Related papers: Generating Generalized Distributions from Dynamica…
In this paper, we suggest a novel sampling method for Monte Carlo molecular simulations. In order to perform efficient sampling of molecular systems, it is advantageous to avoid extremely high energy configurations while also retaining 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…
Molecular dynamics simulations were carried out to test the thermodynamic theory of weakly excited, two-dimensional granular systems [Hayakawa and Hong, Phys. Rev. Lett. 78, 2764 (1997)], where granular materials are viewed as a collection…
Reliable dynamical properties from molecular dynamics simulations require careful control of thermostatting artifacts. We systematically assess how NVE, deterministic thermostats, velocity-rescale dynamics, and stochastic Langevin-type…
We present a class of diffusion-based algorithms to draw samples from high-dimensional probability distributions given their unnormalized densities. Ideally, our methods can transport samples from a Gaussian distribution to a specified…
Gaussian distribution is commonly used as a good approximation to study the trapped one-component Bose-condensed atoms with relatively small nonlinear effect. It is not adequate in dealing with the one-component system of large nonlinear…
Molecular dynamics with the stochastic process provides a convenient way to compute structural and thermodynamic properties of chemical, biological, and materials systems. It is demonstrated that the virtual dynamics case that we proposed…
The particle-in-cell numerical method of plasma physics balances a trade-off between computational cost and intrinsic noise. Inference on data produced by these simulations generally consists of binning the data to recover the particle…
Recent laboratory experiments suggest an intrinsic asymmetry between heating and cooling, with heating occurring more efficiently. Two decades earlier, molecular dynamics (MD) simulations had examined a related setup - heating one side of a…
In this work we introduce a geometric integrator for molecular dynamics simulations of physical systems in the canonical ensemble. In particular, we consider the equations arising from the so-called density dynamics algorithm with any…
An extended Hamiltonian approach to conduct isothermal-isobaric molecular dynamics simulations with full cell flexibility is presented. The components of the metric tensor are used as the fictitious degrees of freedom for the cell, thus…
We apply the Nose-Hoover thermostat and three variations of it, which control different combinations of velocity moments, to the periodic Lorentz gas. Switching on an external electric field leads to nonequilibrium steady states for the…
Heterogeneous multiscale methods (HMM) combine molecular accuracy of particle-based simulations with the computational efficiency of continuum descriptions to model flow in soft matter liquids. In these schemes, molecular simulations…
A flexible model is developed for multivariate generalized spherical distributions, i.e. ones with level sets that are star shaped. To work in dimension above 2 requires tools from computational geometry and multivariate numerical…
We consider and compare four Hamiltonian formulations of thermostated mechanics, three of them kinetic, and the other one configurational. Though all four approaches ``work'' at equilibrium, their application to many-body nonequilibrium…
A Gaussian operator basis provides a means to formulate phase-space simulations of the real- and imaginary-time evolution of quantum systems. Such simulations are guaranteed to be exact while the underlying distribution remains…
We investigate the influence of numerical discretization errors on computed averages in a molecular dynamics simulation of TIP4P liquid water at 300 K coupled to different deterministic (Nos\'e-Hoover and Nos\'e-Poincar\'e) and stochastic…
Estimating the temperature and metal abundance of the intracluster and the intragroup media is crucial to determine their global metal content and to determine fundamental cosmological parameters. When a spatially resolved temperature or…
The molecular dynamics lattice gas method maps a molecular dynamics simulation onto a lattice gas using a coarse-graining procedure. This is a novel fundamental approach to derive the lattice Boltzmann method by taking a Boltzmann average…
This paper introduces an extension to the normal distribution through the polar method to capture bimodality and asymmetry, which are often observed characteristics of empirical data. The later two features are entirely controlled by a…