Introduction

Writing a paper for a peer-reviewed scientific journal is not easy. Here, I share some of my experiences in writing one. A list of my publications can be found on my Google Scholar page.

Text editor

First, what do we use to write? A text editor. Most people I know use either Microsoft Word or LaTeX. I recommend the latter. Similar to that multiple authors can collaborate on a Word document using Google Docs, people can do the same on a LaTeX document using Overleaf. There are other LaTeX online services but Overleaf is the one I use. Just go to its website and create an account. It supports dark mode.

With Overleaf, you do not need to install any LaTeX-related software on your own computer. But if you want, you can. Follow this page.

If you are a beginner of LaTeX, these references may be helpful:

Article type and journal selection

There are two main types of academic papers: research articles and review articles. The former report original research while the latter provide a summary of research on a certain topic and perspective on where the field is heading. Some journals publish research articles only, some review articles only, some both.

Research article

Depending on the length, there are two main types of research articles: full length articles and letters.

A full length article consists of five main parts, each of which has a heading: Introduction, Methods, Results, Discussion, and Conclusion. However, this is not necessarily the order in which these sections appear in a paper because some journals, e.g., npj Computational Materials, want you to put the Methods section at the end. Letters usually do not have any heading, but the structure is largely the same. Some letters, e.g., Nature, want you to have a section with the heading Methods at the end of the text.

Some journals publish full length articles only, some letters only, some both. In some journals, e.g., Physical Review Materials, the letter-size paper is called Rapid Communication. To find out more about a journal, read the recently published work in it. Also read their instructions carefully. Below are some examples:

Once you select a journal, start writing. When I write a paper, I start with Introduction and end with Conclusion, before finishing the Abstract. But some people write Methods, Results, Discussion first, followed by Introduction, Conclusion, and Abstract. Some other people prefer having an outline first and/or having the figures/tables ready before they start writing. It is up to you.

Review article

Writing a review article is different from writing a research article. This video from Elsevier may be useful.

Below is the list of some journals in my field that only publish review articles:

Writing style

The writing style varies greatly depending on the type of article you want to write and the journal you want to submit your manuscript to. For general writing style, I highly recommend this book. Chinese speakers may also be interested in this book.

There are also many good references on this topic, e.g.,

Main text

First, avoid plagiarism, including the words that come from prior published work by the same author(s). Pay special attention to the Introduction and Methods sections in your research articles and all sections in your review articles. Here are some useful resources:

Below I give a list of specific rules in writing the main text of an academic paper using LaTeX:

