IISER BSMS Curriculum 2021

BS-MS Curriculum at IISER Pune
Last revised: August 4, 2021
Contents
1. Historical Introduction to the Curriculum at IISER Pune ............................................................ 2
2. Course Plan for a BS-MS Student .............................................................................................. 3
2.1. Compulsory Courses .................................................................................................................. 4
2.2. Elective Courses in the 3rd Semester .......................................................................................... 4
2.3. Major and Minor Requirements for Each Discipline .................................................................. 5
2.3.1. Biology................................................................................................................................. 5
2.3.2. Chemistry ............................................................................................................................ 6
2.3.3. Data Science ........................................................................................................................ 7
2.3.4. Earth and Climate Science (ECS) ......................................................................................... 8
2.3.5 Humanities and Social Sciences (HSS) .................................................................................. 9
2.3.6 Mathematics ...................................................................................................................... 10
2.3.7 Physics ................................................................................................................................ 11
2.4 Fifth Year Research Project ....................................................................................................... 12
3. Syllabi for the Compulsory Courses .........................................................................................13
4. Syllabi for Elective Courses ......................................................................................................30
4.1 Syllabi for Elective Courses in Biology ....................................................................................... 30
4.2 Syllabi for Elective Courses in Chemistry .................................................................................. 59
4.3 Syllabi for Elective Courses in Data Science .............................................................................. 94
4.4 Syllabi for Elective Courses in ECS ............................................................................................. 95
4.5 Syllabi for Elective Courses in Mathematics ........................................................................... 126
4.6 Syllabi for Elective Courses in Physics ..................................................................................... 147
1
1. Historical Introduction to the Curriculum at IISER Pune
IISER Pune’s BS-MS program started in 2006. For students admitted to the institute from 2006 to
2018, the curriculum of this five year dual degree program was notionally divided into three parts.
The first part, comprising the first two years (or four semesters) had common and mandatory
courses in all disciplines. The second part, comprising the third and fourth years (or four
semesters), had advanced courses in every discipline, and the student was free to choose the
courses that they were interested in. The only constraints were bounds on the number of credits
per semester, and that the student was required to choose courses from at least two disciplines in
the third year. The fifth year (or two semesters) was entirely devoted to a research project, and the
student was expected to submit a thesis at the end of the fifth year and defend it to be eligible for
the dual BS and MS degrees. The degrees of students graduating with this curriculum are not in a
particular branch of science; rather, they are degrees in Science.
After about ten years of this curriculum being in place, sufficient data and feedback from students
and faculty was available on it, following which an internal committee of faculty members called
the Academic Advisory Committee was constituted in December 2017 to review the curriculum and
suggest appropriate changes. After a survey was conducted amongst the faculty, senior students,
and alumni to seek opinions and after several rounds of deliberations, the committee
recommended that the curriculum be changed in the following way:
a. In the first one and a half years (or three semesters), all students take common,
compulsory courses that give them a broad background in the sciences. In the 3rd semester,
besides the compulsory courses, students choose two elective courses.
b. In the 4th semester, all students take two compulsory courses and six elective courses. At
this point, a student can begin to exercise any one of these three options: to major in one
discipline; to major in one discipline and minor in another; to choose not to major or minor
in any discipline. A student who wishes to major or minor has to take a certain number of
prescribed courses in the 4th to 8th semesters (or five semesters) to fulfil the Major or
Minor requirements.
c. In the fifth year (or two semesters), the student works on a research project and writes an
MS thesis.
The changed structure of the BS-MS program was approved by the IISER Pune Senate during its 25th
meeting in November 2018. Following that, the Curriculum Committee, an internal committee of
faculty members representing all disciplines, met several times to deliberate on the nature of the
courses in the new curriculum. Faculty meetings also took place in the various disciplines to discuss
course structure and contents, and requirements for a Major and a Minor. An external review of
the curriculum by distinguished academics and teachers was conducted on October 11, 2019 at
IISER Pune. The present curriculum applies to BS-MS students admitted to IISER from the year 2019
onward.
2
2. Course Plan for a BS-MS Student
The table below outlines the number and nature of courses offered by different disciplines, and the
number of courses that a typical BS-MS student would take during the five year program.
Discipline Sem 1 Sem 2 Sem 3 Sem 4 Sem 5 – 8 Sem 9 – 10
C C C E C E E
Biology 2 1 1 1 – 3 ≥5 Research
Chemistry 1 2 1 1 – 3 ≥5 project and
MS thesis
Mathematics 1 2 1 1 – 3 ≥5
Physics 2 1 1 1 – 3 ≥5
Earth and Climate 1 1 1 1 – 3 ≥5
Science (ECS)
Humanities and – 1 1 – – – ≥3
Social Sciences
(HSS)
Foundation 2 – – – 2 – –
courses
Total courses for a 9* 8 6 2 2 6 6-7 per
student semester
C: Compulsory courses
E: Elective courses offered from which a student chooses an appropriate number as indicated in
the last row
*For the 2019 and 2020 batches, there is no ECS course in Sem 1 and the total courses for a
student in Sem 1 is 8.
To graduate with a BS-MS degree, the student has to obtain at least 216 credits, which are
distributed in the following way: 99 (96 for 2019 and 2020 batches) in years one and two, ≥ 84 in
years three and four, and 36 in year 5 for the MS thesis. More information about credits for
individual courses is provided below.
3
2.1. Compulsory Courses
The table below outlines the compulsory courses in the first three semesters and the two
compulsory courses in the 4th semester. Each course is worth 3 credits (3 contact hours per week).
Discipline Sem 1 Sem 2 Sem 3 Sem 4

Introductory Biology Introduction to Ecology and –
Biomolecules Evolution
Biology
Experiments in – – –
Biology
Principles of Organic Principles of Principles of –
Chemistry Physical Chemistry Inorganic
Chemistry Chemistry
– General Chemistry – –
Practicals I
Calculus I Calculus II Introduction to –
Mathematics Probability
– Linear Algebra – –
Introductory Introductory Introductory –
Mechanics Electricity and Quantum Physics
Physics
Magnetism
Physics Lab I – – –
Earth and Climate Evolution of Earth The Solid Earth Introduction to
Science (ECS) and Life Climate Science
Humanities and – History of Science Science and –
Social Sciences Society
(HSS)
Academic – – Thermodynamics
Foundation Communication Skills
courses Introduction to – – Data Analysis
Computing
Total Number of 9* 8 6 2
Compulsory
Courses
*For the 2019 and 2020 batches, there is no ECS course in Sem 1 and the total number of
compulsory courses for a student in Sem 1 is 8.
2.2. Elective Courses in the 3rd Semester

The table below lists the five elective courses in the 3rd semester of which a student is required to
choose any two. Each course is worth 3 credits (3 contact hours per week).
Discipline Course Title

Biology Introduction to Biological Systems
Chemistry General Chemistry Practicals - II
Mathematics Advanced Linear Algebra
Physics Mathematical Methods for Physics
Earth and Climate Science (ECS) Landscapes and Their Evolution
4
None of the 3rd semester elective courses are a pre-requisite for the courses in the 4th semester and
are not a requirement for a Major or a Minor. If such a course is necessary for a student to acquire
some knowledge essential for courses in the 5th to the 8th semesters, the student may be required
to appear for a qualifying exam offered in the summer to demonstrate proficiency in the subject.
Thus, the student has the flexibility to opt for courses in the 3rd semester without having to commit
to a potential Major or Minor.
2.3. Major and Minor Requirements for Each Discipline

From the 4th to the 8th semesters, students may opt for a Major and a Minor in disciplines of their
choice. In any semester, no discipline requires that a student opt for more than five mandatory
courses for being eligible for a Major. A student can, however, choose to take more than five
courses in a discipline each semester. It should be noted that a student cannot opt for a Minor
without also opting for a Major. Each discipline has different requirements regarding the number
and nature of courses to be completed successfully by a student to qualify for a Major or a Minor in
that discipline. The details are provided below.
It is to be noted that, like the courses of the 1st to the 3rd semesters, each course offered in the 4th
semester is also worth 3 credits (3 contact hours per week). However, in the 5th to the 8th
semesters, courses can be worth either 3 credits (2 contact hours per week) or 4 credits (3 contact
hours per week). The reason for reduced contact hours in relation to credits is that a student is
expected to do more homework and independent self-study in the higher semesters as the course
content becomes more complex.
In addition to these courses, in the 5th to the 8th semesters, each discipline also offers semester
long “Lab Training/Theory Project” courses worth 3 credits (flexible number of contact hours)
wherein a student can work in an experimental lab or take up a theory project with a faculty
member of their choice. A student can register for at most one such project across disciplines per
semester.
While the basic structure of the BS-MS program and the requirements for Major in all disciplines
will remain unchanged, there may be small changes in the course contents, the semester when a
course is offered, and new courses may be added.
The requirements of a Major / Minor in each discipline are specified below.
2.3.1. Biology
Major: At least 15 courses in Biology from the list below, of which a minimum of 8 need to be 4
credit courses. The number of credits for each course is mentioned in parenthesis after the course
name.
Minor: At least 8 courses in Biology from the list below.
5
Note: Lab Training/Theory Projects courses count towards fulfilling the requirements for a Major
and a Minor.
Semester Course Title (Number of credits) Prerequisites

#
Cell Biology (3)
4 Physiology (3)
Genetics (3)
Advanced Molecular Biology (4) [5th Sem only]
Advanced Biochemistry I (4)
Bioinformatics (4)
Cellular Biophysics I (4)#
Chemical Ecology (4)
Developmental Biology (4)
5 and 7 Ecology I (4)
Neurobiology I (4)#
Plant Biology (4)#
Advanced Immunology (3) [7th sem only] Introductory Immunology (4)
Structural Biology (3)
Animal Physiology II (3) [7th Sem only] Animal Physiology I (4)
Literature Review (3) [7th Sem only]
Advanced Biochemistry II (4)
Animal Behaviour (4)
Animal Physiology I (4)#
Data Science (3)
Ecology II (4) [offered in alternate years—either 6th
or 8th Sem]
Evolution (3)
Introductory Immunology (4)#
Mathematical and Computational Biology (4)
6 and 8
Microbiology (4)
Applied Plant Biology (3) Plant Biology (4)
Cellular Biophysics II (3) [offered in alternate Cellular Biophysics I (4)
years—either 6th or 8th Sem]
Genome Biology and Epigenetics (4)
Neurobiology II (3) [offered alternate years — Neurobiology I (4)
either 6th or 8th Sem]
Physical Biochemistry (3)
Biology and Disease (4) [8th Sem only] Cell Biology (Semester 4 elective)
#
This course is a pre-requisite for another course
2.3.2. Chemistry
Major: At least 18 courses in Chemistry from the list below, of which the 12 marked with an
asterisk (*) are mandatory. The remaining 6 courses are as per the student’s preference.
Minor: At least 6 courses in Chemistry from the list below. Of these, only one out of the three
advanced labs will count.
6
Note: Lab Training/Theory Projects courses do not count towards fulfilling the requirements for a
Major and a Minor.
Semester Course Title Prerequisites

Principles of Organic Chemistry II – Organic
Reactions, Transformations, and Stereochemistry*
4 Analytical Chemistry – Separation Principles and
Techniques*
Fundamentals of Molecular Spectroscopy*#
Physical Organic Chemistry*
Chemical Equilibrium and Kinetics*
Main Group Chemistry*
5
Advanced Organic Chemistry Lab*
Symmetry and Group Theory
Self-assembly in Chemistry
Organic Synthesis I*#
Transition Metal Chemistry*
6
Advanced Inorganic Chemistry Lab*
Quantum Chemistry*
Advanced Physical Chemistry Lab*
Polymer Chemistry
Organic Synthesis-II Organic Synthesis I
Bioinorganic Chemistry
Thermal and Photochemical Reactions
7 Solid State Chemistry
Statistical Thermodynamics
Bioorganic Chemistry and Chemical Biology
Electrochemistry
Fundamentals of Solution-State NMR
Spectroscopy: Principles and Applications
Organic Spectroscopy
Advanced Mocleular Spectroscopy Fundamentals of Molecular Spectroscopy
Medicinal Chemistry
Photochemistry and Photophysics Fundamentals of Molecular Spectroscopy
Advanced Materials Science
8 Organometallic Chemistry: Principles and
Applications
Organotransition Metal Catalysis and Beyond
Chemistry for Alternative Energy
Advanced Organic Synthesis – Asymmetric
Synthesis
#
2.3.3. Data Science
Semester Projects in Data Science are open for students in semesters 5—8. A Major or a Minor in
Data Science is currently not an option.
7
2.3.4. Earth and Climate Science (ECS)
Major: At least 18 courses in ECS from the list below of which the 12 marked with an asterisk (*)
are mandatory. The remaining 6 courses are as per the student’s preference.
Minor: At least 6 courses in ECS from the mandatory courses [marked by the asterisk (*)] in the list
below.
Major and a Minor.
For 2021 batch and onwards:
I. The 4th semester courses are Principles of Planetary Climate*, Introduction to Geophysics*,
Atmospheric and Ocean Chemistry
II. Numerical Computation is a mandatory courses in the 5th semester.

Principles of Planetary Climate*
4 The Solid Earth*
Atmosphere and Ocean Chemistry
Applied Mathematical Methods*#
Introduction to Geophysics*#
Physics of Atmosphere*#
5 Earth and Planetary Materials*#
Sedimentology and Stratigraphy*# Earth and Planetary Materials
Numerical Computation
Structural Geology and Tectonics#
Introduction to field technique* (offered during Earth and Planetary Materials,
vacation) Sedimentology and Stratigraphy,
Structural Geology and Tectonics
Geo and Cosmochemistry*# Earth and Planetary Materials
Geophysical Fluid Dynamics*#
6
Physics of Geological processes* (Proposed new Introduction to Geophysics
name: Gravity and Global Tectonics)
Analytical Geochemistry Lab* Geo and Cosmochemistry
Physical Oceanography Physics of Atmosphere
Signal Analysis & Information Theory
Parameter Estimation and Inverse Theory
Exploration Seismology# Introduction to Geophysics
Atmosphere and Ocean Dynamics Geophysical Fluid Dynamics
#
Tropical Meteorology Physics of Atmosphere or Geophysical
7
Fluid Dynamics
Hydrology
Igneous and Metamorphic Petrology # Earth and Planetary Materials,
Geo and Cosmochemistry
8
Igneous and Metamorphic Petrology Lab Igneous and Metamorphic Petrology
#
Paleobiology Sedimentology and Stratigraphy
#
Sequence Stratigraphy Sedimentology and Stratigraphy
Sedimentology and Palaeontology Lab Sedimentology and Stratigraphy,
Paleobiology
Advanced Seismology# Introduction to Geophysics
Geoelectromagnetic Exploration#
Geoelectromagnetic Exploration Lab Geoelectromagnetic Exploration
Exploration Seismology Lab Exploration Seismology,
Sequence Stratigraphy
Geophysical Field Experiments Advanced Seismology,
Exploration Seismology,
Geoelectromagnetic Exploration
Climate Modelling Geophysical Fluid Dynamics,
At least one of of the following: Physics of
Atmosphere / Physical Oceanography /
Tropical Meteorology
8
Science of Climate Change Tropical Meteorology or Physical
Oceanography
Glacial System Modelling Applied Mathematical Methods
Satellite Data Analysis and Image Processing Earth and Planetary Materials
Indian Geology and Resources Sedimentology and Stratigraphy,
Geo and Cosmochemistry,
Igneous and Metamorphic Petrology
Isotope Geochemistry
Geological Field Training Sedimentology and Stratigraphy,
Paleobiology,
Sequence Stratigraphy
#
2.3.5 Humanities and Social Sciences (HSS)
Major: Not applicable
Minor: Minimum 6 courses in HSS as per the student’s preference (not counting the compulsory
courses in Semesters 2 and 3).
Note: No more than 2 Lab Training/Theory Projects courses count towards fulfilling the
requirements for a Minor.
9
2.3.6 Mathematics
Major: Minimum 15 courses in Mathematics (courses with code of the form MTxxxx), of which the
9 marked by the * sign in the list below are mandatory. The remaining 6 courses are as per the
student’s preference.
The courses offered in Semester 5 which are mandatory for a Major in Mathematics (marked *)
can be taken in Semester 7; similarly, the mandatory courses offered in Semester 6 (marked *) can
be taken in Semester 8.
Minor: Minimum 8 courses in Mathematics.
Below is a list of Mathematics courses that are usually offered at IISER Pune. In addition to these,
additional courses not in this list are regularly offered based on faculty and student interest. All
these courses count towards fulfilling requirements for a Major and a Minor.
Note: Lab Training/Theory Projects courses count towards fulfilling the requirements for a Major
and a Minor.

Group Theory*
4 Real Analysis I*
Discrete Structures*
Rings and Modules* Group Theory
Real Analysis II* Real Analysis I
Point Set Topology* Real Analysis I
Ordinary Differential Equations* Real Analysis I
5
Graph Theory* Discrete Structures
Statistical Inference
Numerical Analysis
Fields and Galois theory Group Theory
Complex Analysis* Real Analysis I
Algebraic Number Theory Fields and Galois theory
Measure Theory and Integration Real Analysis II
6 Calculus on Manifolds Point Set Topology, Real Analysis II
Coding Theory Discrete Structures (recommended, but
not mandatory)
Algorithms Graph Theory
Representation Theory Advanced Linear Algebra,
Algebraic Number Theory
Functional Analysis Measure Theory and Integration
7
Differential Geometry and Lie Groups Group Theory
Algebraic Topology Group Theory, Point Set Topology
Probability Measure Theory and Integration
Algebraic Geometry Rings and Modules
Fourier Analysis Functional Analysis
8
Riemannian Geometry Differential Geometry and Lie groups
Cryptography Group Theory
10
Stochastic Processes Probability
Partial Differential Equations Functional Analysis
2.3.7 Physics
Major: At least 18 courses in Physics from the list below of which the 14 marked with an asterisk (*)
are mandatory. The remaining 4 courses are as per the student’s preference.
Minor: At least 8 courses in Physics from the list below.
Major and a Minor.
Semester Course Title (Number of credits) Prerequisites

Classical Mechanics* (3)
4 Thermal and Statistical Physics* (3)
Physics Lab II* (3)
Electrodynamics I* (4)
Electronics 1, with Lab* (4)
Optics* (4)
5 Quantum Mechanics I* (4)
Physics Lab III (3)
Methods of Experimental Physics (3)
Mathematical Methods for Physics II (3)
Quantum Mechanics II* (4) Quantum Mechanics I
Physics Lab IV* (4)
Statistical Mechanics I* (4) Thermal and Statistical Physics
Condensed Matter Physics I* (4) Quantum Mechanics I,
6 Thermal and Statistical Physics
Computational Physics (4)
Electrodynamics II (3) Electrodynamics I
Electronics & Instrumentation (3) Electronics I
Group Theory in Physics (3)
Physics Lab V* (4)
Nuclear and Particle Physics* (4) Quantum mechanics I
Advanced Classical Mechanics (3) Classical Mechanics
Astronomy and Astrophysics (3)
Condensed Matter Physics I,
Condensed Matter Physics II (3)
Statistical Mechanics I
7
Fluid Dynamics (3)
Gravitation (3)
Quantum Mechanics I
Physics at Nanoscales (3)
Condensed Matter Physics I
Math Methods II
Quantum Field Theory I (3)
Quantum Mechanics II
11
Group Theory in Physics
Quantum Information (3) Quantum Mechanics I
Statistical Mechanics II (3) Statistical Mechanics I
Methods of Experimental Physics (3) [Same as 5th
sem course]
Mathematical Methods for Physics II (3) [Same as
5th sem course]
Quantum Mechanics I
Atomic and Molecular Physics * (4)
Statistical Mechanics I
Physics Lab VI (3)
Gravitation
Advanced Gravitation (3)
Quantum Field Theory I
Optics
Advanced Optics (3) Quantum Mechanics I
Electrodynamics I
Astrophysical Processes (3)
Cosmology (3)
Non-linear Dynamics (3) Classical Mechanics
8
Quantum Mechanics II
Particle Physics – Standard Model (3)
Nuclear & Particle Physics
Physics of Soft Matter (3) Statistical Mechanics I
Plasma Physics (3)
Quantum Field Theory II (3) Quantum Field Theory I
Lab/Theory project course (3)
Electronics & Instrumentation (3) [Same as 6th sem
course]
Computational Physics (3) [Same as 6th sem
course]
Group Theory in Physics (3) [Same as 6th sem
course]
Note on prerequisites:
Instructors will assume that the student is familiar with the basic course (prerequisite course) while
teaching the advanced course (the course which requires prerequisites). Physics majors will credit
most of the prerequisites as a matter of course. Non-physics (Major) students may face course
schedule/overload conflicts in crediting all the prerequisites. Non-phyiscs (Major) students
interested in physics courses for a Minor or otherwise may do so without the prerequisites after
seeking permission from the instructor, and at their “own risk”. The teaching of the advanced
course will assume that all students are familiar with the basic courses listed as a prerequisites.
Students should use this table to become familiar with the prerequisites before crediting the
advanced course.
2.4 Fifth Year Research Project

The fifth year project, carried out over the 9th and 10th semesters, is worth 36 credits. A student
who wishes to major in a particular discipline must opt for a Fifth Year Project in that discipline.
Prior approval from the department (at the time of registration for the Fifth Year Project) is
required for the project to be considered suitable for the department's Major requirement.
12
3. Syllabi for the Compulsory Courses
Note: All Compulsory Courses are worth 3 credits each
Discipline Biology
Course title Introductory Biology
Semester 1
Nature of course Lectures and Tutorials
Introduction Students attending this course need not have taken biology at the HSC level. The
course is an introduction to the main conceptual framework of biology as a science,
outlining the diversity, organization, and fundamental principles of living systems.
Course contents Module 1: Concepts in Biology

(approximate number  What is Life? Importance of biology and evolution (2)
of lectures per topic,  Plants, animals, and microorganisms (2)
excluding tutorials,  Logical structure of biology: complexity, emergent properties, adaptation,
are given within diversity (2)
brackets)  Nature of experimentation in biology and statistical inference (1)
Module 2: Genetics and Molecular Biology
 Nature of biological information in cells, nucleus and chromatin architecture (1)
 Genetics, genes, alleles, Mendel’s laws (3)
 Central dogma of molecular biology, DNA replication, transcription and
translation (3)
Module 3: Cell Biology
 Cell theory, prokaryotes and eukaryotes, unicellular, multi-cellular organisms (2)
 Cell structure and compartmentalization: cell wall, cell membrane,
cytoskeleton, actin, microtubules, microfilaments, and motor proteins (2)
 Endomembrane system, ER, Golgi complex, endosomes, lysosomes, and nucleus
(2)
 Cell cycle, mitosis and meiosis (1)
References 1. N. A. Campbell, J. B. Reece, R. B. Jackson, M. L. Cain, L. A. Urry, S. A.

Wasserman, P. V. Minorsky, (2007), Biology, 8th Edn. Benjamin-Cummings Pub
Co.
2. Gadagkar R (1997), Survival Strategies. Harvard University Press.
3. D. Sadava, W. K. Purves, G. H. Orians, and H. C. Heller, (2008), Life: the Science
of Biology, 8th Edn., Sinauer Assoc. & Freeman & Co.
4. Raven, Johnson, Losos and Singer (2005). Biology, 7th edition, McGraw Hill.
5. Alberts, Bray, Hopkin, Johnson, Lewis, Raff, Roberts and Walters (2003).
Essential Cell Biology, 2nd edition, Garland Science.
6. Bruce Alberts, Alexander Johnson, Julian Lewis, Martin Raff, Keith Roberts,
Peter Walter (2007). Molecular Biology of the Cell, 5th Edition, Garland
Science.
7. Principles of Biology, Nature Education (http://www.nature.com/principles)
8. Scitable by Nature Education (http://www.nature.com/scitable)
Discipline Biology
Course title Experiments in Biology
13
Semester 1
Nature of course Laboratory
Introduction The theme for the practical course is “Looking at cells in action”. The course aims to
make students understand the joy of doing experiments in biology. Further,
students will learn about experimental errors. Finally, students will also learn to
keep good records of the experiments performed in a lab journal.
Course contents a. Basics of microscopy

(Tentative list of b. Using the microscope to observe different microorganisms
experiments) c. Model organisms
d. Staining of blood cells and micrometry of different cells
e. Bacterial staining – differentiating between gram positive and gram negative
bacteria
f. Osmosis/Plasmolysis
g. Leaf stomatal density
h. Mitosis/Meiosis
i. Metaphase chromosome spread
j. Pure culture techniques: media, streaking, pour plates
k. Enumeration of bacteria
References 1. Text Book(s) of Introductory Biology course

2. Lectures and associated reading provided by faculty during the course
3. Raven, Johnson, Losos and Singer (2005). Biology, 7th edition, McGraw Hill.
Discipline Biology
Course title Introduction to Biomolecules
Semester 2
Nature of course Lectures, Tutorials, and Laboratory Sessions
Introduction The course aims at introducing basic concepts in biochemistry and provides a
framework to understand basic biomolecular function.
Course contents Basic molecules necessary for life - carbohydrates, lipids, nucleic acids, proteins,
(approximate number enzymes (6)
of lectures per topic, Interrelationships between biomolecules that collectively carry out essential cell
excluding tutorials, functions (2)
are given within Concepts in Metabolic pathways, Bioenergetics (4)
brackets)
List of experiments:
1. Sugar estimation (Colorimetry) and Protein estimation (spectrophotometry)
2. Lipid estimation (Titrimetry)
3. Enzyme assay and kinetics
4. Plasmid DNA isolation, DNA estimation and transformation
5. Agarose gel electrophoresis, Restriction digestion and ligation
6. Polymerase Chain Reaction
References 1. Harper’s Illustrated Biochemistry (2009), 28th edition, McGraw Hill.

2. Biochemistry Voet, D., Voet, J.G. Publisher: Wiley; 3 edition
3. Lehninger Principles of Biochemistry David L. Nelson, Michael M. Cox.
Publisher: W. H. Freeman, Fourth Edition
14
4. Jeremy M Berg; John Tymoczko; Lubert Stryer (2012), Biochemistry, 7th/6th
edition (or older), Wiley.
5. Plummer, D.T. (1988) An introduction to practical biochemistry. 3rd edition.
Tata McGraw-Hill, New Delhi.
6. Primrose, S.B., Twyman, R.M. and Old, R. W. (1994) Principles of Gene
Manipulation. 5th Edition. Blackwell Science, UK.
Discipline Biology
Course title Ecology and Evolution
Semester 3
Nature of course Lectures
Introduction This is an introductory course that will help students in terms of
A) understanding of 1) the basic concepts in ecology and evolution 2) how

organisms interact with each other and the environment, and 3) the ways of
investigating ecological and evolutionary questions
B) ability to 1) visualize how these concepts connect to real-life situations, and 2)

investigate questions in classical genetics, ecology, and evolution in particular, and
biology/science in general using the tools mentioned above
Course contents Introduction: An overview of biological processes: Why study ecology and
evolution?
Population ecology: Survivorship curves, Life-tables, Simple population dynamics

models and their behavior, Deterministic chaos, Lattice effect
Community ecology/ Species interaction: Competition (Competitive exclusion

principle, Niche, Lotka-Volterra Model of Competition, Niche partitioning, Invasive
species); Predation (Lotka-Volterra Model, Classic experiments in predation,
Predator-avoidance strategies);
Applications: Conservation biology (Basic concepts, Reserve designing, Case study:

Passenger pigeons and Project Tiger), Eutrophication, Lake restoration
Evolution: A very brief history of evolutionary thought upto Extended Evolutionary

Synthesis. Selection.
Population genetics: H-W equilibrium; selection; genetic drift
References No single text book can be prescribed. The following booksshall cover much of the
proposed syllabus:
• Molles, M.C. (2009) Ecology Concepts and Applications:McGraw Hill.
• Freeman, S and Herron, J. (2014) Evolutionary Analysis. W.Prentice Hall
Discipline Chemistry
Course title Principles of Organic Chemistry
15
Semester 1
Introduction This course includes structural chemistry of organic compounds with an emphasis
on electronic structure, reactivity, conformation, and stereochemistry. These
concepts will prepare students for a mechanistic-based approach to learn organic
chemistry. Emphasis will be given towards developing problem-solving skills unique
to organic chemistry.
Course contents  Organic Chemistry in day-to-day life: Medicines, petrochemicals, polymers,

soaps and detergents; dyes, cosmetics, artificial sweeteners, food additives
etc
 Introduction to organic chemistry: Carbon compounds and chemical bonding;
a) Ionic bonding; b) Covalent bonding; c) VSEPR theory; d) Hybridization/LCAO
e) Molecular orbital theory; f) Arrow pushing concepts in organic chemistry; g)
Inductive effects; h) Hyperconjugation; i) Mesomeric effects; j) Resonance; k)
Tautomerism
 Aromatic compounds: Aromaticity, anti-aromaticity and non-aromaticity.
 Reactive Intermediates: arbocations, carbanions, free radicals, carbenes, and
nitrenes
 Acidity, basicity, and pKa: Acidity,basicity, definition of pKa, factors that
influence the acidity and basicity, levelling effect, predicting acid strengths,
HSAB Principle
 Stereochemistry: Importance of stereochemistry, chirality, chirality in
biomolecules (proteins, carbohydrates), drugs that interact with chiral
biomolecules, assigning chirality, stereochemical descriptors, R and S, E and Z
notations; interaction of chiral molecules with light, optical activity
 Conformational analysis: Acyclic systems such as ethane, propane and n-
butane and cyclic molecules such as cyclohexane
 Classifications of organic reactions:
- Addition Reactions: Modes of additions reactions; nucleophilic, electrophilic,
free radical addition reactions; nucleophilic addition to carbonyl groups, angle
of nucleophilic attack on aldehydes and ketones; aldol and related reactions;
electrophilic addition reactions to alkenes and alkynes
- Substitution Reactions: Types of substitution reactions: nucleophilic
substitution at saturated carbon; SN1 and SN2 mechanisms for nucleophilic
substitution; aromatic electrophilic and nucleophilic substitutions; examples
for free radical substitutions
- Elimination Reactions: Types of elimination reactions; factors affecting the
elimination reactions; substitution and elimination; elimination happens when
the nucleophilic attacks hydrogen instead of carbon
References 1. Organic Chemistry by Jonathen Clayden, N. Greeves, S. Warren, P. Wothers

Oxford University Press, 1 edition Chapters 6, 10, 12, 14, 16, 17,18, 19, 20 21,
22, 37
2. Organic Chemistry by Solomon, John Wiley & Sons Inc; 2nd or 3 rd edition
3. March’s Advanced Organic Chemistry by M. Smith and J. March, Wiley-
Interscience; 5, or 6 edition
Course title Principles of Physical Chemistry
Semester 2
16
Introduction The objective of this course is to look at chemistry at the level of molecules and
atoms, and make connections between the rules governing such microscopic
particles to what we observe in the macroscopic world.
Course contents  Building blocks of chemistry: Chemistry at the fundamental level is about
molecules, their constituent particles, and the changes they undergo.
 Need for quantum mechanics: Beginning of the electronic era. Thomson's,
Millikan's, and Rutherford's experiments. Necessity to explain Black-body
radiation, Wave-particle duality of light, Wave-particle duality of matter
 Energy quantization: Particle in a box model. Wave function and Schrödinger
equation. Properties of a wave function, calculation of average value of
position, applications to spectra of conjugated polymers and quantum dots.
Particle in a 2D box and ring.
 Hydrogen atom: Stability of the atom is explained by quantum mechanics. The
orbitals are eigenfunctions of the Schrödinger equation. Shape and radial
distribution function of the orbitals.
 Multielectron atoms: Orbital picture
 Chemical bonding: Lewis theory, valence bond theory and molecular orbital
theory using the wave function approach, Potential energy surface
 Intermolecular interactions: Charge-charge, dipole-dipole interaction, H-bond,
differences in covalent and noncovalent interaction
 Molecules to materials: Supramolecular chemistry, molecules of life, surface
and interface, origin of electrode potential
 Interaction between light and matter: Classical picture of interaction between
light and matter, energy states, transition between energy states
References 1. Physical Chemistry by Peter Atkins and Julio de Paula

2. Physical Chemistry: A Molecular Approach by Donald A. McQuarrie
Course title General Chemistry Practicals I
Semester 2
Introduction This course is designed to acquaint students with the practice of experimental
organic chemistry, inorganic chemistry and physical chemistry. Experiments are
based on some of the key topics that are introduced in the theory courses. In
addition, this laboratory course also introduces the synthesis of known medicines,
insect repellents, colorful dyes and other reactions. This course will help students
to develop laboratory skills.
Course contents 1. Synthesis of Aspirin

2. Insect repellent: Synthesis and characterization of N,N-diethyl-3-
methylbenzamide- DEET
3. Dye Formation: Synthesis of azo dyes
4. Chemiluminescence: Synthesis of Luminol and its chemiluminescence
properties
5. Saponification of esters and soap manufacturing
6. Determination of Acid Neutralizing Power of commercial Antacids
7. Kinetic Study of Ester (ethyl acetate) hydrolysis in the presence of HCl at room
temperature
17
8. Verification of Lambert Beer’s Law and simultaneous determination of K2Cr2O7
and KMnO4 with the help of UV Spectrophotometer
9. To investigate the phenomena of Depression in Freezing point and determine
the molar mass of unknown solute
10. Study of oscillatory chemical reaction
References Readings and laboratory manual provided during the course
Course title Principles of Inorganic Chemistry
Semester 3
Introduction This course will introduce students to the most rudimentary principles behind the
chemistry of inorganic compounds. At the end of the course, the students should
be able to derive the structure of various covalent compounds, apply the concept
of acid-base chemistry to various reactions and as a whole understand the
importance of the elements of the periodic table for living matter.
Course contents  Acids and Bases: Various models of Acids and Bases. Concepts of pH, pKa, pKb.
Solvent levelling. Lewis acidity. Reaction and properties of Lewis acidity and
Bases, Superacids, Magic acid, Hard and soft Acids and Bases. Solvents as acids
and bases, Heterogeneous acid base reactions.
 Oxidation and Reduction: Redox half-reaction, standard potentials, The
electrochemical series, The Nernst equation, Redox stability, reactions with
water, oxidation by atmospheric oxygen, disproportionation and
comproportionation, Latimer diagrams, Frost diagrams, The dependence of
stability on pH, Redox titration.
 Representative Chemistry of Transition metals and main- group elements:
Basics of transition metal complexes: Introduction to coordination
compounds, Crystal field theory. Basics of Main group chemistry: Periodic
trends of S and P block elements. Basics of nuclear chemistry, Introduction to
organometallic chemistry.
References 1. Inorganic Chemistry: Shriver and Atkins, 4th Edn., Oxford University Press
2. Inorganic Chemistry by Huheey, Keiter, Keiter, Medhi (4th Ed.)
3. Concise Inorganic Chemistry: J. D. Lee
Discipline Earth and Climate Science
Course title Evolution of Earth and Life
Semester 2
Introduction This course provides an integrated view of the Planet Earth dealing with the Earth’s
internal structure and processes (Earth materials, volcanism, and plate movement),
land forms, surface processes, understanding evolution of life forms through ages
18
and its interaction with the planet.
Course contents Formation of solar system, Structure and composition of the Earth and other
planets, Understanding Earth Processes: Earth material, Plate tectonics and Earth
Interior, continental crust growth, Rock Formation Processes, Weathering and mass
wasting, Hydrological cycles, origin of water, Formation of oceans, Oxygenation of
ocean/atmosphere system
Concept of geologic time, Relative time, Absolute time, Geological time scale,
Nature of paleontological data, Early life on Earth and its indirect evidences, direct
evidence of early life, Great oxygenation and its relationship with life, Evolution and
radiation of metazoans, major evolutionary transitions, Mass extinctions,
Anthropocene and its uniqueness, Sustenance of life and resources during
Anthropocene
References 1. Planet Earth: Cosmology, Geology, and the evolution of life and
Environment (2007) by C. Emiliani, Cambridge University Press, 718 pp
2. Early earth Systems (2007) by H Rollinson, Blackwell Publishing, 285 pp
3. Understanding Earth (2010) by J. Grotzinger and T J Jordan, W H Freeman
and Co., 672 pp
4. Earth Science (2014) by E. Tarbuck, F. Lutgens, and D. Tasa, Prentice Hall,
792 pp
5. The Blue Planet (2011) by B J Skinner and B Murck, John Wiley and Sons,
656 pp
6. How to build a habitable planet (2012) by C. H. Langmuir and W. Broecker,
Princeton University Press, 718 pp
7. History of life (2005) (4th ed.) by R. Cowen, Blackwell publishing, 324pp
Course title Introduction to Climate Science
Semester 3
Introduction This course provides an overview of the Earth’s Climate system, the various forcing
and feedbacks controlling the Earth’s climate variability in short and long timescale.
It will give a brief introduction to the atmosphere and ocean circulation.
Course contents Concept of earth system, climate forcing, responses, feedback loops, equilibrium
states, Daisy world model
Formation and evolution of Earth’s atmosphere, composition and thermal and

dynamical structure
Solar Flux at Earth’s Orbit, Planetary Energy balance, seasonal variability,

Interaction of radiation with atmospheric gases, ozone formation, Greenhouse
effect, Energy budget, Role of clouds
Mean distribution of air temperature, pressure and wind patterns, Centrifugal and
Coriolis force, Geostrophic wind, Three cell structure of atmospheric circulation
19
Temperature, salinity and density variation in the oceans, wind driven circulation,
surface currents, Ekman transport, subtropical gyres, upwelling, downwelling
Thermohaline circulation, formation of deep water masses, North Atlantic Deep

Water, Antarctic Bottom water, Climate impact of Thermohaline circulation
An overview of Earth’s Climate variability, climate archives, Tectonic scale climate

change, CO2 and long term climate, Faint Young Sun Paradox, Milankovitch cycles
Historical and Future climate change, Overview of weather prediction and climate
modelling.
References 1. The Earth System, 3rd Edition (2009), by LR. Kump, JF. Kasting and RG. Crane,
Pearson.
2. Earths Climate: Past and Future 2nd Edition (2008) by William F. Ruddiman,.
W.H. Freeman.
3. Atmospheric Science: An Introductory Survey, 2nd Edition (2006), by JM.
Wallace and PV. Hobbs, Academic Press.
Discipline Humanities and Social Sciences
Course title History of Science
Semester 2
Introduction This course introduces students to key elements in the history of science in
different parts of the world. Any history of science is an inherently multi-
disciplinary subject for the simple reason that modern science was born through a
complex interplay of philosophy, religious beliefs and rituals, political and legal
systems, commerce, ocean-voyages, technology, art, music and many other cultural
practices across many civilizations. This course aims to understand science in these
intersecting contexts to provide a holistic picture of the subject.
Course contents The broad sweep of this course will trace the beginnings of science from the
ancient world, and use developments such as the beginning of geometry in various
parts of the world, early astronomy and theories of the cosmos, rational medicine,
mathematics, theology and science to explicate the rise and consolidation of
scientific knowledge, and then focus on science in the modern era, the scientific
revolution in Europe, and the rise and spread of modern science across the world.
References 1. William Bynum. A Little History of Science

2. The Oxford Companion to The History of Modern Science
3. Encyclopaedia of the History of Science, Technology, and Medicine in Non-
Western Cultures
4. Edward Grant. Physical science in the Middle Ages
Discipline Humanities and Social Sciences
Course title Science and Society
20
Semester 3
Introduction The objectives of this course are:

1. To develop critical reading, visual analysis, and thinkingskills that will enable
students to identify and evaluatearguments, evidence provided, steps of reasoning,
conclusions
2. To understand natural sciences as part of society andexplore their relationships
with humanities and social sciences
Course contents 1. Introduction to CourseWhat is Science? – Systematic Inquiry, hypothesis,

objectivesearch, reproducibility, modelling, theory or framework oftheory,
inductive - deductive reasoning
2. History of Modern Science: Helio-centrism, Galileo(observational science),
Renaissance, Cartesian Dualism andReductionism, Age of Enlightenment, Industrial
Revolution,Positivism, Falsifiabilty
3. History of Indian Science/Non-Western cultures:Mathematics/Astronomy in
India, Vyakarna, Panini,Medicine/Surgery (Charaka), Metallurgy,
Hindi/Arabicnumerals
4. Economic Botany, Botanical Garden
5. Economic Zoology, Art and Science, BotanicalRepresentation
6. Biographies: Different ways of biography writing; Womenscientists
7. Biographies: P C Ray
8. Science and Ethics
9. Science and Cinema
10. Science Fiction
11. Religion and Science
12. Cartography and Calendars
13. Wrap – Up Lecture
References 1. D.P. Chattopadhyaya (general editor), History of Science,Philosophy and Culture

in India (Delhi: Pearson; Center forStudies in Civilisation, 1999).
2. Steve Woolgar, Science: The Very Idea (London; New York:Routledge, 1993)
Discipline Mathematics
Course title Calculus I
Semester 1
Introduction This course introduces the basic tools of calculus of functions of one variable. We
develop the concepts of continuity, differentiability and integrability together with
their geometric and physical meaning. Along with this, we also introduce the key
techniques of mathematical proofs like induction and contradiction. This opens up
our awareness of the logic underlying the world of mathematics, and brings clarity
to our study. Applications include computing extrema of functions and calculating
areas of regions bounded by graphs.
21
Course contents Set and functions, Mathematical induction, finite and infinite sets, proof by
contradiction, properties of real numbers, least upper bound axiom, convergent
sequences, limits of functions, continuity, intermediate value theorem,
differentiability, product and chain rules, mean value theorem, Taylor's Theorem
and Taylor's Expansion, maxima and minima, series, Riemann integration,
fundamental theorem of calculus, integration by parts and change of variables,
applications to area and volume, First and second order linear ODE with constant
coefficients: Methods of solving, statement of existence and uniqueness of solutions
(without proof)
References 1. Calculus Vol. 1 and 2: T .M. Apostol (2007) Wiley

2. Calculus: M. Spivak (2006) Cambridge
3. Calculus: J. Stewart (2012) Cengage Learning
4. Calculus and Analytic Geometry: G.B. Thomas, R. Finney (1995) Addison-Wesley
Course title Calculus II
Semester 2
Introduction This course introduces the basic tools of calculus of functions of several variables.
We generalize the notions of continuity, differentiability and integration to
functions of several variables and discuss their geometric and physical meaning. We
learn the techniques of partial differentiation, integration along curves and surfaces,
and indicate a wealth of applications.
Course contents Vectors and 3-dimensional geometry, functions from R^m to R^n , derivatives and
integrals of vector functions, arclength and curvature of space curves, limits and
continuity, partial derivatives, total derivatives, maxima and minima, statement of
two-variable implicit function theorem, Lagrange multipliers, divergence, curl;
iterated integrals, change of variable formula, line integrals, statement of Green’s
Theorem, surface integrals, statement of Stoke’s Theorem, statement of divergence
theorem, applications to area and volume
References 1. Calculus Vol. 2: T. M. Apostol (2007) Wiley

2. Calculus: J. Stewart (2012) Cengage Learning
3. Calculus and Analytic Geometry: G.B. Thomas, R. Finney (1995) Addison-Wesley
22
Course title Linear Algebra
Semester 2
Introduction The notion of a vector space generalizes our familiar experience of three
dimensional space, with its planes and lines, to any dimension. However in higher
dimensions our geometric intuition should be supported with the mathematical
theory of coordinates. In this course the main objects of study are finite dimensional
space over real numbers, its subspaces, and linear transformations. Our tools are
the algebra of matrices and vectors. By introducing the notion of an “inner
product”, we may also speak of angles and magnitude in any dimension.
The importance of linear algebra to mathematics cannot be overstated. Along with

calculus, linear algebra is one of the two pillars of mathematics, and is fundamental
to any student of science.
Course contents Vector Space structure on R^n, Matrix operations and systems of linear equations,
Gauss-Jordan Elimination, Matrix Inversion, Determinants, Abstract Vector Spaces
with Examples, Subspaces, Linear Combinations, Basis and Dimension, Linear
Transformations and Geometry, Rank-nullity Theorem, Coordinates and Change of
Basis, dot product on R^n, Orthogonality and Gram-Schmidt Process, Eigenvalues
and Eigenvectors, Diagonalizability, Applications to linear ODE, discrete dynamical
systems, least squares method
References 1. Introduction to Linear Algebra: G. Strang (2009) Wellesley Cambridge Press

2. Linear Algebra done right: S. Axler (2014) Springer
3. Linear Algebra with applications: Bretscher (2012) Pearson
4. Linear Algebra: K. Hoffman and R. Kunze (2009) Prentice Hall
Course title Introduction to Probability
Semester 3
Introduction This course provides an introduction to probability and statistics with applications.
Topics included are basic probability models; random variables; discrete and
continuous probability distributions.
23
Course contents Random experiments, events, axiomatic definition of probability, equally likely
outcomes, conditional probability, independence, Bayes theorem, random
variables, Cumulative distribution function, some standard discrete and continuous
variables, mathematical expectation, variance, moments, moment generating
function, Chebyshev's inequality, functions of a random variable, their distributions
and moments, joint, marginal and conditional distributions, independence of
random variables, Law of large numbers, Central Limit Theorem, sampling
distributions. Conditional expectation, Random walk, Markov chains, Introduction to
chi square and T distributions (as sampling distributions derived from normal iid)
References 1. A First Course in Probability: S. Ross (2012) Pearson

