Simulating a chemically fueled molecular motor with nonequilibrium molecular dynamics.

ABSTRACT: Most computer simulations of molecular dynamics take place under equilibrium conditions-in a closed, isolated system, or perhaps one held at constant temperature or pressure. Sometimes, extra tensions, shears, or temperature gradients are introduced to those simulations to probe one type of nonequilibrium response to external forces. Catalysts and molecular motors, however, function based on the nonequilibrium dynamics induced by a chemical reaction's thermodynamic driving force. In this scenario, simulations require chemostats capable of preserving the chemical concentrations of the nonequilibrium steady state. We develop such a dynamic scheme and use it to observe cycles of a particle-based classical model of a catenane-like molecular motor. Molecular motors are frequently modeled with d

SUBMITTER: Albaugh A 

PROVIDER: S-EPMC9033874 | biostudies-literature | 2022 Apr

REPOSITORIES: biostudies-literature