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Biochemical reactions typically occur at low copy numbers, but at once in crowded and diverse environments. Space and stochasticity therefore play an essential role in biochemical networks. Spatial-stochastic simulations have become a…
We introduce Gradient Particle Magnetohydrodynamics (GPM), a new Lagrangian method for magnetohydrodynamics based on gradients corrected for the locally disordered particle distribution. The development of a numerical code for MHD…
Dyadic Green's function is an important tool of computational photonics, giving deeper insights into light-matter interaction. We present an operator approach to the derivation of the dyadic Green's function of a generic anisotropic…
Near- and far-field optical properties of silicon nanostructures under linear polarization (Gaussian beam), and azimuthally or radially focused cylindrical vector beams are investigated by finite-difference time-domain method (FDTD) in Meep…
Matter-RADiation interaction SIMulation (MRADSIM) is an innovative modular software toolkit developed to simulate the effects of radiation on electronic components, human beings and various materials. It incorporates innovative features…
We have developed an efficient simulation tool 'GOLLUM' for the computation of electrical, spin and thermal transport characteristics of complex nanostructures. The new multi-scale, multi-terminal tool addresses a number of new challenges…
We present the first public release (v0.1) of the open-source GADGET Dataframe Library: gadfly. The aim of this package is to leverage the capabilities of the broader python scientific computing ecosystem by providing tools for analyzing…
In this paper we present an advanced numerical method to simulate a real life challenging industrial problem that consists of the non-destructive testing in steam generators. We develop a finite element technique that handles the big data…
Recent advancements in 3D generation models have opened new possibilities for simulating dynamic 3D object movements and customizing behaviors, yet creating this content remains challenging. Current methods often require manual assignment…
Molecular dynamics (MD) simulation has long been the principal computational tool for exploring protein conformational landscapes and dynamics, but its application is limited by high computational cost. We present ProTDyn, a foundation…
Despite advances in physics-based 3D motion synthesis, current methods face key limitations: reliance on pre-reconstructed 3D Gaussian Splatting (3DGS) built from dense multi-view images with time-consuming per-scene optimization; physics…
Magboltz is widely used to compute electron transport properties in gas mixtures for detector applications. Its text-based workflow, however, can be a barrier for routine use, especially for users who are not already familiar with the…
The increasing use of microfluidics in industrial, biomedical, and clinical applications requires a more and more precise control of the microfluidic flows and suspended particles or cells. This leads to higher demands in three-dimensional…
Nonlinear Optical Spectroscopy is a well-developed field with theoretical and experimental advances that have aided multiple fields including chemistry, biology and physics. However, accurate quantum dynamical simulations based on model…
Additive models offer accurate and interpretable predictions for tabular data, a critical tool for statistical modeling. Recent advances in Neural Additive Models (NAMs) allow these models to handle complex machine learning tasks, including…
Rydberg atoms provide a powerful platform for exploring strongly interacting quantum systems, both in free space and in structured electromagnetic environments, with growing applications in quantum technology. Accurately modeling their…
We present yadism, a library for the evaluation of both polarized and unpolarized deep-inelastic scattering (DIS) structure functions and cross sections up to N$^3$LO in perturbative QCD. The package provides computations of observables in…
MNPBEM is a Matlab toolbox for the simulation of metallic nanoparticles (MNP), using a boundary element method (BEM) approach. The main purpose of the toolbox is to solve Maxwell's equations for a dielectric environment where bodies with…
The increasing importance of Computational Science and Engineering has highlighted the need for high-quality scientific software. However, research software development is often hindered by limited funding, time, staffing, and technical…
Sample-induced image-degradation remains an intricate wave-optical problem in light-sheet microscopy. Here we present biobeam, an open-source software package that enables to simulate operational light-sheet microscopes by combining data…