2. Introduction to Probability and Statistics: V.Rohtagi and A.K. Saleh (2000) Wiley-
Interscience
3. Probability and Statistical Inference: Hogg,Tanis and Rao (2007) Pearson
Education
4. Introduction to Probability: J.Blitzstein and J. Hwang , CRC press
Discipline Physics
Course title Introductory Mechanics
Semester 1
Introduction This course is an introduction to the basic concepts of Classical Mechanics. It covers
the basics of statics and dynamics including energy and momentum, central force
motion and angular momentum. Thereafter it covers the fundamental aspects of
waves and oscillations, and concludes with the special theory of relativity.
Course contents Statics, Newton’s Laws, Oscillations, Energy and Momentum, Lagrangian method,
Central Forces, Angular Momentum
Waves: interference, reflection, refraction, Vibrating strings
Travelling waves and pulses
Frames of reference, basics of special relativity
References 1. Introduction to Classical Mechanics With Problems and Solutions

David Morin,
2. Vibrations and Waves, A.P. French
Discipline Physics
Course title Physics Laboratory I
Semester 1
Introduction This course will expose students to how one approaches experiments in physics:
design, observations, data analysis and interpretation.
24
Course contents Torsional pendulum, physical pendulum, Young's modulus, coefficient of friction,
Euler's relation, Faraday's and Lenz's law of electromagnetic induction, Biot-
Savart's law, Stoke's law, numerical experiments
References
Discipline Physics
Course title Introductory Electricity and Magnetism
Semester 2
Introduction This course covers the basics of electromagnetism. It introduces most of the key
concepts including the potential of simple electrostatic configurations, electric
currents and current densities, magnetic field due to wires and solenoids, induction
and electromagnetic waves. The course concludes with a discussion of electric and
magnetic fields in matter.
Course contents Basics of Electrostatics

Electrostatic potential
Electric fields around conductors
Electric currents
Magnetic field
Induction
Electromagnetic waves
Electric and Magnetic Fields in Matter
References Electricity and Magnetism: Purcell and Morin

Introduction to Electrodynamics: David J. Griffiths
Discipline Physics
Course title Introductory Quantum Physics
Semester 3
Introduction This course introduces the basics of “modern physics”, with an emphasis on the
experiments, effects and physical principles that underlie quantum theory.
The objectives of this course are:

To introduce quantum physics and its applications; to understand how we arrived
at quantum rules; learning to apply quantum physics in various physics problems;
Course contents Historical background, Black Body Radiation, Photoelectric effect, discrete spectra,
Wave-particle duality, Wave packets, correspondence Principle, the Uncertainty
principle, The wave function and probability interpretation, Postulates of quantum
mechanics, Schr dinger equation, expectation values, Operators, two-level
systems, entanglement, simple problems of wells, barriers and oscillators in one
dimension, Hydrogen atom (qualitative).
25
References 1. Introduction to Quantum Mechanics, David J. Griffiths (Pearson Education)
2. Quantum Mechanics, C. Cohen-Tannoudji, B. Diu and F. Laloe, Vol. 1 (Wiley-
Interscience)
3. Quantum Mechanics, Bruce Cameron Reed (Jones & Bartlett 2010)
4. Molecular Quantum Mechanics, Atkins and Friedman (Oxford University Press)
Discipline Foundation course
Course title Academic Communication Skills
Semester 1
Nature of course Tutorials
Introduction This course will focus on developing reading, writing, listening, and speaking skills
of students in English with special emphasis on the academic context. Given the
vast disparity of the proficiency levels of English of the students who join the
programme, the class will be split into 3 to 4 divisions, and while each division will
cover the same skill or module, the method of teaching, the scope of the lesson,
and the material used will vary.
Course contents The skills of reading, writing, speaking, and listening, are in themselves critical and
will be practised, taught, and honed in various ways. Through these skills, some of
the modules that will also be covered are:
introductions (self and other) in informal and formal settings;
skills of public speaking and body language;
voice modulation, tone, register;
basic to advanced pronunciation practice;
question-making and back-channelling;
vocabulary clouds and oft-confused words;
email writing for specific formal purposes;
role plays;
grammar topics such as subject-verb agreement, tenses, voice, modal verbs;
analysing the form and structure of different styles/types of written texts;
close and critical reading skills;
listening comprehension;
reading comprehension;
linkers, conjunctions, and relative clauses in reading and writing;
creative/imaginative writing;
analysing and writing for specific purposes
group discussions;
power point presentations;
skills of editing written texts;
reading newspapers and simple journal articles;
learning constructive criticism skills;
References 1. Raymond Murphy. Essential English Grammar
26
2. Raymond Murphy. Intermediate English Grammar
3. Hilary Glasman-Deal. Science Research Writing for Non-Native Speakers of
English
4. J Lebrun. Scientific Writing: A Reader and Writers Guide
Course title Introduction to Computing
Semester 1
Nature of course Lectures and Computer Lab Sessions
Introduction This is an introductory course in programming and algorithms. The course, via an
easy programming language like python, will impart basic coding skills. The student
will also get some experience in breaking up a problem into programmable steps,
and then actually converting them into executable codes. Some basic algorithms
and useful skills, like plotting a graph, will also be covered.
Course contents Basic introduction to a computer, and basic operating system commands to
communicate with the computer. Using an editor (e.g. gedit) and ipython.
Input/Output from the screen and a file. Conditional branching: if...then...elif...else.
Loops: for, do while, while. Functions. Recursion. Introduction to Numpy and
Matplotlib (for plotting graphs and other plots). Data manipulation. Some basic
algorithms, eg bubble and/or merge sort, definite integration, methods of finding
roots of an equation, etc.
References 1. Charles Dierbach, Introduction to Computer Science using Python

2. John Guttag, Introduction to Computation and Programming Using Python.
3. Allen Downey, Jeffrey Elkner, Chris Meyers, How to think like a computer
scientist : Learning with Python
4. Mike McGrath, Python
5. David Evans, Introduction to Computing
Course title Thermodynamics
Semester 4
Introduction Thermodynamics helps us understand the rules that govern the change of matter
and energy. Majority of the subject was developed to make better and more
efficient engines (e.g., cars, pumps, etc. that convert energy to useful work). Many
attempts were made to even make machines that will run perpetually without any
input energy. Thermodynamics puts an end to such efforts and also sets limits to
the efficiency of an engine.
However, the applicability of thermodynamics is much beyond its usages in

machines. Thermodynamics helps us understand the inevitable future of any
27
matter or process. It introduces a non-conserved quantity called entropy that syncs
with the arrow of time and help us to understand why certain things (e.g., heat
transfer from hot to cold or diffusion of molecules) happen spontaneously while
certain other things (formation of ice at room temperature and normal pressure)
are not possible. The rules of thermodynamics are general and thereby applicable
to problems in physics, chemistry, biology and other natural sciences.
In this course, both classical and statistical approaches will be used to understand
the subject. Therefore, it will provide a complete conceptual understanding of one
of the most fundamental topics of science.
Course contents  Thermodynamics in everyday life, system and surroundings, macroscopic and
microscopic systems, concept of equilibrium, thermodynamic state of the
system. 0th law, gas thermometers, equation of state, real gas and virial
equation
 First law of thermodynamics, work, heat, internal energy, equivalence of heat
and work, expansion/ compression work, isothermal processes, reversible
processes, Joule’s free expansion, adiabatic changes, specific heats, enthalpy,
Joule and Joule-Thompson experiment
 Thermochemistry, calorimetry
 Second Law of thermodynamics, concept of entropy, direction of time,
equivalence of the statements of second law, heat engines and efficiency
(internal combustion engine and external combustion engine), refrigerators,
Carnot cycle
 Definition of entropy, Clausius inequality, calculation of entropy
 Microscopic interpretation of entropy, concept of probability, microstates and
distribution, two level and multi level systems, distinguishable and
indistinguishable particles, most probable distribution, Boltzmann distribution,
microscopic estimation of entropy, partition function
 Concept of absolute entropy, third law of thermodynamics
 Fundamental equation, Legendre transformation, Introduction to free energy,
Criteria for spontaneous change, Maxwell relations, general thermodynamic
relations
 Applications of free energy
References 1. Heat and Thermodynamics by Mark W Zemansky and Richard H Dittman

2. Physical Chemistry by Peter Atkins and Julio de Paula
Course title Data Analysis
Semester 4
Introduction The course will introduce students to preliminary techniques of data analysis in
order to equip them with tools to understand and interpret data in the context of
experiments, population statistics and real world numbers in general. It will also
discuss the need to design experiments to generate useful and optimal data.
Course contents Visualization techniques:

 Graphical data representation in one and more dimensions
28
Statistical analysis:
 unweighted, weighted, and robust estimators
 confidence intervals for mean, standard deviation, correlation coefficient,
percentiles and proportions
 hypothesis testing: comparison of means, medians, standard deviations,
and distributions (multinomial, contingency table, and non-parametric) of
two samples
 ANOVA
Relationship between variables:
 curve-fitting: linear least square (2 variables, multiple variables,
generalised); non-linear least square
 goodness of fit
 correlation coefficient
Experiments:
 data reproducibility issues
 causality versus correlation
 measurement errors, error propagation
 experimental design
The course will draw upon real world data, including, but not limited to data from
the lab courses that the students have taken in the first three semesters, and
examples from their own classroom courses too.
References 1. Statistical methods for data analysis, Luca Lista, Springer 2016
2. An introduction to Error Analysis, John Taylor, University Science Books, 1997
29
4. Syllabi for Elective Courses
4.1 Syllabi for Elective Courses in Biology

Discipline Biology
Course title Introduction to Biological Systems
Semester 3
Credits 3
Introduction Biological systems are elaborate machines with parts that interact in surprising
ways. This course can be envisaged as the antithesis of reductionism. Rather than
take the biological machine apart, we will try to put it together and demonstrate
the properties that emerge are often more than a sum of its parts. Using thematic
examples from subcellular to organismal scales, we will try to derive organizational
principles that mediate interactions between components. The course will
introduce quantitative methods necessary to develop a systems perspective.
Course contents Introduction to complexity in Biology
Introduction to complex systems
Emergent properties and evolution of biological complexity
Integration and organization in Cells

Signal transduction – representing the outside and communication
Gene regulation and gene regulatory networks
Integration and organization in Organisms

Early development and pattern formation
Differentiation and hierarchical gene expression
Growth, Regeneration and Stem cells
Cell death
Ageing
Integration and organization in Physiology

The immune system and inflammation
References i] Alberts, Johnson, Lewis, Raff, Roberts & Walter. Molecular Biology of the Cell.
Garland Science, 4th Edition, 2002
ii] Wolpert, Smith, Jessell, Lawrence, Robertson & Meyerowitz. Principles of

Development. Oxford University Press. 3rd Edition, 2006.
iii] Alon. An Introduction to Systems Biology: Design Principles of Biological Circuits

Chapman & Hall/CRC. 1st Edition, 2006.
iv] Murray. Mathematical Biology Vol. I. Springer. 3rd Edition, 2007.
Discipline Biology
Course title Cell Biology
Semester 4
Credits 3
Introduction This course will provide a detailed insight into basic concepts of cellular structure
and function. It also aims to give a sense of the complex regulatory mechanisms
30
that control cell function.
Course contents 1) Cell compartmentalization
2) Cell membrane organization - Lipid Composition, inner and outer leaflets,
protein binding to the lipid bilayer, proteins bypassing the lipid bilayer, receptors
and membrane channels. Receptor mobility and clustering in the lipid bilayer.
3) Bending the cell membrane - What does it take and what does it allow cells to
do. Endocytosis / Exocytosis - Cell receptor function - cellular trafficking
4) Detailed evaluation of the cytoskeletal network - MT vs Actin - their organization,
association with membrane, membrane receptors, role in endocytosis and
exocytosis.
5) Role and regulation of the motor proteins. Directionality and what that means to
cellular function (trafficking, endocytosis, exocytosis). Use this to introduce the idea
of redundancy and what that means to the cell.
6) Cell cyle and Cell Division - An overview - Role for the cell membrane,
cytoskeleton - MT and actin + motor proteins, Golgi disorganization
7) Cell Division check points and their regulation. Role of growth factors.
8) Mutations in the genes that regulate cell cycle and division and their role in
causing cancer.
References 1) Molecular Biology of the Cell by Alberts, Johnson, Raff, Lewis et al. (2007) 5th Ed.
Garland Science;
2) Molecular Biology of the Gene by James Watson et al., (2007) 6th Ed. Benjamin
Cummings;
3) Molecular Cell Biology by Lodish, Berk, Kaiser, et al., (2007) 6th Ed. W.H.Freeman;
4) Reviews recommended on the course website.
Discipline Biology
Course title Physiology
Semester 4
Credits 3
Introduction Physical and chemical functions of molecules, cells, tissue and organs interact to
build an integrative organism. The Physiology course provides a general
background to mechanisms and processes that shape ways of how whole
organisms function. Key topics fundamental to all organisms, including microbes,
plants and animals, will be covered. The course will focus on fundamental unifying
processes and mechanisms making life possible but also take a comparative
approach, wherever possible, to showcase the divergence in strategies employed
by different groups.
Course contents 1) Introduction to homeostasis

 Homeostasis of energy, ions, water and gases
 Enzyme kinetics
 Temperature effects in physiology and biochemistry, including Q10
effects.
2) Gas exchange
 Principles of gas exchange, including diffusion and gas solubility in water
 Respiration
3) Nutrient acquisition, metabolism, thermoregulation
 Photosynthesis and respiration: key enzymes, substrates and products
 Nutritional demands of plants and mechanisms underlying plant nutrient
acquisition
31
 Metabolism: key enzymes, substrates and products
 Size and metabolism
 Thermoregulation in organisms
4) Water management and ionic homeostasis
 Principles of water balance: homeostatic water balance as organismal
environment changes
 Principles of fluid transport in animals
 Water transport in plants; equations for water potential to calculate the
direction of water movement in plants
 Excretory systems and epithelia in ionic regulation in animals
5) Integrative control
 Endocrine and nervous control in animals
 Hormonal and long distance communication in plants
6) Defence mechanisms
 Innate immunity, adaptive immunity, plant immunity, microbial defences
7) Biomechanics
 Size regulation, growth and movement
 Cell and tissue mechanics, including hydraulics in plants
References Hill, R.W., Wyse, G.A. & Anderson, M. 20XX. Animal Physiology, (Latest Edition).
Sinauer.
Taiz, L., Zeiger, E., Møller I.M. & Murphy A. 20XX. Plant Physiology and
Development, (Latest Edition). Sinauer.
Rece, J.B., Urry, L.A., Cain, M.L., Wasserman, S.A., Minorsky, P.V. & Jackson, R.B.
20XX. Campbell Biology, (Latest Edition). Pearson.
Discipline Biology
Course title Genetics
Semester 4
Credits 3
Introduction The goal of this course is to build upon Basic Genetics, which the students learnt in
their high school and the first few semesters at IISER-Pune. This course was
designed to revise basic concepts and then move on to advanced concepts.   A
student who completes this course is expected to be conversant in the Science of
Genetics, its history as well as current advances. A strong emphasis will be laid on
modern tools and techniques as also the utility of model organisms, which are the
workhorses of the science of genetics.  With the above aims in mind, the course
will follow a path wherein the students first read Classic papers, that defined the
field of genetics in the 19th and 20th centuries. This thread of understanding will
be followed till the present, with the latest papers (2000-) being discussed in the
course.
Course contents i) Mendelian Genetics.
ii) Non-Mendelian Genetics: Linkage, Incomplete Dominance, Maternal Inheritance,

Extra-nuclear inheritance, Sex-linked inheritance, Sex determination, Dosage
Compensation, Epigenetics, Genomic imprinting.
iii) The Chromosomal basis of inheritance.
iv) The Genetics of Bacteria and Bacteriophages. Bacterial transposons. Vertical and
Horizontal gene transfer. Transformation, Transfection & Transduction. Genetic
32
Complementation. Genetic Mapping.
v) Genetic screens as a basis for functional genomics. Deficiences, EMS & X-ray
based mutagenesis screens. Creating alleles. Enhancer traps, EP-Lines, RNA-
inheritance, FLP-FRT & Cre- Lox Systems. Nusslein-Volhard & Weischaus Zygotic
and Maternal Screens, Behavior mutant screens.
vi) Gene isolation Manipulation and the techniques that revolutionized modern
genetics. Working with Nucleic Acids and Proteins. Polymerase Chain Reaction.
DNA Sequencing, Southern, Western & Northern Blots. In-situ Hybridization, FISH,
SNP’s, RFLP’s, EST’s, STS & Oligonucleotide Arrays. Gene Cloning vs Animal Cloning,
Nuclear transplantation, stem cells & iPS cells.
The utility of the following Model Organisms will be discussed: Escherichia coli,
Arabidopsis thaliana, Caenorhabditis elegans, Drosophila melanogaster & Mus
Musculus. E. coli and D. melanogaster at different points during the course.
References (i)“Introduction to Genetic Analysis “ Griffiths, AJ et. al. , 2008, 9th Edition. WH
Freeman & Co. New York.
Discipline Biology
Course title Advanced Molecular Biology
Semester 5
Credits 4
Introduction This course helps to provide fundamental concepts from the enormous and ever-
growing field of Molecular Biology to Undergraduate students. This course will help
students to have a sound knowledge of molecular biology, which will also enable
them to carry out research using molecular biology techniques.
Course contents 1) Diversity of Genomes (2) 

(Approximate number
2) Maintenance of the Genome (13) 
of lectures per topic
are given within - DNA, Chromosomes and Genome 
brackets)
- Replication of DNA
- The Mutability and Repair of DNA 
- Homologous Recombination at the Molecular Level
3) Expression of the Genome (12)
- Mechanisms of Transcription and its Regulation
- RNA Splicing
- Translation 
4) Techniques in Molecular Biology (5)
  - Molecular Cloning methods
  - Molecular Tools for Studying Genes and Gene Activity
5) Latest advances in molecular biology (presentations by students/paper
discussion) (8)
References 1. Molecular Biology of the Gene by Watson, Baker, Levine, Losick et al. [2007] 6th
Ed. Benjamin Cummings.
33
2. Principles of Gene Manipulation by Primrose, Twyman, Old [2002] 6th Ed. Wiley-
Blackwell.
3. Molecular Biology by Weaver [2011] 5th Ed. McGraw- Hill Science.
4. Molecular Biology and Genomics by Mulhardt [2006] 1st Ed. Elsevier.
Discipline Biology
Course title Advanced Biochemistry I
Semester 5, 7
Credits 4
Introduction The course aims at introducing advanced concepts in biochemistry and provides a
framework to understand basic biomolecular function. Its special emphasis is on
studying enzymes as biological catalysts and understanding the chemistry of
enzymatic transformations. It also deals with routine and advanced methodologies
used in generating and analyzing biochemical data.
This course is essentially meant to help understand biology from the point of view
of molecules and physicochemical principles.
Course contents Section #1: Biochemical techniques pertaining to biomolecular purification and
characterization. Will cover a range of techniques from the routine lab techniques
(chromatography, electrophoresis, etc) to the more specialized ones (including
HPLC, Mass spectrometry, NMR) (Lectures: 12)
Section #2: Biochemistry underlying information transfer processes, with a focus on

understanding biochemical reactions that underlie transcription and translation
processes. (Paper presentations: 6 classes)
Section #3: Enzyme biochemistry: enzyme catalyzed reactions, steady state enzyme
kinetics, enzyme inhibition, multisite and allosteric enzymes, pH rate profiles,
viscosity effects, isotopic effects in enzyme catalysis, Cleland notations, pre-steady
state enzyme kinetics (Lectures: 8)
Section #4: Enzyme catalyzed reactions: hydrolysis of peptides bonds, phosphate

transfer and hydrolysis, the amidohydrolase family, the enolase family, the
amidotransferases & molecular tunnels, NAD & FAD catalyzed reactions, the radical
SAM superfamily, carboxylations and decarboxylations, strategies to annotate
enzyme function. (Lectures: 10)
References Biochemistry Voet, D., Voet, J.G. Publisher: Wiley; 3 edition
Lehninger Principles of Biochemistry David L. Nelson, Michael M. Cox. Publisher: W.

H. Freeman, Fourth Edition
Jeremy M Berg; John Tymoczko; Lubert Stryer (2012), Biochemistry, 7th /6th edition
(or older), Wiley.
Enzyme kinetics and mechanism, Paul Cook & W. W. Cleland
Enzyme reaction mechanisms, Perry Frey & Adrian D. Hegeman.
Also, primary research articles and reviews would be utilized to provide

contemporary insights into the field.
34
Discipline Biology
Course title Bioinformatics
Semester 5, 7
Credits 4
Introduction This course is an introduction to bioinformatics and computational structural
biology. The systematic acquisition of data made possible by advances in genomics
and proteomics technologies has created a gap between the available data and its
analysis leading to insights from the data. Computational and theoretical
approaches to understanding biological systems are an essential step in closing this
gap. Also included in this course are topics in data-mining, 3D model building,
ligand docking (drug development) and algorithm development. Lectures will be
supplemented with computer labs to understand the algorithms being covered.
Programming assignments may be given, so some familiarity with programming in
any language will help.
Course contents Topics: Sequences analysis (pairwise alignment, multiple sequence alignment, motif
discovery, gene annotation), pattern recognition/discovery in large-scale
expression data, hidden markov models for sequence analysis, inferring
phylogenetic trees (UPGMA, neighbor-joining, maximum parsimony, maximum
likelihood), analysis of next generation sequencing data (Alignment, ChIP-Seq, RNA-
seq, Assembly), Bayesian networks, Protein 3D structure modeling (homology
modeling/comparative modeling, ab inito modeling), molecular docking, drug
design and Introduction to molecular dynamics.
Most topics covered would have either a hands-on session or a computational

assignment and in some cases both.
References 1. R. Durbin, S. R. Eddy, A. Krogh, and G. Mitchison, Biological Sequence Analysis:
Probabilistic Models of Proteins and Nucleic Acids (Cambridge University Press,
1999), ISBN 0521629713 
2. Arthur Lesk, Introduction to Bioinformatics (Oxford University Press, 2008), ISBN-

10: 0199208042 ISBN-13: 978-0199208043 
3. Arthur Lesk, Introduction to Protein Science : Architecture, function and

genomics (Oxford University Press, 2010), ISBN-10: 0199541302 ISBN-13: 978-
0199541300 
4. David W. Mount, Bioinformatics: Sequence and Genome Analysis (Cold Spring

Harbor Laboratory Press), ISBN-10:0879697121 ISMB-13:978-0879697129
Discipline Biology
Course title Biostatistics
Semester 5, 7
Credits 4
Introduction The course introduces biologists to probability and statistics with a strong emphasis
on using computer simulation of random number distributions to understand the
importance of statistical analysis.
This course is a pre-requisite for Data Science.
Course contents 1. Statistical measures

2. Probability: Basic concepts, distribution functions, change of variables;
3. Fitting data: fitting functions, goodness of fit, correlation, regression,
smoothing, interpolation, extrapolation
35
4. Statistical tests: Parametric and non-parametric tests, null hypothesis,
statistical significance, confidence intervals, Type I and II errors, ANOVA,
multiple testing
5. Time series analysis: Correlation, periodicity
6. Resampling statistics including bootstrapping, jack-knifes, permutation
tests
The fortnightly interaction includes 4 hours of lectures, and 2 hours of hands-on
experience of using Matlab or R.
References Sokal and Rohlf (1995) Biometry: the principles and practice of statistics in
biological research. 3rd Ed, W. H. Freeman and Co.
Zar, J.H. (2009). Biostatistical Analysis. 5th Edition, Prentice hall
Discipline Biology
Course title Cellular Biophysics I
Semester 5, 7
Credits 4
Introduction This course will introduce the exciting new interdisciplinary field of “Physical
Biology” of the cell. It will emphasize the role of theoretical models taken from
physics, which allows a unification of biological phenomena.
This course is a pre-requisite for Cellular Biophysics II.
Course contents The biological phenomena that will be examined are:

1) Force spectroscopy of proteins and nucleic acids
2) Cytoskeleton: Actin and microtubules
3) Motor proteins
4) Protein diffusion, ligand-receptor binding and crowding effects
5) Biomembrane mechanics
6) Red blood cells
7) Cell adhesion and migration
The models that will be invoked will build upon concepts from classical and
statistical mechanics. At the end of the course, the student will be expected to
understand the following models in their application to cellular biophysics:
1) Mechanical forces
2) Mass, stiffness and the damping of proteins
3) Thermal forces
4) Polymer mechanics
5) Molecular motor stepping
6) Membrane bending and undulations
7) Simplest models of cell shape
The tutorials will involve a few computational and experimental exercises to
complement theoretical concepts.
References 1) Philips, R., Kondev, J., Theriot, J. (2008) Physical Biology of the Cell. Garland
Sciences.
2) Nelson, P. (2003) Biological Physics: Energy, Information, Life. Freeman
3) David Boal (2001) Mechanics of the Cell. Cambridge University Press.
4) Howard Jonathon (2001) Mechanics of Motor Proteins and the Cytosokeleton
Discipline Biology
36
Course title Chemical Ecology
Semester 5, 7
Credits 4
Introduction The objectives of the course include: i) understanding principles related to
interactions between different organisms ii) understanding the importance of
chemistry in interaction ecology- how chemicals modulate associations, niches and
ecosystems iii) studying different classes of natural chemicals, importance of their
diversity and structure-function relationship iv) understanding the ecological or the
‘real world’ significance of physiology and biochemistry v) understanding the
importance of interdisciplinary research and integrating modern methods like
genomics, transcriptomics, proteomics, metabolomics with classical field ecology.
Outcomes: Students will be trained in formulating research hypotheses from their
observations of nature, using the scientific literature for this, designing
experiments, integrating modern methods with classical ecology and developing a
scientific publication.
Course contents Introduction and overview of Chemical Ecology

(Approximate number
Philosophy of the course. Introduction to various taxa and ecosystems- terrestrial,
aquatic (fresh water), marine, microbial, etc. Importance of chemistry in biotic
are given within
interactions. Introduction to chemically-based interactions like symbiosis,
brackets)
parasitism, predation, mimicry, aposematism, bet hedging, pollination, seed
dispersal, etc. Importance of chemical ecology to the mankind. (3)
Field visit: Observations of ecosystems, safety precautions, field ethics, rules and
tips for eco-friendly field work, sustainable sample collection, etc. (2)
Infochemical classes: pheromones, allomones, synomones, kairomones, etc.
Major natural product classes (alkaloids, amines, amino acids, aryls, fatty acids,
flavonoids, glycosides, phenolics, polyketides, saponins, steroids, terpenoids, etc.),
biosynthetic pathways, structural aspects and structure-function relationships.
Volatiles vs. non-volatiles (6)
Analytical skills: Metabolomics- Application of metabolomics methods in chemical
ecology (8)
Sample preparation: choice of extraction solvent, conditions, compound stability
considerations, etc,
Gas chromatography (Derivatization, Solid phase extraction, Headspace analysis)
Liquid chromatography
Mass spectrometry, NMR
GC-MS and LC-MS instrument demonstration (2)
Other omics methods like genomics, transcriptomics, proteomics, etc. and
supporting techniques like forward and reverse genetics, heterologous expression,
bioassays, field-based assays, etc. (5)
Chemical Defense: Plants, insects, arachnids, reptiles, frogs, fishes, marine
organisms, etc. Importance of chemical diversity, induced vs. constitutive defense,
direct vs. indirect defense, anticipins, cost-benefit economy, primary metabolism-
/growth-defense tradeoffs. Evolutionary perspective of the taxon specific
occurrence of various metabolite groups (4)
Chemistry of counteradaptations: detoxification, sequestration, co-option,
excretion, avoidance. Tissue specificity, transporters of toxins and detoxification
products. Cost-benefit economy. (4)
Chemical ecology of social insects: ants, termites, honeybees, etc. Chemical
37
communication, foraging, path tracing, mate search, etc. (2)
Human chemical ecology: body odor, infectious disease vectors, chemical ecology
of infections, skin and gut microbiota, etc. (2)
References  Chemical Ecology (2016) Anne-Geneviève Bagnères, Martine Hossaert-
Mckey (Eds.), Willey.
 Chemical Ecology: From Gene to Ecosystem (2006) Dicke, Marcel, Takken,
Willem (Eds.), Springer Netherlands.
 Hands-On Chemical Ecology: Simple Field and Laboratory Exercises (2009)
Müller-Schwarze, Dietland, Springer.
 Physiological Ecology How Animals Process Energy, Nutrients, and Toxins
(2007) William H. Karasov & Carlos Martínez del Rio. Princeton University
Press.
 Secondary Compounds in Plants: Primary Functions
 David Seigler and Peter W. Price. (1976) The American Naturalist, 110,
101-105.
 Peirik R., Ballare, C. L. and Dicke, M. (2014), Ecology of plant volatiles:
taking a plant community perspective. Plant Cell Environ, 37, 1845–1853.
 Maud C.O. Ferrari, Brian D. Wisenden, Douglas P. Chivers. (2010) Chemical
ecology of predator–prey interactions in aquatic ecosystems: a review and
prospectus. Canadian Journal of Zoology, 88, 698-724.
 J B. McClintock, B J. Baker. (1997) A Review of the Chemical Ecology of
Antarctic Marine Invertebrates. Integrative and Comparative Biology, 37,
329–342.
 Moore P.A. (2016) Human Chemical Ecology. In: The Hidden Power of
Smell. Springer
 Chemical ecology of interactions between human skin microbiota and
mosquitoes. FEMS Microbiol Ecol. (2010) 74:1-9.
Discipline Biology
Course title Ecology I
Semester 5, 7
Credits 4
Introduction This course will cover the basic theoretical framework of ecology, and deal with
some of the topics that were introduced in Ecology and Evolution in greater detail.
Course contents Introduction (4 lectures):

Definition of Ecology; Hierarchical levels of biological organization; Philosophy of
the Science of Ecology; Complexity in Nature; History of Ecological thought;
Significance of Ecology; Evolution by Natural Selection
I. Ecology of Individual Organisms (8 lectures)

Physiological ecology: conditions vs. resources, niche, tolerance range, optima,
acclimation, limiting factors, energy balance, photosynthesis, respiration, storage,
growth, reproduction, abiotic factors: temperature, moisture, light, soil, fire,
nutrients
II. Population Ecology (10 lectures)

Population growth and regulation: What is a population, birth rate, death rate, life
tables, survivorship curves, population growth functions, carrying capacity,
population pyramids; Evolution of life histories: r and K selection, iteroparous vs.
semelparous reproduction, Ageing and senescence, tradeoffs; Species interactions:
competition, mutualism, herbivory, predation, optimal foraging, parasitism, trophic
cascades
38
III. Community Ecology (8 lectures)
Community structure: emergent properties, dominance, diversity, spatial structure,
assembly rules; Community change: disturbance, succession, climax, phenology,
seasonal patterns
IV. Ecosystem Ecology (8 lectures)

Productivity and energy flow: primary production, secondary production,
consumers, decomposition, energy flow, biomass vs. production, ecological
efficiency, detritus vs. grazing;  Biodiversity, conservation and climate change:
Indices of diversity, causes and consequences of diversity, effects of climate change
References a. Begon, M., Townsend, CR, and Harper, JL. (2005) Ecology - From
Individuals to Ecosystems. 4th Ed. Blackwell Publishing.
b. Ricklefs RE and Miller GL (2000). Ecology. 4th Ed. Freeman and Co.
c. Gurevitch J, Schener SM, and Fox GA (2006). The Ecology of Plants. 2nd Ed.
Sinaeur and Associates.
Discipline Biology
Course title Neurobiology I
Semester 5, 7
Credits 4
Introduction The course introduces neuroscience as a specialized discipline. The overarching
goal of the course is to provide a detailed description of the logic of the nervous
system from the perspectives of evolution, organization, development, physiology
and emergent properties like learning and memory. The course is aimed at
students interested in understanding the fundamental basis of the neural function
and output and those interested in pursuing neuroscience in the future.
Course contents 1. History of Neuroscience (1 lecture)

2. Organization of nervous system (4 lectures)
3. Membrane channels, ionic basis of resting potential and action potential (5
lectures)
4. Diversity in biophysical properties of ion channels and its effects on membrane
excitability (2 lectures)
5. Propagation of action potential and Synaptic transmission (2 lectures)
6. Synaptic plasticity Hebbian theory (2 lectures)
7. Evolution of Nervous systems (1 lecture)
8. Nervous system development (6 lectures)
9. Learning and memory (2 lectures)
10. Experience dependent plasticity (5 lectures)
11. Adult Neurogenesis and Neuropathology (2 lectures)
12. Neural basis of behavior – studying causality using optiogenetics,
chemogenetis, invivo electro/optophysiology (4 lectures)
13. Practicals: Demonstration of stereotaxic surgery, rodent brain histology,
operant conditioning paradigms, ex vivo imaging, optogenetics (4 hours)
References 1) Kandel E, et al. (2000). Principles of Neural Science, 4th Ed. McGraw-Hill Medical;
39
2) Bear M, et al. (2006). Neuroscience. 3rd Ed. Lippincott Williams & Wilkins;
3) Sanes D, et al. (2005). Development of the Nervous System. 2nd Ed. Academic
Press.
4) Johnston and Wu (1994). Foundations of Cellular Neurophysiology
5) Ralph Greenspan (2007), An Introduction to Nervous Systems
6) Gerstner and Kistler (2002), Spiking Neuron Models
Discipline Biology
Course title Plant Biology
Semester 5, 7
Credits 4
Introduction The objective of this course is to understand basic plant biology, plant architecture,
growth & development (signal perception & transduction etc.). This course will also
help students to deal with practical questions in the Applied Plant Biology and use
them in agriculture biotechnology as well as ecology and environmental studies.
This course is a pre-requisite for Applied Plant Biology and would be advantageous
for understanding Ecology II as well.
Course contents Evolutionary plant lineages, Plant Cell, Cytoskeleton, Plasmodesmata, structure -
(Approximate number mode of communication (2)
are given within Water transport, Mineral Nutrition, Mycorrhiza, secondary active transport,
brackets) aquaporins (3)
Photosynthesis- Light and dark reactions, molecular models (5), Ecological

considerations (1)
Translocation in the phloem, Macromolecular (RNA/Protein) transport (4),

transporter genes, Respiration, Lipid metabolism (4)
Plant growth and development, embryogenesis, polarity, signal perception &

transduction, stress tolerance, clock genes and signaling cascades, the control of
flowering, ABC/ABCDE models, Stem cells & SAM architecture, leaf development
and RAM, Molecular regulators (7)
Phytochromes, photoreceptors and light control of plant development, Blue light

responses (4)
Plant Hormones (Auxin, Cytokinin, Gibberellin, Ethylene, ABA, Strigolactone),

history, biosynthesis, mode of action/signal transduction, Senescence and Stress
physiology (6)
References 1. Buchanon, B; Gruissem, W & Jones R (2000): Biochemistry and Molecular

Biology of Plants, American Society of Plant Biologists (ASPB), USA.
2. Taiz, L & Zeiger E (2010): Plant Physiology (5Th ed.) Sinauer Associates Inc.,
Massachusetts, USA
3. Major Plant Science journals such as Plant Cell, Plant Physiology, Frontiers
in Plant Science, Trends in Plant Science, Current opinion in Plant Biology.
40
Discipline Biology
Course title Advanced Immunology
Semester 7
Credits 3
Prequisite Introductory Immunology
Introduction The course will aim to discuss advanced concepts in the biology of the immune
system. Discussions will be in the contexts of evolution of immune system
formation and regulation, and of disease implications involving qualitative and
quantitative immune dysfunction. Current analyses and new technologies used for
them will be one major component. Participants will (hopefully!) emerge with a
sophisticated understanding both of immunological regulation and of current ways
of investigating organismal physiology at multiple levels of biological organisation.
Course contents How does the immune system patrol body barriers and the microbiota found there
How does the immune system know when and how to respond?
How does the immune system respond to phylogenetically diverse pathogens, and
what are the determinants of the utility of such responses?
Are tumors pathogens as far as the immune system in concerned?
Qualitative and qualitative immune dysfunction, with or without ‘disease’
References Fundamental Immunology, Ed. William E. Paul, 7th Edition, Lippincott Williams &
Wilkins (2012)
Janeway’s Immunobiology, 8th Edition, Kenneth M. Murphy, Garland Science (2012)
Selected reviews provided by instructor
Discipline Biology
Course title Structural Biology
Semester 5, 7
Credits 3
Introduction The course provides an introduction to the structure of biomolecules with
emphasis on the techniques used for structure determination and analysis. The
course covers basic aspects of sample preparation, structure determination and
structure analysis. The aim of the course is to introduce students to the process
involved in structure determination and analysis, and how structural information
can be utilized for better understanding of biological processes.
Course contents Introduction to structures of biomolecules: proteins and nucleic acids 
Recombinant technology and purification techniques to isolate biomolecules
Determination of atomic structure using X-ray crystallography
Studying macromolecular assembly using electron microscopy
Biophysical and spectroscopic techniques to understand structures 
Graphics tools to visualize and analyze atomic structure of biomolecules.
References Introduction to Protein Structure by Carl Branden, John Tooze, Garland Science; 2
edition (January 3, 1999)
41
Biomolecular Crystallography: Principles, Practice, and Application to Structural
Biology by Bernhard Rupp, Garland Science; 1 edition (October 20, 2009)
Understanding DNA by Chris Calladine, Horace Drew, Ben Luisi, Andrew Travers,
Elsevier Academic Press (2004)
Textbook of Structural Biology by Anders Liljas, Lars Liljas, Jure Piskur, Goran
Lindblom, Poul Nissen & Morten Kjeldgaard,   Pub. Date: March 2009, Publisher:
World Scientific Publishing
Discipline Biology
Course title Vertebrate Zoology
Semester 5, 7
Credits 3
Introduction This course aims to provide an integrative view of vertebrate morphological and
functional diversity, employing the comparative approach.
Students will learn about evolutionary history, function and comparative anatomy
of vertebrates, using phylogenies to interpret evolution and function. This course
will study the comparative anatomy and function of the vertebrate musculoskeletal
system, employing a basic biomechanics approach. By the end of this course,
students will have a grasp of functional anatomy and the strategies animals have
evolved to deal with the physical demands of their environment, and be able to
map this back using phylogenies to understand how these traits and strategies
evolved. In addition each sub-module listed below will give students a flavour of
the research methodology used to address these questions, from micro-CT
scanning and morphometrics to high-speed videography, computational models
and even robotics.
Course contents 1. Introduction to phylogenetics/cladistics (1 lecture)

2. Brief overview of the evolutionary history and diversity of the craniate
vertebrates (1 lecture)
3. Basic biomechanics, allometry and scaling laws (1 lecture).
4. The cranial musculoskeletal system: Comparative anatomy, the
biomechanics and evolution of feeding. (4 lectures).
5. The axial musculoskeletal system: Comparative anatomy, evolution and
the biomechanics of posture and support. (4 lectures).
6. Vertebrate tracheal systems and the production of biological sound (2
lectures).
7. The appendicular musculoskeletal system: The evolution of limbs, and
biomechanics of locomotion in land, air and water. (4 lectures).
8. Vertebrate integument. Evolution and function of scales, feathers and
skin, and the production of biological color. (3 lectures).
9. The evolution of form and function in vertebrate sensory organs (4
lectures).
10. Paper discussions, dissection demonstrations (4 lectures, interspersed
with other topics).
Using recent advances in CT scanning and the open-source project oVERT, classes
will engage students with three-dimensional skeletal anatomy of diverse
vertebrates (including extinct ones) using “virtual dissection”.
References Vertebrates: Comparative Anatomy, Evolution and Function by Kenneth Kardong

Comparative Anatomy of the Vetrebrates: GC Kent and KC Carr
42
Discipline Biology
Course title Animal Physiology II
Semester 7
Credits 3
Prerequisites Animal Physiology I
Introduction While the students have been given extensive training in human physiology during
Animal Physiology I, this course offers insights into the physiology of sub-
mammalian vertebrates and invertebrates. Special physiological adaptation
displayed by the animals in diverse habitats will be discussed. Thermal relations
encountered in endo- and ectothermic animals will be explained. Selective
pressures that shape to different physiological phenotypes will be addressed.
Some of the seminal research papers in the field will be discussed.
The course will prepare the student for undertaking research in any area of animal
physiology.
Course contents Section #1- (Title and no of lectures)

Physiology of sub-mammalian vertebrates (14 lectures)
Physiology of circulation, respiration, ionic balance and excretion in terrestrial and
aquatic vertebrates, nutrition, feeding and digestion, sensory perception,
physiology of reproduction.
Thermoregulation in ectothermic and endothermic animals.
Section #2 – (Title and no of lectures)

Physiology of invertebrates (12 lectures)
Circulation, ionic balance and excretion, respiration, digestion, metamorphosis,
nervous and neuroendocrine systems, pheromones, olfaction and sound
perception in insects, muscle and locomotion, reproduction and life cycle of
insects.
Special topics (4 lectures)

Photoperception in invertebrates
Number of lectures: 30
References 1. Randall, D. et al. (2002). Eckert Animal Physiology, 5th Ed. Freeman.
2. Hill, R.W. et al. (2008). Animal Physiology. 3nd Ed. Sinaur Associates.
3. Guyton, A.C. et al. (2008), Textbook of Medical Physiology. 12th Ed. W.B.
Saunders Co.
4. Withers, P.C. et al. (1992) Comparative Animal Physiology. 1st Ed., Brooks
Cole
Discipline Biology
Course title Literature Review
Semester 7
Credits 3
Introduction Familiarization with scientific literature including:
a) Use of search tools
43
b) Reading, analyzing, and critically evaluating the primary literature
c) Effectively summarizing and communicating (oral and written) scientific
information based on specific topics
Course contents 1) Primary, secondary, and tertiary scientific literature
2) Database searches – tools and strategies
3) Reading and evaluating the scientific literature
4) Academic writing – plagiarism and referencing, format and style
5) Writing a literature review.
Diverse specialist faculty will contribute to this course. Faculty members will choose
topics from their own area of research expertise, and highlight through readings
and discussions the nuances of reading and evaluating the literature. Topics
covered can range from DNA biochemistry to ecology.
References 1. Goeff Hyde’s “The Science of Scientific Writing”
2. Robert A. Day (1998) How to write and publish a scientific paper. Oryx Press
3. Bredan & van Roy (2006) Writing readable prose. EMBO Reports 6: 846-849.
Discipline Biology
Course title Advanced Biochemistry II
Semester 6, 8
Credits 4
Introduction This course constitutes topics that cover (i) molecular metabolism, and (ii)
membrane biochemistry. The first constitutes a mechanistic study of carbohydrate,
amino acid, lipid and nucleotide metabolism. The course highlights the
intersections and cross-talk between the various different biochemical pathways in
primary metabolism The second deals with understanding physical principles
underlying formation, organization and dynamics of membranes and also includes
case studies from contemporary literature discussing working with artificial
membrane systems and reconstitution of membrane proteins into such systems.
Course contents In the first section, topics include understanding primary metabolism pathways
involved in carbohydrate, nucleotide amino acid, lipid, and glycogen metabolism. A
contemporary view of pathways such as glycolysis, the citric acid cycle, urea cycle,
the electron transport chain, oxidative phosphorylation, and nucleotide and lipid
biosynthesis, and the mechanistic role of vitamins and coenzymes is presented. The
course hones into important primary metabolism intersections that connect the
various different biochemical pathways.
In the second section, topics include structure and organization of membranes,

physical chemistry of membranes, membranes and physiology, analytical tools to
understand biochemistry and biophysics of membranes.
References 1) The Organic Chemistry of Biological pathways. John McMurry and Tadhg
Begley. Roberts and Company Publishers
2) Lehninger Principles of Biochemistry. David L Nelson, Michael M. Cox
3) Molecular Biology of the Cell. B. Alberts, A. Johnson, J. Lewis, M. Raff, K.
Roberts, P. Walter, (2002) Garland Science.
44
4) Life - As a Matter of Fat. O. Mouritsen, (2004) Springer.
5) The Structure of Biological Membranes. P. Yeagle. (2004) CRC Press.
6) Biochemistry. D. Voet & J.G. Voet.
7) Primary research articles and reviews would be utilized to provide
contemporary insights into the field.
Discipline Biology
Course title Animal Behaviour
Semester 6,8
Credits 4
Introduction Animals sense the environment and their own internal state and respond with a
variety of different behaviors that are appropriate for the situation. How and why
do animals produce their different behaviors?
As part of this course, students will be introduced to the scientific study of animal
behavior with diverse examples from the animal kingdom. Students will not only
learn the methods, but will also learn to apply them by carrying out a project
during the course on an animal and behavior of their choice.
Anyone curious about animal behavior will find this course useful. In addition, the
study of animal behavior is useful to a number of other fields including
conservation biology, evolution, ecology, etc.
Course contents 1) Behavioral ecology (21 lectures)

1. Introduction to Tinbergen’s four questions, the ultimate basis of behavior
and the evolutionary approach to studying behavior
2. Concepts – using phylogenies and game theory
3. Behavioral ecology and sociobiology – group selection theory, kin selection,
altruistic behavior
4. How ecology influences behavior – communication, feeding, habitat selection
and migration
5. Social and cultural transmission of Behavior
6. Evolutionary ecology of reproductive behavior, mating systems and
parental care in animals
2) Neuronal control of behavior (21 lectures)

1. Introduction and history of animal behavior
2. Revision of concepts from neurobiology – action potentials, synapses,
neural coding, etc
3. General concepts in ethology
4. Sensory processing – toad prey capture, sound localization in owls,
echolocation in bats
5. Decision making
6. Motor Output – CPGs, leech swimming/crawling, escape behavior, cricket
vocalizations
7. Sensorimotor integration – electric fish, bird song
References 1. Behavioral Neurobiology: An Integrative Approach. (Second Edition 2010)

