Related papers: HSMA: An O(N) electrostatics package implemented i…
Stochastic effect in cellular systems has been an important topic in systems biology. Stochastic modeling and simulation methods are important tools to study stochastic effect. Given the low efficiency of stochastic simulation algorithms,…
Learning how to safely handle Plasma-Material Interaction (PMI) is a key challenge towards the commercialisation of energy from nuclear fusion. In this respect, linear plasma devices are ideal experimental testbeds, and numerical codes play…
High-Performance Computing (HPC) platforms enable scientific software to achieve breakthroughs in many research fields such as physics, biology, and chemistry, by employing Research Software Engineering (RSE) techniques. These include 1)…
We introduce an alternative formulation of the exact stochastic simulation algorithm (SSA) for sampling trajectories of the chemical master equation for a well-stirred system of coupled chemical reactions. Our formulation is based on…
The recent progress of linear-scaling or O(N) methods in the density functional theory (DFT) is remarkable. We expect that first-principles molecular dynamics (FPMD) simulations based on DFT can now treat more realistic and complex systems…
In this paper we present a new three dimensional (3D) full electromagnetic relativistic hybrid plasma code H-VLPL (hybrid virtual laser plasma laboratory). The full kinetic particle-in-cell (PIC) method is used to simulate low density hot…
An algorithm for fast calculation of the Coulombic forces and energies of point particles with free boundary conditions is proposed. Its calculation time scales as N log N for N particles. This novel method has lower crossover point with…
We present teraflop-scale calculations of biomolecular electrostatics enabled by the combination of algorithmic and hardware acceleration. The algorithmic acceleration is achieved with the fast multipole method (FMM) in conjunction with a…
The SLUSCHI (Solid and Liquid in Ultra Small Coexistence with Hovering Interfaces) automated package, with interface to the first-principles code VASP (Vienna Ab initio Simulation Package), was developed by us for efficiently determining…
This article reviews two currently available analytic models of the dielectric function of a plasma consisting of quantum particles interacting via Coulomb forces, namely the Random Phase Approximation (RPA) and the Standard (Simple)…
Kernel matrix-vector product is ubiquitous in many science and engineering applications. However, a naive method requires $O(N^2)$ operations, which becomes prohibitive for large-scale problems. We introduce a parallel method that provably…
Outstanding advances in solid-state laser technology, employing the optical parametric chirped-pulse-amplification (OPCPA) technique, have led physicists to focus laser pulses to highly-relativistic intensities which led to novel schemes…
In advancing parallel programming, particularly with OpenMP, the shift towards NLP-based methods marks a significant innovation beyond traditional S2S tools like Autopar and Cetus. These NLP approaches train on extensive datasets of…
The molecular simulations solve the equation of motion of molecular systems, making 3D shapes of molecules four-dimensional by adding the time coordinate. These methods have a great potential in drug discovery because they can realistically…
We consider dynamically constrained Monte-Carlo dynamics and show that this leads to the generation of long ranged effective interactions. This allows us to construct a local algorithm for the simulation of charged systems without ever…
The high-performance computing (HPC) community has recently seen a substantial diversification of hardware platforms and their associated programming models. From traditional multicore processors to highly specialized accelerators, vendors…
We have developed and implemented a new quantum molecular dynamics approximation that allows fast and accurate simulations of dense plasmas from cold to hot conditions. The method is based on a carefully designed orbital-free implementation…
Machine learning (ML) is increasingly becoming a common tool in computational chemistry. At the same time, the rapid development of ML methods requires a flexible software framework for designing custom workflows. MLatom 3 is a program…
We present recent developments in the parallelization scheme of ECHO-3DHPC, an efficient astrophysical code used in the modelling of relativistic plasmas. With the help of the Intel Software Development Tools, like Fortran compiler and…
The global push for sustainability and energy efficiency is driving significant advancements across various industries, including the development of electrified solutions for heavy-duty mobile manipulators (HDMMs). Electromechanical linear…