How to write

a high-quality research ar cle

Phu Nguyen

Department of Civil Engineering

Monash University

[email protected]
http://nvinhphu.wixsite.com/mysite
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A story
Stephane Bordas
Prof at University of Luxembourg

Lambertus Sluys
Prof at Del Uni. of Technology

Mar jn Stroeven
Del Uni. of Technology

Alban de Vaucorbeil
Deakin University
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 Agenda

what is the problem?

general guidelines to wri ng
tle/abstract/introduc on/conclusion/acknowledgement/references

tables/ gures
how to write a paragraph
some mistakes
wri ng work ow
LaTeX

and possibly QA/discussion

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Have you read any papers lately?

lack the technical sophis ca on?

No! so many papers are poorly wri en

Judy Swan – Associate Director for Wri ng in Science and Engineering at

Princeton University – said: ‘scien c wri ng is bad wri ng’

https://www.youtube.com/watch?v=1pzjxYCwb08
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If you can write clear, accessible papers…

get accepted quicker as reviewers worked on the content

people will enjoy reading them

people will learn something from them

your papers are likely to receive high cita ons

learning to write well is an essen al part of becoming a successful researcher

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General guidelines

To inform not to impress

Aim for clarity and readability and reproducibility
Contribu ons must be clearly stated
Every unit of discourse (a sentence/sec on/ar cle): only a single idea/message
Avoid jargon
Minimize chances for reviewers to raise issues
Clarity > gramma cal exactness
If you can remove a word/sentence/ gure, do it
Explain everything

G. D. Gopen and J. A. Swan. The science of scienti c writing. American Scientist, 78(6):550–558, 1990
https://www.nature.com/scitable/ topicpage/scienti c-papers-13815490/
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Explain everything
choose a method: explain why
choose a test/example: explain why
value for parameters: sources and if you come up with them, explain why
provide all parameters needed to reproduce your paper

Topology op miza on is a method that allows to nd an op mal material layout within a

prescribed design domain so as to maximize or minimize certain objec ves and sa sfying
one or mul ple design constraints [1]. …

Various techniques have been developed for topology op miza on, for example, the solid
isotropic material with penaliza on (SIMP) method [2] and the evolu onary structural
op miza on (ESO) method [3] and its improved version – the bi-direc onal evolu onary
structural op miza on (BESO) method [4]. We choose the BESO method for our work for
the following reasons. First, without needing calcula ng sensi vi es, the BESO is much
easier to implement and can be easily adapted to a wide range of problems. Second,
engineers only care whether the design can be improved, but do not care whether the
solu on is op mal or has rigorous mathema cal founda on. We refer to the review of [5]
for a discussion on the merits of exis ng topology op miza on methods.
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Structure of a research ar cle

Title
Abstract
Introduc on
Method
Result
Conclusion
Acknowledgement
Appendices
References
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 The tle: why do paper tles ma er?
the tle is the part of a paper that is read the most
it is usually read rst
papers with short tles got more cita ons
using a ques on mark in a paper’s tle reduces the cita ons
using a colon tended to improve the cita ons
many researchers (me in the past included) never mind

‘The nucleo de sequence of a 3.2 kb segment of mitochondrial maxicircle DNA from Crithidia
fasciculata containing the gene for cytochrome oxidase subunit III, the N-terminal part of the
apocytochrome b gene and a possible frameshi gene; further evidence for the use of unusual
ini ator triplets in trypanosome mitochondria’ by P. Sloof, J. van den Burg, A. Voogd, R. Benne
Nucleic Acids Research, Volume 15, 1987 [47 cita ons]

C. E. Paiva, J. P. d. S. N. Lima, and B. S. R. Paiva. Articles with short titles describing the results are
cited more often. Clinics, 67(5):509–513, 2012

https://www.timeshighereducation.com/news/long-research-titles-have-lower-impact
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Titles from the old great minds

On the Movement of Small Par cles Suspended in Sta onary Liquids Required by the
Molecular-Kine c Theory of Heat

On the Electrodynamics of Moving Bodies

On the In uence of Gravita on on the Propaga on of Light

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The tle: what makes a good tle?
Indicate accurately the subject/scope of the study.
Avoid using abbrevia ons
Do not include "study of," "analysis of" or similar construc ons.

