Breaking time-reversal symmetry for ratchet models of molecular machines.

Abstract

Biomolecular machines transduce free energy from one form to another to fulfill many important roles inside cells, with dissipation required to achieve directed progress. We investigate how to break time-reversal symmetry at a given dissipation cost by using deterministic protocols to drive systems over sawtooth potentials, which have frequently been used to model molecular machines as ratchets. Time asymmetry increases for sawtooth potentials with higher barriers and for driving potentials of intermediate width. For systems driven over a sawtooth potential according to a protocol, we find that symmetric sawtooths maximize time asymmetry, whereas earlier work examining ratchet models of molecular machines required asymmetric sawtooth potentials to achieve directed behavior. This distinction arises because deterministically driven machines are externally provided with direction, whereas autonomous machines must generate directed behavior.