A statistical thermodynamic development is given of a new implicit solvent model that avoids the traditional system size limitations of computer simulation of macromolecular solutions with periodic boundary conditions. This implicit solvent model is based upon the quasi-chemical approach, distinct from the common integral equation trunk of the theory of liquid solutions. The idea is geometrical...

Chemical and thermodynamic equilibrium of multiple states is a fundamental phenomenon in biology systems and has been the focus of many experimental and computational studies. This work presents a simulation method to directly study the equilibrium of multiple states. This method constructs a virtual mixture of multiple states (VMMS) to sample the conformational space of all chemical states sim...

The effect of reduced dielectric environments on the conformational sampling of DNA was examined through molecular dynamics simulations. Different dielectric environments were used to model one aspect of cellular environments. Implicit solvent based on the Generalized Born methodology was used to reflect different dielectric environments in the simulations. The simulation results show a tendenc...

The heat capacity has played a major role in relating microscopic and macroscopic properties of proteins and their disorder-order phase transition of folding. Its calculation by atomistic simulation methods remains a significant challenge due to the complex and dynamic nature of protein structures, their solvent environment, and configurational averaging. To better understand these factors on c...

We introduce a thermostat based on fluctuating hydrodynamics for dynamic simulations of implicit-solvent coarse-grained models of lipid bilayer membranes. We show our fluctuating hydrodynamics approach captures interesting correlations in the dynamics of lipid bilayer membranes that are missing in simulations performed using standard Langevin dynamics. Our momentum conserving thermostat account...

The correct representation of solute-water interactions is essential for the accurate simulation of most biological phenomena. Several highly accurate quantum methods are available to deal with solvation by using both implicit and explicit solvents. So far, however, most evaluations of those methods were based on a single conformation, which neglects solute entropy. Here, we present the first t...

The distance-resolved effective interaction between two colloidal particles in a subcritical solvent is explored both by an explicit and implicit modeling. An implicit solvent approach based on a simple thermodynamic interface model is tested against grand-canonical Monte Carlo computer simulations using explicit Lennard-Jones solvent molecules. Close to liquid-gas coexistence, a joint gas bubb...

Discrete nature of water plays critical role in protein folding and thermodynamics. Explicit all-atom modeling of solvent severely limits the length and time scales of molecular dynamics simulations of protein. In this project, we evaluated accuracy and computational efficiency of four different solvent models, all-atom solvent models ( SPC/E and TIP3P ), Generalized Born Implicit Solvent, and ...

Intermediate filaments, in addition to microtubules and microfilaments, are one of the three major components of the cytoskeleton in eukaryotic cells, and play an important role in mechanotransduction as well as in providing mechanical stability to cells at large stretch. The molecular structures, mechanical and dynamical properties of the intermediate filament basic building blocks, the dimer ...