Related papers: ESPResSo 4.0 -- An Extensible Software Package for…
PyMembrane is a software package for simulating liquid and elastic membranes using a discretisation of the continuum description based on unstructured triangulated two-dimensional meshes embedded in three-dimensional space. The package is…
Scalable and efficient numerical simulations continue to gain importance, as computation is firmly established as the third pillar of discovery, alongside theory and experiment. Meanwhile, the performance of computing hardware grows through…
Field emission coupled with molecular dynamics simulation (FEcMD) software package is a computational tool for studying atomic structure evolution, structural deformation, phase transitions, recrystallization as well as electron emission…
Toward the goal of using Scientific Machine Learning (SciML) emulators to improve the numerical representation of aerosol processes in global atmospheric models, we explore the emulation of aerosol microphysics processes under cloud-free…
With the development of high-speed electron detectors, four-dimensional scanning transmission electron microscopy (4D-STEM) has emerged as a powerful tool for characterizing microstructures in material science and life science. However, the…
It is desired to equip robots with the capability of interacting with various soft materials as they are ubiquitous in the real world. While physics simulations are one of the predominant methods for data collection and robot training,…
Software Engineering and the implementation of software has become a challenging task as many tools, frameworks and languages must be orchestrated into one functioning piece. This complexity increases the need for testing and analysis…
Small-angle X-ray scattering (SAXS) experiments are increasingly used to probe RNA structure. A number of \emph{forward models} that relate measured SAXS intensities and structural features, and that are suitable to model either…
We describe the software package $\texttt{ESpRESSO}$ - [E]xtragalactic [Sp]ectroscopic [R]oman [E]mulator and [S]imulator of [S]ynthetic [O]bjects, created to emulate the slitless spectroscopic observing modes of the Nancy Grace Roman Space…
Large computer models are ubiquitous in the earth sciences. These models often have tens or hundreds of tuneable parameters and can take thousands of core-hours to run to completion while generating terabytes of output. It is becoming…
Molecular-dynamics algorithms for systems of particles interacting through discrete or "hard" potentials are fundamentally different to the methods for continuous or "soft" potential systems. Although many software packages have been…
Harnessing modern parallel computing resources to achieve complex multi-physics simulations is a daunting task. The Multiphysics Object Oriented Simulation Environment (MOOSE) aims to enable such development by providing simplified…
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)…
Structural Equation Modeling (SEM) is an umbrella term that includes numerous multivariate statistical techniques that are employed throughout a plethora of research areas, ranging from social to natural sciences. Until recently, SEM…
Nuclear and particle physics are the core components of most undergraduate and postgraduate physics courses worldwide. While few fundamental concepts like particle counting and detector characterisation are taught in tandem with laboratory…
Scientific software is often driven by multiple parameters that affect both accuracy and performance. Since finding the optimal configuration of these parameters is a highly complex task, it extremely common that the software is used…
This paper presents a 2D/3D Free Surface Lattice Boltzmann Method simulation package called LBfoam for the simulation of foaming processes. The model incorporates the essential physics of foaming phenomena: gas diffusion into nucleated…
Molecular dynamics simulations have emerged as a fundamental instrument for studying biomolecules. At the same time, it is desirable to perform simulations of a collection of particles under various conditions in which the molecules can…
relentless is an open-source Python package that enables the optimization of objective functions computed using molecular dynamics simulations. It has a high-level, extensible interface for model parametrization; setting up, running, and…
Empirical software engineering faces a critical gap: the lack of standardized tools for rapid development and execution of Test-Driven Software Experiments (TDSEs) -- that is, experiments that involve the execution of software subjects and…