Stochastic dynamics of molecular machine: it's nanomachine which is based on Nyquist theory

Abstract

A new model of actin myosin system named Stochastic Inclined Rods Model (SIRM), whose energy of motion is supplied from random noise (or thermal noise) and always moves to one direction, has been proposed. SIRM has a simple structure, which is composed of an inclined spring, a myosin head, and bundle of rods. In the SIRM, the energy of motion is supplied from random noise (or thermal noise) of water molecules generated through the heat energy of ATP hydrolysis. In an open and dissipative system, the myosin head works as a resonator of random noise, which accepts the energy through resonance. It is shown that the inclined rod and the spherical shape of G-actin are very important elements for the purpose of breaking the symmetry in the vibration of stochastic resonance (SR) and of generating a one directional motion. When the myosin head interacts with the spherical potential of G-actin, the trigonometric wave of stochastic resonance is distorted by the collision between the head and G-actin, and then it obliquely kicks the actin fiber by using the spring. It is thus shown that the inclined rod and the shape of the G-actin makes the SIRM move in one direction, even if the potentials between the myosin head and G-actin are perfectly symmetric.