The rough energy landscapes and tight packing of protein interiors are two of the critical factors that have prevented the wide application of physics-based models in protein side-chain assignment and protein structure prediction in general. Complementing the rotamer-based methods, we propose an ab initio method that utilizes molecular mechanics simulations for protein side-chain assignment and...

We discuss the theory of electron-molecule excitation processes of importance in fusion plasmas. We consider elastic scattering, rotational, vibrational, and electronic excitation in turn and also dissociative attachment and impact dissociation.

Prediction for hyper nuclei multiplicities from GSI to LHC energies the Ultra-relativistic Quantum Molecular Dynamics (UrQMD) model combined with a final state coalescence approach is presented and compared thermal model. The influence of radius on collision energy centrality dependence Λ 3 H/Λ ratio discussed.

On the basis of the antisymmetrized molecular dynamics (AMD) of wave packets for the quantum system, a novel model (called AMD-V) is constructed by the stochastic incorporation of the diffusion and the deformation of wave packets which is calculated by Vlasov equation without any restriction on the one-body distribution. In other words, the stochastic branching process in molecular dynamics is ...

We study radiation-damage events in MgO on experimental time scales by augmenting molecular dynamics cascade simulations with temperature accelerated dynamics, molecular statics, and density functional theory. At 400 eV, vacancies and mono- and di-interstitials form, but often annihilate within milliseconds. At 2 and 5 keV, larger clusters can form and persist. While vacancies are immobile, int...

We study the assembling of small gold clusters subject to collisions and close contact coalescence by using molecular dynamics simulations to simulate events that occur typically in the sputtering process of synthesis. Our results support the notion that the kinetics of coalescence processes strongly determine the geometry and structure of the final particle. While impact velocities, relative o...

Solvent effects on polymer dynamics and structure are investigated using a mesoscopic solvent model that accounts for hydrodynamic interactions among the polymer beads. The simulation method combines molecular dynamics of the polymer chain, interacting with the solvent molecules through intermolecular forces, with mesoscopic multiparticle collision dynamics for the solvent molecules. Changes in...

We study the nonequilibrium statistical mechanics of a system of freely moving particles, in which binary encounters lead either to an elastic collision or to the disappearance of the pair. Such a system of ballistic annihilation therefore constantly loses particles. The dynamics of perturbations around the free decay regime is investigated using the spectral properties of the linearized Boltzm...

We extend the reactive force field ReaxFF to describe the high energy nitramine RDX and use it with molecular dynamics (MD) to study its shock-induced chemistry. We studied shock propagation via nonequilibrium MD simulations at various collision velocities. We find that for high impact velocities (>6 km/s) the RDX molecules decompose and react to form a variety of small molecules in very short ...

Brownian adhesive dynamics (BRAD) is a new method for simulating the attachment of viruses to cell surfaces. In BRAD, the motion of the virus is subject to stochastic bond formation and breakage, and thermal motion owing to collisions from the solvent. In the model, the virus is approximated as a rigid sphere and the cell surface is approximated as a rigid plane coated with receptors. In this a...