Related papers: Accelerating Molecular Dynamics Simulations using …
We consider in this work the convergence of a split-step Euler type scheme (SSM) for the numerical simulation of interacting particle Stochastic Differential Equation (SDE) systems and McKean-Vlasov Stochastic Differential Equations…
The efficient simulation of fluid-structure interactions at zero Reynolds number requires the use of fast summation techniques in order to rapidly compute the long-ranged hydrodynamic interactions between the structures. One approach for…
The physical processes at the interface of a low-temperature plasma and a solid are extremely complex. They involve a huge number of elementary processes in the plasma, in the solid as well as charge, momentum and energy transfer across the…
The simulation of high-energy physics collision events is a key element for data analysis at present and future particle accelerators. The comparison of simulation predictions to data allows looking for rare deviations that can be due to…
Mapping the conformational dynamics of proteins is crucial for elucidating their functional mechanisms. While Molecular Dynamics (MD) simulation enables detailed time evolution of protein motion, its computational toll hinders its use in…
In this paper, we propose a Gaussian Process (GP) emulator for the calculation of a) tomographic weak lensing band-power spectra, and b) coefficients of summary data massively compressed with the MOPED algorithm. In the former case…
Radiative transfer effects need to be taken into account when analysing spectral line observations. When the data are not sufficient for detailed modelling, simpler methods are needed. The escape probability formalism (EPF) is one such…
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…
An extension to the P3M algorithm for electrostatic interactions is presented, that allows to efficiently compute dipolar interactions in periodic boundary conditions. Theoretical estimates for the root-mean square error of the forces,…
The microscopic description of nuclear fission still remains a topic of intense basic research. Un- derstanding nuclear fission, apart from a theoretical point of view, is of practical importance for energy production and the transmutation…
Metasurfaces, consisting of large arrays of interacting subwavelength scatterers, pose significant challenges for general-purpose computational methods due to their large electric dimensions and multiscale nature. This paper introduces an…
We develop an accurate, highly efficient and scalable random batch sum-of-Gaussians (RBSOG) method for molecular dynamics simulations of systems with long-range interactions. The idea of the RBSOG method is based on a sum-of-Gaussians…
Classical Molecular Dynamics (MD) simulations provide insight on the properties of many soft-matter systems. In some situations it is interesting to model the creation of chemical bonds, a process that is not part of the MD framework. In…
The computer simulation of many molecular processes is complicated by long time scales caused by rare transitions between long-lived states. Here, we propose a new approach to simulate such rare events, which combines transition path…
We present our recent code modernizations of the of the ab initio molecular dynamics program CPMD (www.cpmd.org) with a special focus on the ultra-soft pseudopotential (USPP) code path. Following the internal instrumentation of CPMD, all…
We report a novel hybrid method of simultaneous atomistic simulation of solids in critical regions (contacts surfaces, cracks areas, etc.), along with continuum modeling of other parts. The continuum is treated in terms of quasi-atoms of…
Recent advances in fast sampling methods for diffusion models have demonstrated significant potential to accelerate generation on image modalities. We apply these methods to 3-dimensional molecular conformations by building on the recently…
We develop an accurate, highly efficient and scalable random batch Ewald (RBE) method to conduct simulations in the isothermal-isobaric ensemble (the NPT ensemble) for charged particles in a periodic box. After discretizing the Langevin…
Microscopic processes on surfaces such as adsorption, desorption, diffusion and reaction of interacting particles can be simulated using kinetic Monte Carlo (kMC) algorithms. Even though kMC methods are accurate, they are computationally…
The integral equation coarse-graining (IECG) approach is a promising high-level coarse-graining (CG) method for polymer melts, with variable resolution from soft spheres to multi CG sites, which preserves the structural and thermodynamical…