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: