UC San Diego

Molecules at temperatures above 0K are always in motion, translating, rotating, and undergoing conformational changes. In systems that are out of equilibrium, these motions often become more intense and complex, leading to interesting phenomena, including the existence of life. This dissertation presents theoretical and computational modeling for some of these phenomena. First, many enzymes appear to diffuse faster in the presence of their substrates and to drift along concentration gradients of their substrate, phenomena known respectively as enhanced enzyme diffusion and enzyme chemotaxis. Here, experimental findings and proposed mechanisms for these observations are critically reviewed, then we propose a kinematic and thermodynamic analysis to serve as a validity check for any mechanism that attributes enhanced enzyme diffusion to self-propulsion. Second, overcrowded alkene-based molecular motors, a class of synthetic small molecules designed for light-driven rotation of its rotor part relative to its stator part, exhibit fast rotation in the microsecond timescale. Here, the full rotation process is modeled by quantum surface-hopping molecular dynamics simulations coupled with classical molecular dynamics simulations. This study proposes a novel rotation pathway, as well as providing computational predictions for rotation rate and maximal power output. Encouraging agreement with experiments are found, after fitting critical forcefield parameters to reference quantum mechanical energy surfaces. In conclusion, these efforts contribute to better understanding of molecular motions out of equilibrium and how to conceptualize and model them.