Related papers: Multicanonical molecular dynamics by variable-temp…
Macroscopic theories of nucleation such as classical nucleation theory envision that clusters of the bulk stable phase form inside the bulk metastable phase. Molecular dynamics simulations are often used to elucidate nucleation mechanisms,…
Starting with a microscopic (individual-based) Brownian dynamics model of charged particles (ions), its macroscopic description is derived as a system of partial differential equations that govern the evolution of ion concentrations in…
A fundamental objective of materials modeling is identifying atomic structures that align with experimental observables. Conventional approaches for disordered materials involve sampling from thermodynamic ensembles and hoping for an…
We show how to use the multiple histogram method to combine canonical ensemble Monte Carlo simulations made at different temperatures and densities. The method can be applied to study systems of particles with arbitrary interaction…
Current methods to describe the thermodynamic behavior of many-particle systems are often based on perturbation theory with an unperturbed system consisting of free particles. Therefore, only a few methods are able to describe both strongly…
To study materials phenomena simultaneously at various length scales, descriptions in which matter can be coarse grained to arbitrary levels, are necessary. Attempts to do this in the static regime (i.e. zero temperature) have already been…
The thermodynamic approach to non-equilibrium dynamics describes the state of macroscopic systems by means of a collection of intensities or intensive variables. The latter are by definition the differentials of the entropy with respect to…
The internal layers of neutron stars are expected to contain several superfluid components that can significantly affect their dynamics. The description of such objects should rely on hydrodynamic models in which it is possible to…
Microcanonical equations for several thermodynamic properties of a system, suitable for molecular dynamics simulations, are derived from the nonextensive Tsallis entropy functional. Two possible definitions of temperature, the usual one and…
We have investigated by molecular dynamics method the influence of a finite number of particles used in computer simulations on fluctuations of thermodynamic properties. As a case study, we used the two-dimensional Lennard-Jones system. 2D…
We present a detailed account of the technical aspects of stochastic quantum molecular dynamics, an approach introduced recently by the authors [H. Appel and M. Di Ventra, Phys. Rev. B 80 212303 (2009)] to describe coupled electron-ion…
Systems biology uses large networks of biochemical reactions to model the functioning of biological cells from the molecular to the cellular scale. The dynamics of dissipative reaction networks with many well separated time scales can be…
The large-deviation method can be used to study the measurement trajectories of open quantum systems. For optical arrangements this formalism allows to describe the long time properties of the (non-equilibrium) photon counting statistics in…
We present a novel implementation of the parallel tempering Monte Carlo method in a multicanonical ensemble. Multicanonical weights are derived by a self-consistent iterative process using a Boltzmann inversion of global energy histograms.…
Molecular dynamics simulations are widely used across chemistry, physics, and biology, providing quantitative insight into complex processes with atomic detail. However, their limited timescale of a few microseconds is a significant…
We investigate a binary Lennard-Jones mixture with molecular dynamics simulations. We consider first a system cooled linearly in time with the cooling rate gamma. By varying gamma over almost four decades we study the influence of the…
Boltzmann's principle is used to select the "most probable" realization (macrostate) of an isolated or closed thermodynamic system, containing a small number of particles ($N \llsp \infty$), for both classical and quantum statistics. The…
Structure, function and dynamics of many biomolecular systems can be characterized by the energetic variational principle and the corresponding systems of partial differential equations (PDEs). This principle allows us to focus on the…
We present molecular dynamics simulations of mono- or bidisperse inelastic granular gases driven by vibrating walls, in two dimensions (without gravity). Because of the energy injection at the boundaries, a situation often met…
The dynamics of short 1D nonlinear Hamiltonian chains is analyzed numerically at different temperatures (energy per particle). The boundary temperature $T_b$ separating the regular (quasiperiodic) and the stochastic (chaotic) chain motion…