Use one, not two, space after a period, unless you are typing on an actual typewritter - even Microsoft Word has changed their mind. In practice, there is no need to type an additional space, because LaTeX treats multiple, consecutive spaces as if they were a single space.
Italicize all variables, but not non-variables. Follow this rule everywhere, including figures and tables and their captions. For example,
- x axis, y axis, and z axis
- elastic anisotropic index for cubic crystals: A_c. A is italic but the subscript c is not because it stands for cubic
- however, if there is a vector B, which has three components and you use a, b, c to denote each component, do italicize them, e.g., B_c
- do not italicize units, e.g., write mJ/m$^2$ or $\mathrm{mJ/m}^2$ , instead of $mJ/m^2$
- do not italicize chemical elements, e.g., write Mo$_4$Nb$_3$Ta$_2$ which would yield Mo₄Nb₃Ta₂, instead of $Mo_4Nb_3Ta_2$ which would yield Mo₄Nb₃Ta₂
When you want to italicize one or more words because you want to emphasize or quote something, use \emph, e.g., \emph{I have a dream} or \emph{very} important. Do not use the math mode. $I have a dream$ would yield Ihaveadream.
Always use the Oxford comma.
Be aware of the lack of space after \AA. A few tips:
- write \AA\ or \AA{}
- if \AA is followed by a period or a comma, simply write \AA. or \AA,. If you use a backslash in front of a period or a comma, it becomes a space
Sometimes a period does not denote the end of a sentence. In this case, we need to use a backslash or a tilde following the period, otherwise the space would be too wide, e.g.,
- Ref.\ [34]
- Barack H.\ Obama II
- Fig.\ 2 or Fig.~2
- Tab.\ 3 or Tab.~2
- Xu et al.\ [17]
- Grant No.\ 123456 or Grant No.~123456
However, if the period is followed by a comma or a semicolon, e.g., Xu et al.;, do not add the backslash or tilde.
For cross-references, it is recommended that you use the hyperref package. Then
- refer to a figure as \autoref{fig1} instead of Figure \ref{fig1}, a table as \autoref{tab1} instead of Table \ref{tab1}, an equation as \autoref{eq1} instead of Equation \ref{eq1}, a section as \autoref{sec1} instead of Section \ref{sec1}, etc, where fig1, tab1, eq1, and sec1 are labels that you created yourself.
- refer to multiple figures as Figures \ref{fig1} and \ref{fig2} or Figures \ref{fig1}--\ref{fig3} or Figures \ref{fig1}, \ref{3}, and \ref{5}. The same goes for tables, equations, sections, etc. Note the plural form of the noun.
There are two math modes, including the inline (e.g., a single variable) and display (e.g., an equation) modes.
- When you use the in-line math mode, simply write $C_{12}$ instead of \textit{$C_{12}$} or $ C_{12} $.
- For a short line over a number, use \bar, instead of \overline, e.g., \bar{1}\bar{1}0. \overline is too wide, especially when two are used sequentially.
- To create angular brackets in the math mode, write $\left<110\right>$ or $\langle 110\rangle$ instead of $<110>$ which renders less-than and greater-than signs.
- < and > only work in the math mode. For ≥, ≤, and ≠, use $\ge$ , $\le$ , and $\ne$ , respectively.
- For multiplication, write $5\times 3\times 8$ instead of 5 x 3 x 8 or 5 X 3 X 8.
- In most cases, no need to place a number between two dollar signs, e.g., write 64 instead of $64$ .
- A dash in math mode becomes the minus sign, e.g., write $-10$ degree Fahrenheit instead of -10 degree Fahrenheit. Double check this in the main text and tables.
- For an in-line equation, write $\alpha = 10$ instead of $\alpha$=10.
Add a space before the left bracket or the left parenthesis, e.g., molecular dynamics (MD) instead of molecular dynamics(MD).
Add a space before citing a reference, e.g., I have a dream \cite{king1963} instead of I have a dream\cite{king1963}.
Add a space between the number and the unit, e.g., 10 nm or 10~nm instead of 10nm.
Use the correct units, e.g., 100 kelvin is written as 100 K instead of 100 k.
To cite multiple references in the same place, use one \cite, e.g., write \cite{king1963,obama2008} instead of \cite{king1963}\cite{obama2008}.
When using an acronym, spell out the entire phrase once and once only and only when the phrase is used for the first time. Common mistakes include
- writing molecular dynamics (MD) on page 1, then writing molecular dynamics on page 2
- writing molecular dynamics (MD) on page 1, then writing molecular dynamics (MD) again on page 2
- writing molecular dynamics on page 1, then writing molecular dynamics (MD) on page 2
- writing MD throughout the paper, without spelling out molecular dynamics at all
For dash in text mode, use - for an ordinary hyphen, -- for an en dash, and --- for an em dash. For example, to describe a plane in a coordinate system, write the $xy$ plane or the $x$-$y$ plane instead of the $x-y$ plane. For more on the dashes, read this page.
For quotation marks, please refer to this page.
Pay attention to special character(s) in people's names, e.g., Schr\"{o}dinger instead of Schrodinger.
Use cross-referencing whenever you can.
There are two main citation styles: author-year and numeric.
- The author-year style will take care of the authors' names automatically, regardless of how many authors there are. If you want the names to appear at the end of a sentence, write I have a dream \citep{king1963} which would render I have a dream (King, 1963). Do not write I have a dream \cite{king1963} which would render I have a dream King (1963). However, if you want to names to appear at the beginning of a sentence, write \cite{king1963} has a dream which would render King (1963) has a dream. Do not write \citep{king1963} has a dream which would render (King, 1963) has a dream.
- With the numerical style, if presenting the names is desirable, you need to explicitly write the authors' names, and add the citation right after the names. Use their last names only. Note that some last names have more than one word, e.g., de Koning, van Gogh, Van der Ven, Van de Walle, and Díaz de la Rubia.
  - When there is only one author, e.g., King, write King [34] has a dream.
  - When there are two authors, e.g., Lewis and Clark, write Lewis and Clark [44] returned to St. Louis on September 23, 1806.
  - When there are more than two authors, e.g., Weiss, Barish, and Thorne, write Weiss et al. [54] won the 2017 Nobel Prize in Physics.
- With the numberic style, if presenting the authors' names is not desirable, add the citation at the end of the sentence, e.g., I have a dream \cite{king1963}. which would render I have a dream [34]. An exception is when the author name is at the beginning of a sentence, e.g., King \cite{king1963} has a dream which renders King [34] has a dream. Sometimes the citation is a superscript, e.g., I have a dream \cite{king1963} may become I have a dream³⁴. In some cases, the superscript may be confused with the exponent, e.g., 2 \cite{obama2008} would render 2³⁵. In some other cases, the superscript is not desirable, e.g., our results are compared against those in Ref.\ \cite{obama2008} would render our results are compared against thost in Ref.³⁵. In these cases, write 2 [\citenum{obama2008}] and our results are compared against those in Ref.\ \citenum{obama2008}, which would render 2 [35] and our results are compared against those in Ref. 35, respectively.
- In either style, when you want to cite multiple references in the same place, write \cite{obama2008,king1963} instead of \cite{obama2008}\cite{king1963}.
When you mention a code/software (e.g., LAMMPS, VASP, MOOSE, Atomsk, OVITO, Paraview), double check if you need to cite a reference or references.
Some field-specific comments:
- Please read the wikipedia page on Miller index to understand different notations.
- There should be no space between numbers in the notation, i.e., it should be $[1\bar{1}0]$ and $\left<314\right>$ , instead of $[1 \bar{1} 0]$ and $\left<3 1 4\right>$ .
- If you use the full name of a chemical element, do not capitalize the first letter unless it is the first letter of a sentence, e.g., write we study iron instead of we study Iron. However, if you use the symbol of a chemical element, do capitalize the first letter, e.g., always write Fe instead of fe regardless of where it appears.
- For a compound, write the element's name alphabetically, e.g., write MoNbTa instead of NbTaMo or TaMoNb.
- For a non-stoichiometric compound, write the compositional ratios as subscripts, e.g., write Mo$_4$Nb$_3$Ta$_2$ instead of Mo4Nb3Ta2.

