Related papers: Performance Evaluation of the Zero-Multipole Summa…

RPYFMM is a software package for the efficient evaluation of the potential field governed by the Rotne-Prager-Yamakawa (RPY) tensor interactions in biomolecular hydrodynamics simulations. In our algorithm, the RPY tensor is decomposed as a…

The proximal bundle method (PBM) is a fundamental and computationally effective algorithm for solving nonsmooth optimization problems. In this paper, we present the first variant of the PBM for smooth objectives, achieving an accelerated…

A general polarizable embedded (PE) quantum mechanics/molecular mechanics scheme for periodic systems is presented, describing mutual polarization of the two subsystems. The QM system, described with density functional theory (DFT), is…

Ab initio methods for electronic structure of molecules have reached a satisfactory accuracy for calculation of static properties, but remain too expensive for quantum dynamical calculations. We propose an efficient semiclassical method for…

Molecular dynamics (MD) simulations allow investigating the structural dynamics of biomolecular systems with unrivaled time and space resolution. However, in order to compensate for the inaccuracies of the utilized empirical force fields,…

A novel, particle based, probabilistic approach for the simulation of cloud microphysics is proposed, which is named the Super-Droplet Method (SDM). This method enables accurate simulation of cloud microphysics with less demanding cost in…

Computational modeling of assembly is challenging for many systems because their timescales vastly exceed those accessible to simulations. This article describes the MultiMSM, which is a general framework that uses Markov state models…

In this paper, a fast multipole method (FMM) is proposed for 3-D Laplace equation in layered media. The potential due to charges embedded in layered media is decomposed into a free space component and four types of reaction field…

We analyze deficiencies of commonly used Coulomb approximations in Generalized Born solvation energy calculation models and report a development of a new fast surface-based method (FSBE) for numerical calculations of the solvation energy of…

We report an extension of the smoothed profile method (SPM)[Y. Nakayama, K. Kim, and R. Yamamoto, Eur. Phys. J. E {\bf 26}, 361(2008)], a direct numerical simulation method for calculating the complex modulus of the dispersion of particles,…

In this paper, we propose a fast 2-D block-based motion estimation algorithm called Particle Swarm Optimization - Zero-motion Prejudgment(PSO-ZMP) which consists of three sequential routines: 1)Zero-motion prejudgment. The routine aims at…

Multi-modal semantic segmentation (MMSS) faces significant challenges in real-world applications due to incomplete, degraded, or missing sensor data. While current MMSS methods typically use self-distillation with modality dropout to…

We develop a random batch Ewald (RBE) method for molecular dynamics simulations of particle systems with long-range Coulomb interactions, which achieves an $O(N)$ complexity in each step of simulating the $N$-body systems. The RBE method is…

We introduce a general Monte Carlo scheme for achieving atomistic simulations with monoelectronic Hamiltonians including the thermalization of both nuclear and electronic degrees of freedom. The kinetic Monte Carlo algorithm is used to…

-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…

We develop a novel method of replica-exchange molecular dynamics (REMD) simulation, mass-scaling REMD (MSREMD) method, which improves trajectory accuracy at high temperatures, and thereby contributes to numerical stability. In addition, the…

We propose a simple many-body based screening mixing strategy to considerably enhance the performance of the Bethe-Salpeter (BS) approach for prediction of excitation energies of molecular systems. This strategy enables us to nearly…

We present monostatic sampling methods for limited-aperture scattering problems in two dimensions. The direct sampling method (DSM) is well known to provide a robust, stable, and fast numerical scheme for imaging inhomogeneities from…

Many different simulation methods for Stokes flow problems involve a common computationally intense task -- the summation of a kernel function over $O(N^2)$ pairs of points. One popular technique is the Kernel Independent Fast Multipole…

We present a new method to couple the Direct Simulation Monte Carlo (DSMC) algorithm with molecular dynamics (MD). The coupling approach generalizes prior coupling methods using a cell-based decision. The approach is supported by a lifting…