An e cient and robust staggered algorithm applied to the quasi-sta c descrip on of

bri le fracture by a phase- eld approach

⇒ An e cient and robust staggered solver for a phase- eld model of quasi-sta c
bri le fracture

General mesh method: A uni ed numerical scheme

⇒ General mesh method: A uni ed numerical scheme for uid dynamics problems

Data-driven inverse modelling through neural network (deep learning) and

computa onal heat transfer
⇒ Data-driven inverse modelling for heat transfer problems through neural network
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The abstract

the most important sec on of your paper

the rst sec on that is read by journal editors
once published, the rst sec on that is examined by readers
in many cases, it is the only sec on of the manuscript that they will ever read

write the paper rst, abstract is the nal part

abstract: a concise summary of your paper
include: background, gaps, methodology and results
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 The abstract: an example
Fracture of hyperelas c materials such as synthe c rubber, hydrogels, tex le fabrics is an
essen al problem in many engineering elds. The computa onal simula on of such a fracture
is complicated, but the use of phase eld models (PFMs) is promising. Indeed, in PFMs, sharp
cracks are not treated as discon nui es; instead, they are approximated as thin damage bands.
Thus, PFMs can seamlessly model complex crack pa erns like branching, merging, and
fragmenta on. However, previous PFMs for hyperelas c materials, which are mostly based on
a PFM with a simple quadra c degrada on func on without any user-de ned parameters,
provide solu ons that are sensi ve to a length scale (that controls the width of the damage
band). The current prac ce of considering this length scale as a material parameter su ers
from two issues. First, such a calculated length scale.. Second … This paper presents a length
scale insensi ve PFM for bri le fracture of hyperelas c materials. This model is an extension of
the model of Wu [JMPS, 103 (2017)] with a ra onal degrada on func on. This func on has
some user-de ned parameters of which one is de ned to be inversely propor onal to the length
scale in such a way that the damage threshold (and thus maximum stress) is independent of the
length scale. Results of mode-I and mixed-mode fracture problems obtained with the method of
nite elements are in good agreement with previous ndings and independent of the
discre za on resolu on. Most importantly, they are independent of the incorporated length
scale parameter.
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The introduc on sec on

State the problem domain

State the speci c problem that the paper is solving
Demonstrate the importance of that problem
State the current approaches to solving this problem
Explain what is wrong about them
State what are the contribu ons of the paper
Plan the readers for reading the subsequent sec ons
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The introduc on sec on: example
Material hardness values are o en cited in manufacturing speci ca ons and
are used for quality control purposes. Hardness tests are usually convenient
and economical to conduct and can o en be classi ed as nondestruc ve.
However, despite the fact that various types of hardness tes ng have been
quan ta vely conducted for over 150 years, a fundamental, theore cal
understanding of the test is, in many aspects, s ll lacking. This is because the
physical processes that occur during a hardness test are very complex although
such tests are rela vely easy to conduct. Contemporary computa onal
mechanics techniques and computer hardware have made it possible and
prac cal to numerically model hardness tests. The goal of such modeling is to
obtain more informa on from the tes ng and thereby make the results more
useful for valida ng the material models used for impact simula ons.
Numerically modeling Brinell and Rockwell hardness tes ng of metals is the
topic of this paper.

Literature review …
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The introduc on sec on: why not pictures?

a picture can engage the readers to con nue reading your paper
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The conclusion
People o en read the conclusions directly a er the abstract
Do not repeat the abstract
Some journals skip the conclusions sec on
Avoid resta ng the problem/context
Highlight most signi cant things
State limita ons/issues
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The conclusion: one example
We have presented a new method for explicit solid dynamics within the framework of the material
point method. Based on previous works developed in the MPM community, par cularly the Convected
Par cle Domain Integrator, the total Lagrangian MPM and the nite element material point method, a
Generalized Par cle in Cell (GPIC) was presented with the following a ributes:
• Seamless enforcement of Dirichlet and Neumann boundary condi ons;
• Seamless treatment of material interfaces;
• Higher e ciency as fewer par cles (or elements) can be used;
All of these are achieved with the introduc on of a nite element mesh in a supposedly meshfree
method. GPIC can be an e cient tool for modeling mul ple contact large deforma on problem (Fig.
28).

