The derivation and approximation of coarse-grained dynamics from Langevin dynamics

The derivation and approximation of coarse-grained dynamics from Langevin dynamics.

We present a derivation of a coarse-grained description, in the form of a generalized Langevin equation, from the Langevin dynamics model that describes the dynamics of bio-molecules. The focus is placed on the form of the memory kernel function, the colored noise, and the second fluctuation-dissipation theorem that connects them. Also presented is a hierarchy of approximations for the memory a...

Coarse Grained Molecular Dynamics

Kinetics of formation of bile salt micelles from coarse-grained Langevin dynamics simulations.

We examine the mechanism of formation of micelles of dihydroxy bile salts using a coarse-grained, implicit solvent model and Langevin dynamics simulations. We find that bile salt micelles primarily form via addition and removal of monomers, similarly to surfactants with typical head-tail molecular structures, and not via a two-stage mechanism - involving formation of oligomers and their subsequ...

Molecular Dynamics Simulations of Freezing Behavior of Pure Water and 14% Water-NaCl Mixture Using the Coarse-Grained Model

 We performed molecular dynamics simulations using the coarse-grained model to study the freezing behavior of pure water and 14% water-salt mixture in a wide range of temperatures for a very long time around 50 nanoseconds. For the salty water, an interface in nanoscale was used. For both systems, the f...

Simulated annealing using coarse grained classical dynamics: Smoluchowski dynamics in the Gaussian density approximation

A dynamical annealing algorithm for global optimization based on approximate solution of the Smoluchowski equation is presented. The equations of motion in the Gaussian density approximation are interpreted as a steepest descent quench on a time dependent effective potential energy surface. A relation between the convexity condition for the effective potential surface and the size of thermal fl...