相关论文: Velocity jump processes : an alternative to multi-…

We consider the problem of efficiently performing simulation and inference for stochastic kinetic models. Whilst it is possible to work directly with the resulting Markov jump process, computational cost can be prohibitive for networks of…

In this paper we develop a stochastic boundary conditions (SBC) for event-driven molecular dynamics simulations of a finite volume embedded within an infinite environment. In this method, we first collect the statistics of…

It was recently demonstrated that a simple Monte Carlo (MC) algorithm involving the swap of particle pairs dramatically accelerates the equilibrium sampling of simulated supercooled liquids. We propose two numerical schemes integrating the…

We implement a three-body potential to model associative bond swaps, and release it as part of the HOOMD-blue software. The use of a three-body potential to model swaps has been proven to be effective and has recently provided useful…

Large-scale molecular dynamics simulations with high accuracy have been increasingly popular for their capability to bridge the gap between atomistic modeling and mesoscale phenomena. Both machine learning potentials and enhanced sampling…

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…

The use of stochastic models, in effect piecewise deterministic Markov processes (PDMP), has become increasingly popular especially for the modeling of chemical reactions and cell biophysics. Yet, exact simulation methods, for the…

Many stochastic processes in the physical and biological sciences can be modelled as Brownian dynamics with multiplicative noise. However, numerical integrators for these processes can lose accuracy or even fail to converge when the…

With the continuous growth of processing power for scientific computing, first principles Born-Oppenheimer molecular dynamics (MD) simulations are becoming increasingly popular for the study of a wide range of problems in materials science,…

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 multi-level elastodynamics timestep solver for accelerating incremental potential contact (IPC) simulations. Our method retains the robustness of gold standard IPC in the face of intricate geometry, complex heterogeneous…

We present teraflop-scale calculations of biomolecular electrostatics enabled by the combination of algorithmic and hardware acceleration. The algorithmic acceleration is achieved with the fast multipole method (FMM) in conjunction with a…

-Molecular simulations allow the study of properties and interactions of molecular systems. This article presents an improved version of the Adaptive Resolution Scheme that links two systems having atomistic (also called fine-grained) and…

Simulations are vital for understanding and predicting the evolution of complex molecular systems. However, despite advances in algorithms and special purpose hardware, accessing the timescales necessary to capture the structural evolution…

Despite its widespread use in materials science, conventional molecular dynamics (MD) simulations are severely constrained by timescale limitations. To address this shortcoming, we propose an empirical formulation of accelerated MD method,…

As inverter-based resources (IBRs) penetrate power systems, the dynamics become more complex, exhibiting multiple timescales, including electromagnetic transient (EMT) dynamics of power electronic controllers and electromechanical dynamics…

Ab initio molecular dynamics (AIMD) with hybrid density functionals and plane wave basis is computationally expensive due to the high computational cost of exact exchange energy evaluation. Recently, we proposed a strategy to combine…

We perform a series of calculations using simulated QPUs, accelerated by the NVIDIA CUDA-Q platform, focusing on a molecular analog of an amine-functionalized metal-organic framework (MOF), a promising class of materials for CO$_2$ capture.…

Computing long-timescale kinetics of biomolecular processes remains a major challenge for atomistic simulations. A way out is to exploit local kinetic information to construct the global stationary flux across the reaction space. The…

Coulomb interaction, following an inverse-square force-law, quantifies the amount of force between two stationary and electrically charged particles. The long-range nature of Coulomb interactions poses a major challenge to molecular…