Ergodic pumping: A mechanism to drive biomolecular conformation changes

We propose that a significant contribution to the power stroke of myosin and similar conformation changes in other biomolecules is the pressure of a single molecule (e.g. a phosphate ion) expanding a trap, a mechanism we call “ergodic pumping”. We demonstrate the principle with a toy computer model and discuss the mathematics governing the evolution of slow degrees of freedom in large Hamiltonian systems. We indicate in detail how the mechanism could fit with known features of the myosin cycle. Many other biomolecular conformation changes could be driven in part by ergodic pumping. We suggest the use of ergodic pumping as a design principle in nanobiotechnology.