Scribd
Upload
31 views36 pages

Engineering Concepts in Biology-Part 2

Uploaded by

nita achari
Copyright
© © All Rights Reserved
We take content rights seriously. If you suspect this is your content, claim it here.
Available Formats
Download as PDF, TXT or read online on Scribd
31 views36 pages

Engineering Concepts in Biology-Part 2

Uploaded by

nita achari
Copyright
© © All Rights Reserved
We take content rights seriously. If you suspect this is your content, claim it here.
Available Formats
Download as PDF, TXT or read online on Scribd
You are on page 1/ 36

BIOCOMPUTING

Dr. Urmila Saxena


Department of Biotechnology
Nit warangal
Biocomputing
• Operates at the intersection of biology,
engineering, and computer science.

• Seeks to use cells or their sub-component


molecules (such as DNA or RNA) to perform
functions traditionally performed by an electronic
computer.
Cells already Compute
1. Cells store data in DNA

2. Receive chemical inputs in RNA (data input)

3. Perform complex logic operations using ribosomes

4. Produce outputs by synthesizing proteins


What is Biocomputing?

 Biocomputing is a field of technology that uses biology,


engineering, and computer science to create systems
that perform computations using biological molecules.

Use of biological molecules, like DNA and proteins, to


perform computations.

The goal of Biocomputing is to mimic the biological


hardware of the human body.
Examples of Biocomputing
• Biological computers
• These are 3D cultures of brain tissue and neurons that mimic the structure and functions of
the brain. They use chemical inputs and biologically derived molecules to process data.
• DNA computing
• This is a form of biological computing that uses DNA. In DNA computing, specific
oligonucleotides are constructed to represent data items
• Biological Neural Networks
• Researchers study the brain’s neural networks to develop algorithms and architectures that
mimic biological processes, potentially leading to more efficient computational models
• Bioinformatics
• This is the application of statistics and computer science to molecular biology.
Biocomputing
Why DNA?

 High density compact Information encoding base pairing


structure

Replicability
 Chemical Stability

Natural Repair Mechanism Evolutionary Adaptation

Universally common
language
DNA Computing
DNA Polymerase
Tools to make a DNA
Computer
●Watson-Crick Pairing
●Polymerases
●Ligases
●Nucleases
●Gel Electrophoresis
●DNA synthesis
Computation is easy
● To build a computer, two things are really necessary:
● A method of storing information
● A few simple operations for acting on that information
○Any method is good enough
The Hamiltonian Path
Problem

●Arrows: Non-stop flights


●Vertices - Cities
The Hamilton Path Problem
● To determine if a sequence of
connecting flights (a path) exists
that starts in Atlanta (the start
vertex) and ends in Detroit (the
end vertex), while passing
through each of the remaining
cities (Boston and Chicago)
exactly once.

● Such a path is called Hamilton


path.
General Hamilton Path
● Given a graph with directed edges and a specified start vertex and end vertex,
one says there is a Hamiltonian path if and only if there is a path that starts at
the start vertex, ends at the end vertex and passes through each remaining
vertex exactly once.

● The Hamilton path Problem is to decide for any given graph with specified start
and end vertices whether a Hamiltonian path exists or not
An Algorithm
● Given a graph with n vertices
1. Generate a set of random paths through the graph
2. For each path in the set:
○ Path starts with the start vertex and end with the end vertex
○ Path passes through exactly n vertices
○ For each vertex – path passes through that vertex

3. If the set is not empty, report there is a Hamiltonian


path
● Took about 10 molecules of each of the different sequences and put them
14

into a common test tube.

● To begin the computation, simply add water, ligase, salt and few other
ingredients to approximate the conditions inside a cell.

● Within one second, the answer to the Hamiltonian Path Problem is there
Solution to mathematical problem could be stored in a single molecule
Additional steps
●PCR– to amplify our target sequence

●Gel electrophoresis – to check correct length of the


strand is 24

●To check the remaining sequences, for whether their


paths pass through all the intermediary cities:
●Watson and Crick Annealing – affinity separation
●DNA probe molecule encoding complementary name of a particular city
●If the tube contained any DNA at all –
Hamiltonian path exists

●No DNA – No Hamiltonian path


Features of Biocomputing

 Biological Information  Self replication


Processing
Modularity
 Parallelism
 Integration with biological functions
Energy Efficiency

Scalability
Adaptive systems
DNA Based Data Storage
The Growth of Digital Data
Demand for denser and longer-
lived information storage devices
• Current storage technologies:
• Optical devices
• Magnetic devices,

• Energy consumption
• Insufficient data density
• reaching their information density limits and are thus not suitable
for long-term (>50 years) storage

• Valuable information needs to regularly transferred to


newer storage media if it is to be preserved for future
generations

• Innovative data storage solutions are required


Can DNA be a solution?
DNA

• Can encode, transmits and preserve information

• Store all genetic information in the form of 4 nucleotide bases

• Stable for thousands of years –required power consumption is


very low

• Has a theoretical data density of 6 bits for every 1 nm of polymer,


or 4.5 × 107 GB/g, which is orders of magnitude higher than the
densities achievable using traditional devices
Sequence based DNA Data
Storage

Steps:
(1) encoding digital information
(2) Data writing (synthesis of new oligonucleotides)
(3) Storing the DNA in physical or biological conditions
(4) Random access
(5) Data readout via DNA sequencing
(6) Decoding the DNA sequences back into the original digital code
From Encoding to Data Writing
Encoding
• One possible
data storage
approach is to
use a set of
DNA sequences
of 60−200 nt in
length.

• Writing Data on
synthetic DNA
sequence
Storage
• Both aqueous solutions and dried DNA only exhibit a half-
life on the order of months to a few years under ambient
conditions

• Considerations for the physical storage of data-encoding


DNA are crucial

• Environmental factors for DNA degradation:


• Strand breaks
• Nucleotide mutations
• Strand cross-linking by UV, oxidation
• Hydrolysis
• Alkylation
• Mechanical stress
Storage solutions
• Encapsulation within silica particles

• Embedding in alkaline salt, polymer, sugar, or silk protein


matrices

• Coprecipitation with calcium phosphates imitating bone

• Dried or lyophilized DNA is stored on filter paper within


hermetically sealed capsules with inert atmosphere

• Frozen in aqueous solu ons and stored at −20 or −80 °C


Random Access
• To select a sub pool of sequences, usually a file,
from a large pool.
Reading
Illumina NGS Sequencing
Limitations of DNA Storage
• Cost

• Process Time Scales

You might also like