Solvent entropy is a force to consider in protein folding and protein design but is difficult to model. It is investigated here in the context of the hp model: Two types of residues, hydrophobic and hydrophilic, are modeled on a lattice. Nine chains and two- and three-dimensional simulations are compared. We show that considering solvent entropy alone, efficient folding of lattice chains (ident...

An ab initio MP2 vibrational Hamiltonian of HOD in an external electrostatic potential parametrized by the electric field and its gradient-tensor is constructed. By combining it with the fluctuating electric field induced by the D(2)O solvent obtained from molecular dynamics simulations, we calculate the infrared absorption of the O-H stretch. The resulting solvent shift and infrared line shape...

The deconstruction of cellulose is an essential step in the production of ethanol from lignocellulosic biomass. However, the presence of lignin hinders this process. Recently, a novel cosolvent based biomass pretreatment method called CELF (Cosolvent Enhanced Lignocellulosic Fractionation) which employs tetrahydrofuran (THF) in a single phase mixture with water, was found to be highly effective...

We performed molecular dynamics simulations on dipalmitoylphosphatidylcholine (DPPC)/dimethylsulfoxide (DMSO) system that has the same lipid:solvent weight ratio as in our previous simulation done on DPPC/water. We did not observe a large change in the size of DPPC membrane when the solvent was changed from water to DMSO. Also, we did not observe that a large number of DMSO molecules is permeat...

We present a direct numerical simulation method for investigating the dynamics of dispersed particles in a compressible solvent fluid. The validity of the simulation is examined by calculating the velocity relaxation of an impulsively forced spherical particle with a known analytical solution. The simulation also gives information about the fluid motion, which provides some insight into the par...

We report Monte Carlo simulations of phase behavior of colloidal suspensions with near-critical binary solvents using effective pair potentials from experiments. At off-critical solvent composition, the calculated phase diagram agrees well with measurements of the experimental system, indicating that many-body effects are limited. Close to the critical composition, however, agreement between ex...

The physiologicomathematical model with eight compartments described allows the simulation of the absorbtion, distribution, biotransformation, excretion of an organic solvent, and the kinetics of its metabolites. The usual compartments of the human organism (vessel rich group, muscle group, and fat group) are integrated with the lungs, the metabolising tissues, and three other compartments deal...

Fluctuating hydrodynamics (FHD) is a general framework of mesoscopic modeling and simulation based on conservational laws and constitutive equations of linear and nonlinear responses. However, explicit representation of electrical forces in FHD has yet to appear. In this work, we devised an Ansatz for the dynamics of dipole moment densities that is linked with the Poisson equation of the electr...