Gunther K Zupanc. Oxford University Press
2. Animal Behavior: An Evolutionary Approach (Tenth edition 2013) John Alcock.
Oxford University Press
3. Scientific papers from journals – will be provided as a reading list during the
45
course
Discipline Biology
Course title Animal Physiology I
Semester 6,8
Nature of course Lectures and Lab demonstrations
Credits 4
Introduction The aim of the course is to impart in depth knowledge in the physiology of different
systems with focus on the human model. The emphasis will be on understanding
how these systems are inter-linked, and how are they regulated and how they
maintain the homeostasis.
The course will prepare the student for undertaking research in any area of animal
physiology.
This course is a pre-requisite for Animal Physiology II.
Course contents Human Physiology (Number of lectures 36)

Introduction (1 lecture)
The concept of homeostasis
Skeletal muscle system (2 lecture)
Structure and function of skeletal muscle, neuromuscular junction
The cardiovascular system (10 lectures)
The cardiac muscle; The heart as a pump; rhythmical excitation and conduction
system of heart; Frank-Starling’s principle; autonomic control of heart; normal and
abnormal ECG; coronary circulation and ischemic heart conditions. Biophysics of
blood flow and resistance, fluid exchange across capillary, nervous and hormonal
regulation of circulation, circulation in the brain, lymph formation and circulation,
CSF secretion and circulation
The kidneys, body fluids and excretion (6 lectures)
The body fluid compartments, urine formation by the kidneys; glomerular filtration
and tubular processing; renal blood flow; counter-current mechanisms; rennin-
angiotensin system; control mechanisms for regulating sodium and water
excretion; thirst mechanism; antidiuretic hormone, diabetes insipidus, diuretics
The gaseous exchange, transport and tissue respiration (5 lectures)
Pulmonary ventilation, pulmonary circulation, physical principles of gas exchange;
gaseous exchange; transport of oxygen and carbon dioxide in the blood and body
fluids; oxygen dissociation curve; Bohr and Haldane effect; neural regulation of
respiration.
Gastrointestinal physiology (4 lectures)
Physiology of smooth muscles, principles of gastrointestinal function – associated
glands and secretions, motility, nervous control and blood circulation; enteric
nervous system; transport of food in alimentary tracts, digestion and absorption
Endocrinology and reproduction (8 lectures)
Introduction to endocrinology; the pituitary hormones and their control by the
hypothalamus; the thyroid, adrenal cortex and medulla, and hormones of the islets
of Langerhans; disorders of endocrine glands; calcium regulation; sex hormones,
regulation of menstrual cycle, hormones of the placenta
Lab-work
Studies on the various organ systems of teleost fish; anatomy of brain, kidney and
heart of goat; study of histological preparations of various tissues of rat.
46
References Textbook of Medical Physiology by Guyton and Hall (2008) 11th Ed. Saunders
Review of Medical Physiology by Ganong (2003) 23th Ed. Lange
Eckert Animal Physiology by Randall, Burggren and French (2002) 5th Ed. Freeman
Williams Textbook of Endocrinology by Kronenberg Melmed, Polonsky and Larsen
(2008) Saunders
Animal Physiology, by Hill, Wyse, and Anderson (2008) Second Edition, Sinauer
Discipline Biology
Course title Data Science
Semester 6,8
Credits 3
Prerequisites Biostatistics
Introduction Objectives: Data science has recently received a lot of attention in all of science,
because of spectacular advances not only in the availability of large amounts of
data but also in our ability to store and process this. Furthermore, there is a
growing optimism across various science communities that data science methods
can complement ab initio modelling in the discovery of fundamental scientific laws
as well. However, sometimes data science gets confused with “big data” alone;
whereas data science is really a formalism of evidence-structured discovery, which
employs a compendium of several tools such as from statistics, machine learning,
optimization theory and so on, and can be used effectively on both ‘large’ problems
as well as ‘small’.
This course will introduce students to data science, in order to: (1) Empower them
with a sharp knowledge of the domain and scope of data science, and (2) Train
them in its methods so that they can begin to discover how to make the most use
of these tools.
Outcomes: This course aims to introduce the essentials of data science in a broad
manner that highlights central principles and commonly used techniques, and, its
wide applicability across multiple science disciplines, with special focus on biology
and medicine.
Course contents Introduction to statistical learning, problem formulation and assessing model
accuracy. The regression and classification settings, supervised and unsupervised
learning; bias-variance tradeoff.
Methods: Linear and polynomial regression, K-nearest neighbors, classification,

resampling methods, linear model selection and regularization, tree based
methods, support vector machines, neural networks, and unsupervised learning.
References Main text: An Introduction to Statistical Learning: with Applications in R (Springer
Texts in Statistics) by James, Witten, Hastie and Tibshirani. Springer; 1st ed. 2013,
Corr. 7th printing 2017 edition (September 1, 2017)
Additional texts:
The Elements of Statistical Learning: Data Mining, Inference, and Prediction,
Second Edition. Authors: Hastie, Trevor, Tibshirani, Robert, Friedman, Jerome,
Springer Series in Statistics, 2009.
Understanding Machine Learning: From Theory to Algorithms 1st Edition, Authors:
Shai Shalev-Shwartz and Shai Ben-David. Cambridge University Press; 1st edition
(May 19, 2014).
47
Discipline Biology
Course title Developmental Biology
Semester 5, 7
Credits 4
Introduction Objective: To introduce students to mechanisms of pattern formation in animals.
Course contents The course will follow the development of invertebrates and vertebrates from the
egg to the embryo. Basic concepts of developmental biology as also principles and
mechanisms that help form and shape the organism will be taught and discussed.
1. Introduction to positional information, axes, coordinates and morphogen
gradients
2. Commonly used Experimental methods in developmental biology
3. Generation and Interpretation of gradient information and Pattern
formation
4. Physics and Mathematics of morphogen gradients and their interpretation
5. Modes of cell-cell interactions during tissue organization: Self-
organization, lateral inhibition, induction, and recruitment
6. Growth and differentiation
7. Evolution of body plan
8. Stem cell biology and tissue repair
Literature (papers, reviews, lectures) will be made available online and throughout
the course recent papers in the area of developmental biology will be read to
update the class on recent research discoveries.
References 1. Gilbert SF, (2006) Developmental Biology, 8th edition, Sinauer Associates,
Inc.
2. Wolpert L, Beddington R, Jessell T, Lawrence P, Meyerowitz E, Smith J,
(2008) Principles of Development, Oxford University Press.
3. Ethan Bier (2000). The Coiled spring: How life begins. CSH press.
48
Discipline Biology
Course title Ecology II
Semester 6 OR 8 (this course is offered in alternate years)
Credits 4
Introduction This course will cover current topics in Ecology. Instead of attempting a
comprehensive review of general Ecology, the course will focus on in-depth
coverage of select topics. Some of the material introduced in Ecology I will be
covered in greater detail, and other topics like Functional Ecology, Global Warming
and Climate Change, Chemical Ecology, Conservation and Sustainable Development
will be introduced. One of the objectives of this course is to introduce some of the
applied aspects of Ecology. The primary method of organization will be readings
and class discussions from the primary literature in Ecology.
Course contents The broad areas of focus will be:
History, Philosophy and the Practice of Ecology (6)
Functional Ecology/Trait-based Ecology (6)
Community structure and biodiversity (6)
Global warming and Climate Change (6)
Ecology of invasion and introgression (4)
Biodiversity conservation and sustainable development (6)
Ecological impact assessment (2)
Chemical and Molecular Ecology (4)
References Ellison, G. N., & Gotelli, N. J. (2004). A primer of ecological statistics. Sinauer,
Sunderland, Massachusetts, USA.
Ricklefs RE, and Miller (2000). Ecology. Freeman and Co. 4th edition.
Gurevitch J, Schener SM, and Fox GA (2006). The Ecology of Plants. Sinaeur and
Assciates. 2nd Edition.
Begon M, Townsend CR, Harper JL (2006). Ecology: from individuals to ecosystems.
Blackwell Publishing. 4th edition.
Journals: Ecology; Ecology Letters; Journal of Ecology; Annual Reviews in Ecology
Evolution and Systematics; Evolution; Oikos; Oecologia; Functional Ecology;
Molecular Ecology; American Naturalist; and others.
Discipline Biology
Course title Evolution
Semester 6, 8
Credits 3
Introduction This course is aimed at being a slightly non-trivial introduction to evolutionary
theory and its applications to various fields of biology. While some of the topics
listed here have been already introduced in Ecology and Evolution (second year
course), the treatment in this course will be much more detailed as well as
mathematical. This course will be useful for all students in general and biology
students in particular. We are departing slightly from a traditional evolutionary
biology course to explicitly incorporate elements of the ongoing Extended
Evolutionary Synthesis. There will also be a strong component of application of
evolutionary biology in various ways.
Course contents 1. Brief history and an overview of the process of evolution
49
2. Evidence for evolution
3. Population Genetics: Hardy-Weinberg Equilibrium, Selection, Mutation,
Migration, Nonrandom mating, Genetic Drift, Neutral evolution, Linkage
Disequilibrium, Epistasis
4. Quantitative Genetics: Heritability, Breeding Value, Breeder's equation, Price
Equation
5. Sources of variation: Mutation, Recombination, Epigenetic variation, Phenotypic
plasticity, Cryptic Variation
6. Genome Evolution: Mobile genetic Elements, Evolution of Mutation Rates, Gene
Duplication
7. Sex: Asexual and sexual reproduction, Cost of sex, Benefit of Sex, Sexual conflict,
Evolution in asexual systems
8. Life-history evolution: Adaptation, Trade-offs, Number and size of offspring,
Parent-offspring conflict.
9. Evolution and Health: Evolution of Antibiotic Resistance, Virulence, Evolutionary
Medicine, Aging.
References The treatment shall be based on primary literature and multiple monographs. The
following books will cover some of the topics.
Roff, D.A. 1992. The Evolution of Life Histories: Theory and Analysis. Chapman and
Hall, New York.
Herron, J. C. & Freeman, S. (2014). Evolutionary Analysis. Pearson Prentice Hall,
Upper Saddle River, NJ
Discipline Biology
Course title Introductory Immunology
Semester 6, 8
Credits 4
Introduction The objective of this course is to introduce basic concepts in immunology to
students from all disciplines. Students will learn about various components of the
immune system including molecules, cells and organs and their function. The
primary emphasis however will be on how these components are physiologically
integrated into the mechanisms of adaptive immune system development and
function.
This course is a pre-requisite for Advanced Immunology.
Course contents I. The immune framework; evolution, ecology and organisation of immune tissues
 the need for immunity, innate and adaptive immunity, pathogen niches
and effector responses, organisation of immune components
II. Target recognition strategies in the immune system; innate, adaptive and MHC
repertoires
 target identification, non-clonal and clonal receptors, self/non-self
discrimination, contexts of signals, control of immune context of antigenic targets,
MHC structure-function, polymorphisms, classes, presentation pathways
III. Developmental rules in the immune system; innate versus adaptive immune cell
differentiation
 embryogenesis and immune development, sites and lineages, checkpoints
50
and signals, proliferation and differentiation balances, unique characteristics of
lymphocyte differentiation programmes
IV. T cell immune responses

 TCRs and their signalling, proliferation and differentiation, effector and
memory response balances, regulation of commitment to distinct cytokine groups
in T cell responses, CD8 T cell response control, regulatory T cells
V. B cell immune responses
structures and functions of antibody/BCR molecules, BCR-mediated
signalling, accessory signals, germinal centres, isotype class switching,
somatic hypermutation, differentiation of memory B cells versus plasma
cells
VI. Immunity in heath and disease

Ideas of ‘health’ and ‘disease’, immunity to infections, integration of innate and
adaptive components in regulating immune responses to infections, mucosal
immunity, non-infection-targeted immune inflammation, autoimmunity and allergy
References 1. Janeway’s Immunobiology, Murphy and Weaver, 9th edition, Garland
Science (2016), ISBN: 9780815345053
2. Basic Immunology, 5th Edition. Functions and Disorders of the Immune
System. Authors: Abul Abbas Andrew H. Lichtman Shiv Pillai.
Paperback ISBN: 9780323390828. Imprint: Elsevier
Published Date: 2nd November 2015
Discipline Biology
Course title Mathematical and Computational Biology
Semester 6, 8
Credits 4
Introduction The goal of this course is to analyse and simulate mathematical and computational
models of biological systems. Classical examples will be drawn from the literature
that best illustrate the seamless integration of mathematics and biology, such as
modeling in neuroscience (the classification of spiking activity based on different
bifurcation scenarios), enzyme kinetics (slow-fast analysis and the Michaelis-
Menten equations), cell cycle modelling, pattern formation in development and
others.
The target audience is two-fold:
a. Biology students will get introduced to some of the best examples of
mathematical reasoning in biology. This is an excellent first step to
thinking about modeling in your own work.
b. Mathematics students can view the course as an “Introduction to
Mathematical Modeling” with examples drawn from Biology. They will
learn techniques that have been found useful in applied mathematics, and
at the same time they will get a feel for important and interesting
problems arising in Biology (and Chemistry).
Many of the models will also be simulated on a computer. In the process, students
will be introduced to programing in Matlab, and numerical techniques to solve
ordinary and partial differential equations.
Course contents Applications of difference equations. This module will analyse linear and nonlinear
difference equations that describe the dynamics of populations. We will look at
different numerical methods to evaluate difference equations.
Models of continuous processes using ordinary differential equations. We will
51
analyse and simulate equations describing enzyme kinetics, excitable systems
including heart and nervous tissue and oscillations in population models. Methods
to numerically integrate differential equations will be covered.
Spatially distributed systems using partial differential equations. In this module we

will examine models of development and pattern formation based on reaction
diffusion equations. Methods to simulate these partial differential equations will be
covered.
Analysis of stochastic systems. Here we will perform Monte Carlo simulations of of

cellular signaling pathways and compare our simulations with those obtained from
deterministic equations.
References 1. Leah Edelstein–Keshet, Mathematical Models in Biology (Classics in Applied

Mathematics). SIAM: Society for Industrial and Applied Mathematics; 1st
edition (February 2005). This book is available online from SIAM. Multiple
copies are also present in the IISER library.
http://epubs.siam.org/doi/book/10.1137/1.9780898719147
2. Philip Nelson, Physical Models of Living Systems., WH Freeman; 1st ed. 2015
edition
3. Cleve Moler, Numerical computing with Matlab, SIAM. This book is available
online from mathworks and from the SIAM ebooks website.
https://in.mathworks.com/moler/chapters.html
Discipline Biology
Course title Microbiology
Semester 6, 8
Credits 4
Introduction The objective of the course is to give an insightful overview of microbial biology,
with more emphasis on prokaryotes. Since the principles of genetics, molecular
biology, physiology, population biology are covered in other courses this course will
focus on what is unique to microbial systems.
Course contents 1. Brief history of microbiology Classification of microorganisms-virus,
bacteria, fungi, protozoans etc.
2. Principles of virology: structure of viruses, viral life cycle
3. Bacteriophage life cycle and phage genetics
4. Microbial genetics: Concepts and applications
5. Horizontal gene transfer, pathogenicity islands
6. Bacterial defense mechanisms
7. Structure of the bacterial cell and comparison with eukaryotic cell
8. Bacterial growth and culturing- bacterial growth kinetics, media and
culture requirements
9. Bacterial cell cycle, cell division in bacteria
10. Bacterial motility and chemotaxis
11. Microbial communities and inter-bacterial communication
12. Introduction to industrial microbiology
13. Medical microbiology and disease
52
14. Development and differentiation in microorganisms- Dictyostelium,
Neurospora, sporulation in Bacillus
References 1) Tortora GJ, Funke BR and Case CL (2004) Microbiology: An Introduction. 8th
Edition. Pearson Education.
2) Moat AG, Foster JW, Spector MP (2006) Microbial physiology, 4th edition, John
Wiley & Sons.
3) Flint SJ, Enquist LW, Racaniello VR, Skalka AM (2008) Principles of Virology
(Volume I), 3rd Edition.
4) Brock Biology of Microorganisms, Michael J. Madigan and John M. Martinko,
13th edition, ISBN-13: 978-0321649638
5) The Genetic Switch by Mark Ptashne (2001), Cold Spring Harbor Limited
6) Relevant research articles and reviews suggested in class.
Discipline Biology
Course title Applied Plant Biology
Semester 6, 8
Nature of course Lectures and Laboratory sessions
Credits 3
Prerequisites Plant Biology
Introduction The objective of this course is to gain knowledge/skills in applied plant biology.
Students would learn and understand know-how about practical questions and
problems in Plant Biology field. This course would also provide current updates in
advanced technologies that are routinely applied in modern Agricultural
biotechnology. The course includes lectures and hands on laboratory sessions and
will prepare students for future career in Agri-Biotech sector (for food, feed,
environment and health based programs).
Course contents 1. Plant cell tissue and organ culture (Various methods of in vitro plant cell
tissue and organ culture, organogenesis, somatic embryogenesis & micro-
propagation (5 L)
2. Plant genetic engineering (transformation and transgenic plants, various
gene transfer and genetic engineering technologies, molecular mechanism of
inter-kingdom gene transfer (prokaryote to eukaryote). Ti and Ri Plasmids,
Multiple Gene Transfer (MGT) to plants and engineering metabolic pathways
(5 L)
3. Editing plant genomes with CRISPR- CAS9, TALEN, ZFN (2L).
4. Virus Induced Gene Silencing in plants (VIGS) (1 L)
5. A full module of gene identification to its functional validation (prediction,
isolation, cloning, vector construction, and expression in plant, a combination
of lectures and parallel lab sessions) (3 lectures and labs)
6. Exploring model plant genomes (Arabidopsis/ tobacco/ Rice) comparative
genomics leading to plant omics (genomics, proteomics, metabolomics) and
biotechnology (2 L)
7. Phytoremediation and its application (1 L)
8. Molecular Farming and Plantibodies, Production of
phytochemicals/nutraceuticals (1 L)
9. Introduction to Mendelian and quantitative Inheritance (1 L).
10. Molecular markers and Marker Assisted Selection/molecular breeding (2 L).
11. Regulatory Issues and IPR (1 L)
References 1. Indra KV, and Trevor T. (2005) Plant Cell and Tissue Culture, Kluwer Academic
53
Publishers
2. Introduction to plant cell tissue culture. M K Rajdan
3. Rainer F, and Stefan S. (2004), Molecular Farming-plant made pharmaceuticals
and technical proteins, Wiley Verlag & Co.
4. Kan W, (2006) Agrobacterium protocols (Methods in Molecular Biology), Vol. 1
and 2, Humana Press.
5. Introduction to Plant Breeding by B.D. Singh
6. DNA markers in plants by I.K. Vasil
7. In addition to the suggested books, papers are from Current Opinion in
Biotechnology. Trends in Plant Science, Plant Cell Report, Plant Science and
Plant Biotechnology & Nature biotechnology are referred.
Discipline Biology
Course title Biology and Disease
Semester 8
Credits 4
Introduction Objectives: 1) Integrate the biology (cell, molecular and physiology) taught so far, 2)
Develop insights into biology revealed by the disease condition, and 3) Teach
technology development and translation prompted by the disease condition.
Cancer, neurodegenerative disorders, infectious diseases, imprinting disorders are
some of the modules that will be used as disease/disorder models.
Course contents Module Topics Lectures
1 The Nature and Investigation of Diseases 2
2 Neurodegenerative Disorders 3
3 Infectious diseases/ Bacteriology/ Virology 4
4 Metabolic diseases 6
5 Cancer 6
6 Group / Paper / Case Study Discussions 6
References 1. Biology of Disease by Nessar Ahmed, Maureen Dawson, Chris Smith and Ed Wood;
Taylor & Francis; 1 edition (December 13, 2006).
2. One Renegade Cell: The Quest For The Origin Of Cancer (Science Masters) by
Robert A. Weinberg; Basic Books; 1 edition (October 7, 1999).
3. The Biology of Cancer by Robert Weinberg; Garland Science; 1 edition (June 7,
2006).
4. The Biology Of Disease by Murray, Jonathan and Kirk; Wiley-Blackwell; 2 edition
[May 2001]
Discipline Biology
Course title Cellular Biophysics II
Semester 6 OR 8 (Course offered in alternate years)
Credits 3
Prerequisites Cellular Biophysics I
Introduction This course continues from where the previous course Cellular Biophysics I had left
off. Here, we examine how to approach the non-equilibrium aspects of cellular
biophysics. We will begin with a detailed treatment of diffusion and its effect on
cellular motility in water. We will then examine the use of rate-equation theories to
understand fluctuating systems such as ion channels and enzymes. Research paper
reading will highlight case studies of the successful application of physics biological
54
problems. Assessment will be through discussion based research paper reading,
assignments, lab-work as well as a term paper. This term paper topic will be picked
by all students at the beginning of the course, and after a mid-semester half-page
update, will be assessed through oral presentation and written report assessment
at the end of the course. The course aims to help you think about modern topics in
cellular biophysics, appreciate their limitations and come up with a problem and
methodology to solve it.
Course contents Section #1- (Mathematics of water and crowding)

Hydrodynamics of water. Low Reynolds Number world. Macromolecular crowding.
Equilibrium in crowded enviroments. Crowded dynamics.
Section #2 – (Dynamics of macromolecules)
Molecular motors: translation, rotation and the diffusive-limit. Rectified random
walks and their relation to molecular motors. Coordination of motor activity.
Cytoskeleton- The polymerization ratchet, force generation, translocation.
Mechanics of transcriptional regulation. DNA packaging from viruses to eukaryotes.
Protein folding.
Section #3: (Non-equilibrium approaches)
Langevin equation, Smoluchowsky equation and general methods of dealing with
nonequilibrium scenario.
References 1. David Boal (2001) Mechanics of the Cell. Cambridge University Press.
2. Philips, Kondev, Theriot & Orme (2009) Physical Biology of the Cell. Garland
Science, Taylor and Francis Group LLC.
3. Gabor Forgacs and Stuart Newman (2005) Biological Physics of the Developing
Embryo. Cambridge University Press.
4. Philip Nelson (2007) Biological Physics. W. H. Freeman Company.
5. Roland Glaser (2010, 2012) Biophysics: An Introduction. Springer.
6. Steven Vogel (1996) Life in Living Fluids. Princeton University Press.
7. Erich Sackmann & Rudolf Merkel (2010) Lehrbuch Der Biophysik. Wiley VCH
Discipline Biology
Course title Genome Biology
Semester 6, 8
Credits 3
Introduction In the year 2003, the complete human genome sequence was released, which led
to the obvious question – what next? Have we achieved and done everything that
we understand with regard to the human genome? Certainly NOT. This was just the
beginning and has paved the way for some path breaking discoveries and along
with it has brought unprecedented cutting edge technological breakthroughs,
which are only now giving us some glimpses of our own genomes.
The goals of this course are to introduce students to the recent findings and
excitement in Genome Biology and Genomics.
This course is useful to any student with an interest to understand the

fundamentals of genome biology and how recent findings in cell biology and
cytogenetics interface with Genomics and its application to the diagnosis and
treatment of complex human diseases.
55
An ability to design novel experimental strategies and assays to harness the power
of genomics to study both fundamental and applied questions in biology.
Course contents Module 1: Nucleic acids (structure and function): DNA, RNA, proteins, DNA-
hydrogen bonding, base pairing, replication, sequencing, annealing, hybridization,
transcription, amino acids, proteins. Biology of Genomes, Synthetic genomes –
Creation of a Bacterial cell controlled by a chemically synthesized genome. (4)*
Module 2: Biology of the nucleus – Nuclear envelope, Nuclear pore complexes

(Nups), Nuclear bodies, nuclear speckles and their functional significance,
Mechanobiology of the nucleus (4)
Module 3: Advanced Chromosome biology – karyotyping & Spectral Karyotyping

(SKY), FISH methods, chromosome painting studies and molecular cytogenetics,
(Includes lab demonstrations) (4)
Module 4: Functional Genomics: Array-comparative genomic hybridization (a-CGH),

Microarrays, Chromosome conformation capture assays, 3C, 4C and Hi-C, Next Gen
DNA and RNA Sequencing technologies, Chip-Seq, Copy number variations (CNV),
Transcriptomics, Proteomics, Bioinformatics, Applications of systems &
Computational Biology (10)
Module 5: Genome Biology & Disease: Cancer Genomics, Inherit d diseases,

Chromosomal aberrations, Metabolomics, Stem cells & genomics (10)
* No. of lectures/hours/discussions (approx)
References 1) Bruce Alberts, Alexander Johnson, Julian Lewis, Martin Raff, Keith Roberts, Peter
Walter, Molecular Biology of the Cell, 5th Edition, 2007 (Sections: 1-3, Chapters: 1-
8).
2) Gibson et al, Science 2 2010: 329, 52 – 56
3) http://cshperspectives.cshlp.org/cgi/collection/the_nucleus
4) Shivashankar GV Nuclear mechanics and genome regulation, Methods Cell Biol.
2010;98:xiii
5) Vorsanova SG et al Human interphase chromosomes: a review of available
molecular cytogenetic technologies, Mol Cytogenet. 2010 Jan 11;3:1
6) Padilla-Nash HM et al Spectral karyotyping analysis of human and mouse
chromosomes. Nat Protoc. 2006;1(6):3129-42
7) http://my5c.umassmed.edu/welcome/welcome.php
8) Metzker ML, 2010, Nature Reviews Genetics 11, 31-46
9) http://www.nature.com/omics/index.html
Discipline Biology
Course title Neurobiology II
Semester 6 OR 8 (Course offered in alternate years)
Credits 3
Prerequisites Neurobiology I
Introduction This course builds from Neurobiology I and focuses on higher functions of the
nervous system. Systems level functions like, sensory and motor systems,
processing of pain and emotion, arousal and circadian rhythms will be discussed
56
from qualitative and quantitative perspectives. Traditional and new imaging
modalities will be introduced. Emerging areas of astrocytic and glial feedback,
mirror neurons and current understanding of cognition will also be discussed.
This course is essential for students desirous of pursuing research in any branch of
neurosciences.
Course contents 1) Autonomous nervous system

2) Sensory systems and sensory processing (Audition, Vision, Chemosensation
(Olfaction and Gustation) Somatosensory, Pain
3) Motor control and pattern generators
4) Sleep and circadian rhythms
5) Processing of emotion
6) Learning and memory
7) Neurobiology of perception and cognition
8) Techniques: such as Brain imaging, Electro-encephalography, Positron Emission
Tomography, Functional Magnetic Resonance Imaging, Calcium Imaging,
Optogenetics etc.
References 1) Kandel E, et al. (2000). Principles of Neural Science. 4th Ed. McGraw-Hill Medical.
2) Bear M, et al. (2006). Neuroscience. 3rd Ed. Lippincott Williams & Wilkins.
3) Purves D et al. (2011). Neuroscience. 5th Ed. Sinauer Associates.
4) Larry Squire et. al (2008). Fundamentals of Neuroscience, 3rd Ed.
Discipline Biology
Course title Physical Biochemistry
Semester 6, 8
Credits 3
Introduction Objectives: To teach students to think quantitatively about biochemical and
biophysical data concerning biomolecules
Outcomes: Students will gain the self-confidence to tackle basic quantitative
questions at the interface of biology and chemistry
Course contents Basic structural and chemical properties of biomolecules (2 lectures)

Biomolecular fluorescence (3 lectures)
Basic thermodynamics pertaining to biomolecules in solution (3 lectures)
Elementary statistical thermodynamics pertaining to biomolecule conformational
change (3 lectures)
Molecular Interactions (Torsional forces, Electrostatics, hydrogen bonding, vDW
interactions, hydrophobic effect, disulphide bonds, effective concentrations) (6
lectures)
Protein thermodynamics (2 lectures)
Binding (4 lectures)
Basic kinetics for understanding biochemical mechanisms (4 lectures)
References 1. Physical Chemistry –Principles and applications in Biological Sciences.
Tinoco, Sauer, Wang,Puglisi, Harbison, Rovnyak. Pearson. 2014. 5th
57
edition.
2. Principles of Physical Biochemistry. Van Holde, Curtis Johnson, Shing Ho.
Prentice Hall. 1998. 1st edition.
3. Structure and Mechanism in Protein Science. Fersht. Freeman. 1999. 1st
edition.
4. Physical Chemistry for the Life Sciences. Atkins, de Paula. Freeman. 2006.
1st edition
Discipline Biology
Course title Lab training /Theory Project
Semester 5, 6, 7, 8 (a student can credit maximum of 4 of these courses)
Credits 3
Introduction The larger objective of this course is to encourage students to participate in
ongoing research at IISER. This may be in the form of a reading/literature
review/theoretical and computational project/lab based research project.
The student has to identify, talk to and mutually agree on a research project before
registering for this course.
Course contents The scope, duration, structure, expectations, and evaluation criteria for the course
are decided by the project supervisor. The project is evaluated through
midsemester and end semester reports, and poster presentations evaluated by a
departmental committee at the end of the semester.
References As per suggestion of the project supervisor
58
4.2 Syllabi for Elective Courses in Chemistry
Course title General Chemistry Practicals (elective)
Semester 3
Credits 3
Introduction In this UG laboratory course students will be exposed to basic chemistry
experiments. As part of this course, the students will be carrying out regular
chemistry experiments in the lab, experience handling analytical
instruments, and data analysis.
Course contents Experimental procedures/details will be given in the first class. You will be
doing 10-12 experiments in general chemistry topics. Each class will start
with explanation (theory) for 15-30 minutes followed by 2.0 hour lab work,
and 30 minutes laboratory work-book writing.
Tentative list of experiments
1. Synthesis of artificial sweetener (Aspartame/Saccharine)

2. Continuous-Flow Chemistry in Undergraduate Education: Sustainable
Conversion of Reclaimed Vegetable Oil into Biodiesel
3. Biodegradable polymers from organocatalysts
4. Reaction of Dimedone and Benzaldehyde: A Discovery-Based Lab
5. Determination and comparison of acid neutralizing power of commercial
antacids.
6. Preparation of potash alum from scrap aluminum.
7. Synthesis of molybdenum blue and estimation of phosphoric acid in cold
drinks by Mo-Blue Method.
8. Saponification of esters and soap manufacturing with different
ingredients.
9. Acid-base Titrations using Conductivity Method (general concept about
acid-base and electrochemistry).
10. To investigate the phenomena of Depression in Freezing point and
determine the molar mass of unknown solute (Colligative properties).
11. Determination of Heat of Neutralization. (Thermodynamics)
12. Study the second order velocity constant of the hydrolysis of ethyl
acetate by sodium hydroxide using conductivity measurements (Kinetics).
References Readings and laboratory manual provided during the course.
Course title Principles of Organic Chemistry II/ Organic reactions, transformations and
stereochemistry
Semester 4
Nature of course Lectures and tutorials
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Credits 3
Introduction This course brings an exposure to the various concepts for the organic
transformation and reaction mechanism. To gain exposure on the reagents
and reactive intermediates commonly found in the basic organic reactions,
which will be useful for making of the C-X bond formation reactions. The
expected outcome of this course would be strengthening of synthesis
foundations; students would be in a position to begin rationalizes the
fundamental in organic reactions and methodologies.
Course contents Section 1: Name reactions in organic chemistry (12)

Grignard reactions, Aldol reactions, Mukaiyama Aldol Reactions, Stobbe,
Claisen, Knovenagel, Benzoin condensations, Darzens glycidic ester
synthesis; Dieckmann reactions, Wittig reaction, Julia Olefination,
Peterson Reaction, Reformatsky reaction, Robinson annulation, Stark-
enamine synthesis, Mannich reaction, Gattermann aldehyde synthesis,
Friedel-Crafts acylation reaction, Reimer–Tiemann reaction, Henry
reaction, Biginelli Reaction, Prevost reaction, Woodward reaction,
Shapiro reaction.
Section 2: Molecular Rearrangements (8)
Types of rearrangements, Rearrangement to electron-deficient Carbon,
nitrogen and Oxygen, Migratory aptitude, Benzidine, Pinacol, Benzilic
acid, Favorskii, Wolff, Hofmann, Curtius, Schmidt, Lossen, Beckman, Fries,
Demyanov, Baeyer- Villiger, and Wagner-Meerwein, Stevens
Rearrangement, Baker-venkatraman rearrangement, Aromatic
rearrangement: Dienone phenol, etc
Section 3: Free radical reactions (3)
Substitutions and additions, SET mechanisms, Rearrangements involving
free radicals.
Section 4: Basic concepts in stereochemistry: (5)
Chiral induction, Stereochemical descriptors, enantiomeric excess,
diastereomeric excess, Crams rule, Felkin-Ahn model, Cieplak effect,
chirality in nature, stereochemistry in biomolecules (amino acids,
peptides, nucleic acids, carbohydrates and synthetic polymers).
Books for References:

References 1. Organic Chemistry by J. Clayden, N. Greeves, S. Warren, P. Wothers;
Oxford Press, Second Edn.
2. Principles of Organic Synthesis,R. O. C. Norman and J. M Coxan
3. Advanced Organic Chemistry: Part B (Reaction and Synthesis) by F. A.
Carey and R. J. Sundberg; Springer, Fifth Edn
4. March’s Advanced Organic Chemistry, by Michael B. Smith and Jerry
March; Wiley India, 2012, Sixth Edn
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Course title Fundamentals of Molecular Spectroscopy [Necessary for Advanced Molecular
Spectroscopy, and Photochemistry and Photophysics]
Semester 4
Credits 3
Introduction The objective of this course is to teach the fundamentals of major branches of
Spectroscopy and its applications. Spectroscopy is an important research tool in all
areas of science (Chemistry, Physics and Biology). The interaction of light with
matter provides a great deal of physical information about a system of interest and
ultimately defines many of the observational techniques used. In this course, this
radiation-matter interaction and the quantitative information it can provide about
molecular systems will be examined. The students will be exposed to UV/Vis, IR,
Raman, and NMR spectrophotometers and able to build the basic foundation in
spectroscopy which will be an asset throughout their scientific career.
Course contents Section 1
Introduction to radiation-matter interaction
Topics: Electromagnetic spectrum, Electromagnetic radiation, Basic elements of
spectroscopy, selection rules, intensity of spectral lines.
Section 2
Rotational spectroscopy
Topics: Rotation of molecules; Moments of inertia, Rotational spectra: Diatomic
molecules; Rigid rotor approximation, Treatment as a non-rigid rotor, Intensities of
rotational spectral lines, Techniques and instrumentation.
Section 3
Vibrational spectroscopy
Topics: Vibration of diatomic molecules. Harmonic and anharmonic oscillators,
Vibrational-rotational couplings, Vibration of polyatomic molecules, Techniques
and instrumentation, Analysis of molecules by Infrared spectroscopy. Introduction,
Quantum and classical theories of Raman effect, Pure rotational Raman spectra,
Vibrational Raman spectra, techniques and instrumentation.
Applications of vibrational spectroscopy.
Section 4
Electronic spectroscopy of Atoms
Topics: Energy levels in atoms, Coupling of angular momenta, Term symbol and
selection rules, Spectra of hydrogen atom and others.
Section 5
Electronic spectroscopy of molecules
Topics: Electronic energy levels and selection rules, Term symbols, electronic
spectra of diatomic molecules, Franck-Condon principle, Electronic spectra of
polyatomic molecules, Fluorescence and Phosphorescence, Spectrophotometer
and the Beer-Lambert law.
Section 6
Magnetic resonance spectroscopy
Topics: Nuclear magnetic resonance (NMR): The magnetic field; The energies of
nucleus in a magnetic field; Nuclear spins and magnetic moments; The origin of
Nuclear magnetic Resonance Spectra; The NMR spectrometer; The chemical shift;
Spin-spin coupling and the fine structure in NMR; Fourier Transform NMR
spectroscopy; Examples of NMR spectra.
Determination of structure of unknown compounds using NMR spectroscopy
References a. Specific books for each topic will be announced in class. Some general text
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books are listed below.
b. Molecular Spectroscopy, Jeanne McHale, First Edition, Pearson
c. Fundamentals of molecular spectroscopy: C. N. Banwell and E. M. McCash,
4th edition, Tata McGraw Hill.
d. Physical Chemistry - A Molecular Approach; Donald A. McQuarrie and John
D. Simon, Viva Books Private Limited.
e. Physical Chemistry, P. W. Atkins, Oxford University Press.
f. Introduction to spectroscopy, D. L. Pavia, G. M. Lampman, G. S. Kriz, J. R.
Vyvyan, India Edition, Brooks/Cole Cengage Learning.
g. Spectrometric identification of organic compounds, R. M. Silverstein, F. X.
Webster, 6th edition, Wiley India Edition.
Course title Analytical Chemistry/ Separation Principles and Techniques
Semester 4
Credits 3
Introduction Gain a thorough understanding of the basic molecular aspects of separation
processes. At the end of the course, the student should be able to understand
similarities and differences in operating aspects of various separation techniques.
Gain a thorough knowledge of general chromatographic processes. Gain an
overview of mass spectrometric separations both coupled to chromatography
and/or as an independent method.
Training sessions on HPLC, GC, GC MS, Centrifugation, Electrophoresis and few
other Chromatographic techniques will be undertaken; if the number of students
who take this course are large then, we restrict to demonstrations only.
Course contents Separation of mixtures- two solids, two liquids, two gases or combinations (3 h)
Solvent extraction, distillations, Liquid- Liquid extraction and other methods of
separation (3 h)
Types of Chromatography: GC, HPLC, Hyphenated techniques (6 h)
Electrophoresis, Centrifugation DNA/Protein separations/purifications (6 h)
Green Separation Process Separation using Zeolite and Polymer membranes.(2 h)
Chiral separations, Molecular recognition, Molecule imprinting, Polymer
separations ( 2 h)
Demonstrations (9 h)
References Text Book(s):
Analytical Chemistry 2.0 by David Harvey; Free online version. A copy of this book
will be given to all interested students who have a portable drive
An Introduction to Separation Science: B.L. Karger; L.R. Snyder and C. Horvath;
John Wiley & Sons, 1973
Other required course reference material (if any) will be announced/distributed
during the lectures
Course title Physical Organic Chemistry
Semester 5
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Credits 4
Introduction The main objective of this course is to expose students to the fundamental
concepts of structure and mechanism in organic reactions. Experimental tools
including the use of kinetics and thermodynamics to elucidate mechanisms of
reactions will be discussed. At the end of this course, students will be in a position
to predict reactivity patterns and propose reasonable mechanisms for the organic
reactions and transformations.
Course contents A brief introduction to models of bonding, Valance bond theory and Molecular
orbital theory (1 hr)
Solution and solvent properties and Non-covalent binding forces (5 hr)
Solvent scales, dielectric constant, surface tension and wetting, solubility, salvation
energy, thermodynamics of solutions, Ion pair interactions, salt bridges,
electrostatic interactions, dipole-dipole interactions, Hydrogen bonding (strengths
of hydrogen bonds, salvation effects, electronegativity effects, vibrational
properties of hydrogen bonds), cation-pi interactions, polar-pi interactions,
aromatic-aromatic interactions, induced dipole interactions, hydrophobic effects,
ion liquids.
Conformational analysis of acyclic and cyclic systems (4 hrs)
Thermochemistry of stable molecules, types of energies, heat of formation and
combustion, stain energy, relationship between structure and energies,
Conformational analysis of acyclic molecules: examples ethane, butane, pentane
etc., and allylic systems. Conformational analysis of cyclic systems (3-8 membered
rings) bicyclic ring systems, stereo-electronic effects (anomeric effect, electronic
strain, angle strain, hyper conjugation), fused rings.
Aromaticity and electronic effects on structure (3 hrs)
Interactions involving pi-systems, aromaticity, antiaromaticity and non-aromaticity,
energy criterion for aromaticity, structural and electronic criteria, destabilizing
effects, polycyclic aromatic hydrocarbons, annulenes etc.
Structural Effects on Stability and reactivity (10 hrs)
Energy surfaces, rate and rate constants, transition state theory, relationship to
the Arrhenius rate law, activation parameters, postulates and principles related to
kinetic analysis, Kinetic analyses for simple mechanisms, steady state kinetics,
saturation kinetics, Calculating rate constants, Hammond postulate, reactivity vs.
selectivity principle, the Curtin-Hammett principle, microscopic reversibility, kinetic
vs. thermodynamic control. Marcus theory, the Bell-Evans-Polanyi principle
Kinetic Isotope effects and isotopic labeling experiments (5 hrs)
Isotopic effects, primary isotopic effects, exothermicity and endothermicity,
isotopic effects for linier vs. non-linear transition states, secondary isotopic effects,
steric isotopic effects, equilibrium isotopic effects, tunneling, solvent isotopic
effects
Linear free energy relationships (8 hrs)
Origin of subsistent effects, field effects, inductive effect, resonance effect etc.,
Hammett equation, Hammett plots, Deviation form linearity, Taft equation,
solvent effects, Swain-Scott parameters, acid-base related effects, Bronsted
relationships, conditions to create LFER, extending LFER to biological and
pharmaceutical problems.
Organic Reaction Mechanisms (5 hrs)
Organic reaction mechanisms: Substitutions at aliphatic and aromatic centers
Nucleophilic aliphatic substitution reactions, structure function correlation with
nucleophiles, structure-function correlation with leaving group, structure-function-
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correlations with R groups, SN1 reactions involving non-classical carbocations,
nucleophilic additions of carbonyl compounds, radical aliphatic substitution,
electrophilic and nucleophilc aromatic substitution, nucleophilic substitution to
olefins.
Organic reaction mechanisms: Reactions involving additions and eliminations
Electrophilc addition to alkenes and alkynes, regiochemistry and stereochemistry of
addition reactions, hydroboration, epoxidation, carbene addition, elimination
reactions for aliphatic systems, kinetic and experimental observations of E2, E1,
and E1cb, experimental observations of elimination from radical intermediates.
Regiochemistry and stereochemistry of eliminations, orbital considerations,
thermal eliminations.
References Text Book(s)
Anslyn, E.; Dougherty, D. A.; Modern Physical Organic Chemistry, 1st edition, 2006.
University Science Books. (Primary)
Carrol, F. A. Perspectives on Structure and Mechanism in Organic Chemistry.
Brooks/Cole Publishing Company, 1998
Clayden, J.; Greeves, N.; Warren, S.; Wothers, P. Organic Chemistry. Oxford
University Press, 2nd Edition.
Sundberg, R. J.; Carey, F. A. Advanced Organic Chemistry, Part A: Structure and
Mechanism, 4th Edition. Kluwer/Plenum Press, 2000. (Primary)
Isaacs, N. Physical Organic Chemistry, 2nd Edition, Addison-Wesley-Longman,1995
Course title Main Group Chemistry
Semester 5
Nature of course Lectures & Tutorials
Credits 4
Introduction The objective of this course is to focus on the chemistry of main group elements
such as hydrogen, alkali metals and P-block elements from group 13 – 18 of the
periodic table. The central theme of this course is to give a detailed account on the
fundamental concepts relevant to structure and bonding, acids and bases, redox
behavior, reactions and applications of the main group elements and their
compounds. In addition to providing a necessary foundation for inorganic
chemistry, this course will also emphasize the role of main group compounds in
multi disciplinary areas of chemistry such as supramolecular, organometallic,
materials science and catalysis.
Course contents General Chemistry: ( 9 hrs)
The covalent bond: Bonding theories, MO theory of di- and polyatomic molecules;
Acids and bases: technical application of the concepts of acids and bases; main
group based Lewis aids and their anion sensor applications, introduction to
frustrated Lewis acid-base adducts and their applications.
Hydrogen: (2 hrs)
Atomic and physical properties of hydrogen; The classical hydrogen bond; Water;
Hydrates; Hydrogen ions; Metal hydrides; Activation of hydrogen complexes.
Chemistry of Group 1 and 2 Elements: (2 hrs)
The elements and their properties; Alkali metals in liquid ammonia and other
solvents; Coordination complexes.
Chemistry of Group 13 Elements: (7 hrs)
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The elements and their properties; Chemistry of Boron; Borides; Boron hydrides
(Preparation, structure, bonding, reactions and properties); Carboranes; Boron
halides, Boron-Nitrogen chemistry; Boron-Oxygen chemistry; Aluminium-alkyls and
-halides: structure, property and applications.
Chemistry of Group 14 Elements: (7 hrs)
The elements and their properties; Allotropy of Carbon: Diamond, Graphite, and
Fullerenes; Intercalation; Compounds with C-N, C-O, C-S bonds C-X (halogen)
bonds; Silane reagents, double bond rule in heavier main group elements, synthesis
and properties of disilene, disilynes and polysilanes; Silicides; Silicone Polymers;
Oxygen compounds of silicon; overview of the chemistry and properties of
Germanium and Tin.
Chemistry of Group 15 Elements: (5 hrs )
The elements and their properties; Nitrides; Hydrides of Nitrogen; Oxides of
Nitrogen; Oxo acids and anions of Nitrogen; Activation of Nitrogen; Nitrogen
fixation; Reaction of coordinated NO; Phosphides; Phosphorous halides and oxides;
Oxoacids of phosphorous and their salts; Phosphorous-Nitrogen compounds and
polymers.
Chemistry of Group 16 Elements: (4 hrs )
The elements and their properties; Singlet Oxygen; Ozone; Complexes of molecular
oxygen; N-S compounds; Sulfides; Oxides and oxoacids of sulfur; Chalcogenides,
Polychalcogenides and Zintl phases.
Chemistry of Halogens: (2 hrs )
The elements and their properties; Halides; Polyhalides; Interhalogen compounds;
Charge-transfer complexes of Halogens.
The Noble Gases: (1 hrs )
The elements and their properties; Compounds of Xenon and other noble gases.
Main Group Organometallic Chemistry: (3 hrs) Energy, polarity, and reactivity of M-
C bond; Organometallic chemistry of alkali and alkaline-earth metals.
Organometallic compounds of Boron, Carbon and Nitrogen group of elements and
their properties.
References Text Book(s) (one or two text books, with details like author, full title, edn,
publisher, year, chapter numbers etc)
Advanced Inorganic Chemistry by Cotton, Wilkinson, Murillo and Bochmann (6th
Ed.).
Chemistry of the Elements by Greenwood and Earnshaw (2nd ed.)
Concise Inorganic Chemistry by J. D. Lee (5th Ed.)
Inorganic Chemistry by Shriver & Atkins (4th Ed.)
Inorganic Chemistry by Huheey, Keiter, keiter, medhi (4th Ed.)
Organometallics by Christoph Elschenbroich (3rd Ed.)
Course title Symmetry and Group Theory
Semester 5
Credits 4
Introduction The objective of the course is to recognize symmetry in molecules and understand
its role in chemistry. The course will explore the role of symmetry in (A)
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determining molecular properties (e.g. optical activity, dipole moment), (B)
classifying and assigning nomenclature to molecules, molecular states and
molecular motions and (C) bringing about simplifications in the application of
quantum mechanics to molecules, and (D) determining spectroscopic selection
rules based on molecular symmetry. Group theory applied to the study of
molecular symmetry has far reaching consequences in chemistry and the course
will provide an in-depth appreciation of this.
Course contents  Introduction
 Symmetry elements and operations
 Schönflies notation of point group
 Prediction of dipole moment and optical activity from the viewpoint of
symmetry
 Definition of group, subgroup, class
 Matrix representation of a point group
 Reducible & Irreducible representations
 Great Orthogonality Theorem and its corollaries
 Construction of character table and meaning of all the term in character
table
 Mulliken symbol for irreducible representation
 Direct product of irreducible representations
 Application to spectroscopy
 Projection operator and its application to symmetry adapted linear
combination (SALC)
 Application to quantum mechanics
Construction of Molecular Orbital correlation diagram of simple and complex
molecules
Chemical Applications of Group theory: F. A. Cotton (Wiley Interscience)
Molecular symmetry & group theory: R. L. Carter (John Wiley & Sons)
Symmetry and Spectroscopy: D. C. Harris and M. D. Bertolucci (Dover)
Group Theory and Quantum Mechanics: Michael Tinkham (Dover)
Course title Self-assembly in Chemistry
Semester 5
Credits 3
Introduction This chemistry course is aimed to provide fundamental aspects of self-assembly in
chemistry and its application for supramolecular architectures.
Beneficial: Foundation for students who are interested in molecular materials,
nanomaterials, biology-chemistry interface and self-assembly in chemical and
biological systems. The course also consists of student’s seminars on selected
topics, problem solving, idea generation and laboratory experiments on making
and testing of self-assembled objects.
Course contents Concepts: (4 hrs)
Introduction to self-assembly and supramolecular chemistry, types of self-
assembly process, types of non-covalent interactions, importance of pre-
organization.
66
Guest-Host Chemistry-1 (2 hrs)
Receptors for cations: Crown ethers, Cryptands, Metal ion-crown ether
interactions, Metal ion-macro-ligand supramolecular structures, metallo-
supramolecular polymers, π-Receptors, etc.
Guest-Host Chemistry-2 (2 hrs)
Receptors for anions: Amide, Urea based Receptors, π-receptors, etc.
Guest-Host Chemistry-3: (4 hrs)
Complex recognition systems: Cyclodextrins, Calixarenes, Molecular rings & Nots,
Rotaxanes and Dendrimers.
Self-assembly via Hydrogen Bonding: (3 hrs)
Single & self-complementary system, two, three and four and multiple arm
hydrogen bonding systems, switching of recognition functions, hydrogen bonded
supramolecular polymers, etc.
Methods for determining noncovalent interactions (2 hrs)
Determination of association (or) binding constants for various molecular forces,
Job’s and molar ratio method and problem solving.
Amphiphilies: (5 hrs)
Anionic, cationic and neutral Micelles, critical micelle concentration (CMC)
determination by surface tension, dye-encapsulation method, fluorescence-
method and conductance method, Dynamic light scattering techniques.
Bolaamphiphilies, Nano-tapes, nano-fibers, cylinders, Application of micelles in
drug delivery.
Self-Assembly in the lipid membranes: (3 hrs)
Biological model: K+ and Na+ ion channels in biological cells, Synthetic ion
transporters and channels.
Liquid crystals: (2 hrs)
Origin of liquid crystals, mesogens self-organization, Types: nematic, smectic and
cholestric liquid crystals, characterization of LC-materials by DSC, PLM and X-ray.
Experimental Methods (3 hrs)
Making of Micelles and measuring CMC by DLS, Imaging of Liquid Crystalline
patterns, stability of Hydrogen bonded self-assembly via viscosity techniques, etc.
Biological self-assembly: (2 hrs)
Self-assembly in DNA, Protein and Peptides. Drug delivery applications.
References Core concepts in Supramolecular chemistry and Nano-chemistry, J. W. Steed, D. R.
Turner, Karl Wallace, (2007) 1st edition, Wiley
Selected Topics covered in Comprehensive Supramolecular Chemistry, Volume 8
Edited by J. L. Atwood, J. E. D. Davies, D. D. Macnicol, F. Vogtle, J. M. Lehn, (1996)
1st edition, Pergamon/Elsevier, Oxford
Supramolecular Chemistry: Fundamentals and Applications: Advanced Text book,
K. Ariga, T. Kunitake, (2006) 2006 edition, Springer
Supramolecular Chemistry: From Molecules to Nanomaterials by Jonathan W.
Steed and Philip A. Gale, (2012) 1st edition, Wiley
Introduction to Soft mater: Synthetic and Biological Self-Assembling Materials, I.
W. Hamley, (2007) Revised edition, Wiley
Chemistry of Discotic Liquid Crystals From Monomers to Polymers by Sandeep
Kumar, CRC Press (2010)
Review and research articles, communications and notes published in
international journals (will be provided)
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Course title Advanced Organic Chemistry Lab
Semester 5
Credits 3
Introduction This laboratory course will provide reasonable opportunity for the students to
learn the nuances in organic synthesis. Classical name reactions, oxidation,
reduction, rearrangement and multi-step reactions will be performed in this
course. Purification techniques such as column chromatography will be also
included. Synthesized compounds will be characterized using IR, UV, NMR and
Mass spectrometer. Put together this organic chemistry lab course will set a
platform for students who wish to pursue research in experimental chemistry.
Course contents Tentative list experiments
 Separation of ternary quantitative analysis of organic compounds (6 hrs)

