Dynamics of ions in the selectivity filter of the KcsA channel

The statistical and dynamical properties of ions in the selectivity filter of the KcsA ion channel are considered on the basis of molecular dynamics (MD) simulations of the KcsA protein embedded in a lipid membrane surrounded by an ionic solution. A new approach to the derivation of a Brownian dynamics (BD) model of ion permeation through the filter is discussed, based on unbiased MD simulations. It is shown that depending on additional assumptions, ion’s dynamics can be described either by under-damped Langevin equation with constant damping and white noise or by Langevin equation with a fractional memory kernel. A comparison of the potential of the mean force derived from unbiased MD simulations with the potential produced by the umbrella sampling method demonstrates significant differences in these potentials. The origin of these differences is an open question that requires further clarifications

Simulations moléculaires et leur analyse

Ce cours explique les concepts de la simulation moléculaire et son utilisation pour l'étude de la dynamique des macromolécules biologiques, telle qu'elle est étudiée par diffusion de neutrons. La complémentarité des deux techniques permet de comprendre des détails de la dynamique d'un système moléculaire complexe qui sont inaccessibles aux expériences seules. On peut ainsi mieux interpréter les données expérimentales et également développer des modèles physiques qui donnent une vue cohérente des observations. Ce dernier point est illustré par une étude du lysozyme en solution. En utilisant des méthodes provenant du traitement numérique du signal, on peut extraire des spectres de temps de relaxation qui illustrent que la dynamique des protéines est caractérisée par des processus de relaxation multi-échelles

Inelastic neutron scattering from classical systems

International audienceThe scattering law for inelastic neutron scattering from classical systems is derived by treating the wavefunctions of the scattering system in the stationary phase approximation and taking the classical limit of the Wigner phase space distribution function. In this way recoil effects are properly accounted for and the scattering law fulfils the relation of detailed balance. It is shown why classical van Hove correlation functions do not properly describe neutron scattering from classical systems

Quasielastic neutron scattering and relaxation processes in proteins: analytical and simulation-based models

First published as an Advance Article on the web 1st June 2005 The present article gives an overview of analytical and simulation approaches to describe the relaxation dynamics of proteins. Particularly emphasised are recent developments of theoretical models, such as fractional Brownian dynamics. The latter connects dynamical events seen on the pico- to nanoscond time scale, accessible to quasielastic neutron scattering, and functional dynamics of proteins on much longer time scales. I