Dec. 8 — The Blue Waters Graduate Fellowship was awarded to ten outstanding Ph.D. students in computational science. In this series we’re featuring brief introductions to who they are and what they’re trying to accomplish. This program serves to prepare the next generation of science researchers to solve the world’s problems. Follow along as we highlight these young researchers. Read more profiles here.
Tell me a little bit about yourself—where are you studying now, where did you do your undergrad, what was your major, etc.?
I’m currently a physics doctoral candidate at Arizona State University (ASU) and I work in ASU’s Center for Biological Physics. I studied at Cornell University as an undergraduate and M.Eng. student in the Department of Applied and Engineering Physics. My Masters project involved the implementation of radiation transport physics in an existing plasma simulation code based on the extended magnetohydrodynamics continuum model. I came to Arizona State to apply my experience in computational physics to the simulation and study of proteins and other biological macromolecules under the guidance of Professor Oliver Beckstein.
Tell me about your research—what are you trying/hoping to accomplish? What made you want to pursue this topic?
Proteins, such as membrane transporters or enzymes, are much like nanomachines that undergo structural changes—conformational transitions—between multiple states in order to perform chemical or mechanical work. These transitions are rare events that, due to the equilibrium sampling problem, are difficult to reproduce in equilibrium molecular dynamics (MD) simulation. The paradigm for studying these processes is the so-called structure-function connection; in principle, one should be able to infer a protein’s function (its dynamical structural changes) given information about its structure (its 3D “shape” and amino acid sequence). Given the enormous computational difficulty of simulating highly complex, heterogeneous biomacromolecules on sufficiently long time scale, the majority of my research is focused on the development of computational methods and software tools that can help to more effectively sample and quantify protein conformational motions and transitions. Although I have a very broad interest in pretty much all applications of physics-based approaches to science, I find the physics of biology to be especially intriguing: The physical and chemical processes underlying biomacromolecular dynamics take place at the mesoscale—there are too many degrees of freedom to describe them effectively with pen-and-paper approaches, yet they elude fully statistical descriptions that conventionally require many, many more degrees of freedom. Somehow, these mesoscale biological nanomachines leverage thermal fluctuations—much like miniature ratchets—so as to give rise to the processes essential to life. So, I’m not only drawn to the uniquely challenging nature of biomacromolecular systems, but I also find questions surrounding biological processes (and life!) fascinating in and of themselves.
So what was your process like getting involved with Blue Waters? What made you want to apply for this fellowship?
I actually came across the Blue Waters Graduate Fellowship program more by chance than intention; I received a forwarded email from my advisor about the upcoming application deadline. After taking a closer look at the program, I realized it was offering almost exactly the opportunity for which I had been looking. Since I was near the end of my doctoral studies, having already completed a satisfactory amount of research for my dissertation, there would be room for me to pursue more “risky” or difficult avenues of research. Not only was the Blue Waters Graduate fellowship offering very generous funding, it would also afford me a platform and the freedom to be able to pursue a computational project of my own design!
How will the ability to use Blue Waters impact your research?
Working with Blue Waters procures the obvious benefits of having access to a state-of-the-art supercomputer, though the machine provides a model platform—an ideal testbed—for the kind of algorithm development I plan to do and, therefore, offers a kind of convenience for me as a researcher that would be otherwise hard to find.
Would you have been able to do this kind of research on any other machine? Why or why not?
My fellowship project is focused on algorithm and method development, so the research could in principle be carried out on any machine. The development of the method(s) and code(s) essential to my project will nevertheless require extensive performance and correctness testing; the Blue Waters allocation that is provided by the fellowship enables this. Furthermore, my codes should, ideally, be able to effectively leverage the resources of modern HPC systems (i.e. their distributed nature, GPGPU processing, etc.)—indeed, production versions of the code would be used to perform large-scale simulations that efficiently the available resources of an HPC system. As such, Blue Waters serves as a fantastic platform for the carrying out the kind of research I will be doing!
What is the overall impact that your research will have on the science community and the world at large?
There is ever-growing research in mesoscopic systems, ranging from such diverse topics as the understanding of drug-binding kinetics in biophysics, to the study of ocean-atmosphere coupling in computational climate science, to the design and engineering of complex fluids for industry and consumer goods. Multi-physics modeling can enable and/or enhance the efficiency of the simulation of mesoscopic physical systems whose dynamics span many length and time scales; multiple, often disparate, physical models are combined so as to bridge the phenomena of interest, though the challenge lies in how to couple the models effectively. My project exemplifies a multi-physics approach that couples atomistic (N-body) and continuum simulations. In principle, my research has the potential to achieve a manifold impact. Firstly, my project may eventually result in a fully-working simulation code that can then be used to study biomolecular systems. Secondly, given that my research takes steps into the relatively young, but promising, territory of multi-physics simulation methods, there is an opportunity to contribute to the growing understanding of (un)effective approaches to and techniques for hybrid N-body/continuum simulation. Lastly—and, I believe, most importantly—the development of simulation methods is directly fruitful to understanding of the physical models we use and, therefore, the physical systems themselves. My project is thus also an opportunity to build domain knowledge and physical intuition (e.g. for the role of fluctuations and solvent dynamics in modulating protein function).
Is there anything else you’d like people to know about your research/fellowship?
A unique aspect of my proposed research is that it demands a synthesis of many ideas—fluid dynamics and continuum simulation, the theory of hydrodynamic fluctuations, classical molecular dynamics simulation, both equilibrium and nonequilibrium statistical mechanics, numerical algorithms for ordinary and partial differential equations, techniques in high performance computing, just to name a few broad concepts. The Blue Waters Graduate Fellowship provides me with an invaluable opportunity to integrate otherwise disparate ideas and knowledge, which is, for me, one of the most exciting aspects of scientific research and rewarding experiences in learning.