 Wittig reaction (6 hrs)
 Synthesis of substituted Flavones and characterization of the diketo
intermediates and flavones derivatives. (9 hrs)
 Photochemical reaction: Synthesis of benzopinacol from benzophenone
using sunlight (6 hrs)
 Beckmann rearrangement: Acetanilide from Acetophenone Oxime (3 hrs)
 Diels alder reaction: anthracene and maleic anhydride (3 hrs)
 Click reaction (3 hrs)
 Organometallic reactions: Palladium catalyzed cross-coupling reaction (3
hrs)
Selective acylations of amine using thioacetic acid(3 hrs)

References Experimental procedures will be provided from current literature.
1. General Chemistry Experiments by Anil J. Elias, Revised Edition 2007,
Universities Press.
2. Comprehensive Practical Organic Chemistry by V. K. Ahluwalia, Renu Aggarwal,
2000, Universities Press.
Course title Quantum Chemistry
Semester 6
Credits 4
Introduction The objective of this course is to understand the rules governing the behavior of
molecules and atoms – the theory of quantum mechanics – and thereby get a
feeling for how to explain and predict chemical properties.
The course starts by discussing the fundamental principles of quantum mechanics
with an emphasis on the physical implications of this elegant, yet non-intuitive
theory. It then applies quantum mechanics to simple model systems and
eventually to atoms and molecules. It explores one of the most pervasive concepts
in chemistry: the chemical bond. The ideas discussed in this course will be useful
to those who wish to pursue further study in the areas of theoretical and
computational chemistry, spectroscopy, molecular biology and materials science.
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Course contents Introduction to Quantum Mechanics and Quantum Chemistry (1hr)
General Principles of Quantum Mechanics (5 hrs)
A. Postulates of quantum mechanics
B. Operators in quantum mechanics
Particle in a Box (2 hrs)
A. Energy, wave-functions, probability distribution
B. Extension to 3 dimensions. Eigenfunctions of a separable Hamiltonian
C. Particle in a box as a model for conjugated molecules Harmonic Oscillator (3
hrs)
A. Classical harmonic oscillator
B. Quantum mechanical harmonic oscillator
C. Ladder operators and commutation rules
D. Harmonic oscillator as a model for molecular vibration
Rigid Rotor (2 hrs)
A. Energy and wavefunctions of the rigid rotor, rotational constants
B. Rigid rotor as a model for molecular rotation
Hydrogen Atom (3 hrs)
A. Schrödinger equation for the hydrogen atom
B. Energy and wavefunctions
Approximate Methods (4 hrs)
A. Variational method
B. Perturbation theory
Many Electron Systems (7 hrs)
A. Electron spin
B. Antisymmetry, Slater determinants
C. The 2-electron system
D. Born-Oppenheimer approximation
E. Valence bond (VB) theory
F. Molecular orbital (MO) theory
Hartree-Fock approximation and beyond for many electron systems (6 hrs)
A. Hartree-Fock: Self Consistent Field Method, a solution for the Schrödinger
Equation.
B. Approximations beyond Hartree-Fock and the concept of electron correlation

Quantum Chemistry by Donald A. McQuarrie
Modern Quantum Chemistry: Attila Szabo and Neil Ostlund
Quantum Chemistry by Ira N. Levine
Course title Organic Synthesis-I [Necessary for Organic Synthesis –II]
Semester 6
Credits 4
Introduction To gain exposure to various commonly used reagents for functional group
transformations, their mechanisms, and applications. Reactions such as
oxidations, reductions, substitutions, additions and carbon-carbon bond
formations will be discussed. The expected outcome of this course would be
strengthening of synthesis foundations; students would be in a position to begin
69
building complex organic molecules in the ensuing course.
Course contents  The Concept of Protecting Functional Groups: Protection of NH groups,
Protection of OH group of alcohols, Protection of diols as acetals,
Protection of carbonyl groups in aldehydes and ketones, Protection of
carboxyl group, Protection of double bonds, Protection of triple bonds.
(6 h)
 Functional Group Transformations:
Oxidation and reduction: (14 h)
 Oxidation of alcohols to aldehydes and ketones, Reagents and
procedures for alcohol oxidation, Chemoselective agents for oxidizing
alcohols, Oxidation of tertiary alcohols, Oxidation procedures to
caroboxylic acids, Allylic oxidation of alkenes, oxidations such as Swern
oxidation, Sharpless, Woodward hydroxylation etc. and various oxidizing
agents.Nucleophilic reducing agents, Electrophilic reducing agents, Regio
and chemoselective reductions, Diastereofacial selectivity in acyclic
systems, Enantioselective reductions
 The chemistry of carbon-carbon pi bonds and related reactions:
Reactions of Carbon-Carbon Double and triple bonds. (2 h)
 Formation of carbon-carbon single bond via enolates:1,3-Dicarbonyl and
related compounds, Direct alkylations of simple enolates. Imines and
hydrazone anions, enamines, Robinson annulations (2h)
 Organometallic Reagents: Organolithium reagents, Organomagnesium
reagents, Organotitanium reagents, Organosilicon reagents,
Organocerium reagents, Organocopper reagents, Organochromium
reagents, organozinc reagents, organosilicon reagents. (16 h)
References 1) Organic Chemistry by J. Clayden, N. Greeves, S. Warren, P. Wothers; Oxford

Press, Second Edn.
2) Modern Organic Synthesis An Introduction, by G. S. Zweifel and M. H. Nantz;
W. H. Freeman, First Edn
3) Advanced Organic Chemistry: Part B(Reaction and Synthesis) by F. A. Carey
and R. J. Sundberg; Springer, Fifth Edn
4) March’s Advanced Organic Chemistry, by Michael B. Smith and Jerry March;
Wiley India, 2012, Sixth Edn
Course title Transition Metal Chemistry
Semester 6
Credits 4
Introduction The objective of this course is to provide a detailed account to the chemistry of
transition metals and emphasize their relationship to other multi-disciplinary
topics such as bioinorganic chemistry and organometallic chemistry. The central
theme of this course is to focus on the fundamental concepts needed to
understand transition metal chemistry, relevant to their structure, bonding,
properties such as spectral characterizes, reactivity, stereochemistry etc. This
course will be useful for all those students, who have opted for chemistry as a
major subject. At the end of this course, students will also learn about the role of
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transition metals in several other fields like materials science, biology and
catalysis.
Course contents  Nature of Metal-Ligand Bonding: Crystal and ligand field theories. Crystal
field stabilization energies, Irving Williams series, 10Dq and pairing
energies, Jahn-Teller Distortion, High spin and Low spin complexes.
Magnetism, Molecular orbital (MO) theory of Octahedral, Tetrahedral
and Square Planar complexes. Nephelauxetic Series. Pi bonding and MO
Theory (10 hrs).
 Inorganic Spectroscopy: Spectroscopic terms, LS coupling. Selection rules,
Orgel diagrams, Tanabe-Sugano diagrams. Charge transfer transitions (12
Hrs)
 Lanthanides and Actinides: Coordination chemistry, Spectra and
magnetic properties. (3hrs)
 Stability and Reactions of Coordination Compounds: Thermodynamic and
kinetic stability, Labile and inert complexes, Ligand substitutions in
octahedral and square planar complexes, Trans-Effect. Mechanism of
redox reactions, Inner and outer sphere mechanisms, Photochemical
reactions. (8 Hrs)
 Basics of Organometallic Chemistry: The 18-electron rule, Bonding,
Hapticity, Oxidation numbers and stability. Carbonyls, Nitrosyls, Alkyls,
Alkylidines, Allyl and cyclic polyene complexes, Metal-metal bonds,
Metallocenes, Fluxionality, Organometallic reactions, Catalysis. (6 Hrs)
 Basics of Bioinorganic Chemistry: Roles of metals in biology, introduction
to photosynthesis, Oxygen transport and storage by heme and nonheme
proteins, Physical methods to study bioinorganic systems. (3hrs)

Inorganic Chemistry by Huheey, Keiter, Keiter, Medhi (4th Ed.)
Inorganic Chemistry by Shriver & Atkins (4th Ed.)
Concise Inorganic Chemistry by J.D. Lee (5th Ed.)
Course title Lab Training/Theory Project – II
Semester 6
Credits 3
review/theoretical or computational project/lab based research project.
The student has to identify, talk to and mutually agree on a research project
before registering for this course. The scope, duration, structure, expectations,
and evaluation criteria (also see below) for the course are decided by the project
supervisor.
Course contents See above
References As per suggestions of the project supervisor
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Course title Chemical Equilibrium and Kinetics
Semester 5
Credits 4

Introduction This course is an advanced continuation of the one component-one phase
thermodynamics introduced in the fourth semester. In this course the application
of thermodynamics to multicomponent (water/ethanol mixture or reaction
mixture of multiple compounds), or multiphase (water/vapor mixture) systems is
discussed with the help of Gibbs free energy or chemical potential. It is, however,
emphasized the root of the changes that we observe in multicomponent system
(mixing or nonmixing of two liquids or formation of vapor pressure) is the
underlying consequence of the entropy of universe as a driving force.
Therefore, this course will help us understand why a certain reaction will happen,
how the volumes of two mixtures will change, what kinds of phases will be
produced in the mixture of liquids, gases and solids. Moreover, what kinds of
solution an electrolyte will make compared to that of a nonelectrolyte.
After discussing about the equilibrium states of ideal and nonideal mixtures, this
course then will discuss about the rate of change in these equilibrium states,
known as chemical kinetics in which the rate laws of various chemical reactions,
catalysis etc. will be discussed. Finally, this course will discuss various reaction rate
theories which are used even today to understand the rate of a chemical reaction.
Thus the objective of this course is to give a consolidated picture of the

equilibrium and kinetics of multicomponent mixtures in chemical systems.
Course contents  Review of thermodynamics of one component system: Statement of
three laws, basic definition of entropy and its meaning, fundamental
equation of thermodynamics, Legendre transformation, free energies
and their implications (2 hr)
 Introduction to multi-component system: Introduction to chemical
potential and use it to define both chemical equilibria and phase
equilibria, Gibbs-Duhem equation, connection of chemical potential with
partition function, problem solving (3 hr)
 Reaction equilibrium in ideal gas mixtures: Chemical potential in an ideal
gas mixture, reaction equilibrium in gas mixture, equilibrium constant
and its dependence on temperature, van’t Hoff equation, problem
solving (3 hr)
 Phase equilibria in one component (multiphase) system: Phase rule,
Clapeyron and Clausius-Claperon equation, introduction to phase
diagram, problem solving (3 hr)
 Ideal Nonelectrolytic Solutions: Partial molar thermodynamic quantities
(volume, enthalpy, entropy, etc.), calculation of partial molar volume,
thermodynamics of mixing, ideal solution and ideally dilute solution,
calculation of vapor pressure, Raoult’s law and Henry’s law, problem
solving (5 hr)
 Nonideal Solutions: Activity and activity coefficient from both convention
I (deviation from ideal solution) and convention II (deviation from ideally
dilute solution) excess function ( 6 hrs)
 Nonideal electrolytic solution: Activity of electrolytes, Debye-Huckel
theory, problem solving (3 hrs)
 Multicomponent Phase Equilibria: Colligative properties (vapor pressure
lowering, freezing point depression and osmosis), two-component phase
diagram, two component liquid-vapor, liquid-liquid (azetropic
composition), solid-liquid phase diagrams (eutectic and peritectic
composition) and general discussion about other phase diagrams. (4 hr))
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 Chemical Equilibrium: Spontaneous chemical reaction, reaction equilibria
in electrolyte and nonelectrolyte solution, in gas mixtures and in solids,
temperature and pressure dependence of the equilibrium constant (3
hrs)
 Equilibrium Electrochemistry: Half reactions and electrodes, varieties of
cells, cell potentials, standard electrode potential, Nernst equation,
applications and problem solving (3 hrs)
 Chemical Kinetics: Rate and order of a reaction, experimental
determination, mechanism of reactions (parallel, consecutive reactions),
temperature dependence of rate, unimolecular reaction, catalysis,
enzyme catalysis (4 hrs)
 Chemical Dynamics: Theories of reaction rate (collison theory, Eyring
theory, and transition state theory) (3 hrs)
References  Physical Chemistry by Ira N. Levine, 6th edition, McGrawHill Higher
Education Publication, (2008)
 Physical Chemistry by Peter Atkins and Julio de Paula, 9th Edition, W. H.
Freeman and Company (2010)
 Physical Chemistry: A Molecular Approach by D. A. McQuarrie and J. D.
Simon, University Science Books (1997).
 Modern Electrochemistry, volume 1 (chapter 3): Bockris and Reddy
(1998)
Course title Bioorganic Chemistry and Chemical Biology
Semester 7
Credits 3
Introduction This course is intended to provide a basic knowledge on the biosynthesis of
biomolecule precursors and natural products. The content of this course is a
chemistry-based approach to understanding the basic structure, reactivity,
biological functions and biosynthesis of precursors–amino acids, nucleotides, fatty
acids, lipids and secondary metabolites. This course will also provide an overview
of the field of chemical biology, while integrating chemical, biochemical and
biological approaches. The course structure will provide chemists with biologically
relevant new targets and biologists with useful new chemical tools.
Course contents Overview of structure of carbohydrates, nucleic acids, proteins, and lipids (6 h).
2. Primary and secondary metabolism, bioenergetics, biological and organic
reaction mechanisms, coenzymes/cofactors (6 h).
3. Amino acids: biosynthesis of aliphatic and aromatic amino acids, desipeptides,
noncannonical amino acids (6 h).
4. Biosynthesis of nucleosides and carbohydrates (3 h).
5. Beta-oxidation of fatty acids, biosynthesis of fatty acids, various lipids,
polyketides, and representative secondary metabolites (3 h).
6. Ribozymes, aptamers, RNA interference, riboswitches, DNA sequencing, next-
generation sequencing (3 h)
7. Synthetic expansion of genetic code. Chemical and chemo-enzymatic labeling of
nucleic acids and its applications - (3 h)
8. Solid-phase peptide synthesis and its applications, unnatural amino acids and
their incorporation, PNAs. (2 h)
9. Protein engineering – protein design principles, directed evolution, computer-
assisted protein design, enzymes from extremophiles. (4 h)
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10. Chemical glycomics: Chemical probes to illustrate carbohydrates
oligosaccharides functions and applications of oligosaccharides. (3 h).
11. Case studies using chemical biology primary literature which illustrates
methods and techniques taught in the course (3 h)
References The bulk of the material presented in lectures will be drawn from several sources,
and where appropriate, reference information will be provided to the students.
1. Biochemistry, Voet and Voet, 3rd edition.
2. Principles of Biochemistry, Lehninger, 4th edition.
3. Chemical Biology: From small molecules to systems biology and drug
design. Edt. Stuart L. Schreiber, Tarun Kapoor, Gunter Wess. Volume 2,
2007, Wiley-VCH.
4. Chemical Biology, a practical course: Herbert Waldmann, Petra Janning.
1st Edition, 2004, Wiley-VCH
Course title Advanced Inorganic Chemistry Laboratory
Semester 6
Credits 3
Introduction Experiments to understand structure and bonding aspects of
coordination complexes and other inorganic molecules
• To understand redox reaction reactions between metal ions
• To understand qualitative analyses through instrumentation techniques
Course contents Spectrochemical analysis of a coordination complex.
Determination of the stoichiometry of a coordination compound by Job’s method
of continuous variations.
Determination of Iron by reaction with Permanganate - A Redox Titration
Synthesis of SnI4 and analysis by Sn119 NMR
Preparation of Copper (I) Chloride.
The preparation of Potassium tris(oxalato)ferrate(III)trihydrate and analysis by IR
spectroscopy.
Determination of Chloride by Mohr’s Method: Precipitation titration.
Solvent Extraction: Determination of copper as the ‘neo-cuproin’ complex.
Preparation of ‘bouncing putty’ a silicone polymer with unusual properties.
Synthesis and observation of phosphorescent emission of Tris(2,2’-
bipyridine)ruthenium- (II) dichloride hexahydrate
References Since the experiments are selected from various sources, appropriate reading
material will be suggested during the instruction sessions in the laboratory
Course title Advanced Spectroscopy [Prerequisite: Fundamentals of Molecular Spectroscopy]
Semester 8
Credits 4
Introduction This course mainly deals with the applications of advanced spectroscopic
techniques in chemistry, physics, material science and biology.
First part of the course will be an introduction to fundamental concepts of light-
matter interaction, optics, lasers and laser systems, other relevant aspects of
74
instrumentation necessary for spectroscopy.
In the second part of the course we will discuss various modern spectroscopic
techniques. Discussion of each technique will be followed by examples from
classic and contemporary literature.
Course contents Light and Optics (10 hrs)
Topics: Introduction to electromagnetic radiation, Quantum description of light,
Polarization of light, Linearly, circularly and elliptically polarized light and how to
produce them, Various types of polarizers, Snell’s law, Brewster angle, Absorption
and emission of radiation, Einstein coefficients of A and B, Time-dependent
perturbation theory.
Birefringence property of various crystal, concept of ordinary and extraordinary
rays, index ellipsoid and classification of crystals, Concept of various types of wave
plate and their applications.
Fundamentals of lasers and laser systems (12 hrs)
Topics: (i) Concept of spontaneous, stimulated emission and population inversion.
Mechanism of population inversion, two-level, three level and four level laser
systems. Frequency and spatial properties of laser radiation. Components of laser
resonator. Loop gain in laser resonator. Gain in continuous-wave and pulsed
lasers, Q-switching and the generation of nanosecond pulses, Mode locking and
the generation of picosecond and femtosecond pulses.
(ii) Fixed-wavelength gas lasers: He-Ne, rare-gas ion, CO2and excimer lasers, Fixed-
wavelength solid-state lasers: Nd:YAG laser, Semiconductor diode lasers, Tunable
dye laser systems, Tunable Ti:sapphire laser systems.
(iii) Non-linear crystal and frequency-mixing processes, Optical parametric
oscillation.
Section #3: Advanced Laser spectroscopic techniques (15 hrs)
Topics:
(i) Cavity ring-down spectroscopy, Laser induced fluorescence, Steady-state and
time-resolved electronic spectroscopy, transient absorption, (3L)
(ii) Scattering, Steady-state and time-resolved Resonance Raman spectroscopy,
Surface Enhanced Raman Spectroscopy (SERS), Coherent anti-stokes Raman
spectroscopy (CARS). Stimulated Raman spectroscopy, (iii) Ultrafast spectroscopy,
Laser femtochemistry.
X-ray Photoelectron Spectroscopy (XPS)/Ultra-violet Photoelectron Spectroscopy
(UPS) and X-ray Absorption Spectroscopy (XAS) (5 hrs)
(i) Overview, (ii) Photoelectric effect and Photoemission from Solids, (iii) Binding
energy and chemical shift, (iv) Inelastic mean free path and sampling depth, (v)
Quantification, (vi) Spectral features, (vii) Instrumentation, (viii) Valence band and
Ultra-violet photoelectron spectroscopy (UPS), (ix) Introduction to XAS, and (x)
Overall perspectives (importance of XPS, UPS and XAS.
References 1) Modern Spectroscopy, Jeanne McHale
2) Modern spectroscopy, J. M. Hollas (Wiley, New York, 2004)
3) High Resolution Spectroscopy, J. M. Hollas (Wiley, 2ndedition, 1998)
4) Physical Chemistry - A Molecular Approach; Donald A. McQuarrie and John D.
Simon (Viva Books Private Limited, New Delhi, 1997)
5) Laser fundamentals: W. T. Silfvast (Cambridge University press, Published in
South Asia by Foundation Books, New Delhi, 1998)
6) Laser Chemistry: Spectroscopy, Dynamics and Applications by H. H. Telle, A. G.
Urena, R. J. Donovan (Wiley, 2007).
7) Introduction to Fluorescence Spectroscopy, Lackowitz
75
8) Surface Analysis - The Principal Techniques. Editors: John C. Vickerman and
Ian S. Gilmore (Wiley, 2009).
9) Photoelectron Spectroscopy – Principles and Applications. Stefan Hüfner
(Springer, 2003).
Course title Organic Synthesis-II [Prerequisites: Organic Synthesis I]
Semester 7
Credits 4
Introduction Build enough knowledge for independent planning of the total synthesis of an
organic molecule
Develop research skills and critical thinking by application of course content to
practical problem solving
Course contents Formation Carbon-carbon single()bond (9 hrs)
Organometallic reagents in action: Organotitanium, organocerium organozinc,
organoboron reagents. Palladium catalyzed coupling reactions: Heck Coupling,
Negishi Reaction, Stille coupling, Suzuki coupling, Sonogashira coupling.Trost Tsuji
Reaction, Synthesis of Carbocyclic systems: Ring closing Olefin Metathesis
(Grubb’s metathesis)
Retrosynthestic Analysis (6 hrs)

Sketches of synthesis: Tactics in Organic Synthesis. How to achieve the desired
transformation? An Ideal Organic synthesis: A fantasy or an achievable goal.
Synthons as universal (but abstract) building blocks in assembling a molecular
framework and real synthetic equivalents; Synthons are idealized reagents,
Choosing a disconnection approach for multiple step syntheses. Functional group
interconversion Two-group disconnections are better than one C-C
disconnections; Donor and acceptor synthons; Two-group C-C disconnections
Saturated heterocycles and stereoelectronics (3 hrs)

Reactions of heterocycles Conformation of saturated heterocycles: the anomeric
Effect; Making heterocycles: ring-closing reactions
Aromatic heterocyclic: structures, reactions and synthesis (5 hrs)

Aromatcity survives when parts of benzene’s ring are replaced by nitrogen atoms;
Six-membered aromatic heterocycles can have oxygen in the ring; Five-
membered heterocycles are good nucleophiles Furan and thiophene are oxygen
and sulfur analogues of pyrrole More reactions of five-membered heterocycles,
Five-membered rings with two or more nitrogen atoms; Benzo-fused
heterocycles; Putting more nitrogen atoms in a six-membered ring ; Fusing rings
to pyridines: quinolines and isoquinolines; Heterocycles can have many nitrogens
but only one sulfur or oxygen in any ring; Pyrroles, thiophenes, and furans from
1,4-dicarbonyl compounds; How to make pyridines: the Hantzsch pyridine
synthesis Pyrazoles and pyridazines from hydrazine and dicarbonyl
compounds;Pyrimidines can be made from 1,3-dicarbonyl compounds and
amidines. Izoxazoles, Tetrazoles. The Fischer indole synthesis. Quinolines and
isoquinolines
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Asymmetric Synthesis (3 hrs)
Chiral Pool synthesis, Chiral Auxillary, Organocatalysis, Desymmetrisation
Chemistry of Natural Products (6 hrs)

Methods of extraction, isolation, fractionation of naturally occurring organic
compounds. Classification of Natural Products. Steroids, terpenoids, Alkaloids,
Marine Toxins, Antibacterials, Taxol, Vancomycine, Reserpine.
Problem solving session (8 hrs)

References 1. Organic chemistry by Jonathen Clayden, N. Greeves, S. Warren, P.
Wothers Oxford University Press, 1st edition, 2001
2. Organic Synthesis, the Disconnection Approach, Warren, S. G. New York :
Wiley, 2nd edition, 2008
3. The Logic of Chemical Synthesis by E. J. Corey & Xue-Min Cheng, 1995
4. Classics in Total Synthesis by K C Nicolaou & Sorensen,2008
5. Advanced organic chemistry, Parts A and B, Francis A. Carey and Richard
J. Sundberg, Springer, 5th edn, 2007 and 2008
Course title Bioinorganic Chemistry
Semester 7
Credits 4
Introduction To understand the role of metal ions in biology
To understand the mechanistic pathway for reactions carried out by metal
enzymes
To understand long range electron transfer reactions
Need of experimental methods to understand the solution state dynamics of
enzymes.
Course contents Experimental Methods [6 h]
Electron Spin Resonance spectroscopy and Mossbauer spectroscopy.
Inorganic Chemistry of Biological systems [3 h]
Role of metals and non-metals. Significance of trace elements. Coordination
chemistry of metal ions in Biology.
Dioxygen Carriers and its Reactions: [12 h]

Naturally occurring dioxygen carriers. General aspects of chemistry of dioxygen,
Fe, Cu and Co. Other ligands that can bind to biologically occurring carriers. Nature
of M-O2 linkage, ligand affinity, distal effects, structures of hemoglobin. Free
radical autoxidation, toxicity of dioxygen. Biological targets, molecular mechanism
of O2 reduction, oxygenases, cytochrome P-450. Catalase and peroxidase, Cu-Zn
superoxide dismutase.
Electron Transfer Reactions: [8 h]

Biological redox components, energy storage and release. Long range electron
transfer in proteins (related to blue-copper proteins and plastocyanin). Protein-
protein complexes. Respiration, Photosynthesis, Nitrogen fixation and Vitamin B12.
77
Metal Sulfide Proteins [8 h]
Fe-S proteins, Rubredoxins, Ferrodoxins. Detection of Fe-S sites, redox behavior.
Multisite Redox enzymes (hydrogenase and nitrogenase).
Metals in Medicine [5 h]
Metal deficiency and diseases, toxic effects of metals, metals for diagnosis and
chemotherapy, Pt anti-cancer drugs as a case study.
Bio-inorganic Chemistry, I. Bertini, H. B. Gray, S. J. Lippard & J. S. Valentine, 1st
Edn., Viva Books, 1998 (2007 reprint).
Biological Inorganic Chemistry: Structure and Reactivity, I. Bertini, H. B. Gray, E. I.
Stiefel & J. S. Valentine, University Science Books, 2007.
Biological Inorganic Chemistry, Robert R. Crichton, 2nd Edition, Elsevier, 2012
The text books mentioned here are only for reference. Actual study material may
include papers and reviews published in reputed journals.
Course title Advanced Physical Chemistry Laboratory
Semester 7
Credits 3
Introduction This course comprises of laboratory experiments based on the fundamental
concepts in chemistry. Experiments offered in this course provide students an
opportunity to learn advanced instrumentation techniques as well as its
application to study a variety of physical chemistry and chemical physics problems.
One of the main goals of this course is to train students in understanding how
physical techniques can be utilized to probe molecular systems and advanced
materials.
Course contents Measuring a 1D proton NMR on a standard sample
Studying effect of salt on 1H 90 degree pulse width
Studying the effect of solvents on 1H chemical shifts
Experimental demonstration of particle in box model using optical properties of
CdS quantum dots
Measurement of temperature dependent four-probe sheet resistance of thin films
Freely diffusing redox couple- A cyclic voltametric investigation
Experimental Demonstration of electrochromic display
Synthesis and Spectroscopic Characterization of Metal Nanoparticles
Introduction of Structural Anisotropy in Nanoparticle Formation
Bench-top Pattering using Soft Lithography
References 1. Basics of NMR, ebook, http://www.cis.rit.edu/htbooks/nmr/
2. THE BELL SYSTEM TECHNICAL JOURNAL, By F. M. SMITS, MAY 1958, Page
711.
3. Modern Electrochemistry, Bockris and Reddy, 2nd edition (Volume 1 to 3),
Springer 1998
4. Electrochemical Methods: Fundamentals and Applications, A. J Bard and L.
R Fualkner, 2nd edition, Wiley 2001
5. The Chemistry of Nanomaterials: Synthesis, Properties and Applications,
C. N. R. Rao, Achim Müller, Anthony K. Cheetham, Vol. 1, Wiley 2006
78
6. Nanoscale Materials, Liz-Marzán,L. M.; Kamat, P. V. Vol. 1, Springer
2003
Course title Thermal and Photochemical Reactions
Semester 7
Credits 3
Introduction This course will give an idea to the students how organic transformations were
promoted by heat and light. Various concepts in thermal and photochemical
organic transformation will be learned. This course will also help for the students
to understand the mechanistic pathway for the thermal and photochemical
reactions. Further application of these reactions in complex organic molecules and
natural products will be studied.
Course contents Thermal and Photo pericyclic reactions (10)
Cycloaddition reactions; Simple cycloaddition reactions, Frontier orbital theory,
comments on allowed and forbidden reactions, selection rules, Cycloaddition
reactions (m + n cycloaddition reactions, Diels-Alder reactions etc.),
stereochemistry and regiochemistry, experimental observations of 1,3 dipolar
cycloadditions (retrocyclic addition) Cheletropic Reactions.
Electrocyclic reactions: (6)
Examples for electrocyclic reactions; allowed and forbidden reactions; selection
rules, Torquoselectivity, Nazarov Reaction
Sigmatropic rearrangements (12)
[1,3]-sigma tropic, [1,2]-sigmatropic, [2,3]-sigmatropic, [3,3]-sigmatropic, [1,5]-
sigmatropic, allowed and forbidden reactions, Wittig Rearrangement, Sommelet-
Hauser, Meisenheimer Rearrangement, Claisen rearrangement, Cope
rearrangement, ene reaction, group transfer reactions, use of chiral axillaries in
sigmatropic rearrangements;
Photochemical reactions (12)
Introdcution to photo chemistry, Di-Π methane rearrangement, oxadi-Π-methane
rearrangement, Photochemistry of carbonyl compounds, Norrish type I and
Norrish type II reactions, nitrobenzyl photochemistry, Paterno-Buchi reaction, azo
compound and diazocompounds, diazirins, azides and photoaffinity labeling,
Chemiluminenscence, photo reduction, photo oxidation, photoisomerization.
Photochemistry in Natural products synthesis
References Books for References:
1. Synthetic Organic Photochemistry by A. G. Griesbeck.
2. Physical Organic Chemistry by Eric V. Anslyn, D. A. Dougherty.
3. Modern Molecular Photochemistry by Nicholas J. Turro.
4. Introduction to Organic Photochemistry, John D. Coyale
5. Recent review articles
Course title Solid State Chemistry
Semester 7
79
Credits 3
Introduction This course is designed to provide the fundamental knowledge of the crystal
structure, properties, characterization, and synthesis of solids. The course will lay
the foundation for understanding the relationship between the internal structure
of matter and the properties of materials that make them attractive for
applications. Apart from the familiarity with the structure – property correlations,
students would be exposed to some of the most recent developments across the
spectrum of solid state and materials.
Course contents Crystal Structure (4h)
Fundamentals of lattice, unit cell, atomic coordinate, Bravais Lattices, crystal’s
direction and planes, types of closed packed structures, symmetry operations and
symmetry elements, point group, space group and crystal structures, factors which
influences crystal structures.
Crystal Diffraction by X-rays, neutrons and electrons (5h)
Structure determination by X-ray diffraction, Bragg’s law, Concepts of reciprocal
lattices, R factors and structure determination, modern X-ray powder diffraction
techniques and their applications, introduction to neutron and electron diffraction.
Electronic Properties and Band theory of solids (5h)
Introduction - metals, insulators and semiconductors, electronic structure, k space
and Brillouin zones, band structure of metals, insulators and semiconductors.
Magnetic Properties (6h)
Magnetic moment, Curie law, Curie-Weiss law, mechanism of magnetic ordering,
exchange Interaction, domain theory, hysteresis, anisotropy, paramagnetism,
ferromagnetism, ferrimagnetism, antiferromagnetism, classical and quantum
mechanical treatment.
Dielectric Properties (4h)
Polarization, dielectric constant and polarizibility, electronic Polarizability,
ferroelectric domains, Piezoelectricity, ferroelectricity, structure-property
correlations, applications.
Thermal Analysis (2h)
Thermogravimetric analysis (TGA), differential thermal analysis (DTA) and
differential scanning calorimetry (DSC), general theory and applications.
Materials Synthesis (2h)
Solid state reaction and wet chemical synthetic routes.
1. Basic Solid State Chemistry by A. R. West, second edition, John Wiley &
Sons, Ltd, 1999.
2. Solid State Chemistry and its applications by A. R. West, John Wiley &
Sons, Ltd, 2007.
3. Introduction to Solid State Physics by Charles Kittel; John Wiley and Sons,
8th Primary literature for advanced topics
Course title Electrochemistry
Semester 7
Credits 3
80
Introduction A student who has attended the course will be able to:
 Explain the nature of the electrochemical terms and concepts

 Understand the nature of electrochemical reactions
 Understand the kinetics of electrochemical reactions
 Plan and perform electrochemical experiments, for ex. cyclic voltammetry
experiment
 Design an electrochemical cell
 Use the modern electrochemical techniques (chronoamperometry,
chronopotentiometry, pulse voltammetry, square-wave voltammetry)
 Perform an electrochemical impedance experiment and
 obtain the equivalent electric circuit for the studied electrochemical
reaction
Course contents Electrochemistry Fundamentals: Farday’s laws, Measurement of conductance,

theory of electrolytic dissociation, Transport number, degree of dissociation,
Activity and activity coefficients of electrolytes, Theories of acids and bases,
Common ion effect and solubility product, Mechanism of buffer action, Henderson
equation, Acid-base indicators, Galvanic cells, Reversible cells, Reversible
electrodes, Thermodynamics of cell reactions (4 hrs)
Basics of Electronics: Circuit elements, Capacitors, resistors, inductors, different
types of AC circuits, simple capacitor circuit, capacitor resistor circuits, diodes, p-n
junction, breakdown voltage, half wave and full wave rectifiers, Transistors, Zener
diodes (2 hrs)
Modern Electrochemistry:
Electrified Interface (5 hrs)
Electrification of interface, Origin of potential difference across the interface,
Accumulation and depletion regions, Thermodynamics of electrified interface, The
structure of electrified interface, Metal/solution & semiconductor solution
interfaces, Band bending, Photoelectrochemistry
Electrodics (5 hrs)
Electron transfer under an electric field, Butler-Volmer equation, Low potential
case/High Potential case, Polarizable and nonpolarizable interface, The equilibrium
condition-Nernst’s thermodynamic treatment, Symmetry factor and transfer
coefficient, Electrode kinetics of semiconductor solution interface,
Microelectrodes, lessening diffusion control by microelectrodes and reducing
Ohmic errors
Electrochemical Techniques (6 hrs)
Cyclic voltammetry, Impedance spectroscopy concepts and applications, Chrono
methods, Scanning Electrochemical Microscopy, Mott-Schottky plot, Determination
of flat band potentials and carrier concentration. Corrosion – fundamentals and
applications.
Electrochemical Energy Conversion and Storage: Electrochemical energy systems.
Batteries, fuel cells and electrochemical capacitors. Fundamentals and applied
aspects. Primary and secondary batteries. Polymer electrolyte membrane fuel cells,
solid oxide fuel cells etc. Double layer- and pseudo- capacitors. Integration of
electrochemical energy storage systems with other devices. Photo-electrochemical
solar cells and conversion of solar energy, Photoelectrochemical water splitting. (6
hrs)
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References 1. Modern Electrochemistry, Bockris and Reddy, 2nd edition (Volume 1 to
3), Springer 1998
2. Trends in molecular electrochemistry, Armando and Amatore, 1st
Edition, CRC press 2004
3. Electrochemical Methods: Fundamentals and Applications, A. J Bard
and L. R Fualkner, 2nd edition, Wiley 2001
Course title Organic Spectroscopy
Semester 8
Credits 4
Introduction  To learn theories of the major instrumental methods (spectroscopic and
analytical methods) used routinely by organic chemists.
 (IR, UV, Fluorescence, MS and NMR) used for structure elucidation in
organic chemistry.
 To develop critical thinking and problem solving skills with discussions of
spectra of known and unknown compounds.
To develop the necessary level structural elucidation ability for each researchers for
their day to day analysis of new molecules.
Course contents Introduction of the course: Objectives and Outlook [1 h]
Topics: Why would we study the course?
IR Spectroscopy [4 h]
Instrumentation; Principles (Selection Rules and Hooke's Law; Characteristic Group
Vibrations) and Analysis of spectra.
Ultra Violet-Visible Spectroscopy and Fluorescence Spectroscopy [5 h]
(UV-Visible): Interaction of electromagnetic radiation with molecules, Double Bond
Equivalents, Instrumentation; Principles (Selection Rules and the Beer-Lambert
Law; Chromophores), pH, solvent and substituent effects and Applications.
(Fluorescence): Basic principle; factors influencing fluorescence properties.
Application of fluorescence: fluorescence sensing by energy transfer and pH;
solvatochromic fluorophores; conformational sensitive fluorescent molecules;
probes for diagnosis.
CHN Analysis [1 h]
Topics: Principles and Applications.
Mass Spectrometry [4 h]
Methods of ionization, separation and registration of ions; The main rules of
fragmentation of organic compounds; The approaches to the interpretation of
mass spectra; High resolution mass spectrometry; The main pathways of
fragmentation of the principal classes of organic compounds in conditions of
electron ionization; Mass spectrometry of high molecular mass compounds and
biomolecules (electrospray ionization, matrix assisted laser desorption/ionization).
Problem solving sessions [4 h]
Nuclear Magnetic Resonance [10 h]
Topics: Instrumentation; Origin of the NMR Effect; Chemical Shift; Splitting; 1H NMR
Spectroscopy; Decoupled spectra; 1D NOE; 13C NMR Spectroscopy; The principles
of two-dimensional spectroscopy; Correlation 2D spectroscopy (COSY, HMQC,
HMBC); Nuclear Overhouser effect (nature, practical consequences); homo- and
82
hetero nuclear effect; technique of measurement; difference spectra; sample
requirements; Other Nuclei.
Structure Determination [12 h]
Topics: Problem solving sessions using 1H, 13C NMR, Mass, CHN, IR data of known
and unknown samples.
References 1. Spectrometric Identification of Organic Compounds by R. M. Silverstein, F. X.
Webster & D. J. Kiemle. 7th Edition.
2. William Kemp, “Organic Spectroscopy”, 3rd Edition. W.H. Freeman & Company.
3. Principles of Fluorescence Spectroscopy by J. R. Lakowicz, 2nd Edition, 2004,
Springer.
4. Fundamentals of Molecular Spectroscopy by Colin N. Banwell, Elaine M. McCash,
Mcgraw-Hill College; 4th Sub Edition.
5. Journals and Publications.
Course title Polymer Chemistry
Semester 7
Credits 4
Introduction This course is emphasized to provide fundamental knowledge in polymer
chemistry. This course is very important for all the students who wish to learn and
practice chemistry. The students will be benefited with new scientific concepts of
larger and macromolecular science
Course contents Concepts: (5 hrs)
Molecular Weight distribution, Number and weight average molecular weight,
Linear, Branched, Cross-linked, grafted- Polymers, Polymer Crystallization, Glass
Transition, Solution and Melt viscosity, Polymer Rheology and Thermal properties,
Isothermal and Non-isothermal crystallization
Step Polymerization: (5 hrs)
Reactivity of Functional Groups, Kinetics of Step Polymerization and Molecular
Weight Control. Examples- polyesters, polyethers polyamides, polyurethanes,
polyurea, polycarbonate and other condensation polymers.
Addition Polymerization: (5 hrs)
Radical Chain Polymerization, Rate of Radical Chain Polymerization, Initiation,
propagation, Termination, Chain Transfer, Autoacceleration, Molecular Weight
Distribution, Controlled or Living Radical Polymerization, TEMPO-mediated
polymerization and atom Transfer radical Polymerization (ATRP).
Ionic Polymerization: ( 5 hrs)
Comparison of Radical and Ionic Polymerization, Cationic and Anionic
Polymerization of the Carbon-Carbon Double, Distinguishing Radical, Cationic, and
Anionic Polymerizations and Applications of ionic or living polymerizations for Block
polymers and Other Polymer Architectures.
Miscellaneous Topics: ( 5 hrs)
Ring-Opening Polymerization, NMR and FT-IR spectroscopy of polymers,
stereochemistry of Polymers and polymer nano-architectures.
Copolymers: ( 2 hrs)
Topics: Concepts, Alternative, random and block copolymers.
Liquid Crystalline Polymers: ( 2 hrs)
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Topics: Main chain and side chain, Nematic, smectic and cholestric Phases and
application.
Conducting Polymers: ( 5 hrs)
Topics: Concepts of conducting polymers, discovery, polyaniline, Polyfluorene,
polythiophene, polypyrrole, poly(phenylenevinylenes), polyphenylene, low band
gap polymers and other examples, Synthetic methodologies, characterization,
Applications in opto-electronic devices and sensors, one and three dimensional
conducting nano-materials and their applications.
Non-linear Polymers: (3 hrs)
Topics: Dendrimers, hyperbranched polymers, random branched polymers,
branching density, influence of branching on the melt, viscosity, rheological and
thermal properties of polymers.
Polymer Blends and Composites: (3 hrs)
Topics: Physical and Reactive blends, Phase separation, Nano-composites and
synthetic-natural fiber composites.
References Principles of Polymerization: G. Odian
Text Book of Polymer Science – Billmeyer
Polymers: Chemistry and Physics of Modern Materials - J. M. G. Cowie
Review articles and research papers will be provided for specific & emerging topics
Course title Statistical Thermodynamics
Semester 7
Credits 4
Introduction Goal is to explain macroscopic (thermodynamic) properties such as enthalpy,
entropy etc. in terms of microscopic (molecular) interaction.
The course is important for physical chemistry students and essential for students
aiming for computational /theoretical chemistry research.
This course will provide a molecular view to understand and explain
thermodynamically observable properties.
Course contents Review of Thermodynamics (8 hr)
Thermodynamics postulates – Conditions of equilibrium -- Reversible Processes and
Maximum Work Postulate – Extremum Principle -- Maxwell Relations
Review of Probability theory (4 hrs)
Definition -- Distribution Function – Moment, Average etc. -- Central limit theorem
Statistical Mechanical Ensembles and Thermodynamics (12 hrs)
Classical Statistical Mechanics, Classical Partition Function – Phase Space and the
Liouville Equation – Equipartition of Energy
Ensembles and Postulates -- Canonical Ensemble -- Grand Canonical Ensemble --
Microcanonical Ensemble -- Other Ensembles -- Equivalence of Ensembles --
Thermodynamic Connection - Fluctuation
Quantum Statistics (4 hrs)
Boltzmann Statistics -- Fermi-Dirac Statistics -- Bose-Einstein Statistics
Monoatomic gas (2 hrs)
Translational Partition Function – Electronic and Nuclear Partition Function –
Thermodynamic Functions
Ideal Diatomic Gas (4 hrs)
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Rigid Rotor Harmonic Oscillator Approximation – Vibrational Partition Function –
Rotational Partition Function – Thermodynamic Functions
Ideal Polyatomic Gas (2 hrs)
Vibrational Partition Function – Rotational Partition Function – Thermodynamic
Functions
Monoatomic Crystals (2)
Einstein’s Model – Vibrational Spectrum of a Monoatomic Crystal – Debye
Approximation –
Chemical Equilibrium (2)
Equilibrium Constant – Examples
References 1. H. B. Callen, Thermodynamics and Introduction to Thermostatistics, 2nd
Edn, (1985). First six chapters
2. Statistical Mechanics, Donald A McQuarrie, University Science Books,
California, USA ,Viva Books Private Limited, New Delhi (Indian Edn) [First 7
chapters and some other chapters)
3. An Introduction to Statistical Thermodynamics, Terrell L. Hill, Dover
Publications, Inc, New York1.
Course title Medicinal Chemistry
Semester 8
Credits 3
Introduction The main objective of this course is to expose students to the fundamental
concepts of drug discovery. A close look at various approaches including rational
design to new drug discovery will be discussed. Through pertinent case studies, a
variety of diseases and drug design principles will be examined. A major focus of
the course will be on drug targets including ion channel proteins, GPCRs and
enzymes.
Course contents 1. An overview of drug discovery and development (Chapter 8, GLP): 4 h
2. Principles of enzyme structure, catalysis and inhibition (Chapters 3 & 4,
GLP): 4 h
3. Structure and function of receptors (Chapters 5 & 6, GLP): 4 h
4. DNA Interactive agents and chemotherapy (Chapter 7, GLP): 3 h
5. Synthetic methodology in medicinal chemistry - approaches to diversity
(Chapter 12, GLP) : 6 h
6. Lead identification and structure-activity relationships (Chapter 11,
GLP): 6 h
7. Drug metabolism and pharmacology (Chapter 10, GLP): 3 h
8. Case Studies : 12 h
References An Introduction to Medicinal Chemistry, Graham L. Patrick; 2nd Ed.
Lehninger’s Principles of Biochemistry, Cox and Nelson, Fifth Edition
Organic Chemistry of Drug Design and Drug Action, Richard B. Silverman, 2nd Ed
Course title Lab Training/Theory Project – IV
Semester 8
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Credits 3
review/theoretical or computational project/lab based research project.
The student has to identify, talk to and mutually agree on a research project before
registering for this course. The scope, duration, structure, expectations, and
evaluation criteria (also see below) for the course are decided by the project
supervisor.
Course contents See above
References As per suggestions of the project supervisor
Course Title Chemistry of Alternate Energy

