Describing protein folding kinetics by molecular dynamics simulations.1.theory

Article Abstract:

A rigorous derivation of formulas for the computation of transition probabilities from molecular dynamics data from Boltzmann weighted conformations as starting states for microcanonical simulations is presented as a way to study the kinetics of protein folding in the context of a Markov chain. The results revealed that one must examine temporal behavior on progressively longer time scales and look for convergence with respect to a number of properties before believing in an ability to predict long time behavior based on the simulations.

Simulation methods, Simulation, Dynamics, Dynamics (Mechanics)

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Interfacial fluctuations of block copolymers: a coarse-grain molecular dynamics simulations study

Article Abstract:

A coarse-grain molecular dynamics simulations study was carried out to comprehend the undulations and thickness fluctuations of a model block copolymer bilayer. The results from simulation shows that line edge roughness could be reduced by raising the Flory-Huggins parameter or addition of strong specific interactions at block interface.

Science & research, Research, Molecular dynamics, Structure, Chemical properties, Copolymers, Lithography (Circuit fabrication)

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Describing protein folding kinetics by molecular dynamics simulations .2.example applications to alanine dipeptide and a beta-hairpin peptide

Article Abstract:

An approach is developed to support the interpretation of molecular dynamics trajectories toward understanding of peptide folding thermodynamics and kinetics in the context of Markov modeling. The above formula is applied in two example systems, namely, an alanine dipeptide in a vacuum and the beta-hairpin from protein G in water.

Peptides, Matter, Kinetic theory of, Kinetic theory

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