Although some good results were obtained, there are many issues worthy of further inves ga on.
First, we have limited our discussion to… Second, only explicit me integra on was considered due to its
computa onal simplicity. This limits GPIC to fast transient dynamics problems. Third, we did not
consider … We are working on some of these issues.
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The acknowledgement

acknowledge the funding agents

acknowledge anyone helped you with the paper (not in the author list)
References and cita on

Cite originals not deriva ves

Avoid ci ng a list of two many papers e.g. ‘See [1-20] for some relevant work’.
If a author-year reference format is used, all references in a single cita on should
be ordered in chronological orders: (Day, 1998; Ashby, 2000; Plaxco, 2010).’
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References manager

Use a ref manager (Bibdesk, Jabref, …)

Put les in cloud (Dropbox/Google Drive), synced across all devices
Whenever you found a good paper, add it to the ref manager, cite it in your
paper with some sentences.
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Tables

Tables should be clear & focus on the data

avoid ver cal lines
avoid double horizontal lines
avoid boxing up cells and
leave enough space between rows
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Figures
The reader usually starts by reading the abstract,
conclusion and gures

A high quality gure:

a legible font size (font matches the font text)
a high resolu on (should be PDFs)
color-blindness aware (dis nguish red and green)
all axes are clearly de ned
Sketches

Matlab or matplotlib (graphs)

Adobe Illustrator or Inkscape (sketches)
TikZ/Asymptote (coding to make gures)

Graphs
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Figures: how to cite them

Fig. 1: This is a cat.

A cat is given in Fig.1. As can be seen, it has two eyes.

A cat has two eyes (Fig. 1).

Same thing applies to tables

Global paragraph for long sec ons

don’t lose your readers

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Global paragraph for long sec ons

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Don’t start a sec on with a g/equa on/table
2. Formula ons

Fig. 1: This is a cat.

blahblahblahblahblahblahblahblahblahblahblahblahblah
blahblahblahblahblahblahblahblahblahblahblahblahblahblah
blahblahblahblahblahblahblahblahblahblahblahblahblahblah
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 How to write a paragraph: ow
In the phase- eld modeling of fracture in bri le and quasi-bri le solids, it is crucial to
represent the asymmetric tensile/compressive material behavior. Exis ng phase-
eld models generally adopt an intui ve split of the free energy density without
capturing the crack boundary condi ons properly or an ad hoc hybrid formula on at
the loss of varia onal consistency. To address this issue, this work presents a
varia onally consistent phase- eld anisotropic damage model.
⇒
In the phase- eld modeling of fracture in bri le and quasi- bri le solids, it is crucial
to represent the asymmetric tensile/compressive material behavior: fracture does
not occur in domains under compression. To capture this asymmetric behavior,
previous phase- eld models generally adopt either an intui ve split of the free
energy density without capturing the crack boundary condi ons (…) properly ... This
work presents a phase- eld anisotropic model that is able to capture the asymmetric
behavior, varia onally consistent and sa sfy crack boundary condi ons.

sentences start with familiar (old) information and end with unfamiliar (new) information
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How to write a paragraph: ow