Semester 8
Credits 4
Nature of Course L- lectures alone
Introduction The course will mainly cover fundamental physical chemistry phenomena involved
in light to electrical energy conversion (optoelectronics), chemical to electrical
energy conversion (electrochemical), and light to fuel conversion
(photoelectrochemical), and energy storage. Important topics of sustainable and
environment-friendly energy research like solar cell, solar-to-hydrogen, fuel cell,
and batteries will be discussed. In the introductory part, the course will cover
different sources of energy and its consequence to environment and society. Then
a major part (15 hours) will be on fundamentals of semiconductors and
optoelectronics with special emphasis on solar cells. Third and fourth parts of the
course will discuss about electrochemical energy storage and conversion
respectively. Both fundamentals and applied aspects will be discussed. Finally, the
last part of the course will briefly discuss about waste heat harvesting. Present
status of emerging science and technology will be discussed, with a special
emphasis on highlighting challenges and opportunities for a researcher in Physical
Chemistry.
The level of the course will be suitable for PhD, Integrated PhD and 8th semester BS-
MS students. Students taking the course are expected to have basic knowledge of
spectroscopy, electrochemistry and solid state chemistry.
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Course contents 1. Introduction (5 hours): Energy-Environment-Economics, light to electrical energy
(details of topics (optoelectronics), chemical energy to electrical energy (electrochemical), light to
/sections with no. of chemical energy (photo electrochemical), waste heat to electrical energy
lectures for each) (thermoelectrics), nuclear energy, wind energy, solar thermal.
2. Fundamentals of Optoelectronics (15 hours): Basics of semiconductor, solar light
absorption, optical losses, charge excitation, charge separation, charge transport,
carrier (electron and hole) mobility, lifetime and diffusion length, Si solar cell, open
circuit voltage, fill factor, power conversion efficiency, GaAs solar cell, thin film
solar cell, dye and quantum dot sensitized solar cell, perovskite solar cell,
computational prediction of novel solar cell material, photodetector, light emitting
diodes.
3. Electro-Chemical Energy Storage (9 hours): Solar to fuel conversion,
electrochemical and photoelectrochemical water splitting reaction, electrochemical
and photoelectrochemical fuel production, the role of electrocatalysts and
photocatalysts. Basics of batteries, primary and secondary batteries, elements and
operation of electrochemical cells, theoretical cell voltage and capacity, losses in
cells, factors effecting battery performance, batteries for PV system.
4. Electro-Chemical Energy Conversion (9 hours): Basics of polymer electrolyte
membrane fuel cells, hydrogen oxygen cells and hydrogen air cell, hydrocarbon air
cell, alkaline fuel cell, phosphoric acid fuel cell and solid oxide fuel cells. Super
capacitor: Basic components of supercapacitors, double layer and
psuedocapacitors. Types of electrodes like high surface area activated carbons,
metal oxide and conducting polymers, aqueous and organic electrolytes. The
disadvantages and advantages of supercapacitors over battery systems and their
applications in aspects of energy density and power density.
5. Waste Heat Harvesting (2 hours): Basics of thermoelectrochemical cells,
fundamental concepts and operation.
References Jenny Nelson, The Physics of Solar Cells (Properties of Semiconductor Materials),
Imperial College Press.
B. E Conway. Electrochemical Supercapacitors. Fundamentals and Applications.
Kluwer 1999.
C. A Vincent and B. Scrosati. Modern Batteries. Butterworth-Heinemann, 1997.
T. J. Crompton. Battery Reference Book, Elsevier. 2000. Sammes Nigel. Fuel Cell
Technology, Springer 2006
Course title Photochemistry and Photophysics [Prerequisites: Fundamentals of Molecular
Spectroscopy]
Semester 8
Credits 3
Introduction This course will give idea to students how light can take a major role in many
natural and chemical processes? Here the students will also get through knowledge
about excited state processes (e.g. fluorescence, phosphorescence etc.) and the
importance of the above mentioned processes in all field of science.
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Course contents Fundamental Concepts (17 Lectures): Absorption of light and excited state
deactivation pathways (Jablonski Diagram), Photochemistry and photophysics, laws
of photochemistry, Primary processes in photochemical reactions, Fluorescence,
Delayed fluorescence and Phosphorescence, Concept of quantum yield, Lifetime,
Anisotropy, Quenching and Sensitization phenomena, Bimolecular quenching,
Stern-Volmer equation, Static versus Dynamic quenching, Electron transfer reaction
& Marcus theory, Excited state proton transfer, Foster Resonance Energy Transfer
(Coulombic), Dexter (Exchange) mechanisms and examples, Photoisomerisation,
Dimerization reactions, Excimer and Exciplex, Diffusion controlled rate constants,
Photochemical equilibrium, Conical intersections and breakdown of the Born-
Oppenheimer approximation.
2. Natural and Technological Applications (7 lectures): Natural and artificial
photosynthesis, Vision, Photochromism, Photocatalysis, Photochemical damage in
living systems and recovery, Photodynamic therapy, Aggregation-Induced Emission
(AIE), Light powered molecular devices and machines (molecular memories,
sensors, rotary motors, logic gates, Encoding and Decoding, Switches)
3. Techniques and Instrumentation (4 Lectures): Steady-state absorption and
emission spectroscopy (Emission and excitation spectra, Absolute and relative
quantum yield measurements), Time-resolved absorption and emission
spectroscopy (techniques used in measuring lifetime using single photon counting
and fluorescence up-conversion, Flash photolysis, Pulse radiolysis and Data
analysis)
References 1.Photochemistry and Photophysics: Concepts, Research, Applications by
Vincenzo Balzani, Paola Ceroni, Alberto Juris.
2. Modern Molecular Photochemistry by Nicholas J. Turro.
3. Principles of Fluorescence Spectroscopy by J. R. Lakowicz.
4. Fundamentals of Photochemistry by K. K. Rohatgi Mukherjee.
5. Handbook of Photochemistry by Marco Montalti, Alberto Credi, Luca Prodi, M.
Teresa Gandolfi.
6. Physical Chemistry by Ira. N. Levine.
Course title Advanced Materials Science
Semester 8
Credits 3
Introduction First part of Advanced Materials Chemistry Course would be exposing the students
to various aspects of a Range of Materials. Train them to understand the Structure-
Property relationships.
Second part of the course would provide them with practical understanding of
energy materials from a fundamental and application perspective.
Course would be presented in a pitch that can be absorbed equally well by students
from physics and chemistry backgrounds.
Course contents Overview of various materials (6 h): Metal and oxide nanoparticles, semiconductor
nanocrystals, oxides related to superconductivity, organic magnets, conducting
polymers and hybrids materials.
Carbon based materials (2 h): Synthesis: Carbon nanotubes (CNTs), fullerenes,
graphene and graphnoid materials, boron nitride, and boro-carbo-nitrides
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Nano-micro fabrication and synthesis (4 h): Top-down and bottom-up approach
towards micro and nanofabrications, self-assembly, supramolecular chemistry,
electron-beam and UV lithography, focused ion-beam lithography, and X-ray
lithography.
Tutorial on instrumentation (1 h): in chemistry, physics and biology
Part II
Introduction: Molecules to Materials (1hr)
Types of Solids (5 hrs):
Amorphous, polycrystalline & single crystals and their analysis using diffraction.
Zeolites, Metal Organic frameworks, Covalent Organic Frameworks, Inorganic rings
and cages.
Adsorption concepts and application (3 hrs):
Surface area, surface tension, contact angles. Fundamentals of adsorption; theory;
isotherms, fundamental adsorption models, types of isotherms. Adsorbents: Micro,
Meso and Macroporous Materials;
Introduction to advanced characterization techniques (3 hrs)
Plasma and photoelectron spectroscopy and microscopy, Thermal Analysis
1. NB part: The class notes would be the best text book. Notes in the form of
published work in various Journals will be provided.
2. RV part: The class notes would be the best text book. In addition there are
several textbooks useful as references. Some of these are listed below. “Adsorption
by Powders and Porous Solids: Principles, Methodology and Applications” (J.
Rouquerol et al.).
“Characterization of Porous Solids and Powders: Surface Area, Pore Size and
Density” (S. Lowell et al.).
“Solid State Chemistry, Lesley E Smart and Elaine A, Moore.
“Atomic absorption and Plasma Spectorscopy, J.R. Dean.
Course title Organometallic Chemistry: Principles and Applications
Semester 8
Credits 3
Introduction The main objective of this course is to help the students to learn the principles of
organometallic chemistry with emphasis to the understanding of their structure,
properties and applications. Organometallic chemistry has served as a bridge
between traditional inorganic and organic chemistry and contributed to the
development of several important discoveries in synthetic organic chemistry. At the
end of this course students will have a thorough understanding of the classification
and mechanistic aspects of several organometallic reactions and will be able be
identify the role of organometallic complexes in organic synthesis and industrial
applications.
Course contents Section #1- Concepts of Structure and Bonding: (3 hours)
Definition, 18 electron rule, Classes of ligands, Bonding and structural
considerations in organometallics and isolobal analogies.
Section #2: Fundamental Reaction Process (3 hours)
Oxidative addition and reductive elimination; Insertion and elimination; Ligand
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substitution processes, Transmetallation, Nucleophilic and electrophilic addition
and abstraction.
Section # 3: Preparative and characterization methods (6 hours):
General methods for the preparation of organometallic compounds such as metal-
hydrides, -carbonyls, -carbenes, -alkenes, -alkynes, -allyl and -arene complexes. Use
of various spectroscopic and analytical techniques for the elucidation of structure,
properties and reactivates of organometallic compounds. Fluxionally and
stereochemically non-rigid molecules.
Section # 4:Synthetic Applications: (10 hours)

(i) Coupling reactions: Heck, Suzuki, Stille, Negishi, Kumada, Sonogashira, Buchwald,
enolate, Hartwig, Hiyama, Tsuji-Trost allylation reactions. (ii) Cyclization reactions:
cycloaddition (including click chemistry), carbocyclization, electrophilic cyclization,
wacker cyclization. (iii) Addition reactions: Hydrometalation, Hydroalkoxylation,
Hydroamination. (iv) Carbonylation: Pauson-Khand reaction, (v) Olefin oxidation,
(vi) Carbenes, (vii) Activation reactions: C-H bond activation, activation of CO and
CO2, viii) alcohol activation using pincer catalyst
Section # 5: Industrial Applications:(3 hours)
Hydrogenation, hydroformylation, isomerization, metathesis and polymerization
reactions.
Section # 6: Bio-organometallics: (3 hours)
Nitrogen fixation, coenzyme B12, Hydrogenase, CO dehydrogenase and
methanogenesis.
References 1. Ch. Elschenbroich, A. Salzer, Organometallics; 2nd Ed. VCH, 1995.
2. Robert H. Crabtree, The Organometallic Chemistry of the Transition
Metals, 5th Ed. (Jhon Wiley, 2009).
3. Clayden, Greeves, Warren and Wothers, Organic Chemistry, (Oxford
University Press, 2001).
4. Louis S. Hegedus, Transition Metals in the Synthesis of Complex Organic
Molecules, 5th Ed (University Science Books, Mill Vally).
5. B. D. Gupta and A. J. Elias, Basic Organometallic Chemistry, University
Press, 2010.
Course title Organotransition Metal Catalysis and Beyond
Semester 8
Credits 3
Introduction Catalysis is of fundamental importance in chemistry and plays a vital role in basic
research, applied sciences as well as industrial processes. To understand the
essence of catalysis and relationship between catalysis effect and catalyst
structure, it is important to learn the basic principles behind the metal, ligands and
their bonding properties. Emphasis will be placed on structure, bonding and
catalytic cycles and how they are derived from appropriate experimental data;
implicit in this is a complete understanding of the fundamental reaction types
prevalent in these cycles such as oxidative addition, migratory insertion and
reductive elimination; How appropriate ligand design can be used to ‘tailor’
catalytic properties such as reactivity and selectivity. It will serve as a foundation to
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apply this knowledge for better understanding of catalysts and catalysis.
Course contents 1. Introduction: Catalysis - Term and basic principles, Why is catalysis required?,
The development of organotransition metal catalysis, Principles of catalysis:
homogenous and heterogeneous catalysis, selectivity and specificity of catalysts
etc. (3 hrs)
2. Structure and bonding: General properties of ligands: dative (L-type), covalent (X-
type), neutral, anionic, even- or odd- electron, π-bonded, combination of σ and π
donor, and cationic ligands. Properties of metals: oxidation state, relationship
between oxidation state and no. of d-electrons, trends in the properties of
transition metals. (4 hrs)
3. Homogeneous Catalysis and Important reactions: Overview of reactions
catalysed by metal complexes in solution; Detailed discussion of the major
homogeneous catalytic reactions to include hydrogenation, carbonylation
reactions, alkene oligomerisation and polymerisation, oxidation reactions, C-C and
C-X coupling, hydrocyanation and hydrosilylation, hydroamination reactions,
Oxidation of olefins and alkanes, Catalytic C-H functionalization, Allylic substitution.
(8 hrs)
4. Asymmetric Catalysis: Introduction, general principle and practical aspects of
asymmetric catalysis. (2 hrs)
5. Heterogeneous Catalysis: Carbonylation reaction, Polymerization, Ammonia
Synthesis, Fischer-Tropsch synthesis, Methane reforming and the mechanism,
Zeolite catalysis, Hydrodesulfurization, High temperature catalysis, selective
oxidation of propylene, Kinetics in heterogeneous catalytic reactions (5 hrs)
6. Non-classical Catalysis: Introduction of non-classical catalysis, Catalysts based on
main group elements especially Frustrated Lewis pair catalysts (FLPs) and their
application in hydrogen activation and reduction of many functional groups,
Organocatalysis, Lanthanide Lewis acids catalysis, Alkali and alkaline earth metal
catalyzed reactions. (6 hrs)
References 1. Dirk Steinborn, Fundamentals of Organometallic Catalysis, Wiley-VCH .
2. John F. Hartwig, Organotransition Metal Chemistry. From Bonding to Catalysis,
University Science Books, Mill Valley, California.
3. Matthias Beller, A. Renken, R. A. van Santen Catalysis. From Principles to
Applications, Wiley-VCH.
4. Gadi Rothenberg, Catalysis. Concepts and Green Applications. Wiley-VCH.
5. For Asymmetric Catalysis: Walsh, P. J., Kozlowski, M. C., Fundamentals of
Asymmetric Catalysis, University Science Books, California, 2008.
Course Title Asymmetric Synthesis and Catalysis

Semester 8
Credits 3
Introduction This is an advanced level course where students can learn various concepts in
asymmetric synthesis/catalysis and their applications in the total synthesis of
natural products. This course would primarily develop a fundamental
understanding of the concepts of chirality, stereoisomerism and optical activity.
Students can learn the various approaches that are used to prepare stereo-
selective products from achiral starting materials and rationalize the formation of
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the stereoselective products. Students will also learn the several reagents and
catalyst used for the asymmetric construction of C-C and C-hetero bond forming
reactions.
Course contents Introduction to stereochemistry (2 hrs): Chirality and Optical activity,
Stereoselective and Stereospecific reactions, Enantiomeric and Diastereomeric
excess, Different methods for determining enantiomeric and diastereomeric excess.
General concepts in Asymmetric synthesis (2 hrs): Re- and Si-faces, Crams rule,
Felkin-Anh model, Chelation model, Prelogs rule, Horeau’s rule, Cotton effect,
Octant rule.
Separation of stereoisomer (1 hr): Resolution and Racemization.
General Strategies for Asymmetric Synthesis (1hr): Chiral Pool, Chiral auxiliaries,
Chiral reagents.
Metal catalysis (9 hrs):
Substrate, Reagent and Catalyst Controlled Asymmetric Synthesis. Asymmetric C-C
and C-heteroatom bond forming reactions: Asymmetric Oxidations/Reductions and
Modifications. Asymmetric cyclization and Ring opening reactions:
Cyclopropanation, Epoxidation and Aziridination and related examples. Asymmetric
Additions Reactions: aldehydes and ketones, conjugate addition. α-Alkylation and
catalytic alkylation of carbonyl compounds (Fluorination and trifluoromethylation),
Strecker Reactions and related examples.
Asymmetric Ring-Closing metathesis, Asymmetric domino reactions/tandem
reactions, Asymmetric synthesis using carbenoids, Asymmetric
photoredoxcatalysis.
Enantioselective Organocatalysis (9 hrs)
Orgaocatalysis and History. Biomimetic Concept: Catalytic mechanism of Class I
Aldolase. Covalent and Non-Covalent Organocatalysis: Lewis base, Lewis acid,
Bronsted acid and Bronsted base catalysis with examples. Enantioselective Iminium,
enamine and Acid–Base Bifunctional Catalysis and Asymmetric Phase-Transfer and
Ion Pair Catalysis. Selected Organocatalysts-Nucleophilic Substitution and Addition.
Chiral N-heterocyclic carbenes (NHCs) catalyzed organic transformations,
asymmetric phase transfer catalysis. Photoredox organocatalysis.
Asymmetric synthesis in Natural products and Large Scale Synthesis (3 hrs):
Strychnine, Oseltamivir, diazonamide A, Esterone
Asymmetric synthesis in drugs, perfumes and chiroptical switches (1 hr)
References 1. Stereochemistry of Organic compounds by E. L. Eliel, S. H. Wilen and L. N.
Mander, Wiley, 2013.
2. Organic chemistry by Jonathan Clayden, Nick Greevs, Stuart Warren and
Peter Wothers.
3. Principles and Applications of Asymmetric Synthesis by Guo-Qiang Lin, Yue-
Ming Li, Albert S. C. Chan
4. Principles of Asymmetric Synthesis by Robert E. Gawley and Jeffrey Aube
5. Asymmetric synthesis: more methods and application by Mathias
Christmann and Stefan Bräse
6. Asymmetric Organocatalysis: From Biomimetic Concepts to Applications in
Asymmetric Synthesis by Berkessel, A. and Groger, H., Wiley-VCH, 2005.
7. Catalysis in Asymmetric Synthesis by Ojima, I., Wiley-VCH, 2004.
Course Title Fundamentals of Solution-State NMR Spectroscopy: Principles and Applications
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Credits 4
Semester 7
Nature of Course L- lectures alone
Introduction The theoretical basis of NMR experiments that are applied to study molecular
structure and dynamics will be described. Principles of Fourier transform NMR will
be discussed with emphasis on instrumentation, data acquisition, processing and
analysis of multidimensional NMR experiments. Routine experiments would be
understood from the fundamentals on how such spectra are acquired, in addition
to their practical aspects/applications.
Course contents Classical NMR spectroscopy: Nuclear magnetism, the Bloch equations, one-pulse
(details of topics with experiment, line-width and chemical shift, scalar coupling.
no of lectures for Theoretical description of NMR spectroscopy: Brief introduction to quantum
each) mechanics, Liouville-von Neumann equation, rotating frame transformation,
density matrix representations, pulses and rotations, quantum mechanical
description of NMR spectroscopy, extension to multiple spin systems, the one pulse
experiment, concept of coherence, product operator formalism and its applications
to single/multiple quantum coherence experiments.
Practical aspects of NMR spectroscopy: NMR instrumentation, experimental set up,
data acquisition, data processing (introduction to Fourier transformation), pulse, z-
axis gradients and spin-decoupling techniques, extension to methodology to two-
and multidimensional experiments.
Chemical applications: Basic 1D 1H NMR experiments (including solvent
suppression), nuclear Overhauser effect spectroscopy, 2D NOESY and ROESY,
correlation spectroscopy (COSY and its variants), total correlation spectroscopy
(TOCSY), J-resolved spectroscopy, diffusion ordered spectroscopy (DOSY), concept
of polarization and coherence transfer (INEPT), heteronuclear correlation
experiments (HETCOR, HSQC, HMQC, HMBC).
Biological applications: 2D [15N, 1H] and [13C, 1H] HSQC, transverse relaxation
optimized spectroscopy (TROSY), common 3D NMR experiments (HNCO, HNCACB,
CBCA(CO)NH, HBHA(CO)NH, (H)CCH-COSY, (H)CCH-TOCSY, HSQC-NOESY, NOESY-
HSQC), rapid data acquisition techniques, residual dipolar couplings, conventional
and recent advances in structure determination of proteins and nucleic acids.
Relaxation and dynamic processes: Steady-state and transient NOE, Solomon’s
equations and its applications, chemical and conformational exchange, Bloch
equations, the relaxation master equation, spectral density functions, relaxation
mechanisms.
References 1. Cavanagh, J. et al., Protein NMR Spectroscopy, Principles and Practice. 2nd
Ed., Elsevier, 2007.
2. Levitt, M.H., Spin Dynamics: Basics of Nuclear Magnetic Resonance, 2nd
Ed. Wiley, 2008.
3. Ernst, R.R., et al., Principles of Nuclear Magnetic Resonance in One and
Two Dimensions, Clarendon Press Oxford, 1987.
4. Rule, G.S. and Hitchens, T.K., Fundamentals of Protein NMR Spectroscopy,
Springer Netherlands, 2006.
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4.3 Syllabi for Elective Courses in Data Science
Discipline Data Science
Course title Semester Project
Semester 5, 6, 7, 8
Credits 3
Introduction The larger objective of this course is to encourage students to participate in ongoing
research at IISER. This may be in the form of a reading/literature
review/theoretical/computational project. The student has to identify, talk to and
mutually agree with a faculty member on a project before registering for this
course.
Course contents The project is evaluated through mid-semester and end semester reports, and
poster presentations evaluated by a departmental committee at the end of the
semester. Exact details about scope, duration, structure, expectations, and
evaluation criteria for this course are decided by the project supervisor.
References As per suggestion of the project supervisor
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4.4 Syllabi for Elective Courses in ECS
Course title Landscapes and Their Evolution
Semester 3
Credits 3
Prerequistes Knowledge of elementary calculus and computing is required.
Introduction This is a course about various landforms around us. Google-Earth, Digital elevation
models is used to explore various interesting landscapes. The processes behind the
origin and evolution of the landforms are discussed quantitatively, using basics
physics.
Course contents 1. A google-earth tour of Earth and Mars; analysing digital elevation models and
contour maps; spatial scales oflandforms, temporal scales of evolution; force
balance and mass conservation [5]
2. planetary scale landforms and processes: [8]
Oblateness, and the highest peak on any planet; hypsometry of planets;
Isostacy (orogens and ocean basins, isostatic response of glacial/erosional
unloading);
Landscapes near plate boundaries (basic structure of the Himalaya and Western
Ghats); folds, faults, Earth-quakes, distribution, slip & uplift pattern;
3.Erosional processes: [5]
physical and chemical weathering (a typical weathering profile in Deccan plateau);
Climate/Erosion/uplift linkage
5. hillslope processes: (regolith and its creep, landslide) [2]
6. fluvial landscapes: (properties of river networks; river discharge and stream
power, erosion and transport; bedrock and alluvial rivers; equilibrium long-profiles,
knickpoint migration, baselevel; floodplains, meandering, braiding) [5]
7. glacial landscapes: (ice flow; erosion, transport, and deposition; u-shaped valleys,
hanging valleys, moraines, lakes) [2]
8. aeolian landscapes: (dunmorphology and migration; exploring martian dunes) [1]
References 1. Geomorphology: The Mechanics and Chemistry of landscapes, Robert S.

Anderson, Suzanne P. Anderson,Cambridge University Press, 17-Jun-2010
2. Fundamentals of Geomorphology, Richard Huggett, Routledge, 04-Jul-2013
Title Principles of Planetary Climate
Semester 4
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Credits 4
Nature of Course Lectures & Tutorials
Pre-requisites Basic knowledge of programming
This course introduces a hierarchical system of mathematical models to analyse the

Introduction
climate system, and the basic physics behind planetary climate
Energy balance in the climate system; zero dimensional energy balance model;
Notion of radiating temperature; application to snowball earth dynamics and
planetary habitability;
Shell model, implications for surface energy balance, radiating height;
Radiative transfer in planetary atmospheres; optical thickness; solutions in

idealised cases;
Course contents Grey gas approximation; Radiative transfer in a grey gas; radiative equilibrium.
Instability of radiative equilibrium and radiative-convective equilibrium
Real gases and their behaviour; impact on climate of a planet.
Energy balance in a single column model; Surface energy balance; transport of

energy by dynamics; general circulation of the atmosphere and ocean as diffusive
processes.
Principles of Planetary Climate by Raymond Pierrehumbert

References
Selected research papers and popular articles
Course title The Solid Earth

Semester 4
Credits 4
Prerequistes None
Introduction This course introduces the basic streams of Solid Earth Geophysics which broadly
includes Seismology, Geodynamics, and Isostasy. The course is aimed at fresh Earth
Science Students and will introduce them to Solid Earth Geophysics to get started.
Course contents Chemical and Physical Composition of the Earth
Meteorites as indicators of planetary compositions, Irons and stony-irons, Ordinary
and carbonaceous chondrites; Core, Mantle, and Crust; Oceans, Water in the Earth.
Figure of the Earth and gravity-I

Gravity and gravitational potential field; Orbit of Earth, ellipticity, Rotation of
Earth; Milankovitch cycles, Precession, wobble, Length of the day, and rotation
irregularities.; Coupling of the core to rotational variations; Introduction to Geoid
and isostasy; Gravity anomalies
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Earth’s Magnetic field-I
Geomagnetic field and its pattern; The secular variation and the electrical
conductivity of the mantle. The electrical conductivity of the core; Geo-Dynamo;
The westward drift and inner core rotation. Dynamo energy, Magnetic field of
other planets
Rock magnetism and paleomagnetism-I

Magnetic properties of minerals and rocks; Secular variation and the axial dipole
hypothesis; Geomagnetic reversals; Paleointensity; Polar wander and continental
drift; Plate tectonics and its paleomagnetic evidence
Plate tectonics-I
Benioff zones and subduction; Spreading centers and magnetic lineations; Hot
Spots; Plate margin and accompanying geological structures; Plate tectonics and
pattern of mantle convection mantle convection.
G-plates- interactive compute model for plate-tectonic reconstructions
Cooling of the Earth and its age, cooling model by Kelvin and Parry
Introduction to Earthquakes as dislocations; Distribution of Earthquakes
References 1. Stacey, Frank D., and Paul M. Davis. Physics of the Earth. Cambridge
University Press, 2008.
2. Fowler, C. M. R., Fowler, C. M. R., & Fowler, M. (1990). The solid earth: an
introduction to global geophysics. Cambridge University Press.
3. Turcotte, D. L., & Schubert, G. (2002). Geodynamics. Cambridge university
press.
4. Cox, A., & Hart, R. B. (2009). Plate tectonics: how it works. John Wiley &
Sons.
Course Title Atmosphere and Ocean chemistry
Semester 4
Credits 4
Prerequistes None
The objective of this course is to learn the basic chemical mechanisms taking place
in the atmosphere and ocean and to understand how critical chemical interactions
control the state of the Earth’s atmosphere and Oceans.
Introduction
This course will provide an outline of nature of the atmosphere and ocean and
discuss how we are changing this with time and how they eventually feedback and
modify our climate.
Evolution of earth’s atmosphere and Ocean; current composition of the

atmosphere and ocean; The greenhouse effect and the ozone hole; rainwater
Course contents
chemistry, acid rain; Atmospheric aerosols, concentration and size, sources, and
transformation; Sources of anthropogenic pollution; Distribution of chemicals in
the ocean; Estuarine behavior of elements; Nutrient cycling in oceans; Organic
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matter Production, export and remineralization; Carbon cycle, Inorganic carbon
chemistry, air-sea carbon exchanges, solubility and biological carbon pumps;
Productivity in oceans.
1. Global Environment: Water, Air and Geochemical cycles. E K Berner and R A

Berner, Second edition, 2012 Princeton University Press, Oxford.
2. Introduction to Atmospheric Chemistry, Daniel Jacob, Princeton University Press,
References
1999.
3. Chemical Oceanography, IVth Ed., Frank Millero, 2013.
4. Tracers in the sea. W S Broecker and T Peng, 1982.
Course Title Applied Mathematical Methods
Semester 5
Credits 4
Prerequistes None
The course is application of mathematical methods to solve physical problems.

Though most of the examples to be treated are from Earth Science and Physics, the
Introduction concept are equally applicable to any other branch. A certain basic knowledge of
calculus and algebra is needed. We shall have many computer exercises in this
course.
Linear Algebra: Projection and completeness, Eigenvalue decomposition of matrix,

function of matrix, singular value decomposition,
Differential Equations and Dynamical Systems: Methods of solution of DEs,

qualitative theory of DEs: stationary points and their classification, introduction to
Course contents bifurcation theory and its application in climate.
PDEs and their analysis: non-dimensionalization, asymptotic analysis, derivation of

approximate equations
Descriptive and inferential statistics: Moments of a distribution and their

estimation; hypothesis testing
1. Roel Sneider and Kasper van Wijk, 2015, A Guided tour of mathematical
methods for the Physical sciences Third Edition , Cambridge University Press
References 2. Boas, M.L.,2006, Mathematical methods in Physical sciences, John Wiley & sons,
Inc
3. Arfken GB and Weber HJ, 2005, Mathematical method for physicist,

Course title Introduction to Geophysics
Semester 5 (for batches 2019, 2020)
4 (for 2021-batch onwards)
Credits 4
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Prerequistes None
Introduction This course provides an overview of various concepts, physical principles and
mathematical treatment required to understand the making and working of the
solid Earth. Appropriate slides, teaching materials (open source) and relevant
research publications to be provided.
Course contents A Crustal evolution 6 L
L1-Earth properties and processes: Chemical and mechanical subdivisions of earth
L2 and 3- Plate tectonics, and Driving mechanism
L 4-Convergent Margins, Subduction zones, Continental convergence,
L5-Mantle plumes and volcanism through time
L6-Evolution of continents and Major Science Questions
B Seismology 21 L, 7T
L1,2- Wave propagation concept using string
L3-5Stress-strain relationship for a perfectly elastic solid The equation of Motion,
Wave equation in isotropic media
L6-8 Plane wave solution in isotropic media, Spherical waves, P and S waves, Plane
waves in a layered medium
L9-11 Earthquake- recording, location, energy, fault characteristics and earthquake
mechanics, statistical behavior,
L12-15 Surface Waves- Rayleigh and Love waves in Earth, Dispersion, Phase and
group velocity
L16-19 Seismic Imaging using Travel time, receiver function, surface wave
L20-21Seismology and plate tectonics, Global earthquake distribution in 3-D and
tectonics- interlinkage between process,
Tutorials- 7
C) Thermal structure of the Earth 7 L, 2T

L1 Rocks, radio activity, heat generation
L2- Heat flow, Geothermal gradient and diffusion
L3-Thermal structure of ocean lithosphere- Half space and plate cooling models
L4-Model verification, Ocean Floor Topography,
L5-Continental geotherm
L6-7 Seismology and thermal structure of earth
Tutorials -2
References 1. Stein, S., & Wysession, M. (2009). An introduction to seismology, earthquakes,
and earth structure. John Wiley & Sons.
2. Shearer, P. M. (2009). Introduction to seismology. Cambridge University Press.
3. https://www.iris.edu/hq/#
4. Irina Artemieva, The lithosphere, Cambridge University Press

Course title Physics of Atmosphere
Semester 5
Credits 4
Prerequistes None
Introduction The course aims to provides an introduction to meteorology with emphasis on
understanding the transfer of energy, momentum and water vapor fluxes by
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atmospheric circulation, thermodynamics of the atmosphere and cloud and
precipitation processes.
Through gaining an understanding of the concept of atmospheric stability and

cloud processes the students will be able to better appreciate the different
weather systems we experience in our day to day life.
Course contents Atmospheric mean state Observed horizontal and vertical distribution of pressure,
temperature, wind and humidity fields, clouds and precipitation, Global circulation
features.
Various decompositions of circulation: mean, transient and stationary eddies, basic

forms of energy in the atmosphere, meridional transport of potential, kinetic and
internal energy, momentum and water vapor fluxes.
Thermodynamic state of the atmosphere and ocean: Equation of state for air and
seawater, dry and moist adiabatic processes, Clausius–Clapeyron equation,
entropy, potential temperature
Understanding atmospheric convection: Static stability, conditional and convective

instability, analysis of thermodynamic diagrams,
Cloud formation and precipitation processes: colligative properties of water

solutions, nucleation of liquid phase and ice phase; curvature and solute effects,
growth of clouds, warm and cold cloud precipitation processes.
References 1) Physics of the Atmosphere and Climate, Murray L Salby
2) Thermodynamics of Atmospheres and Oceans, by Curry and Webster
3) Atmospheric Science: An Introductory Survey, JM Wallace and PV Hobbs, 2nd
Edition, Academic Press, (2006)

Course Title Earth and Planetary Materials
Semester 5, 7
Credits 4
Nature of course Lectures & Laboratory
Prerequistes None
Introduction This course intends to introduce the students to various earth and planetary
materials. Emphasis is given on the physical and chemical characterization of
minerals and rocks.
After attending the course, the students would appreciate inter-relations between
chemistry, structure and physical properties of minerals. It will also enable the
students to identify various minerals and rocks.
This is a mandatory course for getting major in ECS

Course contents Different types of earth and planetary materials.
Internal order in minerals: two and three dimensional lattices, motif, symmetry of
motif and lattices, point group and space groups.
Structure of minerals: ionic radii, coordination, Pauling’s rules.
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Crystal classes and their symmetry. Use of stereographic projections to represent
symmetry elements and point groups.
Physical properties of minerals and its relation with internal structure.
Analytical methods in mineral sciences

Optical microscopy: petrological microscopes; optical properties of minerals.
XRD: powder method to identify minerals and analyze simple structures.
XRF, ICPAES and EPMA analysis to determine chemical composition of minerals
Chemistry and systematic description of selected mineral groups: carbonates,

silicates, sulfides.
Different ways of formations of minerals: crystallization, precipitation, solid-solid

reactions and weathering.
Rocks types and their classifications.
Meteorites and their compositional variations.

References 1. Earth Materials: Introduction to Mineralogy and Petrology by C. Klein and A. R.
Philpotts, Cambridge University Press, 2nd Edition, 2012.
2. An Introduction to Rock Forming Minerals by W. A. Deer, R. A. Howei, and J.
Zussman, Mineralogical Society of Great Britain and Ireland, 3rd Edition, 2013.
3. Understanding Earth by J. Grotzinger, T. H. Jordan, F. Press and R. Siever, W.H.
Freeman and Co. N.Y. USA, 5th Edition, 2007.
4. An introduction to Igneous and Metamorphic Petrology by J. D. Winter,
Prentice Hall, 2nd Edition, 2009.

Course title Sedimentology and Stratigraphy
Semester 5, 7
Credits 4
Nature of course Lectures and field
Prerequistes Earth and Planetary Materials
Introduction This course will aim to bring into focus the processes that influence the formation of
sediments and sedimentary rocks, their physical, chemical, and biological properties
and evolution of sedimentary processes through geologic time.
Outcomes: The students will become familiar with sediment transport, major
sedimentary rock types and deposition in modern sedimentary environments. They
will be able to establish stratigraphic relationships in sedimentary basins. It is
expected that the students will be able to understand evolution of
sedimentary processes through geologic time as gleaned from sedimentary rock
record.
Course contents 1. Fundamentals of sedimentary geology: Sediments – types
and origin, weathering (physical, chemical, hydrolysis), entrainment and
transportation.
2. Siliciclastic sediments and sedimentary rocks (sandstone, conglomerate, shale).
3. Diagenesis of siliciclastic
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4. Diagenesis of organic matter, hydrocarbon generation
5. Concepts of fluid movement, flow conditions, Hjulström curve, turbidity currents
6. Sedimentary structures at different scales, post depositional
sedimentary structures, mud volcanism.
7.Concepts of sedimentary facies, Walther's Law and depositional
environment (fluvial, lake, transitional, marine)
8. Biogenic sediments and sedimentary rocks key elements of
modern and past carbonate depositional environments.
9. Principles of stratigraphy, Lithostratigraphy, biostratigraphy, chronostratigraphy.
References 1. Principles of Sedimentology and Stratigraphy, (2006), by Boggs, S., Jr., Prentice
Hall.
2. Sedimentary geology, (2004), by Prothero, D. R., & Schwab, F., Macmillan.
3. Sedimentary Petrology, (2006), by Tucker, M. E., Blackwell Publishing.
4. Depositional sedimentary environments; with reference to terrigenous clastics,
(1973), H.-E. Reineck, and I. B. Singh, Berlin, New York, Springer-Verlag.
5. Sedimentology and Stratigraphy, Second Edition (2009), by Nichols, G., Wiley
Blackwell.
6. Sedimentary rocks, (1975), by Pettijohn, F.J., Harper and Row Publ. New Delhi

Course Title Numerical Computation
Semester 5
Credits 4
Prerequistes None
Introduction The course gives an introduction to numerical methods and algorithms widely used
for solving wide ranges of applied mathematical problems. In addition, students will
become familiar with MATLAB based scientific computing/programming
environment.
Course contents Introduction to scientific computing.
Basics of MATLAB programming: basics of MATLAB programming, array operations

in MATLAB, Loops and execution control, working with files: Scripts and Functions,
file input/output operations, visualization.
Floating point arithmetic: Floating point system, measures and types of errors, the
IEEE standards.
Linear algebra: Linear algebra in MATLAB, Gauss elimination, Gauss-Jordan

elimination, LU decomposition and stability, QR decomposition method, Eigen value-
Eigen vectors.
Interpolation: linear interpolation, Newton and Lagrange polynomial interpolation,

Piece-wise interpolation method: cubic spline method.
Least-square method: Design matrix, Matrix method based least-square solver, QR

decomposition based least-square method.
Numerical differentiation: Finite difference method, centered, backward and

forward difference methods.
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Numerical Integration: Trapezoidal and Simpson method, composite Trapezoidal and
Simpson’s method, data adaptive Simpson integration method.
ODE/PDE solvers: Euler method, Runge-kutta 2nd order and 4th order method,
solving coupled ODE/PDEs, MATLAB built-in ODE solvers.
References 1. Numerical Recipes, W.H. Press et al., Cambridge University Press, 2007.
2. Introduction to Numerical Analysis, J. Stoer and R. Bulirsch, Springer, 2003.
3. Linear Algebra and its Applications, Gilbert Strang, 4th edition, 2014.

