相关论文: Metric-tensor flexible-cell algorithm for isotherm…

We propose a method to extend the fast on-the-fly weight determination scheme for simulated tempering to two-dimensional space including not only temperature but also pressure. During the simulated tempering simulation, weight parameters…

An integrator for a class of stochastic Lie-Poisson systems driven by Stratonovich noise is developed. The integrator is suited for Lie-Poisson systems that also admit an isospectral formulation, which enables scalability to…

A very simple explicit integrator for the rotational motion of rigid linear molecules is presented which can preserve the rigidity of the molecules without requiring any constraint force. The integrator is time-reversible and symplectic,…

The development of physical simulators, called Ising machines, that sample from low energy states of the Ising Hamiltonian has the potential to drastically transform our ability to understand and control complex systems. However, most of…

Molecular dynamics is one of the most commonly used approaches for studying the dynamics and statistical distributions of many physical, chemical, and biological systems using atomistic or coarse-grained models. It is often the case,…

We present a brief tutorial on the nuts and bolts computation of a multisymplectic particle-in-cell algorithm using the discretized Lagrangian approach. This approach, originated by Marsden, Shadwick, and others, brings the benefits of…

A new scheme for numerical integration of motion for classical systems composed of rigid polyatomic molecules is proposed. The scheme is based on a matrix representation of the rotational degrees of freedom. The equations of motion are…

We show how to improve the molecular dynamics step of Hybrid Monte Carlo, both by tuning the integrator using Poisson brackets measurements and by the use of force gradient integrators. We present results for moderate lattice sizes.

We have presented some practical consequences on the molecular-dynamics simulations arising from the numerical algorithm published recently in paper Int. J. Mod. Phys. C 16, 413 (2005). The algorithm is not a finite-difference method and…

We discuss a symmetry-adapted algebraic (or vibron) model for molecular spectroscopy. The model is formulated in terms of tensor operators under the molecular point group. In this way, we have identified interactions that are absent in…

We propose a new generalized-ensemble algorithm, which we refer to as the multibaric-multithermal Monte Carlo method. The multibaric-multithermal Monte Carlo simulations perform random walks widely both in volume space and in potential…

Torsional-space Monte Carlo simulations of flexible molecules are usually based on the assumption that all values of dihedral angles have equal probability in the absence of atomic interactions. In the present paper it is shown that this…

Monte Carlo simulations are a powerful tool to investigate the thermodynamic properties of atomic systems. In practice however, sampling of the complete configuration space is often hindered by high energy barriers between different regions…

Studying single-particle dynamics over many periods of oscillations is a well-understood problem solved using symplectic integration. Such integration schemes derive their update sequence from an approximate Hamiltonian, guaranteeing that…

An arbitrary Lagrangian--Eulerian finite element method and numerical implementation for curved and deforming lipid membranes is presented here. The membrane surface is endowed with a mesh whose in-plane motion need not depend on the…

The effect of different move sets on the folding kinetics of the Monte Carlo simulations is analysed based on the conformation-network and the temperature-dependent folding kinetics. A new scheme of implementing Metropolis algorithm is…

We present a reversible and symplectic algorithm called ROLL, for integrating the equations of motion in molecular dynamics simulations of simple fluids on a hypersphere $\mathcal{S}^d$ of arbitrary dimension $d$. It is derived in the…

We present and compare different numerical schemes for the integration of the variational equations of autonomous Hamiltonian systems whose kinetic energy is quadratic in the generalized momenta and whose potential is a function of the…

We study the geometric particle-in-cell methods for an electrostatic hybrid plasma model. In this model, ions are described by the fully kinetic equations, electron density is determined by the Boltzmann relation, and space-charge effects…

A variational formulation for non-equilibrium thermodynamics was developed by Gay-Balmaz and Yoshimura. In a recent article, the first two authors of the present paper introduced partially cosymplectic structures as a geometric framework…