(525f) Calculating Entropy Production with Nonequilibrium Molecular Dynamics

A system with net flows of mass or energy is not in equilibrium, a common feature of industrial and biological systems. These flows can come from many sources: heat baths at different temperatures, moving boundaries, imposed external torques or forces, inflows or outflows of mass, hydrodynamic flows, electric or magnetic coupling---the list is endless. To study nonequilibrium systems with molecular simulations requires the development of methods to model the particular mechanism behind the nonequilibrium behavior.

In this talk I will present a method for treating chemical nonequilibrium in molecular dynamics simulations. By introducing grand canonical Monte Carlo chemostats for reactants and products, the concentrations of species undergoing reactions can be held away from their thermodynamic equilibrium. I will also present a method for calculating the entropy produced in this nonequilibrium chemical state. Entropy production is a necessary component in thermodynamic uncertainty relationships, which bound the precision of a system based on the entropy produced. In this way I can compare how close a nonequilibrium system is to thermodynamic bounds.

I will demonstrate these methods by simulating a model synthetic molecular motor. By holding the system at a high concentration of fuel and low concentration of waste, away from equilibrium concentrations, the motor has a continuous supply of free energy. In the presence of this free energy supply the motor produces mechanical work. By calculating the precision of this work and the entropy produced in the system, I find that the motor model operates far from thermodynamic limits. These results suggest that the performance of synthetic motors can be greatly improved and demonstrate the power of the nonequilibrium simulation method and entropy production calculation.