Related papers: Constant-temperature molecular-dynamics algorithms…
We present here two novel algorithms for simulated tempering simulations, which break detailed balance condition (DBC) but satisfy the skewed detailed balance to ensure invariance of the target distribution. The irreversible methods we…
We report here the experimental realization of multi-step cooling of a quantum system via heat-bath algorithmic cooling. The experiment was carried out using nuclear magnetic resonance (NMR) of a solid-state ensemble three-qubit system.
Atmosphere modelling applications become increasingly memory-bound due to the inconsistent development rates between processor speeds and memory bandwidth. In this study, we mitigate memory bottlenecks and reduce the computational load of…
This paper presents a molecular dynamics simulation of an inelastic gas, where collisions between molecules are characterized by a coefficient of restitution less than unity. The simulation employs an event-driven algorithm to efficiently…
Constructing accurate interatomic potential and overcoming the exponential growth of structural equilibration time are challenges to the atomistic investigations of the composition-dependent structure and dynamics during the vitrification…
A robust, simple and fast procedure for the calculation of uncertainties in relative static dielectric permittivity ($\varepsilon_s$) computed via molecular dynamics (MD) is proposed. It arises as a direct application of well founded…
We present a 3D finite element solver for the nonlinear Poisson-Nernst-Planck (PNP) equations for electrodiffusion, coupled to the Stokes system of fluid dynamics. The model serves as a building block for the simulation of macromolecule…
We propose a new explicit pseudo-energy and momentum conserving scheme for the time integration of Hamiltonian systems. The scheme, which is formally second-order accurate, is based on two key ideas: the integration during the time-steps of…
Respecting the laws of thermodynamics is crucial for ensuring that numerical simulations of dynamical systems deliver physically relevant results. In this paper, we construct a structure-preserving and thermodynamically consistent finite…
Molecular dynamics (MD) simulation is essential for various scientific domains but computationally expensive. Learning-based force fields have made significant progress in accelerating ab-initio MD simulation but are not fast enough for…
Obtaining a rigorous and reliable method for linking computer simulations of polymer blends and composites at different length scales of interest is a highly desirable goal in soft matter physics. In this paper a multiscale modeling…
This paper focuses on discussing Newton's method and its hybrid with machine learning for the steady state Navier-Stokes Darcy model discretized by mixed element methods. First, a Newton iterative method is introduced for solving the…
Simulations of objects with classical dynamics are in fact a particular version of discrete dynamics since almost all the classical dynamics simulations in natural science are performed with the use of the simple ''Leapfrog" or ''Verlet"…
While molecular dynamics (MD) is a very useful computational method for atomistic simulations, modeling the interatomic interactions for reliable MD simulations of real materials has been a long-standing challenge. In 2007, Behler and…
A variational method for computing conformational properties of molecules with Lennard-Jones potentials for the monomer-monomer interactions is presented. The approach is tailored to deal with angular degrees of freedom, {\it rotors}, and…
This article describes algorithms for the hybrid parallelization and SIMD vectorization of molecular dynamics simulations with short-range forces. The parallelization method combines domain decomposition with a thread-based parallelization…
Classical molecular dynamics simulations are based on solving Newton's equations of motion. Using a small timestep, numerical integrators such as Verlet generate trajectories of particles as solutions to Newton's equations. We introduce…
Numerical implementation of an explicit phonon bath requires a large number of oscillator modes in order to maintain oscillators at the initial temperature when modeling energy relaxation processes. An additional thermalization algorithm…
A roughly constant temperature over a wide range of densities is maintained in molecular clouds through radiative heating and cooling. An isothermal equation of state is therefore frequently employed in molecular cloud simulations. However,…
Ab initio molecular dynamics (AIMD) simulations using hybrid density functionals and plane waves are of great interest owing to the accuracy of this approach in treating condensed matter systems. On the other hand, such AIMD calculations…