Abstract
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 t m , 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 t m and carries out a statistical averaging over initial conditions along the trajectory run. Meaning of t m 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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Keywords
- Lyapunov Exponent
- Molecular Dynamic Method
- Quantum Uncertainty
- Stochastic Property
- Velocity Autocorrelation Function
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Morozov, I.V., Norman, G.E., Stegailov, V.V. (2002). Dynamic and Stochastic Properties of Molecular Systems: From Simple Liquids to Enzymes. In: Sloot, P.M.A., Hoekstra, A.G., Tan, C.J.K., Dongarra, J.J. (eds) Computational Science — ICCS 2002. ICCS 2002. Lecture Notes in Computer Science, vol 2331. Springer, Berlin, Heidelberg. https://doi.org/10.1007/3-540-47789-6_120
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