Related papers: SMILEI: a collaborative, open-source, multi-purpos…
Artificial intelligence (AI) and machine learning (ML) are expanding in popularity for broad applications to challenging tasks in chemistry and materials science. Examples include the prediction of properties, the discovery of new reaction…
The particle-in-cell (PIC) method has been widely used for plasma simulation, because of its noise-reduction capability and moderate computational cost. The immersed finite element (IFE) method is efficient for solving interface problems on…
Robustly handling collisions between individual particles in a large particle-based simulation has been a challenging problem. We introduce particle merging-and-splitting, a simple scheme for robustly handling collisions between particles…
We present a computer code written in C that is designed to simulate structure formation from collisionless matter. The code is purely grid-based and uses a recursively refined Cartesian grid to solve Poisson's equation for the potential,…
Next-generation High Energy Physics (HEP) experiments will generate unprecedented data volumes, necessitating High Performance Computing (HPC) integration alongside traditional high-throughput computing. However, HPC adoption in HEP is…
Molecular simulations are an important tool for research in physics, chemistry, and biology. The capabilities of simulations can be greatly expanded by providing access to advanced sampling methods and techniques that permit calculation of…
Virtual screening is a technique used in drug discovery to select the most promising molecules to test in a lab. To perform virtual screening, we need a large set of molecules as input, and storing these molecules can become an issue. In…
SMeagol is a software tool to simulate highly realistic microscopy data based on spatial systems biology models, in order to facilitate development, validation, and optimization of advanced analysis methods for live cell single molecule…
Furthering our understanding of many of today's interesting problems in plasma physics---including plasma based acceleration and magnetic reconnection with pair production due to quantum electrodynamic effects---requires large-scale kinetic…
Machine learning interatomic potentials (MLIPs) enable atomistic simulations with near ab initio accuracy at significantly reduced computational cost, but their broader adoption is often limited by fragmented tooling, limited scalability,…
Complex plasmas are low-temperature plasmas that contain micrometer-size particles in addition to the neutral gas particles and the ions and electrons that make up the plasma. The microparticles interact strongly and display a wealth of…
Computational chemistry allows researchers to experiment in sillico: by running a computer simulations of a biological or chemical processes of interest. Molecular dynamics with molecular mechanics model of interactions simulates N-body…
A massively parallel simulation code, called \textit{dHybrid}, has been developed to perform global scale studies of space plasma interactions. This code is based on an explicit hybrid model; the numerical stability and parallel scalability…
We present a Fortran 95 code for simulating the evolution of astrophysical systems using particles to represent the underlying fluid flow. The code is designed to be versatile, flexible and extensible, with modular options that can be…
We present HONEI, an open-source collection of libraries offering a hardware oriented approach to numerical calculations. HONEI abstracts the hardware, and applications written on top of HONEI can be executed on a wide range of computer…
Simplified Molecular Input Line Entry System (SMILES) is a single line text representation of a unique molecule. One molecule can however have multiple SMILES strings, which is a reason that canonical SMILES have been defined, which ensures…
Molecular simulation is a scientific tool dealing with challenges in material science and biology. This is reflected in a permanent development and enhancement of algorithms within scientific simulation packages. Here, we present…
Merlin++ is a C++ charged-particle tracking library developed for the simulation and analysis of complex beam dynamics within high energy particle accelerators. Accurate simulation and analysis of particle dynamics is an essential part of…
We use electromagnetic Particle-in-Cell codes to investigate the two-stream instability and Weibel instability when two beams of plasma collide head-on relativistically. We compare the dissipation of kinetic energies in the two cases. We…
In a first course to classical mechanics elementary physical processes like elastic two-body collisions, the mass-spring model, or the gravitational two-body problem are discussed in detail. The continuation to many-body systems, however,…