An easy implementation of molecular mechanics and molecular dynamics simulation using a continuum solvent model is presented that is particularly suitable for biomolecular simulations. The computation of solvation forces is made using the linear Poisson-Boltzmann equation (polar contribution) and the solvent-accessible surface area approach (nonpolar contribution). The feasibility of the method...

Most chemistry and biochemistry occur in condensed media, in particular, aqueous solutions. Thus, the proper simulation of these processes has to take into account the solvent effects. Consequently, since the pioneer work of Born on ionic solvation, these solvent effects have been shown to be of fundamental importance for many chemical and biological processes and have then been receiving consi...

Conformations of a zwitterionic bilayer were sampled from a molecular dynamics simulation and their electrostatic properties analyzed by solution of the Poisson equation. These traditionally implicit electrostatic calculations were performed in the presence of varying amounts of explicit solvent to assess the magnitude of error introduced by a uniform dielectric description of water surrounding...

The adsorption of mixtures of alkyl thiol surfactants on the Au(111) surface as well as on icosahedral gold nanocrystals (NCs) was investigated by molecular simulation. We compared the molfraction of each surfactant type on the gold structure with the molfraction of each surfactant type in the surrounding bulk solvent. For alkyl thiol surfactants with 1 to 4 carbon atoms difference, we found th...

In this project I investigate the dynamics of the self-propelled motion of a polymer solvent droplet. Similar movement has been witnessed in a variety of situations. For example oil placed on glass substrate coated with Stearyl Trimethyl Ammonium ions exhibits this motion due to the chemical Marangoni effect. Here the droplet absorbs the hydrophobic molecules on the substrate leaving an absence...

In the previous paper expressions for the partial molar energy and entropy at infinite dilution have been derived based on the inhomogeneous forms of the energy equation and the correlation expansion for the entropy. These expressions are here applied to a series of solutes of varying size in dense hard-sphere and Lennard-Jones solvents, some of which serve as reference systems for comparison w...

A vinylogous series of highly dipolar merocyanines were designed to study their solvatochromism in a wide range of solvents including low-polarity alkanes. It has been revealed that the lower vinylogues indeed have negative solvatochromism in the full range of solvent polarities starting from n-hexane, while the hexamethinemerocyanine exhibits reversed solvatochromism. With the extreme ranges o...

We investigated the performance of the recently developed SPC/L model for liquid water, as a pure liquid, in binary mixtures with DMSO, and as a solvent model in a peptide folding simulation. Additionally, in order to test the compatibility with the GROMOS biomolecular force field, free energies of hydration of a set of representative compounds were computed. The results are compared to those f...

We report a numerical simulation for the phase diagram of a simple two-dimensional model, similar to the one proposed by Noro and Frenkel [J. Chem. Phys. 114, 2477 (2001)] for membrane proteins, but one that includes the role of the solvent. We first use Gibbs ensemble Monte Carlo simulations to determine the phase behavior of particles interacting via a square-well potential in two dimensions ...

The mutual entropic depletion force felt by two solute "big" hard spheres immersed in a binary mixture solvent of nonadditive "small" hard spheres is calculated as a function of the surface-to-surface distance by means of canonical Monte Carlo simulations and through a recently proposed rational-function approximation [R. Fantoni and A. Santos, Phys. Rev. E 84, 041201 (2011)]. Four representati...