Related papers: SEAMM: A Simulation Environment for Atomistic and …
The JETSCAPE simulation framework is an overarching computational envelope for developing complete event generators for heavy-ion collisions. It allows for modular incorporation of a wide variety of existing and future software that…
A large number of powerful, high-quality, and open-source simulation packages exist to efficiently perform molecular dynamics simulations, and their prevalence has greatly accelerated discoveries across a wide range of scientific domains.…
SMILEI is a collaborative, open-source, object-oriented (C++) particle-in-cell code. To benefit from the latest advances in high-performance computing (HPC), SMILEI is co-developed by both physicists and HPC experts. The code's structures,…
Ensemble datasets are ever more prevalent in various scientific domains. In climate science, ensemble datasets are used to capture variability in projections under plausible future conditions including greenhouse and aerosol emissions. Each…
With the increase of research in self-adaptive systems, there is a need to better understand the way research contributions are evaluated. Such insights will support researchers to better compare new findings when developing new knowledge…
The promise of AI-driven scientific discovery hinges on whether AI agents can autonomously design and execute the computational workflows that underpin modern science. Molecular dynamics (MD) simulation presents a natural test bed to…
Sequence alignment is a memory bound computation whose performance in modern systems is limited by the memory bandwidth bottleneck. Processing-in-memory architectures alleviate this bottleneck by providing the memory with computing…
This article illustrates the development of a software named GoldEnvSim for simulation of the dispersion of radionuclides in the atmosphere. The software is written in JavaFX programming language to couple the Weather Research and…
As space exploration advances, underground environments are becoming increasingly attractive due to their potential to provide shelter, easier access to resources, and enhanced scientific opportunities. Although such environments exist on…
We describe AMUSE, the Astrophysical Multipurpose Software Environment, a programming framework designed to manage multi-scale, multi-physics simulations in a hierarchical, extensible, and internally consistent way. Constructed as a…
Human-robot interaction requires a common understanding of the operational environment, which can be provided by a representation that blends geometric and symbolic knowledge: a semantic map. Through a semantic map the robot can interpret…
Summary: The Systems Biology Markup Language (SBML) is an extensible standard format for exchanging biochemical models. One of the extensions for SBML is the SBML Layout and Render package. This allows modelers to describe a biochemical…
Modeling deformable objects - especially continuum materials - in a way that is physically plausible, generalizable, and data-efficient remains challenging across 3D vision, graphics, and robotic manipulation. Many existing methods…
A major challenge in light-matter simulations is bridging the disparate time and length scales of electrodynamics and molecular dynamics. Current computational approaches often rely on heuristic approximations of either the electromagnetic…
One of the key requirements for incorporating machine learning into the drug discovery process is complete reproducibility and traceability of the model building and evaluation process. With this in mind, we have developed an end-to-end…
The Institute for Solid State Physics (ISSP) at The University of Tokyo has been carrying out a software development project named ``the Project for Advancement of Software Usability in Materials Science (PASUMS)". Since the launch of…
Argon molecular dynamics (MD) simulations are performed with a newly developed MD program, Easy M(1)odular M(2)olecular M(3)echanics (EM3). The program was developed in an object-oriented fashion containing classes for each critical part of…
E(A+M)PEC traces the ionization structure, cooling and emission spectra of plasmas. It is written in OpenCL, runs in NVIDIA Graphics Processor Units and can be coupled to any HD or MHD code to follow the dynamical and thermal evolution of…
Electrical machines commonly consist of moving and stationary parts. The field simulation of such devices can be very demanding if the underlying numerical scheme is solely based on a domain discretization, such as in case of the Finite…
We introduce atomicrex, an open-source code for constructing interatomic potentials as well as more general types of atomic-scale models. Such effective models are required to simulate extended materials structures comprising many thousands…