Course Title Structural Geology and Tectonics
Semester 5, 7
Credits 4
Nature of Course Lectures & Tutorials
Prerequisites None
Introduction This course is offered to enable the students to understand crustal deformation and
its association with plate tectonics. This will help students to understand patterns
of rock deformation. The students will also appreciate multiphase crustal
deformation in relation to the regional tectonics. The course has bearing on
exploration of hydrocarbon and economic mineral deposits.
Course contents Behavior of rock material under stress, strain. Dynamic and kinematic analyses of
rocks in two dimensions, stress and strain.
Stress: Uni-axial and Bi-axial stress analysis. Mohr’s Circle and its applications;
Mohr-Coulomb failure Criterion.
Strain: Bi-axial strain analysis. Strain ellipsoids: Flinn’s diagram of strain ellipsoids.
(6)
Folds, Classification and genesis of folds. Mechanism of folding, Biot’s law - strain
within a buckled layer, similar fold and shear fold, kink bands, chevron folds and
conjugate fold. Theory of progressive evolution of fold shapes in single competent
layers, Layer parallel shortening, Dependence of fold shape on high and low
viscosity contrast between different layers, Superimposed folding, type 1, 2 and 3
interference pattern. (6)
Faults– classification and genesis, Mechanism of faulting. Thrust systems. Strike
slips fault systems. Joints and fractures. Classification and Significances. (4)
Lineations. Classification and significance. Boudinage and Fold relations. Foliations,
cleavage. Classification and Significances. Scope of structural analysis, concept of
Tectonite fabric and Tectonite Symmetry (4)
Shear Zones–classification, ductile shear zone. Structural analysis on microscopic,
mesoscopic and macrosopic scales Microdeformation, plastic and brittle
deformation, Deformation of planar structures by flexural slip folding and shear
folding. (4)
Structure and physical characters of continental and oceanic crust Continental drift,
Sea - floor spreading and Plate Tectonics, Structure and Tectonics of divergent
margins, transform faults, convergent margins (4)
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Tectonic framework of India, Different tectonics blocks, Cratons and Mobile Belts
Dharwar, Southern Granulite Terrain, Eastern Ghats Mobile Belt, Aravalli and Delhi
Fold Belts, Central Indian Tectonic Zone, Neotectonics - Features and evidences-
characteristic landforms, Methods of analysis, Case studies of Orogenic belts (4)
References 1. Ramsay, J. G. Folding and fracturing of rocks. McGraw Hills, 1967.
2. Haakon Fossen, Structural Geology. Cambridge University Press.
3. Davis, G. H., Reynolds, S. J. and Kiutth, C. C. 2013. Structural Geology of Rocks
and Regions, John Wiley and Sons, 3rd Ed.
4. Philip Keary and Frederick Vine, Global Tectonics, Blackwell Science, 1996

Course Title Introduction to Field Technique
Semester 6, 8. During winter vacation
Credits 3
Nature of course Field visits of 5 days during winter break. Report writing and presentation.
Prerequisites Earth and Planetary Materials, Sedimentology and Stratigraphy, Structural Geology
and Tectonics
Introduction This course aims at developing ‘an eye’ for the field aspects of geoscience. The
students will be introduced to geological field skills necessary for documenting,
understanding and interpreting field observations.
This course offers an opportunity to get familiarized with the ‘real-world
geosciences’. After attending this course, the students will find it much easier to
visualize what is being taught in the theory courses offered by ECS. This course will
impart skills necessary not only for carrying out actual field-based studies but also
for interpreting the field results.
Course contents Field visits would be planned well in advance and students would be informed.
Main features of the field would include:
Introduction to topographic and geologic maps. Identification of minerals and rocks
in the field. Basic structural measurements, understanding deformation, recent
sedimentary processes and environment, basics of lithological mapping. Field
report writing and presentation.
References 1. The Field Guide to Geology by David Lambert and Diagram Group, 2nd edition,
Checkmark Books
2. Geological Field Techniques by Angela L. Coe (Ed), Wiley-Blackwell

Course Title Geo and Cosmo Chemistry
Semester 6, 8
Credits 4
Prerequistes Earth and Planetary Materials
Introduction This course focuses on developing an understanding of chemical behavior of
elements and processes that lead to the distribution of elements in earth. High
temperature processes will be discussed to make students understand formation of
planetary objects such as earth and their chemical differentiation. Low temperature
processes are introduced to explain earth surface processes such as weathering and
104
ocean chemistry. Applications of stable and radiogenic isotopes are also introduced.
After successful completion, the students will be able to use geochemical principles
to understand formation and chemical evolution of various earth-system reservoirs.
Course contents Origin of elements.
Cosmochemical and Geochemical behaviour of elements and its basis: Properties of

elements (volatiles, semi-volatiles, alkalis, alkaline earths, REE, HFS); Goldschmidt
Classification of elements.
Radioactivity and decay schemes.
Condensation of elements; meteorites and their compositional variations. Timescales

of formation planetary formations.
Concept of distribution coefficients; Mass conservation and elemental fractionation;

Rayleigh fractionation.
Differentiation of the Earth and resultant elemental distribution in the core-mantle-

crust system.
High temperature geochemistry: basic thermodynamic concepts; stability of minerals

at different temperature, pressure conditions; thermodynamics of solutions;
geothermo- and geobarometers.
Low-temperature aqueous geochemistry; Oxidation-Reductions reactions; Carbonate

Equilibria; Chemistry of natural water; Chemical weathering.
Kinetics of reactions: rate of reactions and their temperature dependence.
Stable isotopes: isotope fractionation; applications in geological and climate

sciences.
References 1. W. M. White : Geochemistry, 2013, Wiley-Blackwell
2. F. Albarede: Geochemistry-An introduction. Second Edition, 2009, Columbia
University Press.
3. H. Y. McSween, S. M. Richardson and M. E. Uhle: Geochemistry: Pathways and
Processes. Second ed., 2004, Columbia University Press.
4. K. C. Misra: Geochemistry: Principles and applications. 2012, Wiley-Blackwell.

Course title Geophysical Fluid Dynamics
Semester 6, 8
Credits 4
Prerequistes None
Introduction The main goal of the course is to understand the dynamical processes in the
atmosphere and Ocean and their mathematical-physical formulation.
Course contents Physical properties of fluids: Continuum hypothesis
Framework for describing fluid motion: Lagrangian and Eulerian frameworks,
105
fundamental forces acting on fluids, conservation laws: momentum, mass, and
energy, equation of state, rotating and non-rotating frames of references
Apparent forces: centrifugal and Coriolis forces
Naiver-Stokes equations in a rotating spherical coordinate
Simplifications and approximations of the governing equations (Naiver-Stokes
equation): Traditional approximation, Boussinesq-Anelastic approximations, f and
Beta-plane approximations
Scale analysis: Hydrostatic approximation, Geostrophic approximation, Gradient
wind approximation, Cyclostrophic approximation, Thermal wind balance.
Vertical coordinates: Height, Pressure, Theta (entropy) coordinates
Vorticity and Circulation: Kelvin circulation theorem, physical interpretation of
vorticity equation and their applications, potential vorticity.
Effect of friction on fluid: Effect of friction on large-scale flow, Ekman layer and
pumping, Western boundary intensification.
References 1. Atmosphere, Ocean, and Climate Dynamics, John Marshall and Alan Plumb,
Academic Press, 2008.
2. An introduction to Dynamic Meteorology, J. R. Holton and G. J. Hakim, Academic
press, 2013.
3. Physics of the Atmosphere and Climate, Murray L Salby, Cambridge University
Press, 2012.
4. Atmospheric and Oceanic Fluid Dynamics, Geoffrey Vallis, Cambridge University
Press, 2017.

Course title Physics of Geological Processes
(Proposed new name: Gravity and Global Tectonics)
Semester 6, 8
Credits 4
Prequisite Introduction to Geophysics
Introduction The course presents a physical concept and mathematical framework for using
gravity measurements to study Earth’s structure. The course also provides a
comprehensive view of the working of Earth in the framework of Plate tectonics.
Course contents A) Potential Field theory and gravity
Potential Field theory, The Gravitational potential, The Field Equations (Laplace
equation), Global gravity and spherical harmonics, The Continuation theorem of
Potential fields, Multipole Gravitational field, Moment of Inertia and Gravity,
Calculation of excess mass in 1D and 2D
B) Measurement and interpretation of gravity data

The Lattitude effect, The free-air correction, The Bouger Correction, Topographic
correction, Effects of Isostasy, Downward continuation and interpretation of
residual anomalies, Maximum depth Rules, The Geoid, The method of characteristic
curves, The numerical computation of Gravity Profiles.
C) Isostasy and Flexure of the Lithosphere

Historical Development of the Concept of Isostasy, Success of the Airy and Pratt
Models of Isostasy in Explaining Crustal Structure, The Earth’s Gravity Field and Tests
of Isostasy, Strength of the Earth’s Crust, Putnam and Local versus Regional
Compensation, Principle of Isobary, Isostasy and Plate Tectonics, Flexure of the
Lithosphere
106
Elasticity and Flexure, Linear Elasticity, Uniaxial Stress and Strain, Plane stress and
strain, Pure and simple shear, Isotropic stress, Two-Dimensional Bending or Flexure
of Plates under applied Moments, Vertical and Horizontal Load, Application to the
Earth’s Lithosphere-Periodic and End Load, Bending of the Elastic Lithosphere under
the Loads of Island Chains, Ocean Trench Flexure and the Structure of Sedimentary
Basins, Thin- versus Thick-Plate Flexure
The Lithosphere as a Filter, The Gravitational Admittance, Isostatic Response

Functions, Flexure of a Viscoelastic Plate, Rheology of the Lithosphere: Brittle vs
Ductile, Time-Dependent Flexure, Elastic Thickness, and Earthquakes
References 1. Grant, F. S., Guilford, J. P., & West, G. F. (1965). Interpretation theory in applied
geophysics. New York: McGraw-Hill.
2. Watts, A. B. (2001). Isostasy and Flexure of the Lithosphere. Cambridge
University Press.
3. Trucotte, D. L. and Schubert, G. (2002). Geodynamics. Cabridge University Press

Course Title Analytical Geochemistry Lab
Semester 6, 8
Credits 3
Nature of Course Laboratory
Prerequistes Geo and Cosmochemistry
Introduction This course gives hands-on training on analyzing and interpreting various geological
samples.
Course contents Lab protocols, safety and statistics; Basic principles of sampling and geochemical
analyses of rocks, sediment, and water. Aquatic geochemistry: Salinity, Alkalinity,
Dissolved oxygen, Nutrient analyses; Rock and sediment Geochemistry: Sample
Dissolution; major and trace elemental analyses, Inorganic and organic carbon; Clay
analyses; Aerosol sampling and analyses; Key aspects of data presentation, analysis
and interpretation.
1. P.J. Potts: A handbook of Silicate rock analysis, 1992, First edition, Springer
Science, LLC.
2. K. Grasshoff, K. Kremling, M. Ehrhardt: Methods of seawater Analysis, 1999,
Third Edition, Wiley, VCH.
3. J. Strickland, T. R. Parsons: A Practical Handbook of seawater analysis. Second
edition, 1972, The Alger Press Ltd.

Course title Physical Oceanography
Semester 6, 8
Credits 4
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Prerequisites Physics of Atmosphere
Introduction This course provides students an overview of the oceanography from observational
and dynamical perspectives. The aim will be to provide the student with an
empirical description of the large scale ocean circulation and build further from an
elementary fluid dynamics course and see how ocean circulation can be
understood using dynamical principles.
Course contents The oceans as we observe them: Measurement of temperature and Salinity;
introduction to measurement systems; qualitative description of the large scale
circulation;
Thermodynamics of seawater; Fluid dynamics of the ocean: Inertial Oscillations;

Boundary layers; Ekman layer; Ekman pumping and its consequences; the deep
ocean circulation and relationship to potential vorticity conservation; Western
boundary intensification; Abyssal flow in the ocean
References 1. Introduction to Physical Oceanography by Robert H Stewart
2. Atmosphere and Ocean Dynamics by Geoffrey Vallis.

Course title Signal Analysis and Information Theory
Semester 6, 8
Credits 4
Prerequisites Understanding of linear algebra and probability as well as real and complex analysis.
Introduction Information is a fundamental aspect of the nature and workings of reality, and is also
fundamental to our understanding of reality. This realization has resulted in a
resurgence of interest in the topic of Signal Analysis and Information Theory and its
implementation in the Earth and Environmental Sciences. By the end of the course, the
student must be able to: Formulate the fundamental concepts of signal processing and
information theory, and analyse problems in statistical setting.
Course contents 1. Signal representation: Analog and digital signal, sampling theorem, Signal and
systems, Z-transform, Fourier series, Fourier transform, discrete Fourier transform,
Fast Fourier transform, digital filters
2. Measure of Information: Probability and statistics, Entropy, Theoretical
Foundations and relationship with probability theory.
3. Compression and Quantization
4. Sparsity
5. Exponential Families, Maximum Entropy
6. Detection and Estimation Theory
References 1. Proakis, J.G. and Dimitris, D.K., (2006) ‘Digital Signal Processing’, Prentice-Hall.
2. Oppenheim A. V. (1997), ‘Signals and Systems’, Prentice Hall
3. Jaynes, E.T. (2003) ’Probability Theory — The logic of Science’, Cambridge
University Press, ISBN 978-0521592710
4. Cover and Thomas, Elements of Information Theory (Second Edition), Wiley,
108
2006.
5. MacKay, D. J. (2003) Information theory, inference and learning algorithms.
Cambridge University press, ISBN-13: 9780521642989.

Course title Parameter Estimation and Inverse Theory
Semester 5, 7
Credits 3
Prerequisites None
Introduction This course is intended to discuss fundamental concepts of inverse modeling and
to enable the students to formulate and solve inverse problems
Course contents 1. Introduction: Introduction to forward and inverse problem, Linear and non-
linear inverse problem, Application of inverse theory in different areas of science
and engineering
2. Brief revision of linear algebra: Linear vector space, linear combination, linear
independence, basis and dimension of a vector space, functional, norms and
normed vector space.
3. Ill posed problems: Well posed and ill posed problems, underdetermined,
overdetermined and mix-determined systems.
4. Solution of linear inverse problems: Least square solution, minimum norm

solution, maximum likelihood method, Tikhonov regularization method,
estimation of trade-off parameter using L-curve and generalized cross validation
(GCV) method, Model and data resolution, Backus-Gilbert method
5. Singular value decomposition: Singular value decomposition, singular value and

singular vector, Moore-Penrose generalized inverse, truncated singular value
decomposition method, Impact of noise on inverted model, Relation between
singular value decomposition and Tikhonov regularization method
6. Non-linear inverse problem: Solution of non-linear inverse problem using quasi-

linear methods, Gradient, sensitivity (Jacobian) matrix and Hessian matrix,
Newtons method, Gauss-Newton method, Quasi-Newton method, Levenberg-
Marquardt algorithm, steepest decent method
7. Global optimization techniques: Introduction to stochastic inversion techniques,

Markov chain Monte Carlo method, Bayesian inversion, Simulating annealing,
genetic algorithm
References 1. Parameter Estimation and Inverse Problems: Richard C. Aster, Brian Borchers
Clifford and H. Thurber (2018) Elsevier
2. Geophysical Data Analysis: Discrete Inverse Theory MATLAB Edition: W. Menke
(2012) Academic Press.
3. Inverse Problem Theory: A. Tarantola (2005) SIAM Publication
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Course title Exploration Seismology
Semester 7
Credits 4
Prerequisites Introduction to Geophysics
Introduction This course aims to discuss seismic methods used in subsurface imaging that
include seismic theory, data acquisition and processing.
Course contents 1. Introduction to theory of seismic waves, seismic velocity of minerals and rocks.
Application areas (real life problems in industry, water, engineering)
2. Reflection and refraction of seismic waves in flat and dipping layer earth, use of
intercept-slowness, analysis of travel time curve, primary and multiple reflection.
3. Onshore and offshore data acquisition, Seismometry, Seismic data acquisition

system, seismic sources and their characteristics.
4. 2-D and 3-D survey design, multichannel data, signal enhancement (CMP, CDP),
advantage of 3-D acquisition
5. Data processing workflow- Pre-processing techniques such as reformatting,

editing, muting and geometrical spreading correction; Noise filtering; velocity
analysis and normal move out correction; multiple reflection elimination
techniques such as deconvolution, data stacking and Radon transform; migration of
post stack and pre-stack data
6. Application of seismic data to hydrocarbon exploration. Brief discussion on

borehole seismology (Vertical Seismic Profiling).
References 1. C.L. Liner, Elements of 3D Seismology, Pennwell Corporation, U.S. (2004)
2. Yilmaz, O., “Seismic Data Analysis Processing, Inversion and Interpretation of
Seismic Data”, Society of Exploration Geophysicists (2001)
3. Sheriff, R.E. and Geldart, L.P., “Exploration Seismology”, Cambridge Univ. Press.
(1995)
4. Telford, W.M., Geldart, L.P. and Sheriff, R.E., “Applied Geophysics”, Cambridge
Univ. Press. (1990)
5. Dobrin, M.B. and Savit, C.H., “Introduction to Geophysical Prospecting”,
McGraw Hill. (1988)
6. Robinson, E.A., Durrani, T.S. and Peardon, L.G., “Geophysical Signal Processing”,
Prentice-Hall International (1986) (2004).

Course title Atmosphere and Ocean Dynamics
Semester 7
Credits 4
Prerequisites Geophysical Fluid Dynamics
Introduction The course helps students understand the complex interactions governing the
Earth’s atmosphere and oceans by exploring the basic fluid dynamic and
thermodynamic principles.
Course contents Wave fundamentals
Restoring forces, group velocity, Phase velocity, dispersion relation, wave vector,
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different types of waves in the atmosphere and Ocean.
Common wave modes observed in the atmosphere and Ocean: Surface gravity
waves, Internal gravity waves, Inertio-gravity waves, Rossby waves.
Geostrophic adjustment.
Mid-latitude and equatorial shallow water wave models
Normal modes
Mid-latitude and equatorial wave modes
Horizontal and vertical structure and propagations of waves
Forced waves
Steady forced motion
Transient forced motion
Thermal and Orographically forced waves
References 1. Atmosphere-Ocean Dynamics, A. E. Gill, Academic press, 1982.

2. Geophysical Fluid Dynamics, Joseph Pedlosky, Springer, 1987.
3. Middle Atmosphere Dynamics, D. G. Andrews, J. R. Holton, and C. B.
Leovy, Academic press, 1987.

Course title Tropical Meteorology
Semester 7
Credits 4
Prerequisites Physics of Atmosphere and Ocean or Geophysical Fluid Dynamics
Introduction This is an advanced course which explores the weather and climate phenomena in
the Tropics in detail. Topics on atmospheric physics and dynamics covered in the
previous courses will be used to understand different climate phenomena.
Course contents Basic state of the tropics, Observational overview, Energy and moisture budgets,
Tropical convection, ITCZ, General circulation of the tropics- Hadley and Walker
circulation, Brewer Dobson circulation, Quasi-Biennial Oscillations.
Thunderstorms: CAPE and CINE, Life cycle and structure of thunderstorm, growth
of a thunderstorm to a supercell and multi-cell thunderstorm, Thunderstorm
electrification –sequence of events in a discharge, the mechanism of earth –
atmospheric charge balance – role of thunderstorms
Tropical cyclones: Development and climatology; TC structure; Dynamics and

thermodynamics of TC evolution, Observing and forecasting TCs
Tropical variability:
1) Interannual Fluctuations of the Walker Circulation –El Niño/Southern
Oscillation; Ocean-Atmosphere interaction in the tropics, Bjerkenes
feedback; Genesis and characteristics of ENSO; Global impacts of ENSO;
Indian Ocean dipole
2) Tropical Intraseasonal Oscillations: The Madden Julian Oscillations, life
cycle and evolution.
3) Monsoons: annual cycle, seasonality, a conceptual mechanistic model of
the Indian summer monsoon; ITCZ over Indian ocean – structure and
movement, 30-50 day oscillations, 10-20 day oscillations, the role of the
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oceans in the life cycle of Indian monsoon system, ENSO and the Indian
Monsoon.
References 1. Climate and circulation of the tropics, by S Hastenrath
2. Monsoon Meteorology by C.P. Chang and T.N. Krishnamurti
3. El Nino, La Nina and the Southern Oscillation, George Philander, Academic
press, 1990.

Course title Hydrology
Semester 5, 7
Credits 4
Prerequisites Knowledge of elementary calculus and computing is required
Introduction This is a course about global water cycle, focusing on the physics of various
terrestrial hydrological processes. Global problems related to water would also be
touched upon.
Course contents * Hdrological cycle: (6 L)
Hydrological cycle (with some India-specific data and discussions).; global
reservoirs, fluxes, and residence time; energy/mass balance; water vapor in the
atmosphere, Precipitation and its variability, interception, infiltration; evapo-
transpiration, energy/water limited cases, Budyko curve; soil moisture, ground
water, surface water; measurement methods.
* Stream Flow: (8 L)
Effective rainfall, surface flow/overland flow.
Linear reservoir model;
Streamflow routing, runoff generation; stream flow and hydrograph. Unit and
synthetic hydrographs. St Venant’s equation;
* Ground water: (8 L)
Flow through porous media; soil moisture; infiltration; groundwater recharge. Flow
of ground water; aquifers; anisotropy;
wells. Diffusion equation for water table; steady solutions of diffusion equation;
Measurement methods.
* Tools and models: (4 L)
GIS tools and conceptual numerical model. Introduction to the structures of some
relatively simple hydrological models (eg VIC). Some hands on sessions. Global
water trends and climate-change effects.
References 1. Applied hydrogeology, 4th Edition (2000), by Fetter, Pearson.

2. Applied Hydrology, (1988), by Ven Chow, David Maidment and Larry Mays,
McGraw-Hill.
3. Groundwater hydrology, (2004), by Todd and Mays, Wiley.

Course Title Igneous and Metamorphic Petrology
Semester 7
Credits 4
Nature of Course Lectures and Tutorials
Prerequisites Earth and Planetary Materials, Geo and Cosmochemistry
Introduction This course aims at training the students to use chemical and mineralogical data of
rocks for understanding petrogenesis of igneous and metamorphic rocks.
This course deals with practical and theoretical aspects of formation of igneous and
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metamorphic rocks. Students will be able to explain why certain types of magmas
are associated with different crust forming processes. It will further help students
to appreciate textural and mineralogical changes of a rock when exposed to
different pressure-temperature conditions.
Course contents Significance of the chemical variations of rock forming minerals: olivine, spinel,
pyroxene, amphibole, garnet and feldspars.
Solid-melt and solid-solid partition coefficients of important elements and their

applications. Modelling of trace element distribution among coexisting phases to
understand origin and evolution igneous rocks.
Thermodynamics and kinetics of magma generation in different tectonic settings.

Emplacement and crystallization of magmas. Extrusive basaltic volcanism on earth
and other planetary bodies.
Phase rule, mineral assemblages and metamorphic reactions. Phase

transformations during different paths of pressure, temperature and time changes
(P-T-t paths) and their tectonic relevance.
References 1. An introduction to Igneous and Metamorphic Petrology, 2nd Edition (2009), by J.
D. Winter, Prentice Hall.
2. An Introduction to Rock Forming Minerals, 3rd Edition (2013), by W. A. Deer, R.
A. Howei, and J. Zussman, Mineralogical Society of Great Britain and Ireland.
3. Igneous Rocks and Processes: A Practical Guide, (2010), by Robin Gill, Willey
Blackwell.
4. Igneous and Metamorphic Petrology, 2nd Edition (2003), by M. G. Best, Blackwell
Publishing.
5. Igneous Petrology, 2nd Edition (1996), by A. Hall, Longman.
6. Principles of Igneous and Metamorphic Petrology, 2nd Edition (2009), by A.
Philpotts and J. Ague, Cambridge University Press.
7. Metamorphic Phase Equilibria and Pressure-Temperature-Time Paths, (1994), by
F. S. Spear, Mineralogical Society of America.
8. Petrogenesis of Metamorphic Rocks, (2011), by K. Bucher and R. Grapes,
Springer.

Course Title Igneous and Metamorphic Petrology Lab
Semester 7
Credits 3
Nature of Course Lab
Prerequisites Igneous and Metamorphic Petrology
Introduction This course will cover laboratory aspects of the course Igneous and Metamorphic
Petrology
Course contents To be decided later
References To be decided later

Course Title Paleobiology
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Semester 5, 7
Credits 4
Prerequisites Basic knowledge of programming, Classical mechanics, Sedimentology
Introduction Paleontology is the study of the history of life through time. As with many other
areas of geology, paleobiology sits at the interface between disciplines, in this case
biology and geology. This course is designed to develop an understanding of the
process that govern the development of the fossil and general principles to
understand the fossil record. A quantitative approach is adopted in this course to
establish the patterns inferred from the organismal record in the deep time. The first
part of the course is primarily devoted to develope an understanding of various
Paleontological methods applied to read the record. The second part is designed to
study the evolutionary steps and major events of the life history in this planet as
revealed by the fossil record.
Course contents History of paleontological investigation, Nature of the fossil record, Taphonomy,
Growth and form, Evolutionary morphology, Population and species, Systematics,
Evolutionary rates and trends, Diversification, Extinction, Paleoecology,
Paleobiogeography, Conservation Paleobiology, Biostratigraphy Stratigraphy and
records of events in deep time, Early record of life during Precambrian, Important
events in Paleozoic, Mesozoic and Cenozoic
References 1) Foote, M. and A. Miller. 2008. Principles of Paleontology. 3rd ed. Freeman, NYC.
2) Prothero, D.R. 2004. Bringing Fossils to Life: An Introduction to Paleobiology. 2nd
ed. McGraw-Hill, NYC.
3) A number of peer reviewed articles (listed in the attached page).

Course title Sequence Stratigraphy
Semester 7
Credits 4
Prerequisites Basics of General Geology, Sedimentology and Stratigraphy
Introduction Sequence stratigraphy is the most recent and revolutionary paradigm in the field of
sedimentary geology, and completely revamps geological thinking and methods of
stratigraphic analysis. The concepts embodied by this discipline have resulted in a
sea change in geological thinking and in particular, the methods of facies and
stratigraphic analyses. In recent times, this approach has been embraced by
geoscientists as the preferred style of stratigraphic analysis, which has served to tie
together observations from many disciplines. As opposed to the other, more
conventional types of stratigraphy, such as biostratigraphy, lithostratigraphy,
chemostratigraphy or magnetostratigraphy, which are mostly concerned with data
collection, sequence stratigraphy has an important built-in interpretation
component which addresses issues such as (i) the construction of the allogenic
controls at the time of sedimentation, and (ii) predictions of facies architecture in
yet unexplored areas.
In fact, a key aspect of the sequence stratigraphic approach is to encourage the
integration of data sets and research methods. Blending insights from a range of
disciplines invariably leads to more robust interpretations and consequently,
scientific progress. Thus, the sequence stratigraphic approach has led to improved
understanding of how stratigraphic units, facies tracts, and depositional elements
relate to each other in time and space within sedimentary basins.
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Sequence stratigraphy builds on many exciting data sources. It requires a good
knowledge of sedimentology and facies analysis, fills the gap between
sedimentology, basin analysis, and the various types of conventional stratigraphy.
The study includes integration of disciplines including sedimentology, facies
analysis, depositional systems, biostratigraphy, well logs, seismic, tectonics and
basin analysis among others.
Seismic stratigraphy, which is the precursor of modern sequence stratigraphy, was
specially designed to facilitate the exploration of hydrocarbons. The methods of
seismic and sequence stratigraphy are now increasingly popular, and routinely
employed as part of the exploration strategies for other natural commodities as
well, including coal and mineral resources. What used to be an exclusive asset of
the petroleum industry, has been proven to have value for all types of exploration,
and the mining industries too are now making use of the genetic benefits of the
sequence stratigraphic approach.
For these reasons, sequence stratigraphy is currently one of the most active areas
of research in both academic and industrial environments.
Course contents · Overview

· Early developments
· Definition
· Core concepts
· Accommodation and shoreline shifts
· Base level
· Shoreline trajectories- Transgression and regression
· New approaches- Stratigraphic sequences
· Well logs
· Seismic data
· Unique/non unique stratal geometries
· Stratal stacking patterns in downstream/ upstream controlled settings
· Sequence stratigraphic units
· Sequence stratigraphic surfaces
· Systems tracts
· Sequence Models
· sequences in fluvial systems
· sequences in coastal to shallow-water systems
· sequences in deep water clastics
· Scales in sequence stratigraphy
· Sequence stratigraphic hierarchy
· Sequences in Carbonate Systems
· Depositional sequences in Indian Petroliferous basins
References Selected reviews provided by instructor.
Course title Sedimentology and Paleontology Lab
Semester 7
Credits 3
Nature of Course Laboratory
Prerequisites (if any) Sedimentology and Stratigraphy, Paleobiology
Introduction The laboratory course on Sedimentology and Paleontology is the extension of the
classroom teaching to the hands on training involving rocks and fossils in the
laboratory.
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The sedimentology part incorporates understanding various laboratory techniques
in the study of sedimentary rocks, including identification of microfacies,
sedimentary structures, texture etc. and their attributes in reservoir
characterization and depositional modelling.
The Paleontology part involves study of various group of microfossils including
foraminifera, ostracoda etc. The laboratory course incorporates processing of
samples for extraction of microfossils, sorting, identification and interpretation. The
course will also involve study of rock thin sections for microfossils, role of SEM in
species identification and interpretation of age and environment
Course contents  Megascopic studies of rock specimens (Clastic and Carbonates) and their
interpretations
 Microfacies studies (Petrography)
 Granulometry studies and interpretations
 Heavy mineral Analysis
 Scanning Electron Microscopy
 X-RD and X-RF studies and interpretations
 Cathodoluminescence studies and interpretations
 Clay minerology and its effects on rock porosity
 Carbonate megascopy in hand specimens
 Carbonate microfacies in thin sections
 Carbonate porosity and diagenesis interpretations from thin sections
 Hard rock in megascopy and petrography
 Fossils in hand specimens (Rock Samples)
 Techniques in Sample processing for extraction of microfossils
 Sorting and examination of microfossils
 Fossil identification and data entry
 Thin section examination
 Role of SEM in micropaleontology
Each topic will be preceded by classroom lecture.
References Material will be provided by the instructor

Course title Advanced Seismology
Semester 8
Credits 4
Prerequistes Introduction to Geophysics
Introduction This is an advanced course dealing with aspects of elastic wave propagation in the
earth, methodology of earth and earthquake imaging, statistical seismology,
seismology and plate tectonics and earthquake prediction. This requires basic
knowledge of mechanics, waves, calculus and algebra.
Course will have a number of hands on computer exercises and dealing with real
data
Course contents Stress and strain, seismic wave equation ( a quick review), computing synthetic
seismogram
Ray theory and travel time calculation in flat and spherical earth
Inversion of travel time in 1-D flat and spherical earth. Taup-p method
3-D velocity tomography
Earthquake location in 3-D medium, relative earthquake location, joint hypocenter
determination
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Ray theory: amplitude and phase computation, Attenuation- concept and
computation
Reflection seismology: receiver function, midpoint stacking, Kirchoff theory and
computer code writing
Surface wave and normal mode: Earth parameter estimation
Earthquake source theory
Earthquake and plate tectonics
Earthquake prediction
References Stein, S and Wysession, An introduction to seismology, earthquake and earth
structure, Wiley
Shearer, P, Introduction to seismology
Aki, K, Quantitative seismology

Course title Geoelectromagnetic Exploration
Semester 6, 8
Credits 4
Prerequistes Primary understanding of structure of minerals and rocks
Introduction This course introduces basic concept of electromagnetic wave propagation in
matter and its application in subsurface imaging.
Course contents 1. Introduction: Application of electrical and electromagnetic methods in earth
sciences, electrical properties of rocks and minerals
2. Electrical and Electromagnetic theory: Maxwell’s equations in time and

frequency domain, constitutive relations, Helmholtz equation, wave and diffusion
equation, skin depth, whole space Green’s function, boundary and interface
conditions, solution of the Helmholtz equation for 1- dimension model, depth of
investigation, vertical resolution, apparent resistivity and phase, isotropic and
anisotropic medium.
3. Electrical Method: Introduction to Resistivity methods, Instruments for

Resistivity methods, principle of superposition, principle of reciprocity, resistivity
array configurations (Wenner, Schlumberger, dipole-dipole, pole-pole, pole-
dipole), sounding and profiling techniques, potential distribution over a layered
earth, resistivity transfer function, recurrence relations, apparent resistivity
functions, resistivity data analysis, principle of equivalence, induced polarization
and selfpotential methods.
4. Electromagnetic method: Time and frequency domain electromagnetic

methods, Green’s function & convolution operator and their applications for
different source geometries, active and passive source method, formulation of
Magneto-telluric (MT) response for 1D earth model, MT response function for 1D,
2D and 3D earth model, very low frequency (VLF) technique, controlled-source
electromagnetic techniques, airborne electromagnetic methods, ground
penetrating radar.
References 1. Electrical Methods of Geophysical Prospecting: G. V. Keller (1980) Pergamon
Press.
2. Geosounding Principles: Resistivity Sounding Measurements: O. Koefoed
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(1980) Elsevier.
3. The Geoelectrical methods in Geophysical exploration: M. S. Zhdanov and G. V.
Keller (1994) Elsevier
4. Geophysical Electromagnetic Theory and Methods: M.S. Zhdanov (2009)
Elsevier
5. Electromagnetic Methods in Geophysics, Vol. I Theory: M.N. Nabighian (1987)
Society of Exploration Geophysics
6. Electromagnetic Methods in Geophysics Vol. II Applications: M.N. Nabighian
(1991) Society of Exploration Geophysics
7. Geoelectromagnetism: J.R. Wait (1982) Academic Press

Course title Geoelectromagnetic Exploration Lab
Semester 6, 8
Credits 3
Nature of course Lab
Prerequisites Geoelectromagnetic Exploration
Introduction This course aims to provide hands-on experience in data acquisition and
analysis of electrical/electromagnetic methods. Substantial time will be spent in
computation experiments that include writing commuter programs.
Course contents Field Experiments: Survey design and data acquisition
Electrical Method: Computation of electric potential due to a point source and
dipole source; computation of apparent resistivity for layered earth model for
different arrays types (Wenner, Schlumberger, dipole-dipole, pole-pole);
Sensitivity analysis for different array types; Data analysis of 2D resistivity data
Electromagnetic method: Computation of electric field due to point source in
whole/half space; computation of MT response function due to layered earth;
Computation of controlled-source electromagnetic response of layered model;
Data analysis of MT and EM data
References 1. Electrical Methods of Geophysical Prospecting: G. V. Keller (1980) Pergamon
Press.
2. Geosounding Principles: Resistivity Sounding Measurements: O. Koefoed
(1980) Elsevier.
3. The Geoelectrical methods in Geophysical exploration: M. S. Zhdanov and G.
V. Keller (1994) Elsevier
4. Geophysical Electromagnetic Theory and Methods: M.S. Zhdanov (2009)
Elsevier
5. Electromagnetic Methods in Geophysics, Vol. I Theory: M.N. Nabighian
(1987) Society of Exploration Geophysics
6. Electromagnetic Methods in Geophysics Vol. II Applications: M.N. Nabighian
(1991) Society of Exploration Geophysics.
7. Geoelectromagnetism: J.R. Wait (1982) Academic Press

Course title Exploration Seismology Lab
Semester 8
Credits 3
Nature of course Lab, Tutorials
Prerequisites Exploration Seismology, Sequence Stratigraphy
Introduction The course providse students with the opportunity to develop hands-on
experience of various seismic data analysis techniques. It will cover the essential
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geological and geophysical information necessary to visualize and interpret
seismic data. The students will gain a solid understanding of the applications of
the seismic data that include post-stack seismic attributes, seismic sequence
stratigraphy, seismic geomorphology, and multidisciplinary integration.
Outcome: The course is dedicated to advanced seismic data analysis techniques
using practical exercises. It will guide the students in the understanding that the
integration of geological data into the seismic model will add value in coherent
and successful seismic predictions that result from an interpretation.
Course contents Reflection Seismic data processing:
Data reformatting, geometry update and its QC, random noise attenuation
parameter testing and its application, velocity analysis, muting, deconvolution
parameter testing and its application, Radon filter parameter testing and its
application, dip moveout, Kirchhoff time migration parameter testing and its
application.
Reflection seismic data analysis (2D and 3D):
The processed seismic data and velocity models will be used to develop the
understanding of stratigraphy, structure,, potential hydrocarbon occurrences, etc.
Interpretation will be conducted on both prestack and post-stack seismic data
followed by AVO analysis. 3D seismic data analysis on seismic signal analysis,
attribute analysis and spectral decomposition.
A. SEISMIC DATA ANALYSIS & QC
Elements of Seismic data analysis (pre-stack and post-stack): Marine reflection

seismic data, wavelets, polarity and phase, seismic velocity, lateral and vertical
resolution, acoustic impedance, reflection co-eff, frequency content, noises,
multiples, data formats, visualizing shot gathers, CMPs, common offsets,
migration products.
Process 2D marine reflection seismic line.
Seismic data preparation for interpretation: smoothing/filtering for structural

interpretation vs reservoir interpretation. Parameters for seismic displays (Vertical
sections, time slices, composite sections, 3D vs 2D view).
B. WELL-TO-SEISMIC TYING
Well data calibration to identify main geological markers and main reservoir
layers.
Synthetic seismogram calculation.
C. MAPPING - HORIZONS & FAULTS

Structural interpretation (in time) of key horizons and faults (time picking: manual,
guided, and 3D picking).
Picking results QC and estimation of uncertainties.
Volume and surface attributes calculation and analysis.
Surfaces generation to produce a time model.
Spectral Attributes, Supervised Classification
Bright Spot Interpretation
Correlation and mapping
D. SEISMIC AND SEQUENCE STRATIGRAPHY

Seismic facies, stratal terminations. Identify the sequences and sequence
boundaries, wheeler transform
E. VOLCANIC STRATIGRAPHY
Identifying intrusions, and various facies, determine hydrocarbon potential using
reflection seismic data. Develop an understanding of magmatic emplacements
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and impact on the hydrocarbon system.
F. DEEP WATER ENVIRONMENT

Identify the deep water turbidite, mass transport and channel system. Develop an
understanding of deep water environment.
G. CROSS-CUTTING REFLECTIONS
Seismic Analysis of diagenesis and gas hydrate
References 1. Seismic Data Analysis, by Oz Yilmaz, Publisher: Society of Exploration

Geophysicists
2. 3-D Seismic Interpretation, Bacon, Simm and Redshaw. Cambridge University

Press, ISBN 9780511802416, 2003.
3. Seismic Attributes for Prospect Identification and Reservoir Characterization,

by Satinder Chopra and Kurt J. Marfurt, Pages: 481, Publisher: Society of
Exploration Geophysicists

Course title Geophysical Field Experiments
Semester 8
Credits 3
Prerequisites Advanced Seismology, Exploration Seismology, Geoelectromagnetic Exploration
Introduction This course aims to train students in handling geophysical field equipment and
provide hands-on experience in geophysical data acquisition. Data acquisition and
processing will build on theoretical concepts learnt in introduction to geophysics,
exploration geophysics, seismology and geo-electromagnetic exploration.
Substantial time will be spent on analysing and processing the raw data and
synthesizing the results in a report.
Course contents Course will have following three components
1. Geophysical survey design
2. Field operation and data acquisition
3. Data analysis
Data will be acquired using several geophysical equipment along a profile. The
acquired data will be processed and analyzed after fieldwork.
References 1. Applied Geophysics: W. M. Telford, L. P. Geldart and R. E. Sheriff (1990)
Cambridge Univ. Press
2. Fundamentals of Geophysics: W. Lowrie (2007) Cambridge University Press.
3. Introduction to Geophysical Prospecting: M. B. Dobrin and C. H. Savit (1988)
McGraw Hill
4. Introduction to Applied Geophysics: Exploring the Shallow Subsurface: H. R.
Burger, A. F. Sheehan and C. H. Jones (2006) W.W. Norton

Course title Climate modelling
Semester 8
Credits 4
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Prerequisities 1.Geophysical Fluid Dynamics
2. Physics of Atmosphere and Ocean/Oceanography/Tropical Meteorology
Introduction This advanced course introduces the approaches used in modelling the
geophysical flows from weather to climate timescales. Various models ranging
from simple energy balance models to complex GCMs will be explored. Hands on
training will be given using intermediate complexity models.
Course contents Historical Background, Numerical Weather Prediction as an Initial Value Problem,
Filtering Problem, Finite Difference Techniques, Explicit, Implicit, and semi-implicit
Schemes. Spectral Technique, Galerkin methods, CFL conditions and stability
analysis, Staggered grid, Nonlinear Instability and Aliasing
Hierarchy of Numerical Models: Barotropic Model, Equivalent Barotropic Model,

Two level Baroclinic Model, Shallow Water Equation Model, Primitive Equation
Models, Spectral Model
Basic Concepts of Parameterization, parameterization of boundary layer, cumulus

convection, radiation and clouds.
Components of an earth system model -- Atmosphere, Ocean, Land, Biosphere,

Sea and Land ice. Interactions between different components, energy, mass and
momentum fluxes.
Coupling-Hierarchy of Coupled models-Coupling strategies-spin up problems

Introduction to a full complexity climate model (CESM) -- configuration, compiling
and execution on an HPC machine.
References 1. Fundamentals of Atmospheric Modeling by Mark Z. Jacobson
2. A Climate Modelling Primer by McGuffie and A Henderson Sellers
3. Modeling Dynamic Climate Systems, Walter A. Robinson
4. Dynamic Meteorology & Numerical Weather Prediction : G.J.Haltiner &
Williams
5. Numerical Modelling of Oceans and Oceanic Processes: Lakshmi H.Kantha &
Carol Anne Clayson

Course title Science of Climate Change
Semester 8
Credits 3
Prerequisities Tropical Meteorology/Oceanography
Introduction Aim of this course is to provide understanding of climate changes and challenges
to sustainable development. Spatial and temporal change in the climate system
will be discussed. Various mitigation and adaptation strategies that are required
to face the current and future climate shifts will be discussed.
Course contents Description of the climate system, natural greenhouse effect and the effect of
trace gases and aerosols, feedbacks in the climate system, climate change in the
past, ice ages, proxy records, abrupt climate change, Instrumental record of
climate, climate variability on various time-scales, simple models of climate,
General Circulation Models, natural and anthropogenic climate change: detection
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and attribution, impacts and mitigation of climate change.
References 1. Solomon, S., D. Qin, M. Manning, Z. Chen, M. Marquis, K.B. Averyt,
M.Tignor and H.L. Miller: IPCC, 2007, Changes in Atmospheric
Constituents and in Radiative Forcing. In: Climate Change 2007:
Contribution of Working Group I to the Fourth Assessment Report of the
Intergovernmental Panel on Climate Change
2. J. David Neelin. Climate Change and Climate Modeling, Cambridge
University Press
3. Kevin E. Trenberth. Climate System Modeling, Cambridge University Press
4. Boris A. Kagan. Ocean Atmosphere Interaction and Climate Modeling,
Cambridge University Press

Course title Glacial System Modelling
Semester 6, 8
Credits 3
Prerequisites Applied Mathematical Methods
Introduction Beginning with an introduction to glacial processes, a hierarchy of mathematical
models of glacier dynamics is introduced. These models are used to obtain
quantitative insight into the interaction of glaciers in climate, water and
landsurface systems.
Concepts would be learned with the help of hands-on model exercises.
Course contents Glaciers (mass balance; energy balance; flow; steady state; climatic response; 0, 1
and 2-dimensional glacier dynamics models).
Glacier and Climate (ice-albedo feedback; ice-sheet and global climate; sea-level
fluctuations; snow-ball earth; global warming.)
Glacier and water cycle (Glacier hydrology; Glaciers and Himalayan rivers; climate
change and glacier-fed rivers.)
Glacier and landscape (Glacial erosion and deposition; glacial landforms;
modelling glacier valley long profiles.)
References 1. Geomorphology by Anderson and Anderson, Cambridge University Press
(2010)
2. Glacier and Climate Change by Oerlemans, CRC Press, (2001)
3. Physics of Glaciers by Cuffey and Patterson, 4th Edition, Elesvier (2010)

Course title Satellite Data Analysis and Image Processing
Semester 8
Credits 4
Prerequisite Landscape evolution, Earth and Planetary Materials.
Introduction The main objective of the course is to provide a foundation in satellite-based
remote sensing techniques. It has an equal emphasis on the physics of remote
sensing, digital image processing of remote sensing data, and application of remote
sensing. The course will cover the key image processing approaches and methods
as well as hands-on exercises and analyses. The focus of the course is on the
acquisition, processing, and analysis of remote sensing data and imagery in the
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geosciences. The methods taught are applicable to a wider range of fields such as
microscopy in the geosciences, image analysis in engineering applications, and
societal applications such as change detection as a result of drought or flood, forest
fire etc. Principles of remote sensing learned in the course could also be applied to
exploring planetary surface materials and surface processes. Students are
encouraged to bring a topic of their interest and explore how they can utilize the
concepts learned from the class to help them solve the problem of their interest.
Expected outcomes:
1. Assess how image processing and image analysis may help solve a specific
problem in geosciences or related disciplines.
2. Identify the appropriate imaging approaches or imagery pertinent to the

problem.
3. Develop an approach and workflow that builds on the concept of the image-
processing chain to move from raw imagery or geospatial data to a quantitative
representation and digest information contained in the imagery.
4. Use their acquired proficiency in digital image processing to apply the

appropriate tools out of the major image processing methods to solve geosciences,
geospatial or societal problems.
5. Understand the limitations of the technology
Course contents A. Fundamentals of remote sensing: The Electromagnetic Spectrum, radiation units
and laws, atmospheric scattering, BRDF, Albedo, path radiance, principles of
spectroscopy and spectral signatures.
B. Sensors and sensor technology: (i) Biology and optics of image processing,
cameras, scanners and acquisition devices, digitization, satellite and airborne image
acquisition differences and applications. (ii) Geometric transformations-
interpolation, geometric operations, and projections.
C. Understanding digital image: image, imaging, computer vision, image histogram,

global and local thresholding, gradient detection, linear filtering: neighborhoods,
kernels, convolutions, and their application on satellite images, adaptive
segmentation, frequency-domain operations, texture analysis (measures of texture,
point- and neighborhood-based methods), image fusion. Tutorial: Spatial and
frequency domain filtering.
D. Processing of colour and multi-spectral images: Colour representation and

transforms, multispectral transforms (principal component analysis and minimum
noise fraction transformation) and classification (unsupervised and supervised
techniques). Tutorial: Pre-processing VNIR/SWIR data, image rectification
(geometric and radiometric corrections), multispectral image analysis, image
classification.
E. Thermal remote sensing: Principles, atmospheric corrections, temperature

Estimation, sub-pixel temperatures and atmospheric corrections, emissivity and
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applications of thermal remote sensing. Tutorial: Thermal image processing of
ASTER images. Determine emissivity.
F. Hyperspectral remote sensing: Basics of hyperspectral images, concept of image

cube, hyperspectral image analysis workflow (pre-processing, filtering noisy data,
determining pixel purity index, end-member selection, n-dimensional data
visualization, spectral angle mapping, match filtering, minimum noise fraction
transformation, principal component analysis of hyperspectral images,
decorrelation stretch, applications, and advantages). Tutorial: Complete
hyperspectral processing workflow.
G. Synthetic aperture radar basics and Applications. Tutorial: Basics of SAR data
pre-processing and interpretation. Combine with multispectral image to enhance
interpretation
References 1. Introductory Digital Image Processing: A Remote Sensing Perspective by

John R. Jensen (Prentice Hall, 1996;318 p.; ISBN 0132058405,
9780132058407)
2. Castleman K. R. (1996) Digital image processing, Prentice Hall
3. Articles will be provided by the instructor.

