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I'm a PhD student and I want to start writing my research paper on chemistry modeling. I don't know how to organize my ideas or how to highlight my results.

I'm looking for a strategy to follow, and even though I've been reading a lot of papers about my topic, I still don't get the starting point.

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    en.wikipedia.org/wiki/IMRAD have a look here, it might help. The IMRAD structure is widely used for scientific publications.
    – Sursula
    Jul 5, 2023 at 8:45
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    A Ph.D. student often has an advisor to ask about such questions.
    – GEdgar
    Jul 7, 2023 at 10:27
  • Start by writing a bullet point sentence for each paragraph summarizing in plain language what you want to say in it.
    – mavzolej
    Jul 8, 2023 at 18:06
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    If certain things in your paper took you significant time to understand, and you were not able to find anywhere a clear explanation of those, add this explanation to your paper. If it's too long, add it to appendix. That's helpful for readers and also leads to more citations.
    – mavzolej
    Jul 8, 2023 at 18:09

5 Answers 5

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Congratulations on getting a publishable result!

When you're starting to write a paper, especially if you don't have a lot of experience with manuscript preparation, anything you can do to get past the blank page and start getting text down can help.

You've been reading a lot of related papers. Do you have any target journals picked out for this publication yet? Have you been reading papers from those journals? If you look at a few examples from your target journals, you can get a sense of the basic structure and organization they use. Put those section headings into your document. They will likely be Introduction, Methods, Results, and Discussion, but this can vary. Each section answers specific questions.

The first section to fill out is the Methods. What did you do? How could someone else replicate what you did?

Then fill out Results. What did you find out? What was significant, and what was not?

Now you are ready to write the introduction: What context would the reader need to understand why you picked this research question? Why was your research question important, what differentiates your strategy from other people's, and what was your contribution?

You can now write the Discussion, calling back to the context you established for your research question in the Introduction. Make specific references to your results and discuss what they mean in a more "big picture" way.

Finally, you are ready to write the abstract. This should summarize the whole paper, telling the reader in one or two sentences each why the research is important, what you did, what you found, and what it means. Basically, use one or two sentences to summarize each section of your paper in order.

That's it!

One last piece of advice: Don't be afraid to get feedback early and often, even if it is from your fellow PhD students rather than from your PI. The less developed your paper is when you solicit feedback, the easier it is to change course.

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Beginning writers think of a paper as something that exists in their mind, and that the job of the writer is to 'download' it to paper via hands. This is not how it works. Writing is an iterative process, in which ideas are formed as you write them, and the writer moves from one draft to another, until it's good enough to send to the journal. So don't worry about perfection. Just keep doing drafts, and the paper will come to life, eventually.

Another thing that I think beginners miss is that the difficult part is usually just getting started, so I always advice my students to train themselves to start writing. This is achieved by putting a timer and promising yourself to work for say, 15 minutes. That time is usually short enough that you can avoid procrastination, but long enough to put something in writing. You then stop at 15 minutes, no matter if the writing is going well. You then force yourself to take a break and restart. Let's say you budgeted 2 hours of writing, that's 8 different times you have to force yourself to start. After a few days, your brain will be trained in the skill of starting to write.

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I'm assuming that your paper will have the following sections, more or less in that order (the state of the art can be at the beginning or end of papers depending on fields, and sometimes fused with the intro):

  • Introduction what cool work you did in your paper and why it's important
  • State of the Art what other people did that are similar/related, what you are basing your paper on
  • Methodology the steps you took to achieve your results and why you chose them - sometimes also includes what you expected
  • Results a straight description the actual results and if they matched your hypotheses
  • Discussion now that you discussed the results, how do you interpret them more in depth? what do they tell you about your initial hypothesis? what follow-up questions did they raise?
  • Exploration (optional) if they raised questions and you did more experiments, quick summary (method + results + mini discussion)
  • Conclusion summary of the cool work you did + some perspectives.

If this is your first paper, it will probably be the easiest to start by the methodology and results description. Goal is to describe what you did, some of why, and your results, which you should know at this point. Then, I would suggest writing jointly the state of the art and the discussion, to make sure you are not overlooking things. Questions raised by your results might have answers in the literature, and doing a back and forth between discussion and existing papers will help you build a stronger argument.

