We analyze the structural behavior of a single polymer chain grafted to an attractive, flexible surface. Our model is composed of a coarse-grained bead-and-spring polymer and a tethered membrane. By means of extensive parallel tempering Monte Carlo simulations it is shown that the system exhibits a rich phase behavior ranging from highly ordered, compact to extended random coil structures, and ...

The thermal conductivity of several amorphous solids is numerically evaluated within the harmonic approximation from Kubo linear-response theory following the formalism developed by Allen and Feldman. The predictions are compared to the results of molecular dynamics (MD) simulations with realistic anharmonic potentials and to experimental measurements. The harmonic theory accurately predicts th...

We study the orientational properties of labeled segments in semiflexible dendrimers making use of the viscoelastic approach of Dolgushev and Blumen [J. Chem. Phys. 131, 044905 (2009)]. We focus on the segmental orientational autocorrelation functions (ACFs), which are fundamental for the frequency-dependent spin-lattice relaxation times T1(ω). We show that semiflexibility leads to an increase ...

Utilizing a novel, hybrid molecular dynamics, Monte Carlo simulation, we report on microstructural changes in a polymer network that arise in response to oscillatory shear deformation. We model telechelic selfassociating polymers as a course-grained, bead−spring system. The stress response of the system is obtained from rheological experiments and is reported as a function of frequency and ampl...

We study the driven flow of an unentangled glassy polymer film with a free upper surface and supported below by a substrate using nonequilibrium molecular dynamics simulations based on a bead-spring model. Above the glass transition temperature T(g), simple Poiseuille laminar flow is observed with the film mobility defined as the flow current density per unit pressure gradient scaling as h(3) w...

— Using the Gaussian Ansatz for the monomer–monomer correlation functions we derive a set of the self–consistent equations for determination of the conformational state in the bead–and–spring copolymer model. The latter is based on the Edwards type effective free energy functional with arbitrary two–body interaction matrix. The rate of conformational changes in kinetics may be expressed via the...

We have studied the effect of shape of an amphiphilic molecule on micellization properties by carrying out stochastic molecular dynamics simulation on a bead-spring model of amphiphiles for several sizes of hydrophilic head group with a fixed hydrophobic tail length. Our studies show that the effect of geometry of an amphiphile on shape and cluster distribution of micelles is significant. We fi...

The DNA is treated using the discretized wormlike bead-chain model, where each “bead” represents a 3 nm segment of relaxed DNA (1, 2). Each bead is assigned a salt-dependent charge qdna according to Stigter (3). The DNA bead-chain is also assigned an intramolecular force field comprising of stretching, bending, twisting terms that capture all aspects of DNA mechanics. The stretching energy Ustr...

We present molecular dynamics simulations of a simple model for polymer melts with intramolecular barriers. We investigate structural relaxation as a function of the barrier strength. Dynamic correlators can be consistently analyzed within the framework of the mode coupling theory of the glass transition. Control parameters are tuned in order to induce a competition between general packing effe...

Regions of highly repetitive DNA, such as those found in the nucleolus, show a self-organization that is marked by spatial segregation and frequent self-interaction. The mechanisms that underlie the sequestration of these sub-domains are largely unknown. Using a stochastic, bead-spring representation of chromatin in budding yeast, we find enrichment of protein-mediated, dynamic chromosomal cros...