Course title Indian Geology and Resources
Semester 8
Credits 4
Prerequisites Sedimentology and Stratigraphy, Geo and Cosmochemistry, Igneous and
Metamorphic Petrology
Introduction This course is aimed at providing in-depth information about Indian stratigraphy,
various economically important deposits within India and their genesis.
Course contents To be finalized later
References To be finalized later

Course Title Isotope Geochemistry
Semester 6, 8
Credits 3
Introduction This inter-disciplinary course aims to present application of (inorganic) chemistry in
Earth and Climate sciences. This course will discuss why abundance and distribution
of chemical elements (and their isotopes) in different reservoirs vary and how these
variations can be used to understand various geological processes. The goal is also to
understand the behavior of selected isotopes in the Earth system and apply these
properties in the field of hydrology, ocean and climate sciences.
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Course contents Properties of chemical elements; Stable and radioactive isotopes; Geochemical
cycles; Mass dependent and independent fractionation; Analytical methods and
isotope dilution; Binary Mixing; Solid Earth and magmatic processes; Chemical
geodynamics; Radiogenic tracers and Geochronology; Paleothermometry;
Reconstruction of past climate; Isotopes in the hydrology; Submarine groundwater;
Application of isotopes in oceanography; Atmospheric chemistry
References 1) Faure, G. and Mensing, T.M. (2004) Isotopes: Principles and Applications,
3rd Edition, John Wiley publishers, 928 pp.
2) Dickin, A.P. (2005) Radiogenic Isotope Geology, 2nd Edition, Cambridge
Publishers, 512 pp.
3) Allegre C. (2008), Isotope Geology, Cambridge University Press, 512 pp.
Course Title Geological Field Training
Semester 8, During winter vacation
Credits 3
Nature of course Power point lecture and Geological field work in the outcrops
Prerequisites Basics of General Geology, Sedimentology, Paleobiology and Sequence Stratigraphy
Introduction The field geological course is designed with the objective to train the students in
various aspects of field geological mapping, tectonics, basin evolution ;
understanding fundamentals of sedimentology, clastic and carbonate facies,
sedimentary structures, processes and products of various depositional
environments including fluvial, delta, estuary, coastal, carbonate shelf and coral
banks among others; fundamentals of paleobiology , micro and mega fossils
,biofacies, age and environmental interpretations ;Peleogeographic
reconstructions; fundamentals of sequence stratigraphy including mapping of
sequences, sequence stratigraphic surfaces, concepts of scales, systems tracts at
various hierarchical scales and different elements of petroleum systems including
source and reservoir rocks etc. This will be useful for all Geology students in their
professional and academic pursuits.
Course contents The course will begin with an introductory lecture about the basin Geology,
stratigraphy, evolution etc, followed by 4/5 days field trip to classic sections.
References Field Guide book provided by instructor
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4.5 Syllabi for Elective Courses in Mathematics
Course title Advanced Linear Algebra
Semester 3
Credits 3
Nature of course Lectures and/or Tutorials
Introduction In this course, we study the abstract vector spaces over arbitrary fields,
diagonalization and canonical forms for linear maps. We explore the close
connection between Linear algebra and geometry of Euclidean spaces Rn and Cn via
inner products and quadratic forms
Course contents Theory of abstract vector spaces over a field, basis and dimension, linear maps,
adjoints of linear transformations and dual spaces, quadratic forms and symmetric
matrices, orthogonal and unitary matrices, diagonalization of Hermitian and
symmetric matrices, eigenvectors and eigenvalues, Cayley-Hamilton theorem,
minimal polynomial, trace, determinant, introduction of classical linear groups,
multilinear algebra: tensor product of two vector spaces and, decomposition of V ⊗
V into symmetric and alternating tensors
References (1)Linear Algebra: K. Hoffman and R. Kunze (2009) Prentice Hall
(2) Finite Dimensional Vector Spaces: P. Halmos. (2012) Martino Fine Books
(3) Linear Algebra done right: S. Axler (2014) Springer
(4) Algebra: M. Artin (1991) Prentice Hall
(5) Linear Algebra: Stephen Friedberg, Arnold Insel (2004)
Course title Group Theory
Semester 4
Credits 3
Introduction You will study the three important algebraic structures, viz. Groups and Rings in this
course. Groups are collections of symmetries of objects. They are encountered
throughout mathematics, for instance in polyhedra, wallpaper patterns, and the
irrational roots of polynomials. In this course we introduce abstract groups; that is
we study the symmetries without the objects. The emphasis will both be on finite
groups, for which cardinality plays a decisive role, and on matrix groups, governed
by linear algebra. The notion of a group is one of the basic structures in
mathematics, and worthy of study for every scholar. A chemist will later study the
linear actions of finite groups, and a physicist will later study those of Lie groups. For
mathematicians, group theory is a basic component of their vocabulary.
One of the greatest analogies in mathematics is that between integers and
polynomials. Both have a rich theory of divisibility, with a Euclidean algorithm and
factorization into primes. It is always fruitful to find analogies between the two. The
proper context, which generalizes both integers and polynomials, is “ring theory”,
which you will begin to study in this course.
Course contents Groups, subgroups, normal subgroups, cosets and Lagrange's theorem, quotient
groups, group homomorphisms, isomorphism theorems, examples of groups (C_n,
S_n, A_n, D_n), group actions, Cayley’s theorem, Sylow’s theorem, direct and semi-
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direct products, class equation, general linear group and symmetries, statement of
the structure theorem for finitely generated abelian groups.
References (1) Abstract Algebra: D.S. Dummit and R.M. Foote (2003) Wiley
(2) Topics in Algebra: I.N. Herstein (1975) Wiley
(4) Algebra: T.W Hungerford (2003) GTM Springer
Course title Real Analysis I
Semester 4
Credits 3
Introduction A serious student of mathematics must master the epsilon-delta language of

“limits”.Familiar ideas from calculus, such as continuity, series, derivatives, and
integrals are all describable in terms of limits. In this course we strengthen our
analytic technique to the point where we can blend these ideas gracefully. Full
proofs are the norm in this course. It is very much a prerequisite for courses in the
analysis, topology, and applicable math streams; it is also strongly recommended for
students pursuing theoretical physics.
Course contents Real numbers, least upper bound property, sequences, convergence, suprema and
infima, Bolzano-Weierstrass theorem, limsup, liminf, limit points. Compactness and
connectedness in metric spaces. Heine Borel theorem Cauchy sequences. infinite
series, rearrangement of series, tests for convergence. Functions on R, continuous
functions, intermediate value theorem, uniform continuity, absolute continuity, the
continuity of derivative, L'Hospital rule. Riemann-Stieltjes integral, basic properties,
Riemann integrability of continuous functions, functions of bounded variation as
integrator, fundamental theorem of Calculus. Integration of vector valued functions
and rectifiable curves.
References 1. Analysis I & II: T. Tao, TRIM Series (2006) Hindustan Book Agency
2. Introduction to Real Analysis: R. G. Bartle and D. R. Sherbert (2011) Wiley
3. Mathematical Analysis: T. M. Apostol (1974) Addison-Wesley
4. Principles of Mathematical Analysis: W. Rudin (1976) Tata McGraw Hill
5. Methods of Real Analysis: Goldberg (1976) Wiley
Course title Discrete Structures
Semester 4
Credits 3
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Introduction The purpose of this course is to understand discrete structures that are used not
only in the traditional areas of mathematical application but also in computer
science, information theory, biological sciences, physical sciences, etc.
In particular, this course is meant to introduce sets, relations, functions, counting,
and combinatorics, and graph theory.
Course contents Set, functions, relations, partial ordered sets, chains and antichains in posets,
Counting and Combinatorics: Permutations and combinations of multisets, Binomial
identites, Set partitions, Bell, Catalan, and Stirling numbers, The Pigeonhole
Principle (strong form), The Inclusion and Exclusion Method and applications,
Mobius Inversion, Recurrence Relations and Generating Functions.
Graph Theory: Paths and Cycles, Eulerian and Hamiltonian Graphs, Bipartite graphs
and Matching, Trees, Cayley's tree formula.
References 1. Introductory Combinatorics: R. Brualdi (2009) Prentice Hall.

2. Combinatorics: P. Cameron (1994) Cambridge.
3. Enumerative Combinatorics: R. Stanley (2012) Cambridge.
4. A Course in Combinatorics: J. H. van Lint, R. M. Wilson (2001) Cambridge.
5. Combinatorics: Russell Merris (2003) Wiley-Interscience.
6. Introduction to Graph Theory: D.B. West (1996) Prentice Hall.
Course title Fields and Galois Theory
Semester 5
Credits 4
Prerequisites Group Theory
Introduction Galois theory arose from the study of “adjoining” roots of polynomials to the
rational numbers to generate larger number sets, such as the Gaussian numbers.
These larger fields of numbers enjoy the group of symmetries of the irrational roots
of these polynomials, which is called the Galois group. Such fields correspond
inversely to their Galois groups in a beautiful correspondence beloved to
algebraists. A clear understanding of Galois theory allows one to settle classical
questions such as whether we can or cannot use radicals to express the roots of
various polynomials. It is also prerequisite to modern questions in number theory
and algebraic geometry.
Course contents Fields and extensions, examples, algebraic extensions and algebraic elements,
transcendental elements, existence of algebraic closure, separable extensions,
normal extensions, automorphisms, solvable groups and solvability, main theorem
of Galois theory, finite fields, Galois groups of finite fields, cyclotomic extensions,
impossibility of solving polynomial equations of degree 5 or more by radicals.
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References 1. Abstract Algebra: Dummit and Foote (2003) Wiley India
2. Galois Theory: I. Stewart (2003) Chapman Hall/CRC Math. Series
3. Algebra: S. Lang (2005) GTM Springer
4. Field and Galois Theory: Patrick Morandi (2011) GTM Springer
5. Galois Theory (lectures delivered at the University of Notre Dame): E. Artin
(1997) Dover
6. Galois Theory: Edwards (1984) Springer
7. Field Theory: Roman (2006) Springer
8. Galois Theory of Algebraic Equations: J.P. Tignol (2001) World Scientific
9. Lectures on the Algebraic Theory of Fields: K.G. Ramanathan,
10. TIFR Lecture notes (available online)Galois Theory: Murthy, Ramanathan,
Seshadri, Shukla and Sridharan,
11. TIFR Pamphlets (available online)
Course title Rings and Modules
Semester 5
Credits 4
Prerequisites Group Theory, Advanced Linear Algebra (Recommended, but not mandatory)
Introduction In this course, you will study modules over rings which are generalisations of vector
spaces.
Course contents Rings, integral domains, PIDs, UFDS, polynomial rings, ideals, prime ideals, maximal
ideals, quotient rings, Chinese remainder theorem, modules over commutative
rings, isomorphism theorems, submodules, quotients, direct sums, tensor products,
free modules, structure theorem for modules over a PID, canonical forms (Jordan
and rational), localization of rings and modules.
References (1) Abstract Algebra: D.S. Dummit and R.M. Foote (2003) Wiley
(2) Topics in Algebra: I.N. Herstein (1975) Wiley
(4) Algebra: T.W Hungerford (2003) GTM Springer
Course title Real Analysis II
Semester 5
Credits 4
Prerequisites Real Analysis I
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Introduction In this course, we study the analysis on n-dimensional Euclidean space R^n. Though
some of these ideas are encountered previously in Multivariable Calculus, in this
course there is more emphasis on rigorous proofs than computations. This course is
a prerequisite for the courses in geometry sequence.
Course contents Pointwise and uniform convergence of sequences of functions, uniform

convergence and continuity, uniform convergence and differentiation, uniform
convergence and integration, Arzela-Ascoli theorem, Stone-Weierstrass theorem.
Uniform convergence of series of functions, Weierstrass M-test, introduction to
power series and analyticity, Fourier series. Differentiation on R^n, definition of
total derivative, Contraction principle, Inverse function theorem, implicit function
theorem, Leibniz's rule for differentiation under the integral sign. Multiple integrals,
Change of variable formula, Stokes theorem for regions in R^n.
References 1. Mathematical Analysis: T. M. Apostol (1974) Addison-Wesley

2. Principles of Mathematical Analysis: W. Rudin (1976) Tata McGraw Hill
Course title Point Set Topology
Semester 5
Credits 4
Introduction Topology, along with Algebra and Analysis, is one of three foundational areas of
pure mathematics. Roughly speaking, Topology can be thought of as ‘rubber-sheet
geometry’. Whereas Euclidean notions of lengths between points and angles
between lines do not make much sense on a stretchable sheet of rubber, some
properties such as that of having a hole in the rubber sheet do not change under
any amount of stretching or deformation. Topology is the study of those properties
which are invariant under such deformations. It is useful and enriching for all
students of science.
Course contents Metric spaces, topological spaces, continuous functions, product topology,
quotient topology, compactness, Heine-Borel theorem, Tychonoff’s theorem,
connectedness and path connectedness, separation axioms such as Hausdorff,
normal and regular, Urysohn’s Lemma, Urysohn’s metrization theorem, Tietze’s
extension theorem, paracompactness, partition of unity, introduction to CW-
complexes.
References 1. Topology: J. Munkres (2000) Prentice Hall

2. Basic Topology: Armstrong (2004) UTM Springer
3. Introduction to Topology and Modern Analysis:G. Simmons (2004) Tata
McGraw Hill
Course title Graph Theory
Semester 5
Credits 4
130
Prerequisites Discrete Structures
Introduction This course is an introduction to the theory of graphs intended for students of
mathematics and other sciences. The course introduces in an elementary way some
basic knowledge and primary methods in Graph Theory. We start from basic
definitions and examples, but hope to move on quickly and cover a broad range of
topics.
Course contents The Basics: graphs, paths and cycles, connectivity, trees and forests, bipartite
graphs, contraction and minors, Euler tours, Hamilton Cycle. Matching and Covers:
Maximum bipartite matching algorithms, Konig’s Theorem, Independent Set. Cuts
and Connectivity: 2-connected Graphs, Menger's theorem; Network Flow: Max-flow
Min-cut and the Ford-Fulkerson algorithm. Planar Graphs: drawing, Euler's formula,
Kuratowski's theorem, plane duality. Coloring: coloring maps and planar graphs,
coloring vertices, coloring edges. Cayley graph, Spectrum of a graph.
References 1. Introduction to Graph Theory: D.B. West (1996) Prentice Hall

2. Graph Theory: F. Harary (1969) Addison-Wesley
3. Modern Graph Theory: B. Bollobas (2008) Springer
4. Graph Theory: R. Diestel (2006) Springer
5. Graphs: C. Berge (1989) North-Holland
6. Graph Theory and its Applications: J.L. Gross and J. Yellen (2006) CRC Press
7. A First Course in Graph Theory and Combinatorics: S. M. Cioaba, M. Ram Murty
(2009) Hindustan Book Agency
Course title Ordinary Differential Equations
Semester 5
Credits 4
Introduction The laws of physics are written in differential equations, providing an eternal
challenge for mathematicians. In this course we consider ordinary differential
equations (ODEs), those only depending on one parameter (time). Students are
likely to have seen methods for producing explicit solutions for sanitized classes of
ODEs, particularly linear ones with constant coefficients. But nature usually gives
differential equations for which we do not have explicit solutions. One nonetheless
has a robust theory which qualitatively describes the behavior of common ODEs.
We will analytically prove existence, uniqueness, and stability, and rigorously
discuss the dynamic behavior of solutions to ODEs (meaning their long-term
evolution).
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Course contents Brief review of methods in solving common ODEs. Higher order constant coefficient
linear ODEs, matrix exponentials and the Linearity Principle, Wronskian theory,
inhomogeneous systems, Sturm-Liouville theory, phase plane analysis, stable,
unstable and center subspaces, stability, asymptotic stability. Non-autonomous
Linear Systems. Non-linear Systems: Dynamical Systems, local existence and
uniqueness, Peano's Theorem, Gronwall's Inequality: Continuous dependence of
solutions, Contraction mappings, Picard approximations, Extending Solutions, the
maximal interval of existence, global existence theorem, Differentiability of the
flow. Linearization, The Stable Manifold Theorem, The Hartman-Grobman
Theorem, Stability and Lyapunov functions, Introduction to the Poincare map,
Statement of the Poincare-Bendixson Theory.
References 1. An Introduction to Ordinary Differential Equations, Dover Books on

Mathematics: E. Coddington (1990) Dover
2. Differential Equations and Dynamical Systems: L. Perko (2010) Springer
3. Differential Equations with Applications and Historic Notes, International
Series in Pure and Applied Mathematics: George F. Simmons (1991)
McGraw Hill
4. Differential Equations, Dynamical Systems, and an Introduction to Chaos:
Hirsch, Smale and Devaney (2004) Elsevier Academic Press
5. Theory of Ordinary Differential Equations: Coddington and Levinson
(1987) Tata McGraw Hill
6. Geometrical Methods in the Theory of Ordinary Differential Equations:
V.I. Arnold (1988) SpringerScience and BusinessMedia
Course title Statistical Inference
Semester 5 & 7 (alternate years)
Credits 4
Introduction The course covers the mathematical development and application of various
statistical techniques that are useful in drawing conclusions about a population,
based on information obtained from a sample. It is useful for a student wishing to
pursue advanced mathematical statistics as well as for a student wishing to analyze
commonly collected experimental data in a scientific manner.
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Course contents Reduction of data, sufficient statistics, minimal sufficient statistics, Neyman
factorization theorem, complete statistics, exponential families. Ancillary statistics,
Basu’s theorem. Estimation of real and vector parameters. Method of moments and
maximum likelihood, Bayes’ estimation. Methods of evaluating estimators, Cramer-
Rao Inequality, Fisher Information, Rao-Blackwell theorem, Lehmann‐Scheffe
theorem. Testing of hypotheses, likelihood Ratio tests, Bayesian tests, error
probabilities, P-values, power function, most powerful tests, Neyman-‐Pearson
lemma, uniformly most powerful tests, monotone likelihood ratio. Confidence
intervals, construction of confidence intervals, one-sided confidence intervals and
their relation with UMP tests, pivotal quantities, Bayesian intervals. Large sample
approximations (without proofs) for: maximum likelihood estimators, log likelihood
ratio, confidence intervals, posterior density. One and two way analysis of variance,
F-statistics and their null distributions.
References 1. Statistical Inference: George Casella, R. L. Berger (2002) Cengage

Learning
2. All of Statistics, A Concise Course in Statistical Inference (Springer Texts in
Statistics): Larry Wasserman (2004) Springer
3. Linear Statistical Inference and its Applications: C. R. Rao (2001) Wiley
4. Parametric Inference: B. K. Kale (1999) Narosa
5. An Introduction to Probability and Statistics: V. K. Rohatgi, A. K. Md. Saleh
(2000) Wiley
6. Mathematical Statistics and Data Analysis, 3e: John A. Rice (2007)
Cengage Learning
Course title Numerical Analysis
Semester 5/7 (Alternate years)
Credits 4
Introduction This course aims at teaching various methods and their theoretical aspects for
solving problems from calculus and linear algebra numerically. Although this course
does not aim to teach how to write a code for solving a numerical problem, but
acquaintance of flow chart is essential. It emphasizes on examining the quality of
approximation and the estimation of errors for a given numerical scheme. Many
problems demand a clear understanding of these, irrespective of using a self-written
code or some mathematical software. Therefore, it is useful for all those who wish
to pursue a carrier in a quantitative study which involves computations.
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Course contents Significant digits, round-off errors. Finite computational processes and
computational errors. Condition number. Loss of significant digits. Numerical
solution of a nonlinear equation in one variable: Methods of bisection, convergence
and error analysis, Fixed point iterative method for contractions, Newton-Raphson
method, the order of convergence and degree of precision, comparison between
the two approaches. Interpolation with one variable: Newton's methods, Horner's
algorithm, divided differences, Lagrange form, Vandermonde matrix, error estimate.
Cubic splines, existence and uniqueness, Gershgorin circle theorem. Numerical
integration: Newton-Cotes; composite trapezoidal, composite Simpson rule, error
estimate. Numerical differentiation: Richardson extrapolation, the order of
convergence, loss of significance.
Computation in Linear Algebra: Numerical solution of a system of linear equations

and matrix inversion: Gaussian elimination, L-U decomposition, Cholesky
decomposition. Iterative methods: Richardson, Jacobi, Gauss-Seidel. Numerical
computation of principal eigenvalue and eigenvector: power method. Numerical
solution of ordinary differential equations: one step method, Euler's, Taylor series,
Runge-Kutta's methods, errors and accuracy. Second-order boundary value
problem, shooting method, finite difference method. Numerical parabolic PDE:
Explicit, implicit and Crank-Nicolson implicit method, stability. A multigrid method
for differential equations.
References 1. Kincaid, D. and Cheney, W.- Numerical Analysis: Mathematics of Scientific

Computing, 3rd Edition, AMS 2002.
2. Hohmann, A. and Deuflhard, P.- Numerical analysis in modern scientific
computing: An Introduction, Springer 2003.
3. G Shanker Rao & Shanker G. Rao - Numerical Analysis, New Age International,
2006.
4. Biswal, Purna Chandra - Numerical Analysis, PHI Learning
Course title Algebraic Number Theory
Semester 6
Credits 4
Prerequisites Fields and Galois Theory
Introduction Algebraic number theory is a major branch of number theory where one studies
various algebraic properties related to algebraic integers. The ring of algebraic
integers O in an algebraic number field K is the basic object in algebraic number
theory. This course aims at the discussion of algebraic properties of O such as
factorization, the behavior of ideals, and field extensions. The usual properties of
the integers such as unique factorization need not hold in this general setting. This
course is essential for a student studying branches of modern mathematics such as
modular forms, arithmetic geometry, automorphic forms and analytic theory of L-
functions.
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Course contents Algebraic numbers and algebraic integers: definitions and basic properties, Integral
extensions, Dedekind domains, prime ideals, ideal factorization, ramification index
and inertial degree, Decomposition groups and inertia groups, proof of the law of
quadratic reciprocity using number fields, finiteness of class groups, Dirichlet’s Unit
Theorem, Riemann and Dedekind zeta functions, class number formula, Dirichlet
L‐functions.
References 1. Number Fields: Marcus (1995) Springer

2. Problems in Algebraic Number Theory: Esmonde, Ram Murthy (2005)
Springer
3. Algebraic Number Theory: J.W.S. Cassels and A. Frohlich (1993) Academic
Press
4. Algebraic Number Theory: Lang (1984) Springer
5. Algebraic Number Theory: Neukirch (1999) Springer
6. Algebraic Number Fields: Janusz (1996) AMS
7. Algebraic Number Theory and Fermat’s Last Theorem: I. Stewart and D.
Tall (2001) AK Peters
8. Algebraic Number Theory: Narasimhan, Raghavan, Rangachari and Lal,
TIFR Pamphlets (available online)
9. Algebraic Number Theory: J. Milne (available online)
Course title Complex Analysis
Semester 6
Credits 4
Introduction Consider a complex-valued function f of one complex variable. If f is complex-

differentiable, an analytic condition, then it is locally expressed by convergent
power series. Moreover its line integral about a loop in its domain vanishes. These
equivalent conditions thus blend topology, analysis, and algebra in the beautiful
realm of complex analysis, one of the great stories of mathematics. Its scope of
application cannot be overestimated, finding use throughout pure and applied
mathematics.
Course contents Complex differentiation, Cauchy-Riemann equations, power series, exponential and
logarithms. Complex line integrals, Cauchy's theorem on a triangle, Cauchy's integral
formula, power series representations, Morera's theorem, Schwarz reflection
principle. Zeros of an analytic function, singularities, Residue theorem, argument
principle, homotopy version of Cauchy's theorem. Conformal mappings, linear
fractional transformations, maximum modulus principle, Schwarz lemma,
automorphisms of the unit disc, Montel's theorem, Riemann mapping theorem.
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References 1. Function Theory of One Complex Variable: R.E. Greene and S.G. Krantz (2006)
AMS
2. Complex Analysis: L. Alhfors (1979) McGraw Hill
3. Functions of One Complex Variable I: J.B. Conway (1978) GTM Springer
4. Complex Analysis (Princeton Lectures in Analysis): E.M. Stein, R. Shakarchi (2003)
Princeton University Press
5. Complex Function Theory: Donald Sarason (2007) AMS
Course title Measure Theory and Integration
Semester 6
Credits 4
Prerequisites Real Analysis I, Real Analysis II
Introduction Measure theory is a generalization of the theory of volumes, one which is reconciled
with the subtleties of analysis. Sets which are negligible for the purposes of
integration have “measure zero”, and it is central to determine which these are. For
instance, sets of rational numbers, and the Cantor set have measure 0, but the set
of irrational real numbers has infinite measure.
The theory of integration is central to analysis, being a method to assimilate

quantities. Delicate problems with integrals, such as those arising in Fourier series,
require more sophistication than Riemann’s naive integral. The Lebesgue integral
focuses attention on the domain of a function, and defines the integral in terms of
measures of subsets of that domain. The Lebesgue theory is now standard, and
gives a robust way to handle limits of integrals.
In particular this course introduces the famous “L^2”-spaces comprised of square-

integrable functions. This is the basic example of a Hilbert space, spaces which are
studied more thoroughly in Functional Analysis. Many concepts in probability
theory may be expressed in terms of measure theory, so this course is also
prerequisite for Stochastic Processes
Course contents Lebesgue Integration: Algebra and sigma-algebra of sets, Lebesgue measure, real
valued measurable functions of a real variable, existence of a non-measurable sets,
nowhere dense sets with positive measure, Cantor sets, Integrability, Monotone
and Dominated convergence theorems, Fatou's lemma, Vitali’s convergence
theorem, Egorov's theorem and Lusin's theorem, change of variables, Jensen's
Inequality, General Measure & Integration theory: Definition and examples of
general measures, integration of measurable functions, absolute continuity of
measures, Radon-Nikodym theorem, outer measure, the extension theorem, L^p
spaces, Holder's inequality, Minkowksi's inequality, convolution, differentiation of
measures, product measure and Fubini's theorem.
References 1. Real and Complex Analysis: W. Rudin (2006) McGraw Hill

2. Real Analysis: H. L. Royden (1997) Prentice-Hall
3. Measure Theory: V. L. Bogachev (2006) Springer
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Course title Calculus on Manifolds
Semester 6
Credits 4
Prerequisites Real Analysis II, Point Set Topology
Introduction In calculus we found that many important phenomena in the geometry of R, R^2,
R^3, occur “locally”, that is in small neighborhoods of points. But there are other
topological spaces, such as the circle, the sphere, etc. which locally “look like” R,
R^2,... These are manifolds, and on such objects one may generalize familiar
concepts from multivariable calculus. This course will lead students through these
ideas. This course is particularly important for students of geometry and theoretical
physics.
Course contents Curves and surfaces in R^2 and R^3: Geometry of Gauss maps, Intrinsic geometry of
surfaces, Theorema egregium, Gauss Bonnet Theorem, manifolds in R^n, Smooth
functions on manifolds, Tangent space, Inverse / Implicit function theorems, Sards’
theorem, Regular value theorem, Smooth partition of unity, Integration of scalar
functions on manifolds
References 1. Calculus on Manifolds: M. Spivak (1998) Westview Press

2. Analysis on Manifolds: J. R. Munkres (1991) Westview Press
3. Topology From the Differentiable Viewpoint: J. Milnor (1997) Princeton
University Press
4. Differential Geometry of Curves and Surfaces: Manfredo P. do. Carmo (1976)
Prentice Hall
5. Elementary Differential Geometry, A.N. Pressley, Springer UM 2010
Course title Coding Theory
Semester 6 & 8 (Alternate years)
Credits 4
Prerequisites Discrete Structures (Recommended, but not mandatory)
Introduction Error-correcting codes are the main systems used to ensure the high degree of
reliability required in modern data transmission and storage systems. This course
introduces the mathematical theory of error-correcting codes. We will also explore
the connections of this subject to other areas of mathematics such as the theory of
finite fields, combinatorics, group theory, projective and algebraic geometry.
Course contents Linear codes: Basic definitions, properties and problems. Basic theory of Finite
Fields. The projective geometric point of view of linear codes. The MacWilliams
identity and Weight enumerators. Construction and properties of special codes and
families of codes like MDS codes and Reed Solomon codes. Structure of finite fields
in more detail. A flavour of Algebraic Geometry codes.
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References 1. Fundamentals of Error-Correcting Codes: C. Huffman and V. Pless (2010)
Cambridge
2. Introduction to Coding Theory: Ron Roth (2006) Cambridge
3. The Theory of Error-Correcting Codes (North-Holland Mathematical Library):
MacWilliams and Sloane (1977) North Holland Publishing Co.
Course title Algorithms
Semester 6
Credits 4
Prerequisites Graph Theory
Introduction This course covers the core material of algorithms and computational complexity.
The subject matter is essential for all students wishing to continue in computer
science or discrete mathematics. It is moreover suitable for all mathematics
students since computational questions are ubiquitous throughout pure and applied
mathematics.
Course contents Asymptotic order of growth: big O notation and its relatives. Data structures:
Priority queues, heaps, queues, stacks, Union-Find. Basic Graph Algorithms: breadth
first search, depth first search, DAGs (directed acyclic graphs) and topological
ordering, strongly connected components. Greedy Algorithms: interval scheduling,
Dijkstra's algorithm for finding shortest paths in a graph, minimum spanning trees,
Huffman codes for data compression. Divide and Conquer and Recurrences: The
master theorem, application to the complexity of recursive algorithms, example of
an algorithm with running time O(n^{1.59}).
References Algorithm Design: J. Kleinberg and E. Tardos (2006) Pearson Education

2. Introduction to Algorithms: H. Cormen, C.E. Leiserson and R.L. Rivest (2009) MIT
Press
3. Design and Analysis of Algorithms: A.V. Aho, J.E. Hopcroft and J.D. Ullman (1975)
Addison-Wesley
4. Fundamentals of Computer Algorithms: E. Horowitz and S. Sahni (1999) Galgotia
Publishers
5. Algorithms and Data Structures: K. Mehlhorn and P. Sanders (2008) Springer
6. Combinatorial Optimization: Algorithms and Complexity: C.H. Papadimitriou and
K. Steiglitz (1982) Prentice Hall
Course title Representation theory
Semester 7
Credits 4
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Prerequisites Advanced Linear Algebra, Rings and Modules, Fields and GaloisTheory
Introduction The basic theme of Representation Theory is actions of groups (and some other
related algebraic objects) on vector spaces via linear maps. One studies the
interplay between the structure of the group and the properties of representations.
It is one of the active research areas in mathematics and has connections to many
branches of mathematics, Algebra, Arithmetic, Geometry and Analysis as well as
Particle Physics and Molecular structures in Chemistry.
Course contents Basic definitions and properties of representations, character theory and
decomposition of regular representations, examples of irreducible representations
and character tables, group rings, induced representations and Mackey theory.
Additional topics at the discretion of the instructor. For example, Artin and Brauer
theorems, rationality questions, representation theory of S_n, representation
theory of GL(2,q), representation theory of compact groups.
References 1. Linear Representations of Finite Groups, Serre J. P., 1977 Springer GTM
2. Representation Theory of Finite Groups Benjamin Steinberg 2012 Springer-
Verlag New York
3. Representation TheoryA First Course : William Fulton, Joe Harris 2004 Springer-
Verlag New York
Course title Functional Analysis
Semester 7
Credits 4
Prerequisites Measure Theory and Integration
Introduction Pure linear algebra does not itself suffice in the study of infinite-dimensional vector
spaces. Linear combinations are typically replaced with infinite series or integrals of
vectors. To make sense of such series or integrals, one can use an inner product or
norm, leading to the theory of Hilbert spaces or Banach spaces. Functional analysis
thus investigates this interplay between analysis and linear algebra. One major
discovery is that many important operators between these spaces have a theory of
eigenvectors akin to that of symmetric matrices. This course especially finds
application in the representation theory of Lie groups and in mathematical physics
Course contents Normed linear spaces: Definition and examples, bounded linear operators, Hahn-
Banach theorem, Banach spaces, Definition and examples, L^p spaces, Arzela-Ascoli
theorem, uniform boundedness principle, open mapping theorem, closed graph
theorem, quotient spaces, projections, dual spaces, weak and weak* convergence,
reflexivity, compact operators, spectrum of compact operators, Hilbert spaces:
Definition and examples, geometry of Hilbert spaces, orthonormal sets, orthogonal
projections, Riesz representation theorem, Spectral theory: Adjoint of an operator,
unitary operators, normal operators, spectral theorem for compact self-adjoint
operators.
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References 1. Functional Analysis: B. V. Limaye (1996) New Age International Publishers
2. Functional Analysis, Sobolev Spaces and Partial Differential Equations: H. Brezis
(2010) Springer.
3. Real and Complex Analysis: W. Rudin (2006) McGraw Hill
4. Introductory Functional Analysis with Applications: E. Kreyszig (1989) Wiley
5. Notes on Functional Analysis: R. Bhatia (2009) Hindustan Book Agency
Course title Differential Geometry and Lie groups
Semester 7
Credits 4
Prerequisites Group Theory, Calculus on Manifolds
Introduction In this course, you will continue learning about manifolds but in a more abstract
way. You will also learn about differential forms and integration of smooth functions
on a manifolds using differential forms and the Stokes theorem for manifolds.
A group may be given a manifold structure so that it becomes a “Lie Group”;

naturally a manifold with many symmetries. Lie groups and their quotients, called
homogeneous spaces, furnish a wealth of interesting examples in geometry. Their
infinitesimal generators form interesting algebraic objects called “Lie algebras”. The
beautiful correspondence between Lie groups and Lie algebras is introduced in this
course.
This is an important course for both future topologists and theoretical physicists.
Course contents Abstract Manifolds, Smooth maps and their derivatives, Tangent spaces, Whitney
embedding theorem for compact manifolds, Introduction to Lie groups and Lie
algebras, Homogeneous spaces, Immersions and submersions, Vector fields,
Statement of Frobenius theorem, Flows and exponential map, Tensor fields,
Orientation, Differential forms, Exterior derivatives, Integration on manifolds using
differential forms, Stokes theorem
References 1. Foundations of Differentiable Manifolds and Lie Groups: F.Warner (1983) GTM
Springer
2. An Introduction to Manifolds: L. Tu (2011) Springer
3. Introduction to Differentiable Manifolds and Riemannian Geometry: W. M.
Boothby (2003) Academic Press
4. A Course in Differential Geometry and Lie Groups: S. Kumaresan (2002)
Hindustan Book Agency
5. Introduction to Smooth Manifolds, John Lee, 2003, Springer GTM
Course title Algebraic Topology
Semester 7
140
Credits 4
Prerequisites Group Theory, Point Set Topology
Introduction It is possible to detect “holes” in a topological space in the following manner. You
trace out a path with some string, but make it a closed path, meaning it starts and
ends at the same point. (All of this must happen within the space.) If you can
contract the string to a point, then you have not found any hole, but if you cannot,
then that says something about your space. For instance, on a sphere you can
contract any closed path, but on a torus, or on a “punctured plane” you can detect
such holes.
The fundamental group of a topological space is a group obtained using these paths.
Moreover a continuous map between topological spaces corresponds to a
homomorphism between groups. In this way, one can transform questions in
topology into questions in algebra.
In this same spirit, the abelian groups of “homology” quantify how simplices fit
together in your space, and can also be used to apply algebra to the world of
topology.
Course contents Paths and homotopy, fundamental groups, fundamental group of a circle, free
groups and free products, Van Kampen Theorem, application to CW complexes,
covering spaces, lifting criteria, deck transformations, Introduction to homology
theory, definition of singular homology, Hurewicz isomorphism, Axioms of
homology, homology groups of spheres, Applications of homology: Brouwer fixed
point theorem, Invariance of domain theorem.
References 1. Algebraic Topology: Allen Hatcher (2002) Cambridge

2. Topology: J. Munkres (2000) Prentice Hall
3. Elements of Algebraic Topology: J. Munkres (1996) Westview Press
4. Topology and Geometry: G. Bredon (1995) GTM Springer
5. Algebraic Topology: Spanier (1996) Springer
Course title Probability
Semester 7
Credits 4
Prerequisites Measure Theory and Integration
Introduction This course gives an introduction to probability theory. The goal of this course is to
start with some basic notions in probability and then move to important topics like
Martingales, Markov chain etc. The topics included in this course are essential for
those who are interested in advanced probability theory, mathematical finance,
mathematical biology, time series analysis etc.
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Course contents Kolmogorov’s model of probability: The Probability Space, Events, properties of
probability measures, independence of events, Bayes’ formula, Kolmogorov 0-1 law.
Borel-Cantelli lemmas. Random variable, distribution functions, joint distributions.
Conditional expectation and conditional probability, regular conditional probability,
independence of σ algebras and random variables. Limit theorems: Weak/Strong
law of large numbers, Central limit theorem. Martingales, Stopping time, Azuma’s
inequality, Doob’s inequality. Discrete time discrete space Markov chain, Chapman-
Kolmogorov equation, classification of states, and limit theorems.
References 1. Introduction to Probability Models: S. M. Ross (2014) Academic Press

2. Introduction to the Theory of Probability and its Applications, Vol. 1: W.
Feller (2008) Wiley
3. Introduction to Stochastic Processes: P. G. Hoel, S. C. Port and C.J. Stone
(1986) Waveland Press Inc.
4. Probability: A Graduate Course (Springer Texts in Statistics): A. Gut (2010)
Springer
5. Probability Theory, Courant Lecture Notes: S. R. S. Varadhan, (2001) AMS
6. Probability: Theory and ExamplesRick Durrett (legally and freely available
on https://services.math.duke.edu/~rtd/PTE/PTE5_011119.pdf
Course title Algebraic Geometry
Semester 8
Credits 4
Prerequisites Group Theory, Rings and Modules
Introduction We aim to introduce the basics of algebraic geometry through an interplay of

geometric objects like curves, surfaces and algebraic objects like rings, ideals, fields
and solutions of polynomial equations. This course will be useful for all mathematics
students and possibly useful for physics students.
Course contents Affine Algebraic Varieties: Zariski Topology, Morphisms, Dimension,

Algebraic Foundations: Nullstellensatz, Coordinate Ring, Noether Normalization
(optional, left to the instructor)
Projective Varieties: morphisms
Quasi-Projective Varieties: Regular Functions
Examples: Curves, Veronese maps, Segre maps, Grassmannians
Degree, statement of Bezout theorem, statement of theorem relating Hilbert
function and Hilbert Polynomial,
Smoothness: Tangent space, statement of Bertini theorem
Rational Maps, Blowing up a point, Birational Equivalence
Maps to projective space, Statement/Sketch of theorem about embedding smooth
curves in P^3, Line bundles and rational maps
Introduction to Sheaves and Abstract Algebraic Varieties.
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References 1. An Invitation to Algebraic Geometry by Karen E Smith, Universitext
2. Algebraic Geometry, A first Course by Joe Harris, GTM 133
3. Basic Algebraic Geometry, by Shafarevich
4. Algebraic Geometry, by Hartshorne GTM
Course title Fourier Analysis
Semester 8
Credits 4
Prerequisites Measure theory and Integration, Functional Analysis
Introduction Classical Fourier Analysis studies the phenomenon that many periodic functions on
real line can be expanded as a Fourier series in terms of sine and cosines and as a
continuous analogue there is a notion of Fourier transform. In this course, you will
learn the mathematical theory of Fourier analysis in terms of L^2 spaces and
Schwartz spaces.
Course contents Basic theory of Fourier series on circle: Fourier series of periodic functions on real
line, orthogonality of Sines and Cosines, criterion for convergence of Fourier series,
example of expansions in Sine and Cosine series, Fourier series w.r.t. orthogonal
system, convergence in the mean, Fourier series expansion of absolutely integrable
functions: sufficient condition for convergence at continuity points.
Fourier transform on R^n: Plancherel theorem, Schwartz space, Fourier inversion,

Poisson summation formula, Paley-Wiener theorems for Fourier transform
Optional topics
Character theory for finite abelian groups, Basics of Topological groups, Pontryagin
duality and generalisation of Plancherel theorem for locally compact abelian groups
(other examples: p-adic numbers, Adeles over a number field)
or
Topological vector spaces, Distributions, Tempered distributions, application of

Fourier transform: solving heat and wave equation.
References 1. Fourier Analysis An Introduction: Stein \& Shakarachi, Princeton University Press
2. Fourier analysis and its applications: G. B. Folland, AMS.
3. Topics in Functional Analysis and Applications: Kesavan, New Age International,
Limited.
Course title Riemannian Geometry
Semester 8
Credits 4
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Prerequisites Differential Geometry and Lie groups
Introduction This capstone class in geometry continues into the deeper terrain of Riemannian
Geometry. This Riemannian metric can be used to define the geometry of lengths
and area on submanifolds of M, and moreover notions of geodesics, curvature and
parallel transport. This course will introduce you to the delicate interplay between
curvature and topology. This is an important course for both future topologists and
theoretical physicists.
Course contents Vector bundles, Tensor bundles, Riemannian metrics, model spaces (space forms),
Connections, Geodesics, Riemannian connections, exponential maps, normal
neighbourhoods, Hopf-Rinow theorem, Hadamard theorem, Curvature tensor, Ricci
and scalar curvature, Gauss-Bonnet theorem
Additional topics (up to the instructor): Symmetric spaces, Principal bundles and
Connections
References 1. Riemannian Geometry, Manfredo do Carmo, 1992 Birkhäuser Basel

2. Riemannian Manifolds: An Introduction to Curvature, John Lee 1997, Springer
GTM
3. An Introduction to Manifolds: L. Tu (2011) Springer
4. Introduction to Differentiable Manifolds and Riemannian Geometry: W. M.
Boothby (2003) Academic Press
5. A Course in Differential Geometry and Lie Groups: S. Kumaresan (2002)
Hindustan Book Agency
6. Differential Geometry, Lie Groups and Symmetric Spaces: S. Helgason (2001)
AMS
Course title Cryptography
Semester 8
Credits 4
Prerequisites Group Theory
Introduction Cryptography, especially public key cryptography, is extremely important in
modern society. It serves us with the required tools for online transactions and
trading, i.e., online commerce. Online commerce is the call of our day and is
considered as one of the foundations of a modern civilization. It is the tool that
makes it possible for a farmer in a remote village to sell his produce to the city,
avoiding the middleman. This course teaches you the mathematical aspects of
cryptography. Mathematical aspects of cryptography can be broadly divided into
two distinct streams: one, the private key cryptography and, the other, public key
cryptography. This course will try to introduce a student to these two aspects.
However the instructor will have leeway in choosing the topics.
Course contents Private key cryptography: DES, differential and linear cryptanalysis, AES. Public Key
Cryptography: RSA, Rabin's cryptosystem, discrete logarithm problem, difference
between the discrete logarithm problem in the group of rational points of an
elliptic curve with that of the group of units of a finite field, protocols using the
discrete logarithm problem like the El Gamal cryptosystem and the Diffie-Hellman
key exchange. Attacks on RSA, like the factoring algorithms. Attacks on the discrete
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logarithm problem, like Pollard's rho algorithm and other square-root algorithms.
Sub-exponential attacks like the number field sieve and its variants in solving the
discrete logarithm problem in finite fields. MOV attack and pairing based
cryptosystems.
References 1. An Introduction to Mathematical Cryptography: J. Hoffstein, J. Pipher

and J.H. Silverman (2008) UTM Springer
2. A Course in Number theory and Cryptography: N. Koblitz (1994) Springer
3. Cryptography: Theory and Practice: D.R. Stinson (2005) Chapman and
Hall/CRC
Course title Stochastic Processes
Semester 8
Credits 4
Prerequisites Probability
Introduction This course introduces the measure theoretic aspects of probability. This course also
introduces Brownian motion which serves as the backbone to the stochastic analysis.
This course will benefit anyone interested in studying queuing theory, mathematical
finance, stochastic control theory and other fields of stochastic analysis.
Course contents Recapitulation of regular conditional probability, definition and examples of

stochastic processes, random walk, linear time series models. continuous time
Markov pure jump processes, transition probabilities and holding time distributions,
semigroup property of Transition functions. Chapman-Kolmogorov equation:
backward and forward. Birth & death processes. continuous time martingale. Finite
dimensional distribution of a stochastic process, probability measure on the path
space, Kolmogorov’s extension theorem. Notion of convergence, Monotone class
theorem, weak convergence, Portmanteau theorem, Skorohod’s representation
theorem, tightness and compactness, characteristic functions and its properties.
Markov processes. Brownian motion (BM): definition, construction, path property,
computation of quadratic variation of BM, Strong Markov and martingale properties
of BM, Geometric Brownian motion. Stochastic calculus, Ito integration, Ito’s
formula, stochastic differential equations, strong/weak solutions.
References 1. Measure Theory and Probability Theory (Springer Texts in Statistics): K. B.

