Studying dynamics and solvation of small biomolecules and enzymes.

Advisor - Prof. Teresa Head-Gordon, Department of Bioengineering, University of California, Berkeley

Solvent Entropy Schematic

PhD Research:

  • Developing computational methods to analyze dynamics of biomolecules
  • Implemented codes in Fortran within existing simulation packages to enable calculations of dynamic observables
  • Developing an understanding of the influence of specific residue modification on protein function
  • Understanding the influence of solvent on biomolecule behavior
  • Developed scripts in python and matlab for determining observables from simulation data

Research Collaborations:

Studying entropic contributions to enzyme solvation using a polarizable force field [May 2016-June 2017]
Collaborators: Prof. Matthias Heyden, MSc. Viren Pattni, Max Planck Institut fur Kohlenforschung, Mulheim

  • Performed molecular dynamics simulations of Kemp Eliminase artificial enzymes and MMP enzyme using the AMOEBA polarizable force field
  • Analyzed the solvation entropy trends over evolved variants in Kemp Eliminase to explain solvent contribution to improved catalytic activity
  • Analyzed solvation around MMP active site with zinc cofactor, to understand influence of polarization and solvation in entropic contribution to MMP activitya

Studying small molecule dynamic modes via classical simulations [May 2015-January 2017]
Collaborators: Prof. Dominik Marx, MSc. Alexander Esser, Institute for Theoretical Chemistry, Ruhr University Bochum

  • Modified existing classical simulation approaches to compare with Ab-Initio Simulation approaches
  • Developed a formulation for localizing charges to allow mode decomposition
  • Obtained significantly improved agreement of classical simulations with Ab-Initio methods

Publications from these project led and contributed to:

Saurabh Belsare
Senior Scientist

Senior Scientist, Bioinformatics at Pacific Biosciences