Directed motion of periodically driven molecular motors: A graph-theoretical approach

Abstract

We propose a numerical algorithm for calculation of quantized directed motion of a stochastic system of interacting particles induced by periodic changes of control parameters on the graph of microstates. As a main application, we consider models of catenane molecular motors, which demonstrated the possibility of a similar control of directed motion of molecular components. We show that our algorithm allows one to calculate the motion of a system in the space of its microstates even when the considered phase space is combinatorially large (∼1 × 10 6 microscopic states). Several general observations are made about the structure of the phase diagram of the systems studied, which may be used for rational design and efficient control of new generations of molecular motors.

Libra: An open-Source “methodology discovery” library for quantum and classical dynamics simulations

“…In particular, the routines for finding minimum spanning tree of a graph and ring‐search procedure are implemented. The former had been used previously in analyzing the fluctuation‐induced directional motion in models of molecular machines . The latter is used in the “libchemobjects” module of the present code for automatic assignment of atom types in the functional group determination and in the force field setup procedures.…”