Date of Award
Doctor of Philosophy (PhD)
The grand challenge of biophysics is to use the fundamental laws of physics to predict how biological molecules will move and interact. The atomistic HIPPO (Hydrogen-like Intermolecular Polarizable Potential) force field is meant to address this challenge. It does so by breaking down the intermolecular potential energy function of biomolecular interactions into physically meaningful components (electrostatics, polarization, dispersion, and exchangerepulsion) and using this function to drive molecular dynamics simulations. This force field is able to achieve accuracy within 1 kcal/mol for each component when compared with ab initio Symmetry Adapted Perturbation Theory calculations. HIPPO is capable of this accuracy because it introduces a model electron density on every atom in the molecular system. Since the model is built on first-principles physics, it is transferable from small model systems to bulk phase. In the first test case, the HIPPO force field for water was able to reproduce the experimental density, heat of vaporization and dielectric constant to within 1%. Importantly, HIPPO has been shown to be only 10% more computationally expensive than the widely-used AMOEBA force field, meaning that more accurate simulations of larger biological molecules are well within reach.
Chair and Committee
Jay W. Ponder
Garland Marshall, Gregory Bowman, Anders Carlsson, Li Yang,
Rackers, Joshua Andrew, "A Physics-Based Intermolecular Potential for Biomolecular Simulation" (2019). Arts & Sciences Electronic Theses and Dissertations. 1942.