Nonequilibrium molecular-dynamics simulations are used to investigate the molecular shape of dendrimers and linear polymers in a melt and under shear. Molecules are modeled at the coarse-grained level using a finitely extensible nonlinear elastic bead-spring model. The shape of dendrimers and linear polymers at equilibrium and undergoing planar Couette flow is analyzed quantitatively and it is ...

We discuss the advantages of parallelization by multithreading on graphics processing units (GPUs) for parallel tempering Monte Carlo computer simulations of an exemplified bead-spring model for homopolymers. Since the sampling of a large ensemble of conformations is a prerequisite for the precise estimation of statistical quantities such as typical indicators for conformational transitions lik...

In this work, we incorporated a quartic bond potential into a coarse-grained bead-spring model to study lubricant adsorption on a solid surface as well as depletion instability. The surface tension density and the number density profiles were examined to verify the solid-liquid and liquid-vapor interfaces during heat treatment. It was found that both the liquid-vapor interfacial thickness and t...

The structure of a single, grafted polyelectrolyte, DNA, is investigated by molecular dynamics simulations. The polyelectrolyte is treated as a bead–spring model with explicit charges using parametrizations of both flexible ~ssDNA! and stiff ~dsDNA! polyelectrolytes. In this single chain limit with no added salt, the flexible ssDNA is always highly extended. Counterion condensation on both mole...

Differential growth processes play a prominent role in shaping leaves and biological tissues. Using both analytical and numerical calculations, we consider the shapes of closed, elastic strips which have been subjected to an inhomogeneous pattern of swelling. The stretching and bending energies of a closed strip are frustrated by compatibility constraints between the curvatures and metric of th...

Primitive path analyses of entanglements are performed over a wide range of chain lengths for both bead spring and atomistic polyethylene polymer melts. Estimators for the entanglement length N_{e} which operate on results for a single chain length N are shown to produce systematic O(1/N) errors. The mathematical roots of these errors are identified as (a) treating chain ends as entanglements a...

The notion of a bead metric space is defined as a nice generalization of the uniformly convex normed space such as $CAT(0)$ space, where the curvature is bounded from above by zero. In fact, the bead spaces themselves can be considered in particular as natural extensions of convex sets in uniformly convex spaces and normed bead spaces are identical with uniformly convex spaces. In this paper, w...

A coarse-grained bead-spring-dashpot chain model with the dashpots representing presence of internal friction is solved exactly numerically for case chains more than two beads. Using a decoupling procedure to remove explicit coupling bead’s velocity that its nearest neighbors, governing set stochastic differential equations are Brownian dynamics simulations obtain material functions in oscillat...

Relatively short peptides, such as toxins and antimicrobial-peptides, are known to insert themselves into cell membranes. On the basis of simple bead-spring models for the membrane lipids, the peptide, and water, detailed processes of the peptide insertion is investigated by molecular dynamics simulation; our special concern is in the highly cooperative motions of membrane lipids and the peptid...

There are contradictory published data on the behavior of fluid slip at high shear rates. Using three methodologies (molecular dynamics simulations, an analytical theory of slip, and a Navier-Stokes-based calculation) covering a range of fluids (bead-spring liquids, polymer solutions, and ideal gas flows) we show that as shear rate increases, the amount of slip, as measured by the slip length, ...