Related papers: Symplectic algorithm for constant-pressure molecul…
In this paper, we develop a stochastic Asymptotic-Preserving (sAP) scheme for the kinetic chemotaxis system with random inputs, which will converge to the modified Keller-Segel model with random inputs in the diffusive regime. Based on the…
Here we present Symplectically Integrated Symbolic Regression (SISR), a novel technique for learning physical governing equations from data. SISR employs a deep symbolic regression approach, using a multi-layer LSTM-RNN with mutation to…
We propose an open-boundary molecular dynamics method in which an atomistic system is in contact with an infinite particle reservoir at constant temperature, volume and chemical potential. In practice, following the Hamiltonian adaptive…
In this paper, we propose a multiphysics finite element method for a quasi-static thermo-poroelasticity model with a nonlinear convective transport term. To design some stable numerical methods and reveal the multi-physical processes of…
Long ranged electrostatic interactions are time consuming to calculate in molecular dynamics and Monte-Carlo simulations. We introduce an algorithmic framework for simulating charged particles which modifies the dynamics so as to allow…
We show that the symplectic reduction of the dynamics of $N$ point vortices on the plane by the special Euclidean group $\mathsf{SE}(2)$ yields a Lie--Poisson equation for relative configurations of the vortices. Specifically, we combine…
Anderson acceleration (AA) has a long history of use and a strong recent interest due to its potential ability to dramatically improve the linear convergence of the fixed-point iteration. Most authors are simply using and analyzing the…
Isothermal-isobaric molecular dynamics simulations have been performed to examine a broad set of properties of the model water-1,2-dimethoxyethane (DME) mixture as a function of composition. The SPC-E and TIP4P-Ew water models and the…
In this paper, we develop an asymptotic-preserving and energy-conserving (APEC) Particle-In-Cell (PIC) algorithm for the Vlasov-Maxwell system. This algorithm not only guarantees that the asymptotic limiting of the discrete scheme is a…
A new methodology is developed to integrate numerically the equations of motion for classical many-body systems in molecular dynamics simulations. Its distinguishable feature is the possibility to preserve, independently on the size of the…
Dynamic simulation of elastic bodies is a longstanding task in engineering and computer graphics. In graphics, numerical integrators like implicit Euler and BDF2 are preferred due to their stability at large time steps, but they tend to…
A simple proof and detailed analysis on the non-ergodicity for multidimensional harmonic oscillator systems with Nose-Hoover type thermostat are given. The origin of the nonergodicity is symmetries in the multidimensional target physical…
The thinning method for numerical generation of the nonhomogeneous Poisson process (NHPP) arrival times has been adapted to accelerate Monte Carlo simulations of the kinetic Ising models (KIMs) with the Glauber spin-flip dynamics. The…
We present a modified simulated annealing method with a dynamical choice of the cooling temperature. The latter is determined via a closed-loop control and is proven to yield exponential decay of the entropy of the particle system. The…
We introduce a new path integral Monte Carlo method for investigating nonadiabatic systems in thermal equilibrium and demonstrate an approach to reducing stochastic error. We derive a general path integral expression for the partition…
Extended Lagrangian molecular dynamics (XLMD) is a general method for performing molecular dynamics simulations using quantum and classical many-body potentials. Recently several new XLMD schemes have been proposed and tested on several…
A new particle-based sampling and approximate inference method, based on electrostatics and Newton mechanics principles, is introduced with theoretical ground, algorithm design and experimental validation. This method simulates an…
An important process for antimatter experiments is the cooling of particles in a Penning-Malmberg trap to experimentally useful temperatures. A non-neutral plasma of one species (e.g. antiprotons) can be collisionally cooled on another…
We derive minimal discrete models of the Boltzmann equation consistent with equilibrium thermodynamics, and which recover correct hydrodynamics in arbitrary dimensions. A simple analytical procedure of constructing the equilibrium for the…
We demonstrate an efficient and accurate, general-purpose first-principles blueprint for calculating anharmonic vibrational free energy and predicting structural phase transition temperatures of solids. Thermodynamic integration is…