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We propose an enhanced approach to the extrapolation of mean potential forces acting on atoms of solute macromolecules due to their interactions with solvent atoms in complex biochemical liquids. It improves and extends previous…
The approximate computation of all gravitational forces between $N$ interacting particles via the fast multipole method (FMM) can be made as accurate as direct summation, but requires less than $\mathcal{O}(N)$ operations. FMM groups…
We develop a computational method for modeling electrostatic interactions of arbitrarily-shaped, polarizable objects on colloidal length scales, including colloids/nanoparticles, polymers, and surfactants, dispersed in explicit ion…
Fast Ewald summation efficiently evaluates Coulomb interactions and is widely used in molecular dynamics simulations. It is based on a split into a short-range and a long-range part, where evaluation of the latter is accelerated using the…
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 propose an algorithm for molecular dynamics or Monte Carlo simulations that uses an interpolation procedure to estimate potential energy values from energies and gradients evaluated previously at points of a simplicial mesh. We chose an…
The interaction of condensed phase systems with external electric fields is crucial in myriad processes in nature and technology ranging from the field-directed motion of cells (galvanotaxis), to energy storage and conversion systems…
Smoothed particle hydrodynamics (SPH) is positioned as having ideal conservation properties. When properly implemented, conservation of total mass, energy, and both linear and angular momentum is guaranteed exactly, up to machine precision.…
Molecular dynamics simulations of biomolecules have been widely adopted in biomedical studies. As classical point-charge models continue to be used in routine biomolecular applications, there have been growing demands on developing…
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,…
The meshless/meshfree radial basis function (RBF) method is a powerful technique for interpolating scattered data. But, solving large RBF interpolation problems without fast summation methods is computationally expensive. For RBF…
In dislocation dynamics (DD) simulations, the most computationally intensive step is the evaluation of the elastic interaction forces among dislocation ensembles. Because the pair-wise interaction between dislocations is long-range, this…
Among the algorithms that are likely to play a major role in future exascale computing, the fast multipole method (FMM) appears as a rising star. Our previous recent work showed scaling of an FMM on GPU clusters, with problem sizes in the…
Most atomistic machine learning (ML) models rely on a locality ansatz, and decompose the energy into a sum of short-ranged, atom-centered contributions. This leads to clear limitations when trying to describe problems that are dominated by…
To address the computational challenges of ab initio molecular dynamics and the accuracy limitations of empirical force fields, the introduction of machine learning force fields has proven effective in various systems including metals and…
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…
In this work, an implicit scheme for particle-in-cell/Fourier electromagnetic simulations is developed and applied to studies of Alfv\'en waves in one dimension and three-dimensional tokamak plasmas. An analytical treatment is introduced to…
Quantum-mechanically-driven charge polarization and charge transfer are ubiquitous in biomolecular systems, controlling reaction rates, allosteric interactions, ligand-protein binding, membrane transport, and dynamically-driven structural…
Quasi two-dimensional Coulomb systems have drawn widespread interest. The reduced symmetry of these systems leads to complex collective behaviors, yet simultaneously poses significant challenges for particle-based simulations. In this…
We present a simulation capability for micro-scale light-emitting diodes (uLEDs) that achieves comparable accuracy to CPU-based finite-difference time-domain simulation but is more than 10^7 times faster. Our approach is based on the…