Dynamic and Stochastic Properties of Molecular Systems: From Simple Liquids to Enzymes

Molecular dynamics method (MDM) supplies to the solution of fundamental contradiction between macroscopic irreversibility and microscopic reversibility with data which help to reveal the origin of stochastization in many-particle systems. The relation between dynamic memory time tm, fluctuation of energy dE and K-entropy (Lyapunov exponent) is treated. MDM is a method which retains Newtonian dynamics only at the times less than tm and carries out a statistical averaging over initial conditions along the trajectory run. Meaning of tm for real systems is related to the quantum uncertainty, which is always finite for any classical system and influence upon particle trajectories in a coarse-graining manner. Relaxation of kinetic energy to equilibrium state was studied by MDM for non-equilibrium strongly coupled plasmas. Two stages of relaxation were observed: initial fast non-Boltzmann oscillatory stage and further relatively slow Boltzmann relaxation. Violation of the microscopic reversibility principle in some enzymatic reactions is discussed.

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