Related papers: Constant-temperature molecular-dynamics algorithms…
We derive and validate a partition function for low-dimensional systems interacting with a heat bath, addressing the general issue of thermodynamic modeling of nanoscale systems. In contrast to bulk systems in the canonical (NVT) ensemble…
DL_POLY Quantum 2.1 is introduced here as a highly modular, sustainable, and scalable general-purpose molecular dynamics (MD) simulation software for large-scale long-time MD simulations of condensed phase and interfacial systems with the…
We develop a novel method of replica-exchange molecular dynamics (REMD) simulation, mass-scaling REMD (MSREMD) method, which improves trajectory accuracy at high temperatures, and thereby contributes to numerical stability. In addition, the…
An algorithm is derived for computer simulation of geodesics on the constant potential-energy hypersurface of a system of N classical particles. First, a basic time-reversible geodesic algorithm is derived by discretizing the geodesic…
Machine learning potentials have emerged as a means to enhance the accuracy of biomolecular simulations. However, their application is constrained by the significant computational cost arising from the vast number of parameters compared to…
Recent developments in analog quantum simulators based on cold atoms and trapped ions call for cross-validating the accuracy of quantum-simulation experiments with use of quantitative numerical methods; however, it is particularly…
We discuss the development and implementation of a constant temperature (NVT) molecular dynamics scheme that combines the Nos\'e-Hoover chain thermostat with the extended Lagrangian Born-Oppenheimer molecular dynamics (BOMD) scheme, using a…
The modeling and simulation of heat source trajectories through phase-change materials is a relevant problem both for space exploration and for terrestrial climate research, among other fields. In space, the DLR and NASA are both interested…
We present a new and improved method for simultaneous control of temperature and pressure in molecular dynamics simulations with periodic boundary conditions. The thermostat-barostat equations are build on our previously developed…
Accelerated molecular dynamics (MD) simulations are implemented to model the sliding process of AFM experiments at speeds close to those found in experiment. In this study the hyperdynamics method, originally devised to extend MD time…
This paper develops and tests a deep-atmosphere, nonhydrostatic dynamical core (DyCore) targeted towards ground-thermosphere atmospheric prediction using the spectral element method (SEM) with Implicit-Explicit (IMEX) and Horizontally…
We use molecular dynamics computer simulations to investigate a critical temperature T_c for a dynamical glass transition as proposed by the mode-coupling theory (MCT) of dense liquids in a glass forming Ni_{0.8}Zr_{0.2}-system. The…
Molecular dynamics (MD) simulation is applied to the condensation process of supersaturated vapors of methane, ethane, and carbon dioxide. Simulations of systems with up to a million particles were conducted with a massively parallel MD…
Vlasov solvers that operate on a phase-space grid are highly accurate but also numerically demanding. Coarse velocity space resolutions, which are unproblematic in particle-in-cell (PIC) simulations, can lead to numerical heating or…
A new pairwise hybrid machine-learning/molecular mechanics (ML/MM) potential is introduced that is conceived for application to large, heterogeneous condensed-phase systems. The PhysNet ML method describes monomers and short-range dimer…
Operational forecasting centers are investing in decadal (1-10 year) forecast systems to support long-term decision making for a more climate-resilient society. One method that has previously been employed is the Dynamic Mode Decomposition…
The Markov entropy decomposition (MED) is a recently-proposed, cluster-based simulation method for finite temperature quantum systems with arbitrary geometry. In this paper, we detail numerical algorithms for performing the required steps…
Molecular dynamics is based on solving Newton's equations for many-particle systems that evolve along complex, highly fluctuating trajectories. The orbital instability and short-time complexity of Newtonian orbits is in sharp contrast to…
We developed a general theoretical approach and a user-ready computer code that permit to study the dynamics of collisional energy transfer and ro-vibrational energy exchange in complex molecule-molecule collisions. The method is a mixture…
We simulate dynamic mechanical analysis experiments for the Kob-Andersen binary Lennard-Jones system. For this, the SLLOD algorithm with time-dependent strain rates is applied to give a sinusoidally varying strain at different densities and…