Fig. 1: Molecular motor model with nonequilibrium simulation setup.
From: Simulating a chemically fueled molecular motor with nonequilibrium molecular dynamics
Top: a tetrahedral cluster formed from two types of particles can transition between filled tetrahedral cluster (FTC) and empty tetrahedral cluster (ETC) plus central particle (C) states while executing Langevin dynamics at a fixed temperature. Chemical potentials for each species (μFTC, μETC, and μC) are regulated with grand canonical Monte Carlo chemostats to drive the reaction away from equilibrium. Bottom: a simulation cell containing a model motor driven at the nonequilibrium steady state fuel concentrations. The motor is constrained to occupy the inner box (shaded yellow) through a Lennard–Jones wall potential while the GCMC chemostats insert and remove FTC, ETC, and C only from the space between the inner and outer boxes (white background). FTC, ETC, and C do not experience the Lennard–Jones wall potential and freely diffuse between the inner and outer boxes. The motor consists of a small shuttling ring (green particles) that diffuses around a larger ring composed of two shuttling-ring–binding sites (orange particles), each adjacent to a three-particle catalytic site (white particles). The remainder of the larger ring is made of inert particles (black) that only have mildly repulsive interactions with other particles. The catalytic sites speed up the FTC → ETC + C decomposition due to attractions between white catalytic particles and the blue and red particles of FTC. Upon their escape, the red C particles can linger around the catalytic sites, blocking the shuttling ring and ultimately gating diffusion to generate net directed current.
