Computer-Aided Understanding of Perturbations in Soft Matter Systems

Abstract

This dissertation aims to advance the fundamental knowledge on the structure and dynamics of condensed matter, focusing on systems relevant to emerging problems in biotechnology and energy. We aim to do this using tools and techniques derived from statistical mechanics with the aid of computer simulations, and when appropriate, combined with principles from experimental science.

In the first part, we study the effects of solution composition on the electrochemical response of a double layer capacitor using electrical impedance spectroscopy measurements and molecular dynamics simulations in a constant potential ensemble. We find that capacitance first increases with ion concentration following its expected ideal solution behavior but decreases upon approaching the pure ionic liquid limit.

In the second part, we use atomistic replica-exchange molecular dynamics simulations and thermodynamic analysis to investigate the effects of ionic liquid-induced perturbations on the folding/unfolding thermodynamics of the Trp-cage miniprotein, and compare our findings to circular dichroism measurements. We find that ionic liquid-induced denaturation resembles cold unfolding, where unfolded states are populated by compact, partially folded structures in which elements of the secondary structure are conserved, while the tertiary structure is disrupted.

In the third part, we perform a fully atomistic computational study of Trp-cage in explicit water, and construct the complete stability diagram in the (P,T) plane. At ambient temperature, we find that application of pressure shifts the equilibrium of conformational states towards denaturation. Below 250K, the stability of the native fold depends non-monotonically upon pressure. Our simulations also show while cold unfolding and thermal denaturation mechanisms differ significantly at ambient pressure, they exhibit progressive similarity at elevated pressures.

In the final part, we consider three commonly used molecular water models (ST2, TIP4P/2005, and TIP5P) that support the existence of the metastable liquid-liquid transition. We demonstrate that a corresponding-states-like rescaling of pressure and temperature results in a significant degree of universality in the pattern of thermodynamic response function extrema. We also report an intriguing correlation between the location of the liquid-liquid critical point, the density extrema locus, and the liquid-vapor stability limit, and demonstrate a similar correlation for two theoretical models.