Athreya, S.N. Lahiri (2010) Springer
2. Paul G. Hoel. Sidney C. Port. Charles l. Stone: Introduction to Stochastic
Processes.
3. Bernt Oksendal: Stochastic differential equations. Springer
4. Brownian Motion (Cambridge Series in Statistical and Probabilistic
Mathematics): Peter Moerters and Yuval Peres (2010) Cambridge
5. Brownian motion and stochastic calculus: I. Karatzas and S. E. Shreve
(1991) GTM Springer
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Course title Partial Differential Equations
Semester 8
Credits 4
Prerequisites Measure Theory and Integration, Functional Analysis
Introduction A solution of an ODE is typically specified by finitely many constants. In contrast, a

solution to a PDE is typically specified by finitely many functions. Both initial
conditions of time and boundary conditions of space play a decisive role. PDE theory
is thus much vaster than the theory of ODEs. This course focuses on four primary
PDEs arising from nature: the transport equation, Laplace’s equation, heat equation,
and wave equation, representing first order PDEs, second order elliptic, parabolic,
and hyperbolic PDEs, respectively. Each of these leads to its own branch of
mathematics that one could study for a lifetime. As well as being an engaging
mathematical topic in its own right, PDE theory is essential for many topics in
analysis, geometry, probability theory, mathematical physics, etc. Students of PDEs
may go on to study topics like harmonic analysis, geometric analysis, operator theory,
control theory, differential geometry, and the calculus of variations.
Familiarity with the contents of ODEs is helpful but not mandatory.
Course contents A. Introduction and Classification of PDEs

B. Four important Linear PDEs:
(1) Transport Equation: Initial Value Problem, Non-homogeneous problem,
(2) Laplace’s Equation: Fundamental Solution, Mean Value Property, Maximum
Principles, Properties of Harmonic functions, Green’s function, Energy Methods,
(3) Heat Equation: Fundamental Solution, Mean Value Property, Maximum Principles,
Properties of solutions, Energy Methods,
(4) Wave Equation: Solution by Spherical Means, Non-homogeneous problem, Energy
Methods.
C. Solution via Separation of Variables
References 1. Partial Differential Equations, Methods and Applications: R. McOwen

(2002) Pearson Education
2. Partial Differential Equations: L. Evans (2010) Graduate Studies in
Mathematics, AMS
3. Introduction to Partial Differential Equations: G. Folland (1995) Princeton
University Press
4. Partial Differential Equations: F. John (1995) Springer
5. An Introduction to Partial Differential Equations: Y. Pinchover and J.
Rubinstein (2005) Cambridge
146
4.6 Syllabi for Elective Courses in Physics
Discipline Physics
Course title Mathematical Methods for Physics
Semester 3
Credits 3
Introduction To provide the key mathematical tools needed for a physics student. This is a key
course for students wanting to study physics. Students from other disciplines will
also find it useful if they plan to study any quantitative science.
Course contents Linear vector spaces
Matrix algebra
Vector calculus
Complex algebra
Ordinary Differential Equations-I
Probability and statistics
Fourier series and transforms
References 1. Mathematical Methods for Physicists: G. Arfken and H. Weber (2012) 7th
edition, Academic Press
2. Fundamentals of Complex Analysis: E.B. Staff and A.D. Snider (2008) Dorling
Kinderley (India) Ltd
3. Ordinary Differential Equations: G. Birkhoff and G.C. Rota (1989) 4th edition,
Wiley India
4. Differential Equations with Applications and Historical Notes: G. Simmons
(2003) Tata McGraw Hill
5. Linear Partial Differential Equations for Scientists and Engineers: Tyn Myint-U
and Lokenath Debnath (2006) 4th edition, Birkhauser
6. Mathematics for Physicists – Dennery and Krzywicki, Dover.
Discipline Physics
Course title Classical Mechanics
Semester 4
Credits 3
Introduction To provide a detailed survey of the basic formalism and practical applications of
classical mechanics. This is a foundational course for physics students but could
also appeal to those majoring in other disciplines, including mathematics.
Course contents Euler-Lagrange equation from variational principle, constraints and Lagrange
multipliers, integrals of motion, symmetries and conservations laws. Hamiltonian
formalism: Hamilton equations, Poisson brackets, symplectic formulation,
canonical transformations, Hamilton-Jacobi theory, action-angle variables.
Central force motion: integrals, Kepler problem, classical scattering. Small
oscillations, normal modes, applications.
References 1. Classical Mechanics: H. Goldstein, C. Poole and J. Safko (2002) 3rd edition,
Pearson
2. Classical Dynamics of Particles and Systems: Thornton and Marion (2003)
Thomson Learning EMEA Ltd
3. Classical Mechanics: R.D. Gregory (2008) Cambridge University Press
4. Mechanics: L.D. Landau and E.M. Lifshitz (2007) 3rd edition, Butterworth-
Heinemann
5. Classical Mechanics A Contemporary Approach: J.V. Jose and E.J. Saletan
(2006) Cambridge University Press
6. Classical Mechanics- W Greiner- 2nd ed-Springer-2010
147
Course title Thermal and Statistical Physics
Semester 4
Credits 3
Introduction This course covers common background material required in many branches of
science including physics, chemistry, some branches of biosciences and
atmospheric sciences as well as many areas of engineering.
Course contents Thermodynamic systems, internal energy, thermodynamic equilibrium, walls and
constraints, heat, entropy-maximization postulates, conditions of equilibrium,
intensive parameters, equations of state, thermal equilibrium and temperature,
mechanical equilibrium, matter-flow equilibrium, chemical equilibrium, Euler and
Gibbs-Duhem relations, the ideal gas, Van der Waals fluid, reversible processes and
maximum work, quasi-static and reversible processes, heat engines, the Carnot
cycle, refrigerator, thermodynamic potentials, the Helmholtz and Gibbs potentials,
enthalpy, throttling process, Maxwell relations, stability of thermodynamic
systems, phase transitions and latent heat, third law of thermodynamics.
References 1. Heat and Thermodynamics, M.W. Zemansky and R.H. Dittmann, Tata McGraw
Hill (2005).
2. An Introduction to Thermal Physics, D.V. Schroeder, Pearson Eduction (2006).
3. Thermodynamics and an Introduction to Thermostatistics, H.B.Callen, Wiley
student edition (2005).
Discipline Physics
Course title Physics Lab II
Semester 4
Credits 3
Introduction Aims to train students in experiments in Heat & Thermodynamics and Classical
optics.
Course contents Thermal Expansion of Solids
Thermal Conductivity by Lee’s method
Specific Heat of Solids
Stefan’s Law of Radiation
Temperature dependence of a Thermistor
Resolving power of Telescope
Newton’s Rings
Malus’ Law
Spectrometer and Gratings
References 1. Daryl Preston, Art of Experimental Physics (John Wiley and Sons 1991)
2. Francis A. Jenkins & Harvey E. White, Fundamentals of Optics ( McGraw-Hill
1957)
3. Mark Zemansky and Richard Dittman, Heat and Thermodynamics (McGraw-
Hill Special Indian Edition 2011)
Discipline Physics
Course title Electrodynamics
Semester 5
Credits 4
Introduction To provide a basic understanding of electric and magnetic fields in matter,
electromagnetic waves in vacuum and in matter and the electromagnetic field
148
equations in a covariant way.
Course contents Review of electro- and magnetostatics, Maxwell’s equations, conservation laws,
electromagnetic waves in vacuum and in matter, guided waves, dipole radiation,
scalar and vector potentials, retarded potentials, gauge transformations,
relativistic electrodynamics, electromagnetic field tensor, covariant formulation of
Maxwell’s equations.
References 1. Introduction to Electrodynamics: D.J. Griffths (2012) Pearson Education
2. Modern Electrodynamics: A. Zangwill (2013) Cambridge University Press
3. Feynman Lectures on Physics: R.P. Feynman, R.B. Leighton and M. Sands
(2011) The Millenium edition, Vol 2, Basic Books
4. Electrodynamics of Continuous Media: L.D. Landau and E.M. Lifshitz (2007)
3rd edition, Butterworth-Heinemann
Discipline Physics
Course title Quantum Mechanics I
Semester 5
Credits 4
Introduction This course introduces quantum physics, its mathematical formulation, and its
applications in various physical scenarios. It
is a pre-requisite for many advanced courses in physics and chemistry, and is
indispensible for understanding the behavior of molecules, atoms and elementary
particles.
Course contents Linear vector spaces, Postulates of QM, Schrodinger Equation, Quantum
measurements, Density operator and its evolution, One-dimensional problems,
Harmonic oscillator, applications, classical limit, Perturbation theory, Fermions and
bosons, Symmetries in Quantum Mechanics, Angular momentum, Spin, Addition
of angular momenta, Applications
References 1. Principles of Quantum Mechanics: R. Shankar (2010) 2nd edition, Springer
2. Introduction to Quantum Mechanics: D.J. Griffiths (2004) 2nd edition,
Addison-Wesley
3. Modern Quantum Mechanics: J.J. Sakurai (1999) Revised Edition, Addison-
Wesley
4. Quantum Mechanics: C. Cohen-Tannoudji, B. Diu and F. Laloe (1977) Vol 1 and
2, Wiley-Interscience
5. Eugen Merzbacher, 3rd edition, 2003, Quantum Mechanics.
Discipline Physics
Course title Physics Lab III
Semester 5
Credits 3
Introduction This lab course is for introducing students to experiments in Modern Physics.
Course contents Photo-electric effect, Cornu's method to determine Young's modulus, e/m by
Thomson's method, Rydberg's Constant,  Millikan's oil drop Method, Michelson
interferometer, Constant Deviation spectrometer, 4 probe resistivity, Hall effect,
Dielectric constant of a polar liquid
References 1. Advanced Practical Physics: B.L. Worsnop and H.T. Flint, Asia Publishing House
2. The Art of Experimental Physics: D.W. Preston and E.R. Dietz (1991) John
Wiley
3. Analytical Experimental Physics: Michael Ference Jr., Harvey B. Lemon,
Reginald J. Stephenson (1970) University of Chicago Press
149
Discipline Physics
Course title Classical Optics
Semester 5
Credits 4
Introduction To understand, what is light, and how it is used in various branches of science
Course contents Modern day classical optics – an introduction
Interference
Diffraction
Polarization
Scattering of light
Introduction to lasers
Optical techniques and instrumentation
Introduction to optical imaging: Microscopes, Telescopes, Interferometry,
Holography, Polarimetry
Optics in physics, chemistry, biology and engineering
References 1. Optics by Eugene Hecht; Addison-Wesley; 4 edition (2001)
2. Optical physics by Lipson, Lipson, and Lipson; Cambridge University Press; 4
edition (2010)
Discipline Physics
Course title Methods of Experimental Physics
Semester 5
Credits 3
Nature of course Lectures and Lab Sessions
Introduction This course is meant for students interested in experimental physics. It aims to
introduce a broad range of experimental techniques and critical experimental
concepts routinely used in modern research laboratories.
Course contents Uncertainties in measurements (2) (Random and systematic errors, and their
analysis)
Electronic measurements & Signal Processing (Basics of Electrical Wiring/Circuits,
Use of Basic Measuring devices, Nature of electronic noise, Filters, Phase Sensitive
Detection) (2+1)
Vacuum Technology (Introduction to gas flow regimes; vacuum pumps, pressure
gauges, and their operation)
Thermometry (Temperature Sensors, temperature measurement & control, PID
controller)
Optical Techniques (Generation & measurement of light, Polarization Control,
Interferometry)
Cryogenic Technology (Introduction to cryogenics & low temperature physics)
X-ray measurements (production & measurement of x-rays, absorption & emission
processes, diffraction)
Physical & Magnetic Property Measurements (Measurement of thermodynamic,
magnetic and dielectric properties of materials)
Optical Spectroscopic Techniques
Modern Experiments including electron microscopy, Quantum Optical
measurements, NMR etc.
References 1. Art of Experimental Physics by Daryl W. Preston, Wiley
2. Introduction To Error Analysis: The Study of Uncertainties in Physical
Measurements by John R. Taylor.
3. The Art of Electronics by Paul Horowitz and Winfield Hill. Also see Student
Manual for the Art of Electronics by Thomas C. Hayes and Paul Horowitz.
4. Methods of Experimental Physics By M. I. Pergament, CRC Press.
5. Statistical Methods in Experimental Physics By Frederick James, World
Scientific.
6. A Laboratory Course in Experimental Physics by W J Loudon.
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7. Data Reduction & Error Analysis for the Physical Sciences, P. R. Bevington & D.
K. Robinson,
8. McGraw Hill.
9. Experimental Physics: Modern Methods by R. A. Dunlap, Oxford University
Press.
Discipline Physics
Course title Gravitation and Cosmology
Semester 5
Credits 3
Introduction The course will introduce students to the basics of the general theory of relativity
and its application to cosmology.
Course contents Brief review of special relativity, Equivalence principle and motivation for
geometric view of gravity, some tools from differential geometry (manifolds,
tensors , metric, curvature), Einstein equation, geometry outside a spherical star,
geodesic equation, predictions of Einstein equation for orbits around the star,
Precession of mercury perihelion. Black holes. Introduction to cosmology, FRW
metric. If time permits, one or two lectures on gravitational waves.
References 1. Gravity – J. Hartle
2. Gravity – Eric Poisson
3. Spacetime and geometry: an introduction to general relativity – Sean Carroll.
4. A first course in general relativity – B Schutz
Discipline Physics
Course title Nonlinear Dynamics
Semester 5
Credits 3
Introduction This is an introductory course that will introduce the novelties of nonlinear
dynamics and provide a basic training on working out fixed points, stability and
bifurcations in dynamical systems and applying these to real-world systems like
population dynamics, epidemics, chemical reactions, lasers, neurons, nonlinear
oscillators etc.
Course contents Nonlinear dynamical systems: classification, chaos, features of chaos, continuous
and discrete dynamical systems; 1-d flows: fixed points and stability, linear stability
analysis, bifurcations, flows on a circle, population dynamics; 2-d flows:
classification of fixed points, stability analysis, limit cycles, bifurcations, predator-
prey systems; higher-dimensional systems: stability, attractors, bifurcations,
chaos, Lorenz system, Rossler system, pendulum.
Discrete dynamical systems, 1-d systems: logistic map, bifurcations, period
doubling, chaos, Lyapunov exponent, circle map; 2-d systems: Henon map,
quasiperiodicity, Arnold tongue; measures of chaos, Poincare map, basin
boundary, FFT, Lyapunov exponents; Fractals: dimensions, multi-fractals, f-alpha
spectrum.
Special topics: control of chaos, stochastic resonance, synchronization, spatio-
temporal chaos, time series analysis, complex networks.
References 1. Nonlinear Dynamics and Chaos: Steven Strogatz (2001) Westview Press
2. Chaos and Nonlinear Dynamics: Hilborn (2009) Oxford University Press
3. Chaos: An Introduction to Dynamical Systems: K.T. Alligood, T.D. Sauer and
J.A. Yorke (1996) Springer
4. Chaos in Dynamical Systems: E. Ott (2003) Cambridge University Press
5. Nonlinear Dynamics: M. Lakshmanan and S. Rajasekar (2003) Springer
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Discipline Physics
Course title Quantum Mechanics II
Semester 6
Credits 4
Introduction The course will cover standard but relatively advanced topics that are required for
every physicist.
Course contents Symmetries of quantum systems, Angular momentum, Addition of angular
momenta, Approximation methods: Variational and WKB methods, Time-
independent and time-dependent perturbation theory, Scattering theory,
Relativistic quantum mechanics, Landau levels, Coherent states
References 1. Quantum Mechanics: Vol I and 2, C. Cohen-Tannoudji, B. Diu and R. Laloe
(2005) John Wiley and Sons
2. Modern Quantum Mechanics: J.J. Sakurai (2009) Revised edition, Addison
Wesley
3. Principles of Quantum Mechanics: R. Shankar (2010) 2nd edition, Springer
Introduction to Quantum Mechanics: D.J. Griffiths (2004) 2nd edition, Addison-
Wesley
Discipline Physics
Course title Physics Lab IV
Semester 6
Credits 3
Introduction Gain an understanding of the key concepts in solid state physics using different
experimental set ups
Course contents Magnetic susceptibility by Quincke’s method  
Lorenz number of copper by electrical and  thermal conductivity  
Verification of Curie- Weiss law  
B-H curve  
Thermal Diffusivity measurement  
Solar cell characteristics  
Resistivity measurement ( four probe)  
Scanning probe microscopy – AFM  
Hall effect  
References 1. Elementary Solid State Physics: Principles and Applications -M. Ali Omar
2. Introduction to solid state physics - Charles Kittel
Discipline Physics
Course title Statistical Mechanics
Semester 6
Credits 4
Introduction The objective of this course is to introduce the microscopic formulation of
thermodynamics for both classical and quantum systems.
Course contents Review of Classical Thermodynamics: Laws of Thermodynamics, Heat engines,
Carnot Efficiency, Maxwell relations, Stability conditions, Probability, Random
variables, Central limit theorem, laws of large numbers, Principle of Statistical
Mechanics: Ergodic hypothesis, postulate of equal apriori probability, phase space,
Liouville’s theorem, BBGKY Hierarchy, Boltzman equation, H theorem, Three
ensembles: Microcanonical Ensemble, Canonical Ensemble, Grand Canonical
Ensemble, fluctuations, Examples: Ideal gas, Mixing entropy, Classical spins,
Paramagnetism, Ferromagnetism, Curie’s law, Interacting particles, Cumulant
Expansion, Cluster expansion, Quantum Statistical Mechanics: density matrix,
152
Liouville equation, Ensembles, Quantum Ideal gas, Bose and Fermi statistics, Black-
body radiation, vibrations of a solid, Bose Einstein Condensation
References 1. Statistical Physics of Particles: Mehran Kardar (2007) Cambridge University
Press 
2. Statistical Mechanics : R. K. Pathria (1996) 2nd Edition, Butterworth-
Heinemann
3. Statistical Mechanics: K. Huang (1987) 2nd Edition, Wiley 
4. Fundamental of Statistical and Thermal Physics: F. Reif (2008) Waveband Pr
Inc.
Discipline Physics
Course title Condensed Matter Physics
Semester 6
Credits 4
Introduction The course covers fundamental principles of solid state physics of crystalline
materials. It will discuss those aspects that can be understood using effectively
non-interacting models of electrons and phonons.
Course contents Macroscopic thermal and electrical properties of solids, Drude theory, Classical
Hall effect
Toy models of solids - one dimensions, introduction to reciprocal lattice, tight
binding models
Geometry of solids in 2 and 3 dimensions, crystal structures, reciprocal lattices,
diffraction
Electrons in solids - band theory, insulators, metals, semiconductors, devices
Magnetism and mean field theories
Phenomenological aspects of superconductivity
Basics of Landau quantization and IQHE
References 1. Oxford Solid State Basics Steve Simon, Oxford University Press (2013)
2. Solid State Physics Ashcroft and Mermin (1979)
3. Introduction to Solid State Physics Kittel (1953)
4. Superconductivity of metals and alloys P G deGennes, CRC Press (1999)
5. The Quantum Hall Effect: Novel Excitations and Broken Symmetries
6. S Girvin Ecole d'Ete Les Houches Lectures 1998
Discipline Physics
Course title Astronomy and Astrophysics
Semester 6
Credits 3
Introduction To introduce students to the basic concepts of astrophysics. The course is intended
both for students interested in pursuing a career in this general area, and for those
specialising in some other area who would like an overview of astrophysics.
Course contents Electromagnetic processes, thermal and synchrotron emission, spectral lines;
stellar physics: structure, composition, evolution; active galactic nuclei, radio
galaxies, quasars, galaxies and galaxy clusters, galaxy structure and composition; X-
ray clusters, cluster radio sources; dark matter, gravitational lensing, rotation
curves; cosmology, big bang model, cosmic microwave background, reionisation.
Other topics (time permitting): pulsars, extra solar planets, telescopes.
References 1. Galaxies in the Universe: An Introduction: L.S. Sparke and J.S. Gallagher III
(2000) Cambridge University Press
2. Galactic and Extragalactic Radio Astronomy: G.L. Verschuur and K.I.
Kellermann (1988) Springer-Verlag
3. The Physics of Stars (Manchester Physics Series): A.C. Phillips (1999) John
153
Wiley & Sons
Discipline Physics
Course title Physics of Soft Matter
Semester 6
Credits 3
Introduction This course will introduce soft matter physics, the physics of macromolecules. It is
relevant inside living matter, polymeric materials, nano-composites, liquid crystals
(LCD displays), and smart materials with tunable properties. The aim is to use
statistical mechanics to understand the generic properties (statistical physics) of
long-chain molecules such as polymers.
Course contents Polymer Static and Dynamics
Molecular weight distributions, Molar mass distributions, Radius of Ideal chains

(random walk model) vs. Real chains with Excluded volume, Semiflexible (Rigid
Polymers), Solvent properties: Polymers in Good/Bad/Theta solvents, Flory Theory,
and Flory Huggins Theory, Blob picture of Semidilute polymers vs. Dilute polymers
& Dense polymers (Melts), Polymers within confining walls, Entropic origins of
rubber elasticity of un- entangled/ entangled polymers, Polymers with cross-links
(Networks and Gels), Linear Visco-elastic reponse of polymeric materials, Polymer
Dynamics: Rouse model of dilute polymers, Zimm Model (with hydrodyamics),
Reptation in melts.
Colloidal (Brownian) Particles.
Intermolecular forces between uncharged Particles: Induced dipole and dispersion

forces, screened Coulomb interactions between charged particles, DLVO Theory,
Hamakers constants, Depletion Interactions, Colloidal Phase diagram. The relevant
statistical mechanics concepts: Random walks, Fluctuation dissipation theorem,
Stokes Einstein relation, fluid physics will be covered.
References 1. Polymer Physics Michael Rubinstein and Ralph H. Colby, Oxford University

Press.
2. Soft Machines (nanotechnology and life) by R.A.L. Jones. Oxford publications.
Discipline Physics
Course title Mathematical Methods II
Semester 6
Credits 3
Introduction To teach more advanced methods that will be essential for some areas of Physics.
Course contents Complex analysis
Ordinary Differential Equations-II (Series solutions, Special functions)
Sturm-Liouville theory
Partial differential equations
Integral transforms
Tensors and basic group theory
References
154
Discipline Physics
Course title Electronics
Semester 7
Credits 4
Introduction To provide an overview of the design principles of electronic circuits. By the end of
this course, students are expected to be able to understand simple circuits, and
also design new circuits on their own.
Course contents Familiarization of students with Basic concepts of the following, leading to a
preparation of foundations for advanced electronics:
Network Analysis
Electronic devices and circuits
Applications of basic semiconductor devices
Fundamentals of operational amplifier and circuits
References 1. Electronic Principles: A. Malvino and D. Bates (2006) 7th edition, Mc-Graw-Hill
2. The Art of Electronics: P. Horwitz and W. Hill (1989) 2nd edition, Cambridge
University Press
3. Electronic devices and circuits’ by Robert L. Boylestad & Louis Nashelsky,
Pearson-2009
Discipline Physics
Course title Atomic and Molecular Physics
Semester 7
Credits 4
Introduction A formal introduction to atoms, molecules, and their interactions with one another
as well as with electric, magnetic, and electromagnetic fields. Experiments
supporting theoretical concepts will be highlighted throughout. Applying
theoretical concepts via solving problems is emphasized.
Course contents Experiments leading to the concept of atoms, molecules, and their structure
Quantum theory of single-electron atoms
Single-electronatomsinelectromagneticfields,fineand hyperfine structures, Stark
effect, Zeeman effect  
Quantum theory of two-electron atoms, influence of orbital and spin angular
momenta; their excited states  
Quantum theory of multi-electron atoms, central field approximation, periodic
table, Thomas-Fermi and Hartree-Fock models, L-S and J-J coupling  
Interaction of atoms with electromagnetic radiation, dipole approximation,
oscillator strengths  
Masers and Lasers, Einstein coefficients, atom optics, trapping atoms and ions,
laser cooling, BEC, atomic clocks  
Electron-Atom,Ion-Atom,Atom-AtomScattering  
Molecules, Born-Oppenheimer approximation, diatomic molecules and their
energy levels, polyatomic molecules  and their structure.  
Electronic, vibrational, and rotational degrees of  freedom; optical, infrared,
Raman, microwave, and magnetic resonance spectroscopies.
References 1. Physics of Atoms and Quanta: H. Haken and H.C. Wolf (2005) Springer
2. Physics of Atoms and Molecules: B.H. Bransden and C.J. Joachain (2003)
Pearson Education India
3. Atoms, Molecules and Photons: W. Demtroder (2010) Springer
4. Atoms, Molecules, and Lasers, K P R Nair, Narosa (2006)
155
Discipline Physics
Course title Nuclear and Particle Physics
Semester 7
Credits 4
Introduction The course will focus on basic concepts in particle and nuclear physics, intended
for students seeking an introduction to the fundamental constituents of matter
and their interactions. The course should serve as a fair prelude to an advanced
course on the Standard Model of particle physics and gauge theories.
Course contents Historical introduction, Classification of fundamental particles, Relativistic
kinematics, Interactions and particle dynamics, Symmetries and invariance
principles, Bound States and the Quark model, Neutrinos, Neutral kaon system,
Higgs mechanism, High energy physics experiments, Nuclear models.
References 1. Introduction to Elementary Particles: D. Griffiths(1987) 2nd edition, Wiley
2. Particle Physics: R.R. Martin and G. Shaw (2008) John Wiley & Sons
3. An Introduction to Nuclear Physics: W.M. Cottingham and D.A. Greenwood
(2001) 2nd edition, Cambridge University Press
Discipline Physics
Course title Physics Lab V
Semester 7
Credits 3
Introduction This lab course offers some interesting experiments that a student frequently
comes across during the lecture courses in advanced electrodynamics and basic
quantum physics. These experiments illustrate physics of the electromagnetic
radiation, their propagation, and interaction with matter. The experiments are
aimed to illustrate the quantum nature of interactions at the subatomic scales.
Course contents Ionic conductivity  
Magnetic Susceptibility measurement by Gouy's method  
Skin depth measurement  
Faraday effect  
Generation and transmission of Electromagnetic waves  (Lecher Wire)  
Constant deviation spectrometer  
Blackbody radiation  
Franck Hertz experiment  
Determination of ionization potential  
References 1. The Art of Experimental Physics: D.W. Preston and  E.R. Dietz (1991), John
Wiley.  
2. An introduction to Error Analysis, John R. Taylor,  University Science Books.  
3. Advanced Practical Physics: B.L. Worsnop and H.T.  Flint, Asia Publishing
House  
4. Analytical Experimental Physics: M. Ference Jr.,  H.B. Lemon and R. J.
Stephenson (1970) University of Chicago Press.  
5. The Art of Electronics: P. Horowitz and W. Hill (1989) 2nd edition, Cambridge
University Press.
Discipline Physics
Course title Computational Physics
Semester 7
Credits 3
Nature of course Computational laboratory and lectures
Introduction This advanced course aims to give the students competence in the methods and
156
techniques of calculations using computers. At the end of the course the student
is expected to have a hands on experience in modeling, algorithm development,
implementation and calculation of physical quantities of relevance in interacting
many body problems in physics. Both classical and a few quantum computational
tools will be introduced.
Course contents Introduction to FORTRAN programming language. Random numbers and
numerical and Monte Carlo integration. Monte Phase Carlo simulation (Phase
transitions in classical 2D Ising model). Differential equaations. Quantum spin
chains, Molecular dynamics.
References 1. Computational Physics, by N. J. Giordano and H. Nakanishi (Pearson Prentice
hall, 2006)
2. Fortran 90/95 for Scientists and Engineers, by S. Chapman (McGraw Hill, 2004)
3. Fortran 90/95 Explained, by M. Metcalf and J. Reid (Oxford university Press,
2002)
4. Numerical Recipes, by W. H. Press, S. A. Teukolsky, W. Vetterling, and B. P.
Flannery (Cambridge University Press)
5. Computer simulation of liquids by M. P. Allen, D. J. Tildesley, (Clarendon Press,
1987)
6. Understanding Molecular Simulation: From Algorithms to Applications by
Daan Frenkel, Berend Smit (Academic Press, 2002)
Discipline Physics
Course title Fluid Dynamics
Semester 7
Credits 3
Introduction This course will be useful for students wishing to gain an overview of the vast field
of fluid dynamics. The course is aimed at imparting basic knowledge of the subject
to facilitate research career in plasma physics, astrophysics, soft matter,
biophysics, and computational fluid dynamics.
Course contents Governing equations: Basic conservation equations, inviscid fluids, viscosity, the
Navier-Stokes equations, jumps and discontinuities
Applications and advanced topics: Applications to Astrophysics, and possibly some
engineering applications. An introduction to turbulence in fluids
References 1. Fluid Mechanics, P. K. Kundu, I. R. Cohen and D. R. Dowling, Elsevier, 5th
edition
2. Fluid Mechanics: L.D. Landau and E.M. Lifshitz (2007) 2nd edition, Pergamon
Press
Discipline Physics
Course title Group Theory in Physics
Semester 7
Credits 3
Introduction This course will explain the role of symmetries in physics. It is important for
students who plan to work in theoretical physics. It should also prove useful to
students studying any subject/topic that is related to symmetries.
Course contents Discrete symmetries.
Continuous symmetries – U(1), SO(2), SO(3), Parameter spaces, Noether’s
theorem.
SU(2) in detail, SU(3), spinors, applications to particle physics.
Group theory of relativity.
References 1. Group Theory: A Physicist's Survey: P. Ramond (2010) 1st edition, Cambridge
University Press
2. Lie Algebras in Particle Physics: H. Georgi (1999) Westview Press, 2nd edition
157
3. Mathematical Methods for Physicists, G. Arfken and H. Weber, Academic
Press, 4e, 1995.
Discipline Physics
Course title Quantum Field Theory
Semester 7
Credits 3
Introduction The goal of this course is to introduce students to the fundamentals of quantum
field theory, as a framework that underlies a large part of contemporary Physics.
This course will be particularly useful for students in theoretical physics and
experimental high energy physics.
Course contents Classical theories of fields, symmetries, Canonical quantisation, Scalar field theory,
Dirac, Weyl and Majorana fermion fields, Electromagnetic field, Gauge invariance,
Quantum Electrodynamics, applications
References 1. An introduction to Quantum Field Theory, M. Peskin & D. Schroeder
2. Quantum Field Theory, Ryder
Discipline Physics
Course title Advanced Condensed Matter Physics
Semester 7
Credits 3
Introduction This course will cover various interacting many-body phenomena, which will be a
good foundation for those who are interested in theoretical, experimental, and
computational research in condensed matter.
Course contents Interacting electrons (Many-body problem, Hartree-Fock approximation in second
quantization, Brief overview on Density Functional Theory); Linear response theory
(Fluctuation-dissipation theorem, Scattering, F-sum rule); Physics of disorder (Kubo
formula for conductivity, Scaling theory of localization, Quantum hall effect);
Magnetism (Local moment magnetism, exchange interaction, Band magnetism-
Stoner theory, spin density wave, Anderson model, Kondo problem); Fermi liquid
theory (Electron spectral function, Quasi-particles and Landau interaction
parameter, Fermi liquid in Kondo problem); Superconductivity (Landau
diamagnetism, London equation and effect of disorder, Ginzburg-Landau theory,
vortices, Type II superconductor )
References 1. Advanced Solid State Physics – Phillip Phillips
2. Solid State Physics, by N W Ashcroft and N D Mermin, Harcourt College
Publishers. (College Ed.)
3. Theory of Quantum liquid, Pines and Nozieres, Westview Press
4. Theory of Superconductivity. J. Robert Schrieffer, Westview Press
Discipline Physics
Course title Advanced Optics
Semester 8
Credits 3
Introduction This course is aimed at students who are majoring in physics, with interest in
experiments. The objective of the course is to introduce advanced aspects of
optics and connect them to some contemporary research topics in optics and
photonics.
Course contents Beam optics: Solutions to wave equation, Gaussian beams and their propagation
and diffraction, Laguerre-Gaussian and Hermite-Gaussian beams, Bessel beams,
158
basic aspects of orbital and spin angular momentum of light (8 hours)
Waveguides: fundamental principles,1D and 2D waveguides, optical coupling, basic
aspects of fiber optics (4 hours)
Optical resonators: Physics of optical cavity, planar resonators, spherical
resonators, Fabry-Perot resonance, Purcell effect (4 hours)
Coherence – definition of spatial and temporal coherence, measurement of
coherence length and time, relationship with interference (4 hours)
Statistical aspects of light – fluctuations and correlations, partially coherent light –
propagation and interference, partial polarization (4 hours)
Photons – Quantization of electromagnetic field, bunching and anti-bunching of
photons, Hanbury Brown-Twiss experiment, Hong-Oh-Mandel experiment (8
hours)
References 1. Fundamental of Photonics, B.E.A. Saleh and M.C. Teich (2007, 2nd edition,
Wiley Pub.)
2. Optical Physics, S.G. Lipson, H. Lipson and D.S.Tanhausser(1995, 3rd edition or
further, Cambridge U. Press)
3. Principles of Optics, M.Born and E.Wolf (1999, 7th edition or further,
Cambridge U. Press)
4. Introductory Quantum Optics, C.C. Gerry and P.L. Knight (2005, Cambridge U.
Press)
Discipline Physics
Course title Physics Lab VI
Semester 8
Credits 3
Introduction The aim is to teach experiments on light and electron emission, spin resonance
phenomena, atomic physics, solid state physics, interaction of radiation with
matter.
Course contents Each student will do some of the following experiments: Field emission, Zeeman
effect, Electron diffraction, characteristics of X-rays and X-ray absorption, Electron
spin resonance, Principle of phase sensitive detection, Thermionic emission, Field-
emission microscopy and Lock-in amplifiers. γ-ray spectroscopy, Scanning
tunneling microscopy, Compton Scattering, X-ray Diffraction, Rutherford
scattering, thermoluminescence, superconductivity, molecular spectroscopy
References 1. Advanced Practical Physics: B.L. Worsnop and H.T. Flint, Asia Publishing House
2. Analytical Experimental Physics: M. Ference Jr., H.B. Lemon, and R.J.
Stephenson (1970) University of Chicago Press
3. The Art of Experimental Physics: D.W. Preston and E.R. Dietz (1991) John
Wiley
Discipline Physics
Course title Special Topics in Condensed Matter Physics
Semester 8
Credits 3
Introduction To introduce students to topics of contemporary research interest in condensed
matter physics, primarily topological materials and phases.
Course contents Su Schrieffer Heeger model: Edge modes, winding number, chiral symmetry and 1D
Dirac Eqn,
Berry Phase: Berry phase, connection, curvature, Chern number, band topology,
Chern Insulators: Hall conductance, Quantum anomalous Hall effect, Edge dispersion,
Integer quantum Hall effect: Landau levels, IQH ground states, chiral edge modes,
Quantization of Hall conductance, plateaus and plateau transitions,
Kane Mele and BHZ model: Chiral spin transport and spin Hall effect,
159
2D and 3D Topological Insulators: Z2 invariants, Effective Hamiltonian of the surface
states,
Dirac and Weyl points: Symmetry protection of Dirac points, surface states and
Hamiltonian, Visualization of edge modes, Weyl points,
Fractional quantum Hall effect: Laughlin state, fractional charge, flux attachment, Jain
states, Chern Simons effective description, boundary Lagrangian,
Spin liquids: Classical spin liquids, Quantum spin liquids, mean field quantum gauge
theories, Kitaev spin liquid
References 1. Bernevig, Hughes: Topological insulators and topological superconductors
2. Asboth: A short introduction to topological insulators
3. X G Wen: QFT of many body systems
4. Les Houches school notes: Topological aspects of condensed matter systems
Discipline Physics
Course title Quantum Field Theory II
Semester 8
Credits 3
Introduction To introduce students, primarily those interested in theoretical physics, to the
formalism and concepts underlying modern developments in both particle and
condensed matter theory, namely path integrals, semi-classical methods,
renormalisation and the renormalisation group.
Course contents General perspective on quantum field theory, Statistical systems, partition and
correlation functions, Transfer matrix method.
Path integral for non-relativistic quantum mechanics, determinants of differential
operators, free non-relativistic particle, applications to simple systems, Gel'fand-
Yaglom formula.
Path integral for scalar fields in QFT, correlation functions, semi-classical
expansion as saddle-point approximation, computation of spectrum from path
integral, semi-classical expansion and its meaning.
Solitons as classical solutions, topological sectors and conservation laws,
quantisation of solitons, instantons, physical interpretation, multi-instantons,
tunneling in quantum mechanics via instantons.
Scalar QED and the Abelian Higgs Model (AHM), solitons of 2+1d AHM as magnetic
vortices.
Feynman diagrams from path integrals. Loop diagrams, divergences, one-loop
amplitudes in scalar field theory, dimensional regularisation, renormalised
perturbation theory, counterterms, minimal subtraction, beta-function.
Renormalisation group equation, physical consequences of the beta-function:
momentum-dependence of coupling constants,
effective action in continuum QFT, Wilsonian view of the renormalisation group.
References 1. Quantum Field Theory and Condensed Matter: An Introduction – R. Shankar
2. An Introduction to Quantum Field Theory – Peskin and Schroeder
3. Quantum Field Theory and The Standard Model – Matt Schwartz
4. Condensed Matter Field Theory - Alexander Altland and Ben Simons
Discipline Physics
Course title Standard Model of Particle Physics
Semester 8
Credits 3
Introduction To introduce particle physics students, both experimental and theoretical, to the
quantum field theoretic model underlying all elementary particle phenomena,
namely the Standard Model.
Course contents Introduction to Non-Abelian gauge theory
160
Global Symmetries of SM and anomalies
Spontaneous electroweak symmetry breaking
Quark and lepton flavor physics and CP-violation
Examples of Electroweak processes
QCD processes and LHC
Non-perturbative topics in SM
Selected topics in Beyond Standard Model physics
References 1. Quarks and Leptons: An introductory course in modern particle physics –
Halzen and Martin
2. Quantum Field Theory and The Standard Model – Matt Schwartz
3. An Introduction to Quantum Field Theory – Peskin and Schroeder
Discipline Physics
Course title Quantum Information
Semester 8
Credits 3
Introduction Involves a theoretical treatment of quantum information, the goal is to prepare
students towards understanding (and contributing to) current research in the
area.
Course contents Fundamental Concepts-Qubits and their measurements, superdense coding,
ensembles, Schmidt decomposition, Bell inequality.
Quantum Computation-Circuits, quantum Fourier transform, search and
factorization, physical implementations.
Quantum Information-Noise, fidelity measures, error-correction, entropy and
information.
References 1. Quantum Computation and Quantum Information: M.A. Nielsen and I.L.
Chuang(2011) Cambridge University Press
2. Lecture notes on Quantum Information and Quantum Computation, John
Preskill – http://www.theory.caltech.edu/people/preskill/ph229/
3. An Introduction to Quantum Computing: P. Kaye, R. Laflamme and M. Mosca
(2007) Oxford University Press
Discipline Physics
Course title Advanced Gravitation
Semester 8
Credits 3
Introduction To prepare students for research in areas of astrophysics, gravitation, string theory
and theoretical particle physics by introducing the basics of gravitational radiation,
black hole physics, the relation between gravity and thermodynamics, etc. Will
also be useful to those working on the holographic formulation of strongly coupled
systems in condensed matter and other areas of physics.
Course contents Gravitational radiation:  the weak-field limit, linearised Einstein equations, plane
waves, polarizations, gravitational radiation by sources.
deSitter and anti deSitter spacetimes.
Black holes and their physics: Rindler space and horizons, spherical symmetry,
Birkhoff’s theorem and the Schwarzschild solution, geodesics in the Schwarzschild
geometry, the event horizon, black hole formation, Penrose diagrams, no hair
theorems, charged and rotating black holes, cosmic censorship, extremal black
holes, Hawking temperature and radiation, Bekenstein-Hawking entropy and black
hole thermodynamics.
References 1. Gravity – Eric Poisson
2. Spacetime and geometry: an introduction to general relativity – Sean Carroll.
3. The large-scale structure of space-time – Hawking and Ellis
161
Discipline Physics
Course title Plasma Physics
Semester 8
Credits 3
Introduction Plasmas in various forms constitute over 95 % of the observable universe. An
understanding of plasma physics in the laboratory context is key to the important
push towards harnessing energy from nuclear fusion. This course will provide an
overview of the theory of magnetohydrodynamics and plasma physics with a view
to applications in astrophysics and in the laboratory
Course contents Basics of plasma physics: Kinetics: Particle orbits, guiding center theory, the BBGKY
hierarchy, Moments of the distribution function, wave-particle interactions (e.g.,
Landau damping), transport coefficients, Transition to the fluid description:
Magnetohydrodynamics: basic governing equations, instabilities (sausage
instability, kink instability, two stream instability, etc), waves in plasmas,
applications to astrophysics (the solar dynamo, the solar wind, jets from compact
objects) and laboratory plasma (column pinches, confinement)
References 1. Plasma Physics: An Introduction to the theory of astrophysical, geophysical
and laboratory plasmas: Peter A Sturrock (Cambridge)
2. The physics of plasmas: T J M Boyd, J J Sanderson (Cambridge)
3. The Physics of Fluids and Plasmas; Arnab Rai Choudhuri (Cambridge)
Discipline Physics
Course title Phase Transitions and Critical Phenomena
Semester 8
Credits 3
Introduction The course will present a coherent description of the theory of continuous phase
transition in classical systems with an extension of the concepts to topological
phase transitions.
Course contents Second order critical behavior, order parameter, response function, related
thermodynamics and the concept of universality.
Models – Spin-1/2 and spin-1 Ising model, q-state Potts model, XY and Heisenberg
model, mean field theory and transfer matrix method.
Ginzburg-Landau theory, Gaussian integrals, symmetry breaking, Goldstone
modes, fluctuation correlations, Ginzburg criterion.
The Scaling hypothesis, homogeneity, self-similarity.
Renormalization Group, Gaussian model, Wilson’s perturbative renormalization
group, epsilon expansion.
Topological phase transition, XY-model, High and low temperature expansions,
vortices, BKT transition.
References 1. Phase transitions and collective phenomena, by Ben Simons, (online available
notes).
2. Statistical mechanics of phase transitions, J M Yeomans, Oxford Science
Publications.
3. A modern approach to critical phenomena, Igor Herbut, Cambridge University
Press.
4. Statistical physics of fields, M Kardar, Cambridge University Press.
162

IISER BSMS Curriculum 2021

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BS-MS Curriculum at IISER Pune

Last revised: August 4, 2021

Discipline Sem 1 Sem 2 Sem 3 Sem 4 Sem 5 – 8 Sem 9 – 10

Discipline Sem 1 Sem 2 Sem 3 Sem 4

2.2. Elective Courses in the 3rd Semester

Discipline Course Title

2.3. Major and Minor Requirements for Each Discipline

The requirements of a Major / Minor in each discipline are specified below.

Minor: At least 8 courses in Biology from the list below.

Semester Course Title (Number of credits) Prerequisites

Semester Course Title Prerequisites

2.3.3. Data Science

For 2021 batch and onwards:

Semester Course Title Prerequisites

2.3.5 Humanities and Social Sciences (HSS)

Major: Not applicable

Minor: Minimum 8 courses in Mathematics.

Semester Course Title Prerequisites

Minor: At least 8 courses in Physics from the list below.

Semester Course Title (Number of credits) Prerequisites

2.4 Fifth Year Research Project

Course title Introductory Biology

Nature of course Lectures and Tutorials

Course contents Module 1: Concepts in Biology

References 1. N. A. Campbell, J. B. Reece, R. B. Jackson, M. L. Cain, L. A. Urry, S. A.

Course title Experiments in Biology

Nature of course Laboratory

Course contents a. Basics of microscopy

References 1. Text Book(s) of Introductory Biology course

Course title Introduction to Biomolecules

Nature of course Lectures, Tutorials, and Laboratory Sessions

References 1. Harper’s Illustrated Biochemistry (2009), 28th edition, McGraw Hill.

Course title Ecology and Evolution

Nature of course Lectures

Introduction This is an introductory course that will help students in terms of

A) understanding of 1) the basic concepts in ecology and evolution 2) how

B) ability to 1) visualize how these concepts connect to real-life situations, and 2)

Population ecology: Survivorship curves, Life-tables, Simple population dynamics

Community ecology/ Species interaction: Competition (Competitive exclusion

Applications: Conservation biology (Basic concepts, Reserve designing, Case study:

Evolution: A very brief history of evolutionary thought upto Extended Evolutionary

Population genetics: H-W equilibrium; selection; genetic drift

Course title Principles of Organic Chemistry

Nature of course Lectures and Tutorials

Course contents  Organic Chemistry in day-to-day life: Medicines, petrochemicals, polymers,

References 1. Organic Chemistry by Jonathen Clayden, N. Greeves, S. Warren, P. Wothers

Course title Principles of Physical Chemistry

References 1. Physical Chemistry by Peter Atkins and Julio de Paula

Course title General Chemistry Practicals I

Nature of course Laboratory

Course contents 1. Synthesis of Aspirin

References Readings and laboratory manual provided during the course

Course title Principles of Inorganic Chemistry

Nature of course Lectures and Tutorials

Discipline Earth and Climate Science

Course title Evolution of Earth and Life

Nature of course Lectures and Tutorials

Discipline Earth and Climate Science

Course title Introduction to Climate Science

Course contents 1) Diversity of Genomes (2) 