My 1st Experience with Writing a Scientific Journal Article

For starters, I’ve been doing research under Dr. Meenakshi Dutt in the Chemical and Biochemical Engineering Department at Rutgers University since my sophomore year as an undergraduate student. (Here’s the new website, which I helped design.) She’s an amazing research advisor. I’ve learned so much from her about the process of doing research and presenting the research at conferences, in PowerPoint presentations and in poster presentations. She expects a lot from her research group, but at the same time, she understands that we have other obligations and lives outside of research. Because of her, and a few other amazing professors, I’ve decided to become a chemical engineering professor.

My project deals with simulating nanoparticles with polymers tethered to them — think hairy ping pong balls. They bounce around in a box and  since the “hairs” are attracted to each other, they form clusters. The application of this can range from bioimaging for diseases and disorder to forming nanomaterials to targeted drug delivery. The “hair” can change based on the particular desired function or application.

This project started in the fall of 2013. Then, my graduate mentor and I worked on deciding which virus capsid — which virus’s protein shell — is the most effective and versatile. Then we had to coarse grain it. We didn’t want to simulate every atom on this protein shell. It would be too computationally expensive for the time scales we were aiming for (a few picoseconds). So coarse graining is a method of combining atoms into a single “bead” with certain attractive and repulsive properties. These properties change based on which atoms are coarse grained together. Then we had to choose the right polymer and coarse grain that.

Fast forward about 2 months later. We were able to coarse grain everything. Now we had to simulate the hairy nanoparticle. The simulations took FOREVER. We were using an IBM bluegene supercomputer, but even then, it took me probably 6 months to run all of my initial simulations.

About a year into this project, as a junior, Dr. Dutt decided that we should also look at a different version of the “hair”. We were initially just looking at a “hair” being one type of polymer. But what if the “hair” was a co-polymer? What hydrophobic effects would we see? What clustering effects would we see? So another collaborator, and a pretty good friend of mine, joined this project. So her version of the project took about another few months or so to finish her simulations.

And around this time, we had been working on writing different codes in MATLAB to analyze all of our data. To see how the clusters actually look. Shape, size, etc. Analyzing the data took another few months. Now we had to find places to publish the papers, and we had to wait for the call for papers, to submit a manuscript. So the waiting for the call from a materials research paper took a few months, in which we worked on the manuscript.

Now I’m a senior. We got the call, wrote the manuscript, edited all of our many graphs and charts and pictures, and submitted the manuscript. And waited. A few months later, we got our revisions. With about a month to finish editing and submit the revision. Basically, they said that our definition of what a cluster was needed to be changed. That meant we had to start with our first code, in which we found the average cluster size and so on. That meant that that new code with the new clustering code took a few days to run. With some of my data, that code took about 48hrs per simulation data. I had 20 to get through. And only a regular laptop to work with, no supercomputer. Imagine how stressed I was with getting everything finished. And the editing of the manuscript. And the editing of the graphs and charts and pictures.

Thankfully we just made the deadline. And now, we wait some more. And hope and pray that the reviewers accept our revisions and don’t ask us to submit another revised manuscript.

This got me thinking though… is it a wonder that the scientific academic community is so cutthroat? If 3 years’ work can be useless based on reviewers’ of a journal, imagine a Ph.D student’s work?



About squishymaru

Master's student in chemical engineering with a B.S. in chemical engineering as well. Loves chemistry, math, increasing diversity in STEM, politics, and public health advocacy. Loves reading, writing, and being active -- mentally and physically.

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