Pursuing the scholarship of a non-traditional scientific computing research in a discovery-dominant field, Promita’s dissertation included a research tool of a physical model of a polypeptide chain. One chapter tested how well it served as an instructional tool in a science museum. Promita received her PhD (2014) in Computer Science and Applications at Virginia Polytechnic Institute and State University.

A Computational Framework for Interacting with Physical Molecular Models of the Polypeptide Chain


Could you describe your dissertation topic to us? In what ways was your dissertation non-traditional/innovative in your field?

I am a seer and I see the world in terms of motion. My dissertation reflects that aspect of my thought process. That’s what you will see in your dissertations as well. If you are working on your vision, at some point your dissertation and its subsequent work will just become you. I know you all have it in you to bring your inner self out into more structured and analyzed form, which will then become your dissertation. Good luck! In my PhD dissertation, I have pointed out a new direction of exploration, a new field of study at the intersection of computational science, scientific experiments and accurate physical models. As an example of the unexplored area of study, I have built physical models for polypeptides that focus on the scientific unsolved problem of protein folding and its theory. I have designed and fabricated Peppytide (www.peppytides.org), the first mechanically flexible, scaled, physical model of the polypeptide chain that accurately demonstrates the molecular dynamics behind protein folding such as degrees of freedom on rotatable bonds, barriers to bond rotation, bond lengths and angles, and short- and long-range (nonbonding) interactions between amino acids. Reported in PNAS here and it is quite fun to read. Unlike most 3-D printed protein models, Peppytide features a backbone chain that can be folded or unfolded to make at-scale, all of the common protein secondary structure elements, such as alpha helices, beta sheets and turns, and small tertiary structures and protein motifs. See pictures and details of the model in action at the Peppytide website. Going further back in time, this work builds upon my master’s work on molecular dynamics in distributed grid computing and scientific computing, as well as my knack for dynamics of things. The point here is that, my PhD work didn’t just start with my PhD or my masters. It started in my thoughts, dreams and every waking moments before that, and slowly culminated into what it is today. Just be yourself. Because of its spatial relevance as well as the focus on precision models, my work caters to an entire range of audience from young students to scientists, where everyone finds some use out of these models at different levels of expertise. Amazingly, people are generally very intuitive with handling of any 3d object with ease whereas computers struggle to do so. It is here that these physical models become powerful and serve to complement computational models.

As you conceived to follow this path, what was the reaction of the key actors in your university (such as your supervisor, committee, department, other)? Did you receive any resistance?

There will always be resistance to new ideas. But if you are confident about your work, it ultimately shows through. It is not only about defending to your committee, the main challenge is to defend your work to the world. For that, you have to be able to articulate your work in very precise terms. This is hard work, but I am sure you will be able to do that if you see it through in your mind. You also need patience — the world needs time to get adjusted to new ideas. There were times when nobody believed that I could do what I was talking about. It sounded undoable and like fairy tales hand waving. Even before that it was hard for me even to put those mind-imagery into words. Years later, when I had built the model ultimately and people were able to play with it, they were like ‘Ah, I see now what you were talking about.’ Those are the moments we work for, don’t we?

How do you think your non-traditional dissertation helped you develop professional competencies and prepared you for academic/non-academic career prospects?

Over the last four years after my PhD, the scope of my work has widened. Besides working on the protein folding dynamics at nano-scale, I am now also working on precise models for brain that will focus on a scientific unsolved problem of the brain function. I hope it will prove to be as fascinating over time. My new field, Physical Scientific Computing, deals with accurate physical models and their temporal change and dynamics in space – and how that goes back and forth with traditional scientific computing as well as experimental data. People have started building on top of my work, which feels very rewarding as well.

Did you face any challenges regarding the evaluation of your dissertation (such as from the external examiner)?

At the beginning, yes. I changed many labs as well trying to get funding for my topic. It would have been easier to work on a well defined project in one of those labs, but I had my vision-bug to handle. Later, a committee of diverse backgrounds couldn’t see at the outset how any of this is ever connected to computer science or chemistry or biology or anything of scholarly importance, but they were encouraging. Few years later, everything fell into place into the dissertation, and at the end, my committee was quite excited with the outcome. But again, your dissertation is not the end, it is the beginning of a new work and has to find its place in world. So, your committee is the least of your worries. Try to think about how it will benefit the world. If it benefits people or a small subset of them, they will ultimately accept the significance of your work. See beyond your degree and committee and defense — see the world and its people and how your work fits in it. Yes, you can do it. There will be barriers. Let it not be a deterrent. If needed, you have to fight your battle.

What would you have done differently if you could do it all over again? What advice do you have for doctoral students who would like to produce a non-traditional dissertation?

When you do ground-breaking work, you have to protect your work. Keep a track of your work and accomplishments and date it well. There is of course arxiv and many, many other online resources and public repositories. Use them well and wisely. Document document document. Find grad students and post-docs who will be your future colleagues. Grow together and support each other in panels and conferences. Find good mentors who will help you get to your NEXT step.

Do you have additional comments?

I hope you feel encouraged to do your visionary work, and I wish you luck. Feel free to reach out to me if you have any questions. If interested, find more about my work at my homepage: http://people.cs.vt.edu/~promita9