Security proofs of cryptographic protocols are crucial for the security of everyday
electronic communica on. However, these proofs tend to be complex and di cult to
get right. To make it easier to manage such proofs, Jones et al. have proposed a new
design principle, called the game-playing technique. This technique follows a code-
based approach where the security proper es are formulated in therms of
probabilis c programs, called games.
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How to write a paragraph: ow
Within the framework of the material point method, a generalized particle
in cell method for explicit solid dynamics is presented. In this method, the
solids are discretized by nite element meshes, and these meshes are
embedded in a background Eulerian grid. The external and internal forces
of the solids are calculated on their respective nite element meshes
and are mapped to the background grid for solving the momentum
equation. Two formulations for computing these forces are presented:
one using the original con guration of the solids and the other employs
the current con guration. Two and three dimensional numerical examples,
covering massive tensile, compressive elastic and plastic deformation,
demonstrate that the former formulation performs much better for
extremely large deformation problems. Compared with previous material
point methods, the proposed method offers these advantages: (i) better
representation of solid boundaries, (ii) seamless enforcement of Dirichlet
and Neumann boundary conditions, (iii) seamless treatment of material
interfaces and (iv) higher ef ciency. All of these are achieved with the
introduction of a nite element mesh in a supposedly meshfree method.
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How to write a paragraph: original version
The material point method (MPM) is a par cle-grid method suitable for solving large
deforma ons of complicated geometries. A tradi onal MPM implementa on treats each
par cle as a lumped mass. The generalized interpola on material point (GIMP) method is a
generaliza on of the MPM that accounts for finite spa al extent occupied by each par cle.
MPM and GIMP have been successfully used in simula on of a range of complicated
engineering problems… In MPM, the material domain is represented by a set of material points
or par cles and uses a mixed Eulerian–Lagrangian method in which Lagrangian par cles carry
history-dependent state data and an Eulerian background grid is used for calcula on of
deriva ves and solving the momentum equa on. In summary, the MPM has the advantages of
both Eulerian and Lagrangian formula ons. Another interes ng feature of tradi onal MPM is
that this method enforces no-slip contact between bodies automa cally without any further
computa onal costs. However, the MPM su ers from a ‘cell crossing instability’ for problems
involving large displacements. This instability occurs whenever par cles cross boundaries of any
cell in the computa onal background grid and is due to the lack of smoothness of the grid basis
func ons used as the interpola on and mapping func ons in the MPM. By introducing
weigh ng func ons and gradient …, the GIMP is capable of reducing these errors and improving
accuracy [3]. These func ons, which can be interpreted as averages of the basis func on and its
gradient over the par cle domain, are used for mapping and interpola ng data between
par cles and grid nodes as well as calcula ng internal and external forces.
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How to write a paragraph: analyse
The material point method (MPM) is a par cle-grid method suitable for solving large
deforma ons of complicated geometries. A tradi onal MPM implementa on treats each
par cle as a lumped mass. The generalized interpola on material point (GIMP) method is a
generaliza on of the MPM that accounts for finite spa al extent occupied by each par cle.
MPM and GIMP have been successfully used in simula on of a range of complicated
engineering problems… In MPM, the material domain is represented by a set of material points
or par cles and uses a mixed Eulerian–Lagrangian method in which Lagrangian par cles carry
history-dependent state data and an Eulerian background grid is used for calcula on of
deriva ves and solving the momentum equa on. In summary, the MPM has the advantages of
both Eulerian and Lagrangian formula ons. Another interes ng feature of tradi onal MPM is
that this method enforces no-slip contact between bodies automa cally without any further
computa onal costs. However, the MPM su ers from a ‘cell crossing instability’ for problems
involving large displacements. This instability occurs whenever par cles cross boundaries of any
cell in the computa onal background grid and is due to the lack of smoothness of the grid basis
func ons used as the interpola on and mapping func ons in the MPM. By introducing
weigh ng func ons and gradient …, the GIMP is capable of reducing these errors and improving
accuracy [3]. These func ons, which can be interpreted as averages of the basis func on and its
gradient over the par cle domain, are used for mapping and interpola ng data between
par cles and grid nodes as well as calcula ng internal and external forces.
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How to write a paragraph: be er version?
The material point method (MPM) is a par cle-grid method suitable for solving large
deforma ons of complicated geometries. In MPM, the material domain is represented by a set
of material points or par cles, which are treated as lumped masses, and uses a mixed …
However, the MPM su ers from a ‘cell crossing instability’ for problems involving large
displacements. This instability occurs … the lack of smoothness of the grid basis func ons used
as the interpola on and mapping func ons in the MPM.

