block copolymer nano-micelles are especially important in cancer treatment because of their fine dimensions. in this article, three systems of amphiphilic copolymers with similar lengths and different ratios of the hydrophobic and hydrophilic chains are studied using implicit-solvent coarse-grained molecular dynamics simulations. the factor fphil is defined as the ratio of the number of hydroph...

We report the implementation of an atomistic Brownian dynamics simulation of proteins. A protein was described by united-atom model with AMBER91 force field. The solvent was treated by distance-dependent dielectric/surface area model. The computation time of the Brownian dynamics and the calculated results on structure and dynamics of 28-mer ββα fold peptide with the implicit solvent model were...

molecular dynamic simulation is a powerful method that monitors all variations in the atomic level in explicit solvent. by this method we can calculate many chemical and biochemical properties of large scale biological systems. in this work all-atom molecular dynamics simulation of polyalanine (pa) was investigated in the presence of 0.224, 0.448, 0.673, 0.897 and 1.122 m of guanidinium chlorid...

Simulation of DNA electrophoresis facilitates the design of DNA separation devices. Various methods have been explored for simulating DNA electrophoresis and other processes using implicit and explicit solvent models. Explicit solvent models are highly desired but their applications may be limited by high computing cost in simulating large number of solvent particles. In this work, a coarse-gra...

Simulation of small molecules, polymers, and proteins in dense solvents is an important class of problems both for processing of materials in liquids and for simulation of proteins in physiologically relevent solvent states. However, these simulations are expensive and sampling is inefficient due to the ubiquitous dense solvent. Even in the absence of the dense solvent, rigorous sampling of the...

A novel Stochastic Event-Driven Molecular Dynamics (SEDMD) algorithm is developed for the simulation of polymer chains suspended in a solvent. SEDMD combines event-driven molecular dynamics (EDMD) with the Direct Simulation Monte Carlo (DSMC) method. The polymers are represented as chains of hard-spheres tethered by square wells and interact with the solvent particles with hard-core potentials....

The dynamic and static properties of molecular dynamics simulations using various methods for treating solvent were compared. The SH3 protein domain was chosen as a test case because of its small size and high surface-to-volume ratio. The simulations were analyzed in structural terms by examining crystal packing, distribution of polar residues, and conservation of secondary structure. In additi...

The swelling of regular, tightly meshed model networks is investigated by a molecular-dynamics-Monte Carlo hybrid technique. The chemical equilibrium between two simulation boxes representing the gel phase and a solvent bath, respectively, is obtained by subjecting the Lennard-Jones particles of a binary mixture, serving as explicit solvent, to the particle transfer step of Gibbs ensemble-Monte...

Molecular dynamic simulation is a powerful method that monitors all variations in the atomic level in explicit solvent. By this method we can calculate many chemical and biochemical properties of large scale biological systems. In this work all-atom molecular dynamics simulation of polyalanine (PA) was investigated in the presence of 0.224, 0.448, 0.673, 0.897 and 1.122 M of guanidinium chlorid...