The goal of this work is the development of novel peptides with high efficacy of inhibiting activity of CDK6/CyclinD complex. The peptides were derived from primary sequence of P16 protein and its homologues. The interactions between CDK6 and P16/INK4a-derived peptides are studied with molecular dynamics simulation employing umbrella sampling method. The SASA implicit solvent model was used for...

The immersion precipitation process makes most commercial polymeric membranes, which enjoy widespread use in water filtration and purification. In this work, a ternary Cahn-Hilliard formulation incorporating a Flory-Huggins homogeneous free energy function is used to model both initial diffusion and the liquid-liquid demixing stage of the immersion precipitation process, which determines much o...

This paper describes a Monte Carlo simulation technique designed to predict the sign and magnitude of the helical twisting power, bM, of a chiral material. The method calculates the chemical potential difference, Dm, between a chiral dopant and its enantiomer when they are placed in a twisted nematic solvent. In the low concentration limit, Dm is directly proportional to bM. In the simulations ...

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...

This article describes the collisional dynamics (CD) method adapted for molecules with geometrical constraints within a description using Cartesian coordinates for the atoms. In the CD method, stochastic collisions with virtual particles are included in usual molecular dynamics simulations to couple the considered polymer molecule to a solvent. The actual presence of the solvent is not explicit...

The liquid-liquid phase separation of a binary solvent can be arrested by colloidal particles trapped at the interface [K. Stratford, Science 309, 2198 (2005)]. We show experimentally that the colloidal network so formed can remain stable after fully remixing the liquids, creating a new type of gel in which colloids in a single-phase solvent have locally planar coordination. We argue that this ...

To investigate the effects of implicit solvents on peptide structure and dynamics, we performed extensive molecular dynamics simulations on the penta-peptide Cys-Ala-Gly-Gln-Trp. Two different implicit solvent models based on the CHARMM22 all-atom force field were used. Structural properties of the peptide such as distributions of end-to-end distances and dihedral angles obtained from molecular...

A fast stable finite difference Poisson-Boltzmann (FDPB) model for implicit solvation in molecular dynamics simulations was developed using the smooth permittivity FDPB method implemented in the OpenEye ZAP libraries. This was interfaced with two widely used molecular dynamics packages, AMBER and CHARMM. Using the CHARMM-ZAP software combination, the implicit solvent model was tested on eight p...

Long-range hydrodynamics between colloidal particles or fibers is modelled by the fluid particle model. Two methods are considered to impose the fluid boundary conditions at colloidal surfaces. In the first method radial and transverse friction forces between particle and solvent are applied such that the correct friction and torque follows for moving or rotating particles. The force coefficien...

We illustrate the effects of dielectric inhomogeneity on the statistical properties of polyelectrolytes in solution, by a lattice Monte Carlo simulation that combines the bond fluctuation model with a local algorithm for computing the electrostatic interactions. Our model accounts for the difference in the dielectric properties between the polymer backbone and the solvent. Taking the coil–globu...