For the treatment of equilibrated molecular systems in a heat bath we propose a transition state theory that is based on conformation dynamics. In general, a set-based discretization of a Markov operator P does not preserve the Markov property. In this article, we propose a discretization method which is based on a Galerkin approach. This discretization method preserves the Markov property of t...

The strength and ductility of nanolayered materials are determined by a delicate balance between dislocation and interface motion under applied mechanical loading. We present here studies of dislocation and interface motion in single crystal and nanotwinned copper, utilizing molecular dynamics simulations. Motion of twin boundary interfaces themselves is dictated by the stress state at the inte...

Molecular dynamics simulations were used to study the initial growth of single-walled carbon nanotubes (SWNTs) on a supported iron cluster (Fe50). Statistical analysis shows that the growth direction of SWNTs becomes more perpendicular to the substrate over time due to the weak interaction between carbon nanotube and the substrate. The diameter of the nanotube also increases with the simulation...

The structural properties of model microgel particles are investigated by molecular dynamics simulations applying a coarse-grained model. A microgel is comprised of a regular network of polymers internally connected by tetra-functional cross-links and with dangling ends at its surface. The self-avoiding polymers are modeled as bead-spring linear chains. Electrostatic interactions are taken into...

Born-Oppenheimer dynamics is shown to provide an accurate approximation of time-independent Schrödinger observables for a molecular system with an electron spectral gap, in the limit of large ratio of nuclei and electron masses, without assuming that the nuclei are localized to vanishing domains. The derivation, based on a Hamiltonian system interpretation of the Schrödinger equation and stabil...

We introduce a novel wavelet-based compound matrix to bridge models (LennardJones model simulated with molecular dynamics and a lattice Q-states Potts model with a Monte Carlo simulation) that describe grain growth over different ranges of spatial and time scales. The compound wavelet matrix provides full statistical information on the microstructure at the range of scales that is the union of ...

based on the notion of micro-structure in linear elasticity presented by mindlin, a newextended continuum mechanics (ecm) formulation is derived which can be utilized to model thematerial behavior at atomic scale. an attempt has been made to present a formulation capable ofproducing the molecular dynamics (md) simulation results with less computational effort. to thisend, some new kinematical v...

htlv-1 and hiv-1 are two major causes for severe t-cell leukemia disease and acquired immune deficiency syndrome (aids). htlv-1 protease, a member of aspartic acid protease family, plays important roles in maturation during virus replication cycle. the impairment of these proteases results in uninfectious htlv-1virions.similar to hiv-1protease deliberate mutations that confer drug resistance on...

We present a Monte Carlo technique for sampling from the canonical distribution in molecular dynamics. The method is built upon the Nosé-Hoover constant temperature formulation and the generalized hybrid Monte Carlo method. In contrast to standard hybrid Monte Carlo methods only the thermostat degree of freedom is stochastically resampled during a Monte Carlo step. Mathematics Subject Classific...

Detailed simulations of the interaction of energetic C60 beams with amorphous targets are presented here. The spatial evolution of the cluster components is calculated accounting for multiple scattering and Coulomb explosion by means of Monte Carlo and molecular dynamics, respectively. The charge states of the individual cluster components ~atoms, atomic ions, fragment cluster ions! as a functi...