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A crucial aspect in the simulation of electrochemical interfaces consists in treating the distribution of electronic charge of electrode materials that are put in contact with an electrolyte solution. Recently, it has been shown how a…
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.…
Fast Multipole Methods (FMMs) based on the oscillatory Helmholtz kernel can reduce the cost of solving N-body problems arising from Boundary Integral Equations (BIEs) in acoustic or electromagnetics. However, their cost strongly increases…
An implementation of the fast multiple method (FMM) is performed for magnetic systems with long-ranged dipolar interactions. Expansion in spherical harmonics of the original FMM is replaced by expansion of polynomials in Cartesian…
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…
We evaluate the practical performance of the zero-multiple summation method (ZMM), a method for approximately calculating electrostatic interactions in molecular dynamics simulations. The performance of the ZMM is compared with that of the…
A proper treatment of electrostatic interactions is crucial for the accurate calculation of forces in computer simulations. Electrostatic interactions are typically modeled using Ewald based methods, which have become one of the…
A large share of today's HPC workloads is used for Ab-Initio Molecular Dynamics (AIMD) simulations, where the interatomic forces are computed on-the-fly by means of accurate electronic structure calculations. They are computationally…
The FFT EnKF data assimilation method is proposed and applied to a stochastic cell simulation of an epidemic, based on the S-I-R spread model. The FFT EnKF combines spatial statistics and ensemble filtering methodologies into a localized…
For inhomogeneous systems with interfaces, the inclusion of long-range dispersion interactions is necessary to achieve consistency between molecular simulation calculations and experimental results. For accurate and efficient incorporation…
We investigate a hybrid numerical algorithm aimed at the large-scale cosmological N-body simulation for the on-going and the future high precious sky surveys. It makes use of a truncated Fast Multiple Method (FMM) for short-range gravity,…
Large classes of materials systems in physics and engineering are governed by magnetic and electrostatic interactions. Continuum or mesoscale descriptions of such systems can be cast in terms of integral equations, whose direct…
We report the implementation of a multi-CPU and multi-GPU massively parallel platform dedicated to the explicit inclusion of nuclear quantum effects (NQEs) in the Tinker-HP molecular dynamics (MD) package. The platform, denoted Quantum-HP,…
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…
We derive a Fast Multipole Method (FMM) where a low-rank approximation of the kernel is obtained using the Empirical Interpolation Method (EIM). Contrary to classical interpolation-based FMM, where the interpolation points and basis are…
Simulating the dynamics of charged particles in quasi-two-dimensional (quasi-2D) nanoconfined systems presents a significant computational challenge due to the long-range nature of electrostatic interactions and the geometric anisotropy. To…
Non-uniform fast Fourier Transform (NUFFT) and inverse NUFFT (INUFFT) algorithms, based on the Fast Multipole Method (FMM) are developed and tested. Our algorithms are based on a novel factorization of the FFT kernel, and are implemented…
The fast multipole method (FMM) has had great success in reducing the computational complexity of solving the boundary integral form of the Helmholtz equation. We present a formulation of the Helmholtz FMM that uses Fourier basis functions…
Massively-parallel molecular dynamics simulation is applied to systems containing electrolytes, vapour-liquid interfaces, and biomolecules in contact with water-oil interfaces. Novel molecular models of alkali halide salts are presented and…
In computational molecular science, calculation of electrostatic interactions involving charged atoms - the strongest interactions in condensed phases, is a major bottleneck. We propose a quantum-classical algorithm for fast, yet, accurate…