In the Dissipative Particle Dynamics (DPD) simulation of suspension, the fluid (solvent) and colloidal particles are replaced by a set of DPD particles and therefore their relative sizes (as measured by their exclusion zones) can affect the maximal packing fraction of the colloidal particles. In this study, we investigate roles of the conservative, dissipative and random forces in this relative...

By utilizing Graphics Processing Units, we show that constant pH molecular dynamics simulations (CpHMD) run in Generalized Born (GB) implicit solvent for long time scales can yield poor pKa predictions as a result of sampling unrealistic conformations. To address this shortcoming, we present a method for performing constant pH molecular dynamics simulations (CpHMD) in explicit solvent using a d...

The global production and consumption of plastics have continued to increase. Plastics degrade slowly, causing persistent environmental pollution Developed waste plastic recycling methods are discussed in this report, with a focus on the dissolution/reprecipitation technique restore low-density polyethene (LDPE) wastes. Aspen HYSYS is used simulate LDPE. Turpentine/petroleum ether (TURP/PetE) c...

We compare a newly developed hybrid simulation method which combines classical molecular dynamics (MD) and computational fluid dynamics (CFD) to a simulation consisting only of molecular dynamics. The hybrid code is composed of three regions: a classical MD region, a continuum domain where the dynamical equations are solved by standard CFD methods, and an overlap domain where transport informat...

Searching conformational ensembles of proteins remains a challenge in atomistic simulation of biomolecules. One approach to accelerate the protein sampling is to take advantage of rough energy surface from the coarse-grained model and, at the same time, to persist atomistic details from the all-atom model. Multiscale enhanced sampling (MSES) of all atoms and topology-based coarse-grained replic...

We coupled statistical-mechanical, molecular theory of solvation (a.k.a. 3D-RISM-KH) contracting solvent degrees of freedom with MD simulation in the Amber package. This included a number of accelerating schemes with cutoffs and iterative guess for the correlation functions, and extrapolating solvent-induced forces and applying them in large multi-time steps (up to 20 fs) to enable simulation o...