Related papers: DynamO: A free O(N) general event-driven molecular…
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…
Neural network potentials (NNPs) enable large-scale molecular dynamics (MD) simulations of systems containing >10,000 atoms with the accuracy comparable to ab initio methods and play a crucial role in material studies. Although NNPs are…
We present a multiscale simulation algorithm for amorphous materials, which we illustrate and validate in a canonical case of dense granular flow. Our algorithm is based on the recently proposed Spot Model, where particles in a dense random…
We present a novel simulation-free framework for training continuous-time diffusion processes over very general objective functions. Existing methods typically involve either prescribing the optimal diffusion process -- which only works for…
Multiscale dynamical systems, modeled by high-dimensional stiff ordinary differential equations (ODEs) with wide-ranging characteristic timescales, arise across diverse fields of science and engineering, but their numerical solvers often…
In this work, we analytically examine the validity of molecular dynamics for a soft potential system by considering a simple one-dimensional system with a piecewise continuous linear repulsive potential wall having a constant slope $a$. We…
We propose novel particle swarm optimization (PSO) variants incorporated with deep neural networks (DNNs) for particles to pursue globally optimal positions in dynamic environments. PSO is a heuristic approach for solving complex…
While several numerical techniques are available for predicting the dynamics of non-Markovian open quantum systems, most struggle with simulations for very long memory and propagation times, e.g., due to superlinear scaling with the number…
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…
Classical molecular dynamics simulations are a common component of multi-modal analyses from scattering measurements, such as small-angle scattering and diffraction. Users of these experimental techniques often have no formal training in…
Complex plasmas are low-temperature plasmas that contain micrometer-size particles in addition to the neutral gas particles and the ions and electrons that make up the plasma. The microparticles interact strongly and display a wealth of…
Efficient simulations of quantum evolutions of spin-1/2 systems are relevant for ensemble quantum computation as well as in typical NMR experiments. We propose an efficient method to calculate the dynamics of an observable provided that the…
Enhanced sampling algorithms have emerged as powerful methods to extend the utility of molecular dynamics simulations and allow the sampling of larger portions of the configuration space of complex systems in a given amount of simulation…
A framework for performing event-driven, adaptive time step simulations of systems of rigid bodies interacting under stepped or terraced potentials in which the potential energy is only allowed to have discrete values is outlined. The…
We propose a computational method to simulate anomalous self-diffusion in a simple liquid. The method is based on a molecular dynamics simulation on which we impose the following two conditions: firstly, the inter-particle interaction is…
The existing Neural ODE formulation relies on an explicit knowledge of the termination time. We extend Neural ODEs to implicitly defined termination criteria modeled by neural event functions, which can be chained together and…
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…
For complex molecules, nuclear degrees of freedom can act as an environment for the electronic `system' variables, allowing the theory and concepts of open quantum systems to be applied. However, when molecular system-environment…
In applied sciences, we often deal with deterministic simulation models that are too slow for simulation-intensive tasks such as calibration or real-time control. In this paper, an emulator for a generic dynamic model, given by a system of…
The optimal conversion of a continuous inter-particle potential to a discrete equivalent is considered here. Existing and novel algorithms are evaluated to determine the best technique for creating accurate discrete forms using the minimum…