Molecular simulation is used to elucidate hydrophobic interaction at atmospheric pressure where liquid water between apolar walls is metastable with respect to capillary evaporation. The steep increase of the estimated activation barrier of evaporation with surface–surface separation explains the apparent stability of the liquid at distances more than an order of magnitude below the thermodynam...

We performed a detailed molecular dynamics study of the interfacial structure of aqueous solutions of 1-butyl-3-methylimidazolium tetrafluoroborate in order to explain the anomalous dependence of the surface tension on concentration. At low concentrations the surface tension decreases with concentration. At higher concentrations the surface becomes saturated; a plateau is observed in simulation...

We incorporate the Poisson-Boltzmann (PB) theory of electrostatics into our variational implicit-solvent model (VISM) for the solvation of charged molecules in an aqueous solvent. In order to numerically relax the VISM free-energy functional by our level-set method, we develop highly accurate methods for solving the dielectric PB equation and for computing the dielectric boundary force. We also...

Implicit solvent-based methods play an increasingly important role in molecular modeling of biomolecular structure and dynamics. Recent methodological developments have mainly focused on the extension of the generalized Born (GB) formalism for variable dielectric environments and accurate treatment of nonpolar solvation. Extensive efforts in parameterization of GB models and implicit solvent fo...

Theories of solvation free energies often involve electrostatic potentials at the position of a solute charge. Simulation calculations that apply cutoffs and periodic boundary conditions based on molecular centers result in centerdependent contributions to electrostatic energies due to a systematic sorting of charges in radial shells. This sorting of charges induces a surface-charge density at ...

Systems in which particles can self-assemble into mono-or bilayers can form variety of stable and metastable structures on a nanometer length scale. For this reason confinement has a particularly strong effect on such systems. We discuss in some detail effects of confinement on lamellar and cubic phases with double-diamond structure. Structural deformations in slit geometry are described for la...

We discuss an application of a density functional approach to describe a bilayer, or a simplified model of a membrane, that is built of tethered chain molecules. The bilayer integrity is maintained by tethering chain particles to two common sheets. We study the structure of a two-component mixture in contact with the bilayer, as well as the solvation force acting between two bilayers, immersed ...

A Yukawa-field approximation of the electrostatic free energy of a molecular solvation system with an implicit or continuum solvent is constructed. It is argued through the analysis of model molecular systems with spherically symmetric geometries that such an approximation is rational. The construction extends non-trivially that of the Coulomb-field approximation which serves as a basis of the ...

Recently, the combination of state-of-the-art molecular mechanical force fields with continuum solvation models enables us to make relatively accurate predictions of both structures and free energies for macromolecules from molecular dynamics trajectories. The first part of this review is focused on the history and basic theory of free energy calculations based on physically effective energy fu...

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