About me

I am a research scientist in the department of  Chemistry and Chemical Biology at Harvard University.  Until recently, I was affiliated with the group of the late Professor Martin Karplus, where I performed and co-directed research on a universal influenza vaccine.  My main research interests are the development and application of molecular simulation methods for understanding protein dynamics, with emphasis on large scale conformational transitions.  On the theoretical front, I develop and implement classical molecular dynamics and free energy simulation methods for biomolecules, which serve to make a 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.  Some applied ongoing projects involve in silico design of peptide inhibitors for bacterial drug efflux pumps in the SMR family, which is motivated by a growing need for new antimicrobials in health and medicine, and of peptide checkpoint blockade inhibitors for immuno-oncology.  I am also a developer of the Chemistry at HARvard Molecular Mechanics (www.CHARMM.org) biomolecular simulation program, in which some of my simulation methods are implemented, and a former 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) and in theoretical immunology.  The topic of my doctoral dissertation was numerical simulations of laminar-turbulent transition in boundary layers.