Related papers: Isothermal-isobaric molecular dynamics using stoch…
A new approach is developed to integrate numerically the equations of motion for systems of interacting rigid polyatomic molecules. With the aid of a leapfrog framework, we directly involve principal angular velocities into the integration,…
The integration time step is a critical determinant of performance in molecular dynamics simulations, governing the trade-off between speed and fidelity. Although 2 fs remains the standard in atomistic biomolecular simulations, the push for…
In the dynamics of driven impurity models, there is a fundamental asymmetry between the processes of emission and absorption of environment excitations: most of the emitted excitations are rapidly and irreversibly scattered away, and only a…
A recent proposal (see quant-ph/9803068) to simulate semiclassical corrections to classical dynamics by suitable classical stochastic fluctuations is applied to the specific instance of charged beam dynamics in particle accelerators. The…
We consider dynamical systems evolving near an equilibrium statistical state where the interest is in modelling long term behavior that is consistent with thermodynamic constraints. We adjust the distribution using an entropy-optimizing…
We study the behavior of an assembly of $N$ granular particles contained in two compartments within a simple kinetic approach. The particles belonging to each compartment collide inelastically with each other and are driven by a stochastic…
A rigorous two-thermostat formulation for ab-initio molecular dynamics using the fictitious Lagrangian approach is presented. It integrates the concepts of mass renormalization and temperature control for the wave functions. The new…
This paper is concerned with classes of models of stochastic reaction dynamics with time-scales separation. We demonstrate that the existence of the time-scale separation naturally leads to the application of the averaging principle and…
We present a thermodynamically consistent mesoscopic model of protein adsorption at liquid-solid interfaces. First describing the equilibrium state under varying protein concentration of the solution and binding conditions, we predict a…
We describe a new technique to estimate the mean square velocity of a Brownian particle from time series of the position of the particle sampled at frequencies several orders of magnitude smaller than the momentum relaxation frequency. We…
Thermodynamics of nanoscale devices is an active area of research. Despite their noisy surrounding they often produce mechanical work (e.g. micro-heat engines), display rectified Brownian motion (e.g. molecular motors). This invokes…
The dynamical properties of a tracer or impurity particle immersed in a host gas of inelastic and rough hard spheres in the homogeneous cooling state is studied. Specifically, the breakdown of energy equipartition as characterized by the…
Molecular dynamics simulations of a three dimensional relativistic gas with a soft potential are conducted with different interactions and particle masses. For all cases the velocity distribution agrees numerically with the J\"uttner…
Time-dependent dynamical properties of a fluid can not be estimated from a single configuration without performing a simulation. Here we show, however, that the scaling properties of both structure and dynamics can be predicted from a…
We study the transport and the relaxation properties of a molecular supercooled liquid by molecular-dynamics numerical simulations. The focus is on the translational motion. Jump motion is detected. At lower temperature the Stokes-Einstein…
We show that macroscopic irreversible thermodynamics for viscous fluids can be derived from exact information-theoretic thermodynamic identities valid at the microscale. Entropy production, in particular, is a measure of the loss of…
We present a microscopic derivation of the laws of continuum mechanics of nonideal ordered solids including dissipation, defect diffusion, and heat transport. Starting point is the classical many-body Hamiltonian. The approach relies on the…
Fluctuations of the instantaneous local Lagrangian strain $\epsilon_{ij}(\bf{r},t)$, measured with respect to a static ``reference'' lattice, are used to obtain accurate estimates of the elastic constants of model solids from atomistic…
We use a standard Monte-Carlo algorithm to study the slow dynamics of a binary Lennard-Jones glass-forming mixture at low temperature. We find that Monte-Carlo is by far the most efficient way to simulate a stochastic dynamics since…
We describe a method to explore the configurational phase space of chemical systems. It is based on the nested sampling algorithm recently proposed by Skilling [Skilling J. (2004) In AIP Conference Proceedings, vol. 735, p. 395.; Skilling…