Figures

Every figure should be accompanied by a caption, which appears below the graphic. LaTeX provides several options to handle figures.

Say that you are writing a paper A for journal B and you want to use a figure that is modified or taken directly from a paper C in journal D. You should cite paper C and add a few words such as Reproduced with permission from Ref. [C]. Refer to the published work or instructions in journal B for the exact words. In addition, obtain permission from the copyright holder of that figure, which is most likely the publisher of journal D, to reuse the figure. Here are guidelines from Elsevier. Other publishers have their own guidelines.

There may be some scenarios in which you do not need to obtain permission. For example, the image or figure has been substantially modified. In this case, you still need to cite journal D. However, if you use a TEM or SEM image or photo, you need to obtain permission from the copyright holder even if you add in the caption that the image has been modified.

Another common mistake is that the letters/numbers contained in figures are too small. The rule of thumb is that the letters/numbers in figures should have the same font size as those in the main text. If they are too small, you can either enlarge the figure or increase the font size when making the figure.

In addition, adjust the legend's position so that it won't overlap with any curves or symbols.

Last but not least, use scientifically derived colour maps, as appropriate.

Tables

Like figures, every table should be accompanied by a caption too. But unlike figures, the caption appears above, not below, the tabulated content. Check this page for more on using tables in LaTeX.

In most journals, vertical lines are not allowed in a table, neither are most horizontal lines. Again, refer to recent papers in the journal and/or its instruction.

