Unveiling molecular mechanism underlying inhibition of human islet amyloid polypeptide fibrillation by benzene carboxylic acid-peptide conjugate

Journal of Molecular Liquids, Journal Year: 2024, Volume and Issue: 416, P. 126426 - 126426

Published: Nov. 7, 2024

Language: Английский

Nonequilibrium Molecular Dynamics Method to Generate Poiseuille-Like Flow between Lipid Bilayers

Journal of Chemical Theory and Computation, Journal Year: 2024, Volume and Issue: 20(22), P. 10199 - 10208

Published: Nov. 11, 2024

There are various flows inside and outside cells in vivo. Nonequilibrium molecular dynamics (NEMD) simulation is a useful tool for understanding the effects of these on biomolecules. We propose an NEMD method to generate Poiseuille-like flow between lipid bilayers. extended conventional equilibrium MD produce by adding constant external force terms water molecules. Using Lagrange multiplier method, center mass bilayer constrained so that does not sweep away bilayer, but individual molecules fluctuate. The temperature system controlled properly solution membrane using Nosé-Hoover thermostat. found velocity increases linearly as applied term increases. It possible estimate appropriate value acceleration with arbitrary this proportional relation once single short performed. also two bilayers slower than analytical Navier-Stokes equations rigid parallel plates due interactions membrane. This can be only membranes soft surfaces generally.

Language: Английский

Simulation study of solvent effect on competitive degradation of aggregation of homo- and hetero- amyloid-β dimers

Journal of Molecular Liquids, Journal Year: 2024, Volume and Issue: unknown, P. 126658 - 126658

Published: Dec. 1, 2024

Language: Английский