You should finish by the introduction and conclusion: as they are summaries of your overall paper and how it fits in the rest of the science, as well as a way for you to sell your ideas, it will be easier (especially as a PhD student) to do them once you already actually have a paper.

Then you can do an overall re-reading to make everything simpler to read.

Good luck and have fun!

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  • I really liked to work with this structure, where each section was one different latex file. Much easier to work ... and to rework for the second paper (or the first paper, resubmitted somewhere else :D ). I had the "rambling" section, which was equal to your "exploration". A lot of things put there, all related but all useless for the current paper...
    – EarlGrey
    Jul 7, 2023 at 9:58
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Your starting point is reading tonnes of papers about your topic and in the type of journals you're targeting. You're already to good start.


A research paper conveys a key message to target audience and highlights the key contribution to the body of knowledge. It is not as broad as a Thesis.

Hence, in drafting a research paper, one needs to figure out and be clear in their mind ... what's the message I'm putting out there, what's significant about the work done, what's the purpose.

In your instance as you've narrated, you've got ideas already. Storyboard them and write them down.
Your results, itemise them and write them down. Also, write how you went about getting the results you've gotten. Slowly, the research paper is taking shape. With more ingredients, the paper is 'cooked', ready your 'dishing'.

There're different structures for research papers across different fields. For chemistry modelling, you should broadly fall under the IMRaD model.

I'll talk a bit more on this, before then take a look for instance at this GEOS-Chem chemistry model v10 by Keller and Evans (2019).
They have a structure introducing their work, the method used, deep dive into the work, followed by discussion and then conclusion.

1) Introduction; 2) Methods; 3) Long-term simulation using the random; forest model; 4) Discussion; 5) Conclusions.

[Extract from IMRaD Wikipedia]
Introduction – Why was the study undertaken? What was the research question, the tested hypothesis or the purpose of the research? Methods – When, where, and how was the study done? What materials were used or who was included in the study groups (patients, etc.)? Results – What answer was found to the research question; what did the study find? Was the tested hypothesis true? Discussion – What might the answer imply and why does it matter? How does it fit in with what other researchers have found? What are the perspectives for future research?


Please note that some have literature review (related works) as part of Introduction or better still just after introduction and before methods.
The literature review is rapid or purposeful. It's different from systematic review. However, some chemistry modelling papers are actually chemistry modelling reviews in which case they might be systematic review (aligning with PRISMA) or narrative review or even rapid following the PRISMA-ScR.

Also, take note that in some fields, methodology covers not just the methods, but the philosophical underpinning, research approach and strategy, methods and data collection tools. See the research onion in Saunders et al. (2023), now in the 9th edition.
Saunders, M., Lewis, P., & Thornhill, A. (2023). Research Methods for Business Students. (9th ed.) Pearson

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Other answers give good advice on how to do this in general, I want to give some tips on how to do the practical thing. This is something I used to write all my papers. In my opinion, separating the task of thinking from the task of doing is essential in overcoming mental blocks. If I'm trying to think about the overall story of the paper or proper language while I write down the content, I get stuck.

I employ a two-step process: First, I write everything down that I can think of. Anything related to the paper, what I did, why this is good, why it is better than other papers, what the application is etc. Crucial for this step is to not think about whether those claims made are correct or even make sense. After this, I usually have a draft of a paper that comes close to the required pages but the content is probably 50% nonsense, the language is bad, the pictures look bad... So then you go to step two: Improving the content.

Now that there are some ideas on paper, it becomes much easier to get the actual paper that you want to write. Since judging content is simpler than creating content, I can now dissect everything I wrote. I find a lot of nonsense during this process, but some ideas stick and turn out to be good ones. It is also easier to judge the overall story from this, which helps to improve the structure. You do this a few times, filter out the bad stuff and keep the good stuff.

Two additional points: First, I like to get a bit tipsy to do the first part, but that is just me. Whatever helps you to produce a large amount of 'nonsense'. Second, an important skill is to not be afraid of reading your own text. This is something I struggled in the beginning of my PhD. Try to get over this, it is crucial for becoming good and fast.

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