By introducing weigh ng func ons and gradient …, the GIMP is capable of reducing these errors
and improving accuracy [3]. These func ons, which can be interpreted as averages of the basis
func on and its gradient over the par cle domain, are used for mapping and interpola ng data
between par cles and grid nodes as well as calcula ng internal and external forces. The
generalized interpola on material point (GIMP) method is a generaliza on of the MPM that
accounts for finite spa al extent occupied by each par cle. MPM and GIMP have been
successfully used in simula on of a range of complicated engineering problems…
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Explicit contribu on statements: be careful

In this paper, we present the following contribu ons:

• A uni ed fourth order phase eld fracture framework for bri le and quasi-
bri le solids ;
• A semi-analy cal (analy cal-numerical) approach for PF-CZM;
• A almost length scale insensi ve fourth order PFM;
• The rst fourth order PFM for cohesive fracture;
• The PF-CZM is applied to study the phenomena of crack kinking in anisotropic
bri le fracture
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Explicit contri. statements: parallel structure

In this paper, we present the following contribu ons:

• A uni ed fourth order phase eld fracture framework for bri le and quasi-bri le
fracture;
• A semi-analy cal approach for the fourth order PF-CZM;
• A comparison of the fourth order PF-CZM against the second order PF-CZM;
• A study of the phenomena of crack kinking and sawtooth cracking in strongly
anisotropic bri le fracture.

Parallel structure
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Parallel structures: Mar n Luther King's "I Have a Dream"

I have a dream that one day this na on will rise up and live out the true meaning of
its creed: "We hold these truths to be self-evident, that all men are created equal."
I have a dream that one day on the red hills of Georgia, the sons of former slaves and
the sons of former slave owners will be able to sit down together at the table of
brotherhood.
I have a dream that one day even the state of Mississippi, a state sweltering with the
heat of injus ce, sweltering with the heat of oppression, will be transformed into an
oasis of freedom and jus ce.
I have a dream that my four li le children will one day live in a na on where they will
not be judged by the color of their skin but by the content of their character.
I have a dream today! . . .
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Parallel structures

Pairs of ideas—two ideas joined by “and” “or” or “but”—should be wri en in

parallel form.

We hoped to increase the response and to improve survival.

If you want to be a good doctor, you must study hard, cri cally think about the
medical literature, and you should be a good listener.

If you want to be a good doctor you must study hard, listen well, and think cri cally
about the medical literature. (impera ve, impera ve, impera ve)

If you want to be a good doctor, you must be a good student, a good listener, and a
cri cal thinker about the medical literature. (noun, noun, noun)
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Dont’s and dos
Dont’s and dos
end results → results
completely eliminate → eliminate
completely lled → lled
equal halves → halves
as men oned above: remove it or be more speci c, as men oned in Sec. 2.
very small → ny (avoid very which is not precise)
always, never: avoid them
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‘The’: When to use and not to use
The tensile membrane structures are widely used for lightweight and long-span
roofs. These structures are de ned as a combina on of tensioned fabric
membrane and suppor ng elements such as rigid structural frame or exible
cables (Gale and Lewis, 2016). The fabric membrane uses the pre-stress of
tension and its shape to resist the external loading, while the suppor ng
elements are compressed and bent by the tension in membrane. The design
process of these structures involves three steps as form nding, load analysis
and cu ng pa ern genera on. The rst step is to nd the shape of structures
in which the prescribed pre-stress are in equilibrium with a given boundary
condi on, while the second step inves gates the behavior of [the] fabric
membrane and suppor ng elements under service loads. The shapes obtained
by [the] form nding process are usually in doubly curved surface, so they
cannot be a ened into plane without distor ng. In addi on, the fabric
membrane itself is manufactured in plane panels of 1-5m widths (Ishii, 1999).
As a result, a specialist design process, third step of cu ng pa ern, have to be
conducted.
read out loud
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What the di erences i.e and e.g?

“i.e.” = id est, which is La n for “that is.”

“e.g.” = exempli gra a, meaning “for example.”

All employees will receive the standard discount; i.e., 20 percent.

One meal (i.e., breakfast) is included in the price of the room.

Certain fur-bearing mammals, e.g., nutria and o ers, spend much of their lives
in the water.

https://www.warnell.uga.edu/sites/default/ les/inline- les/ieVeg.pdf

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Passive or ac ve voice?
A common belief: passive voice makes wri ng more formal & objec ve

a personal tone can help to engage a reader

And the sentences are shorter and thus easier to understand

Use both

https://www.youtube.com/watch?v=1pzjxYCwb08
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Ac ve voice in the literature review
Although dynamics is an interdisciplinary subject today, it
was originally a branch of physics. The subject began in
the mid-1600s, when Newton invented di eren al
equa ons, discovered his laws of mo on and universal
gravita on, and combined them to explain Kepler's laws
of planetary mo on. …

The breakthrough came with the work of Poincare in the

late 1800s. He introduced a new point of view that
emphasized qualita ve rather than quan ta ve
ques ons.

