Current advisor: Jay W. Ponder, PhD
Undergraduate university: SUNY-Buffalo
To fully characterize the function of proteins and biomolecules, we must understand both the static structure and time evolution dynamics of the protein molecule. As more structures are discovered by experimentalists there is an ever growing need for accurate molecular dynamics simulations. In principle, if we know the force on each atom that comprise the biomolecule, we can evolve the system in time and “see” how the protein behaves as a function of time. However, to calculate forces accurately, we must have a physics based force field that captures the quantum mechanical nature of atoms. HIPPO, which stands for Hydrogen-like Interatomic Polarizable POtential, is a physics based biomolecular force field designed to capture these quantum mechanical effects while still having the computational speed of a classical force field. In our lab, we continue to develop the HIPPO force field so that we will eventually be able to use them to study biomolecules.
Chung MKJ, Wang Z, Rackers JA, Ponder JW. 2022 Classical Exchange Polarization: An Anisotropic Variable Polarizability Model. J Phys Chem B, (epub ahead of print):.
Ward MD, Zimmerman MI, Meller A, Chung M, Swamidass SJ, Bowman GR. 2021 Deep learning the structural determinants of protein biochemical properties by comparing structural ensembles with DiffNets. Nat Commun, 12(1):3023.