Publications by authors named "B Le Roux"
Article Synopsis
- Molecular dynamics (MD) simulations are essential for studying biological membranes, but their complexity and chemical diversity pose challenges, especially for low-abundance lipids.
- Using a large simulation can help, but it becomes costly and impractical, particularly when low-abundance lipids strongly interact with proteins.
- To address this, a new hybrid approach called non-equilibrium Monte Carlo (neMD-MC) is proposed, allowing for lipid swapping between the simulation and a thermodynamic reservoir to maintain an equilibrium state and desired lipid composition.
Many voltage-gated potassium (Kv) channels display a time-dependent phenomenon called C-type inactivation, whereby prolonged activation by voltage leads to the inhibition of ionic conduction, a process that involves a conformational change at the selectivity filter toward a non-conductive state. Recently, a high-resolution structure of a strongly inactivated triple-mutant channel kv1.2-kv2.
View Article and Find Full Text PDFSince its inception nearly a half century ago, CHARMM has been playing a central role in computational biochemistry and biophysics. Commensurate with the developments in experimental research and advances in computer hardware, the range of methods and applicability of CHARMM have also grown. This review summarizes major developments that occurred after 2009 when the last review of CHARMM was published.
View Article and Find Full Text PDFArticle Synopsis
- The Smoluchowski-Kramers treatment is a common framework for calculating the permeability coefficient of molecules, relying on the potential of mean force and position-dependent diffusivity.
- Current methods to measure these factors, particularly position-dependent diffusivity, are estimates and do not account for memory effects along reaction coordinates, necessitating alternative approaches for better accuracy.
- Using Green-Kubo linear response theory, the study develops new expressions for the permeability coefficient and compares them through stochastic simulations and molecular dynamics, particularly focusing on water's permeation through lipid bilayers.