The inven on of the high-speed computer in the 1950s

was a watershed in the history of dynamics. … Such
experiments led to Lorenz's discovery in 1963 of chao c
mo on on a strange a ractor. He studied a simpli ed
model of convec on rolls… Lorenz found that the
solu ons to his equa ons never se led down …
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A table of main symbols might be useful
 Wri ng ow: ine cient way

Formula on (equa ons)

Coding
me

Simula ons (experiments)

Wri ng
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Wri ng ow: e cient way

Formula on (equa ons)

Title
Abstract
Introduc on

Coding
Method
Wri ng Result
Conclusion
Acknowledgement
Appendices
References

Simula ons (experiments)

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Wri ng ow: e cient way

Write from the beginning

When stuck, move to other parts, or do something else (e.g. walking)
First dra when the last experiment/simula on is done
Don’t worry about the length: a report/paper/book chapter
No order! Write whatever part you like to
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Wri ng ow: an example
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Wri ng ow: an example
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Wri ng ow: an example
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Wri ng ow: an example
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 Submission

only send it to your supervisors when typos were carefully checked

do not submit your paper un l you’re happy about it
ask peers to read over your work: e.g. another PhD student
e ec ve to get feedback sequen ally rather than in parallel
When should you submit your paper? The answer is when you think it is ready
Don’t be too picky as Voltaire once said, “The best is the enemy of the good”
Try not to think about the paper un l reviewers/editors come back with comments

Rudyard Kipling’s advice: “Trust yourself when all men doubt you, but make
allowance for their doub ng too.” Change text where useful, and where not, politel
explain why you’re keeping your original formula on.
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Use of LaTeX in scien c publica ons

https://www. the- scientist.com/uncategorized/dont- format- manuscripts- 44040.

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Use of LaTeX in scien c publica ons

it is open source (free)

created by scien sts for scien sts
do not worry about format
high quality pdf
beau ful equa ons
automate the wri ng
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If you’re a MS Word guy, why LaTeX?

why not?
In LaTeX, you are not programming, but simply a markup language
if you know another tool, you can use Word be er
people using non-default browser (Firefox/Chrome), ended up staying at their
jobs about 15% longer than ones with Safari/Internet Explorer. They
performed be er on the job
increases career opportuni es

what if your supervisor is a Word guy??? …

https://www.theatlantic.com/business/archive/2015/03/people-who-use- refox-or-
chrome-are-better-employees/387781/
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Wri ng well is a skill can be learned

mimic the wri ng of your favourite researcher

mimic the wri ng of your favourite author
read a lots: not only content but also the wri ng
read papers from a di erent eld
re-write your published papers un l you’re sa s ed
write a lot (besides papers: blog, reports, …)

feel free to deviate from all these wri ng styles!

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Some excellent scien c writers

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I write a lot!!!

~ 500 pages

~ 100 pages

~ 110 pages
I write a lot!!!

~ 200 pages

1000 pages

…
Connec ng the dots…
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Connec ng the dots…
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But wri ng is me consuming 😪

Strang ‘I get up early’

Paul Nahin ‘write one page a day’
‘everyday not without a line’

365 days → 365 pages!

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Take home messages (1)

iden fy the selling point of your paper

explicitly state your contribu ons
use simple, direct language
Clarity > gramma cal exactness
high-resolu on graphics with legible font size
don’t lose your reader:
— ideas rst, data/result second
— plan their reading
— explain everything
— provide all data required to reproduce your results

write early
write a lot
learn something new write about it
read a lot (read books/papers from elds far from yours)
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Take home messages (2)
 One more thing

h ps://www.youtube.com/watch?v=WP-FkUaOcOM
h ps://www.youtube.com/watch?v=jLPCdDp_LE0&t=912s
h ps://www.youtube.com/watch?v=1pzjxYCwb08
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 The end
Phu Nguyen

Department of Civil Engineering

Monash University

[email protected]
http://nvinhphu.wixsite.com/mysite

Tri-Uni Workshop, November 2020