A recently developed implicit membrane model (IMM1) is supplemented with a Gouy-Chapman term describing counterion-screened electrostatic interactions of a solute with negatively charged membrane lipids. The new model is tested on peptides that bind to anionic membranes. Pentalysine binds just outside the plane of negative charge, whereas Lys-Phe peptides insert their aromatic rings into the hy...

We introduce an implicit solvent Molecular Dynamics approach for calculating ionic fluxes through narrow nanopores and transmembrane channels. The method relies on a dual-control-volume grand-canonical molecular dynamics (DCV-GCMD) simulation and the analytical solution for the electrostatic potential inside a cylindrical nanopore recently obtained by Levin [Europhys. Lett. 76, 163 (2006)]. The...

Molecular dynamics simulations with an implicit model of the solvent have allowed to investigate the reversible folding of structured peptides. For a 20-residue antiparallel beta-sheet peptide, the simulation results have revealed multiple folding pathways. Moreover, the conformational heterogeneity of the denatured state has been shown to originate from high enthalpy, high entropy basins with ...

Developing accurate solvers for the Poisson Boltzmann (PB) model is the first step to make the PB model suitable for implicit solvent simulation. Reducing the grid size influence on the performance of the solver benefits to increasing the speed of solver and providing accurate electrostatics analysis for solvated molecules. In this work, we explore the accurate coarse grid PB solver based on th...

Structure prediction and computational protein design should benefit from accurate solvent models. We have applied implicit solvent models to two problems that are central to this area. First, we performed sidechain placement for 29 proteins, using a solvent model that combines a screened Coulomb term with an Accessible Surface Area term (CASA model). With optimized parameters, the prediction q...

Previous DFT in vacuo studies on the conformational preferences for cellobiose showed that upon optimization the φ(H)-anti conformations were of lower energy than the syn forms. Upon optimization using an implicit solvation method, COSMO, the syn or observed form was still not predicted to be of lower energy than the φ(H)-anti form, even though optimization after addition of several explicit wa...

We have used systematic structure-based coarse graining to derive effective site-site potentials for a 10-site coarse-grained dimyristoylphosphatidylcholine (DMPC) lipid model and investigated their state point dependence. The potentials provide for the coarse-grained model the same site-site radial distribution functions, bond and angle distributions as those computed in atomistic simulations ...

We applied the single-replica multiple-state transition-interface sampling method to elucidate the equilibrium kinetic network of the 35-residue-fragment (HP-35) villin headpiece in implicit water at room temperature. Starting from the native Protein Data Bank structure, nine (meta)stable states of the system were identified, from which the kinetic network was built by sampling pathways between...

A mean-field approach to the electrostatics for solutes in electrolyte solution is revisited and rigorously justified. In this approach, an electrostatic free energy functional is constructed that depends solely on the local ionic concentrations. The unique set of such concentrations that minimize this free energy are given by the usual Boltzmann distributions through the electrostatic potentia...

This paper implements efficient techniques for cloth simulation in the area of cloth model, numerical integration, collision detection and response. The whole procedure combines the accurate bending model with implicit integration and collision response. Collision response remains a serious difficulty in cloth simulation, especially with implicit integration. We propose a general scheme that in...