Perspective on Integrative Simulations of Bioenergetic Domains

Abstract

Bioenergetic processes in cells, such as photosynthesis or respiration, integrate so many time and length scales that they hinder the simulation of energy conversion with a mere single level of theory. Just like the myriad of experimental techniques required to examine each level of organization, an array of overlapping computational techniques is necessary to model energy conversion. Here, a perspective is presented on recent efforts for modeling bioenergetic phenomena with focus on molecular dynamics simulations and its variants as a primary method. An overview of the various classical, quantum mechanical, enhanced sampling, coarse-grained, Brownian dynamics, and Monte-Carlo methods is presented. Example applications discussed include multi- scale simulations of membrane-wide electron transport, rate kinetics of ATP turnover from electrochemical gradients and finally, integrative modeling of the chromatophore, a photosynthetic pseudo-organelle.