相关论文: Performance Evaluation of the Zero-Multipole Summa…

Scientific software is often driven by multiple parameters that affect both accuracy and performance. Since finding the optimal configuration of these parameters is a highly complex task, it extremely common that the software is used…

We report a development of a new fast surface-based method for numerical calculations of solvation energy of biomolecules with a large number of charged groups. The procedure scales linearly with the system size both in time and memory…

The multipole-expansion (MPE) model is an implicit solvation model used to efficiently incorporate solvent effects in quantum chemistry. Even within the recent direct approach, the multipole basis used in MPE to express the dielectric…

In this paper, we design and analyze a new zeroth-order online algorithm, namely, the zeroth-order online alternating direction method of multipliers (ZOO-ADMM), which enjoys dual advantages of being gradient-free operation and employing…

We propose a method for efficiently coupling the finite element method with atomistic simulations, while using molecular dynamics or kinetic Monte Carlo techniques. Our method can dynamically build an optimized unstructured mesh that…

The increasing number of protein-based metamaterials demands reliable and efficient theoretical and computational methods to study the physicochemical properties they may display. In this regard, we develop a simulation strategy based on…

The fast multipole method (FMM) performs fast approximate kernel summation to a specified tolerance $\epsilon$ by using a hierarchical division of the domain, which groups source and receiver points into regions that satisfy local…

In plasma edge simulations, kinetic Monte Carlo (MC) is often used to simulate neutral particles and estimate source terms. For large-sized reactors, like ITER and DEMO, high particle collision rates lead to a substantial computational cost…

In order to numerically solve high-dimensional nonlinear PDEs and alleviate the curse of dimensionality, a stochastic particle method (SPM) has been proposed to capture the relevant feature of the solution through the adaptive evolution of…

Typical biomolecular systems such as cellular membranes, DNA, and protein complexes are highly charged. Thus, efficient and accurate treatment of electrostatic interactions is of great importance in computational modelling of such systems.…

Multiparticle collision dynamics (MPCD) is a flexible and robust mesoscale computational technique for simulating solvent-mediated hydrodynamic interactions in soft materials. Here, we provide a critical overview of the MPCD method and…

We present an NPT extension of Ewald summation with prolates (ESP), a spectrally accurate and scalable particle-mesh method for molecular dynamics simulations of periodic, charged systems. Building on the recently introduced ESP framework,…

This paper introduces a random-batch molecular dynamics (RBMD) package for fast simulations of particle systems at the nano/micro scale. Different from existing packages, the RBMD uses random batch methods for nonbonded interactions of…

Atomistic spin dynamics simulations provide valuable information about the energy spectrum of magnetic materials in different phases, allowing one to identify instabilities and the nature of their excitations. However, the time cost of…

The long-range magnetic field is the most time-consuming part in micromagnetic simulations. Improvements both on a numerical and computational basis can relief problems related to this bottleneck. This work presents an efficient…

We design a quantum molecular dynamics method for strongly correlated electron metals. The strong electronic correlation effects are treated within a real-space version of the Gutzwiller variational approximation (GA), which is suitable for…

In this letter, we first propose a \underline{Z}eroth-\underline{O}rder c\underline{O}ordinate \underline{M}ethod~(ZOOM) to solve the stochastic optimization problem over a decentralized network with only zeroth-order~(ZO) oracle feedback…

The paper describes the coupling of the MercuryDPM discrete element method (DEM) code and the implementation of the kernel-independent fast multipole method (KIFMM). The combined simulation framework allows addressing the large class of…

We use machine learning to enable large-scale molecular dynamics (MD) of a correlated electron model under the Gutzwiller approximation scheme. This model exhibits a Mott transition as a function of on-site Coulomb repulsion $U$. The…

Hybrid quantum mechanical-molecular mechanical (QM/MM) simulations are widely used in enzyme simulation. Over ten convergence studies of QM/MM methods have revealed over the past several years that key energetic and structural properties…