Related papers: On Metropolis Integrators for Molecular Dynamics
Chemical potential of species in solution is essential for understanding various chemical processes at interfaces. Molecular dynamics (MD) simulations, constrained by fixed compositions, cannot satisfy a constant chemical potential…
Molecular dynamics is widely used to study various phenomena, such as diffusion, shock wave propagation, and plasma dynamics. A wide range of software packages supports the expanding scope of molecular dynamics applications. However, the…
Molecular dynamics (MD) enables the study of physical systems with excellent spatiotemporal resolution but suffers from severe time-scale limitations. To address this, enhanced sampling methods have been developed to improve exploration of…
Monte Carlo simulations are widely employed to measure the physical properties of glass-forming liquids in thermal equilibrium. Combined with local Monte Carlo moves, the Metropolis algorithm can also be used to simulate the relaxation…
A new approach is developed to integrate numerically the equations of motion for systems of interacting rigid polyatomic molecules. With the aid of a leapfrog framework, we directly involve principal angular velocities into the integration,…
Since its inception the Metropolis-Hastings kernel has been applied in sophisticated ways to address ever more challenging and diverse sampling problems. Its success stems from the flexibility brought by the fact that its verification and…
Quantum mechanics/molecular mechanics (QM/MM) molecular dynamics (MD) simulations have been developed to simulate molecular systems, where an explicit description of changes in the electronic structure is necessary. However, QM/MM MD…
Due to its non-crystalline nature, the glassy state has remained one the most exciting scientific challenges. To study such materials, Molecular Dynamics (MD) simulations have been extensively used because they provide a direct view into…
We present a highly efficient molecular dynamics scheme for calculating the concentration profile of dopants implanted in group-IV alloy, and III-V zinc blende structure materials. Our program incorporates methods for reducing computational…
We present a MATLAB toolbox for five different classes of exponential integrators for solving (mildly) stiff ordinary differential equations or time-dependent partial differential equations. For the efficiency of such exponential…
Molecular dynamics simulations have emerged as a potent tool for investigating the physical properties and kinetic behaviors of materials at the atomic scale, particularly in extreme conditions. Ab initio accuracy is now achievable with…
A new approach for integration of motion in many-body systems of interacting polyatomic molecules is proposed. It is based on splitting time propagation of pseudo-variables in a modified phase space, while the real translational and…
Molecular dynamics (MD) simulations provide atomistic insights into the structure, dynamics, and function of biomolecules by generating time-resolved, high-dimensional trajectories. Analyzing such data benefits from estimating the minimal…
Molecular Dynamic (MD) approach is applied to study the converging cylindrical shock waves in a dense Lennard-Jones (LJ) fluid. MD method is based on tracking of the atom motions and hence it has an fundamental advantages over hydrodynamic…
A multi-scale framework was recently proposed for more realistic molecular dynamics simulations in continuum solvent models by coupling a molecular mechanics treatment of solute with a fluid mechanics treatment of solvent, where we…
Molecular dynamics (MD) simulations allow atomistic insights into chemical and biological processes. Accurate MD simulations require computationally demanding quantum-mechanical calculations, being practically limited to short timescales…
Dependable numerical results from long-time simulations require stable numerical integration schemes. For Hamiltonian systems, this is achieved with symplectic integrators, which conserve the symplectic condition and exactly solve for the…
Physics simulators are widely used in robotics fields, from mechanical design to dynamic simulation, and controller design. This paper presents an open-source MATLAB/Simulink simulator for rigid-body articulated systems, including…
Machine learned interatomic potentials (MLIPs) have emerged as powerful tools for molecular dynamics (MD) simulations with their competitive accuracy and computational efficiency. However, MLIPs are often observed to exhibit un-physical…
Since its first description fifty years ago, the Metropolis Monte Carlo method has been used in a variety of different ways for the simulation of continuum quantum many-body systems. This paper will consider some of the generalizations of…