Related papers: Processed Splitting Algorithms for Rigid-Body Mole…
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,…
We present a new molecular-dynamics algorithm for integrating the equations of motion for a system of particles interacting with mixed continuous/impulsive forces. This method, which we call Impulsive Verlet, is constructed using operator…
Computational chemistry allows researchers to experiment in sillico: by running a computer simulations of a biological or chemical processes of interest. Molecular dynamics with molecular mechanics model of interactions simulates N-body…
Robustly handling collisions between individual particles in a large particle-based simulation has been a challenging problem. We introduce particle merging-and-splitting, a simple scheme for robustly handling collisions between particles…
Hamiltonian splitting methods are an established technique to derive stable and accurate integration schemes in molecular dynamics, in which additional accuracy can be gained using force gradients. For rigid bodies, a tradition exists in…
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…
Modern analog computers are ideally suited to solving large systems of ordinary differential equations at high speed with low energy consumtion and limited accuracy. In this article, we survey N-body physics, applied to a simple water model…
The computational cost of exact methods for quantum simulation using classical computers grows exponentially with system size. As a consequence, these techniques can only be applied to small systems. By contrast, we demonstrate that quantum…
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…
Multiple time-scale algorithms exploit the natural separation of time-scales in chemical systems to greatly accelerate the efficiency of molecular dynamics simulations. Although the utility of these methods in systems where the interactions…
Understanding the complex behavior of molecular systems is fundamental to fields such as physics, materials science, and biology. Molecular dynamics (MD) simulations are crucial tools for studying atomic-level dynamics. This work focuses on…
Particle methods are less computationally efficient than grid based numerical solution of the Navier Stokes equation. However, they have important advantages including rigorous mass conservation, momentum conservation and isotropy. In…
A new approach to simulating warm and hot dense matter that combines density functional theory based calculations of the electronic structure to classical molecular dynamics simulations with pair interaction potentials is presented. The new…
Spatial stochastic molecular simulations in biology are limited by the intense computation required to track molecules in space either in a discrete time or discrete space framework, meaning that the serial limit has already been reached in…
Real-life control tasks involve matters of various substances---rigid or soft bodies, liquid, gas---each with distinct physical behaviors. This poses challenges to traditional rigid-body physics engines. Particle-based simulators have been…
We present a method for differentiable simulation of soft articulated bodies. Our work enables the integration of differentiable physical dynamics into gradient-based pipelines. We develop a top-down matrix assembly algorithm within…
The method of choice for integrating the equations of motion of the general N-body problem has been to use an individual time step scheme. For the sake of efficiency, block time steps have been the most popular, where all time step sizes…
We study numerical methods for dissipative particle dynamics (DPD), which is a system of stochastic differential equations and a popular stochastic momentum-conserving thermostat for simulating complex hydrodynamic behavior at mesoscales.…
Molecular Dynamics simulations are becoming a powerful tool for examining and predicting atomic and molecular processes in various environment. The present review shows how, in the fields of plasma physics, chemistry and interactions with…
In ab initio molecular dynamics simulations of real-world problems, the simple Verlet method is still widely used for integrating the equations of motion, while more efficient algorithms are routinely used in classical molecular dynamics.…