About me

I am a research associate in the Computational Chemistry and Biophysics group of Professor Martin Karplus at Harvard University. My current research is, broadly, the study and application of simulation techniques for understanding protein folding and protein conformational transitions. On the theoretical end, I am involved in the development and computer implementation of free energy simulation methods for biomolecules, which serve to make a theoretically rigorous connection between simulation and experimental measurements (such as dissociation and rate constants) with an emphasis on large proteins. Some of the particular proteins - "molecular machines" - to which I have applied these methods include Myosins and the ClpX degradation complex. A recent project focuses on the in silico design of stapled peptide inhibitors for the EmrE bacterial drug efflux pump in the SMR family, which is motivated by a growing need for new antimicrobials in medicine.I am also a developer of the Chemistry at HARvard Molecular Mechanics (www.CHARMM.org) biomolecular simulation program, in which my simulation methods are implemented, and a co-administrator of the CHARMM Development Project at Harvard.I have a broad interest in numerical methods for the simulation of continuum problems (e.g. elliptic PDEs for incompressible fluid flow). The topic of my doctoral dissertation was numerical simulations of laminar-turbulent transition in boundary layers under the direction of Professor Ugo Piomelli.