Reference list

The reference style differs greatly among journals. Read their instructions carefully. In LaTeX, there are two main ways to manage the reference list: BibTeX and non-BibTeX. I strongly recommend the former. With BibTeX, simply write these two lines at the end of the paper (but before \end{document}):

\bibliographystyle{unsrt}
\bibliography{ref}

which would require two files: unsrt.bst and ref.bib. Most likely the first file is provided by the journal. In practice, however, Overleaf can retrieve a lot of .bst files from its server, so you may only need to provide the file ref.bib.

If you want to cite a paper, e.g., this one, click on Cite, then choose Export citation to BibTeX. Then you will get a .bib file. Open it, copy its content, and add it to your ref.bib file. Then in your main text, write \cite{XU2019160} to cite it. Do this for all other references to cite all of them.

Alternatively, use reference management software. I use Zotero. Go to its website and install Zotero and Zotero Connector. When you read a paper in your browser and want to cite it, use the Zotero Connector to add the bibliographic information to Zotero, which should be already open. Read this page for more on Zotero. Then, in Zotero, select entries you want to export, right-click on them, choose Export Items, change Format to BibTeX, select Use Journal Abbreviation, then click on OK. The entries will be exported to a local .bib file. Open it, then copy and paste its content to your ref.bib file.

Double check the reference list for typos as if it were the main text. Pay attention to these :

Write $\left<110\right>$ and \{110\} instead of <110> and {110}.
Write dislocations in Mo and dilute Mg-based alloys instead of dislocations in mo and dilute mg-based alloys. Unfortunately, in the article title, most BibTeX styles automatically convert all uppercase letters to lowercase ones, except the very first letter. To enforce the usage of uppercase letters, add curly brackets around certain words/letters in your .bib file, e.g., dislocations in {Mo} or dislocations in {M}o.
If the page numbers have a range, use -- instead of -, e.g., 91--126.
Make sure that the special character(s) are properly used in authors' names.
Make sure that the greek letters appear correctly, e.g., $\alpha$ iron instead of a iron; another example is it should be {$\Sigma$}3 grain boundary instead of S3 grain boundary or $\sigma$3 grain boundary which would yield "σ3 grain boundary".
When necessary, use math mode, e.g., ($\bar{1}10$) instead of (-110).
In most cases, use abbreviated journal names, e.g., Acta Mater. instead of the full journal name, i.e., Acta Materialia. Check this webpage for the correct abbreviated journal names. Omit all articles (a, an, the) and prepositions (e.g., at, in, of, for, with). Also capitalize the first letter of each word. For example, write J. Chem. Phys., instead of The J. of Chem. Phys. or J. chem. phys. If you do want to use the full names, be sure to write Acta Materialia and The Journal of Chemical Physics instead of Acta materialia and The journal of chemical physics.
Make sure that any journal article has volume number, page number (or article number), and year. A common mistake made by Zotero (not by you! but it is your job to correc it) is that it collects the page number (starting from 1) when it should collect the article number. For example, the Zotero Connector would take the page number of this paper as 1-9 while it only has an article number 15016. The rule of thumb is to double check any page number range that starts from 1.
If you want to cite a paper that is in an open-access repository of e-prints such as arXiv, ChemRxiv, bioRxiv, engrXiv, or Preprints.org, please check if it has already been published in a peer-reviewed journal or conference proceeding. If yes, cite the peer-reviewed version.

Response to reviewers

A sample response to reviewer letter, which was used for one of my papers, can be found in this GitHub repository. A few suggestions:

Be respectful. Start each response by thanking the reviewer for his/her comment.
Respond to the (associate) editor's comments too, if any.
Refer to your submission as manuscript instead of paper because it is not a paper yet.
Highlight the changes made in both manuscript and response letter. In the response letter, describe the page number (and line number if applicable) or the section name/number where the changes are made.
Try to incorporate what is presented in the response letter into the manuscript. For example, if you prepared a new figure for the reviewer, include it in the manuscript as well. If you don't want to do that, explain the reason.

Name		Name	Last commit message	Last commit date
Latest commit History 51 Commits
.DS_Store		.DS_Store
README.md		README.md
response_to_reviewers_v1.docx		response_to_reviewers_v1.docx

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