Related papers: Efficient Parallel Algorithm for Statistical Ion T…
We compare different methods for sampling from discrete probability distributions and introduce a new algorithm which is especially efficient on massively parallel processors, such as GPUs. The scheme preserves the distribution properties…
We propose an efficient simulation algorithm based on the dissipative particle dynamics (DPD) method for studying electrohydrodynamic phenomena in electrolyte fluids. The fluid flow is mimicked with DPD particles while the evolution of the…
Parallel replica dynamics is a method for accelerating the computation of processes characterized by a sequence of infrequent events. In this work, the processes are governed by the overdamped Langevin equation. Such processes spend much of…
We develop an efficient parallel multiscale method that bridges the atomistic and mesoscale regimes, from nanometer to micron and beyond, via concurrent coupling of atomistic simulation and mesoscopic dynamics. In particular, we combine an…
The implicit 2D3V particle-in-cell (PIC) code developed to study the interaction of ultrashort pulse lasers with matter [G. M. Petrov and J. Davis, Computer Phys. Comm. 179, 868 (2008); Phys. Plasmas 18, 073102 (2011)] has been parallelized…
In this work, we investigate the potential utility of parallelization for meeting real-time constraints and minimizing energy. We consider malleable Gang scheduling of implicit-deadline sporadic tasks upon multiprocessors. We first show the…
Engineering simulations are usually based on complex, grid-based, or mesh-free methods for solving partial differential equations. The results of these methods cover large fields of physical quantities at very many discrete spatial…
We apply the multigrid-reduction-in-time (MGRIT) algorithm to an eddy current simulation of a two-dimensional induction machine supplied by a pulse-width-modulation signal. To resolve the fast-switching excitations, small time steps are…
Molecular dynamics (MD) simulations of complex electrochemical systems, such as ionic liquid supercapacitors, are increasingly including the constant potential method (CPM) to model conductive electrodes at specified potential difference,…
A novel Stochastic Event-Driven Molecular Dynamics (SEDMD) algorithm is developed for the simulation of polymer chains suspended in a solvent. The polymers are represented as chains of hard spheres tethered by square wells and interact with…
The presented work demonstrates the training of recurrent neural networks (RNNs) from distributions of atom coordinates in solid state structures that were obtained using ab initio molecular dynamics (AIMD) simulations. AIMD simulations on…
Only a small fraction of the data generated in state-of-the-art all-atom multi-microsecond molecular dynamics (MD) simulations is typically analyzed. With femtosecond integration steps, microsecond simulations generate billions of time…
We propose a hybrid deterministic and stochastic approach to achieve extended time scales in atomistic simulations that combines the strengths of molecular dynamics (MD) and Monte Carlo (MC) simulations in an easy-to-implement way. The…
The phenomena that emerge from the interaction of the stochastic opening and closing of ion channels (channel noise) with the non-linear neural dynamics are essential to our understanding of the operation of the nervous system. The effects…
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…
The Ray-Casting algorithm is an important method for fast real-time surface display from 3D medical images. Based on the Ray-Casting algorithm, a novel parallel Ray-Casting algorithm is proposed in this paper. A novel operation is…
We describe novel subgradient methods for a broad class of matrix optimization problems involving nuclear norm regularization. Unlike existing approaches, our method executes very cheap iterations by combining low-rank stochastic…
A simple method for improving cache efficiency of serial and parallel explicit finite procedure with application to casting solidification simulation over three-dimensional complex geometries is presented. The method is based on division of…
Particle tracking has several important applications for solute transport studies in aquifer systems. Travel time distribution at observation points, particle coordinates in time and streamlines are some practical results providing…
Large-scale observational health databases are increasingly popular for conducting comparative effectiveness and safety studies of medical products. However, increasing number of patients poses computational challenges when fitting survival…