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Chemical reaction networks (CRNs) provide a convenient language for modelling a broad variety of biological systems. These models are commonly studied with respect to the time series they generate in deterministic or stochastic simulations.…

Molecular Networks · Quantitative Biology 2019-07-11 Ozan Kahramanoğulları

When using multiple software tools to analyze, visualize, or optimize models in MBSE, it is often tedious and error-prone to manually coordinate the execution of these tools and to retain their respective input and output data for later…

Software Engineering · Computer Science 2022-07-12 Jan Flink , Robert Mischke , Kathrin Schaffert , Dominik Schneider , Alexander Weinert

Computed Tomography (CT) image guidance enables accurate and safe minimally invasive treatment of diseases, including cancer and chronic pain, with needle-like tools via a percutaneous approach. The physician incrementally inserts and…

Stress, or pressure, is a central quantity in engineering and remains vital in molecular modelling. However, the commonly used virial stress tensor is invalid for an inhomogeneous fluid, which is essential in fluid dynamics and…

Chemical Physics · Physics 2026-01-13 E. R. Smith

Droplets are the core functional units in microfluidic technologies that aim to integrate computation and reaction on a single platform. Achieving directed transport and control of these droplets typically demands elaborate substrate…

Soft Condensed Matter · Physics 2025-10-03 Zixuan Wu , Gavin Linton , Stefan Karpitschka , Anupam Pandey

We have built an integrated computational platform for material properties at extreme conditions, ProME (Professional Materials at Extremes) v1.0, which enables integrated calculations for multicomponent alloys, covering high temperatures…

To reduce the carbon footprint of computing and stabilize electricity grids, there is an increasing focus on approaches that align the power usage of IT infrastructure with the availability of clean energy. Unfortunately, research on…

Distributed, Parallel, and Cluster Computing · Computer Science 2024-06-21 Philipp Wiesner , Ilja Behnke , Paul Kilian , Marvin Steinke , Odej Kao

NOMAD CAMELS (short: CAMELS) is a configurable, open-source measurement software that records fully self-describing experimental data. It has its origins in the field of experimental physics where a wide variety of measurement instruments…

Instrumentation and Detectors · Physics 2024-03-13 Alexander D. Fuchs , Johannes A. F. Lehmeyer , Heinz Junkes , Heiko B. Weber , Michael Krieger

To cope with the unprecedented surge in demand for data computing for the applications, the promising concept of multi-access edge computing (MEC) has been proposed to enable the network edges to provide closer data processing for mobile…

Information Theory · Computer Science 2020-08-14 Qiqi Ren , Jian Chen , Omid Abbasi , Gunes Karabulut Kurt , Halim Yanikomeroglu , F. Richard Yu

This paper presents a new C++ framework, DELPHES, performing a fast multipurpose detector response simulation. The simulation includes a tracking system, embedded into a magnetic field, calorimeters and a muon system, and possible very…

High Energy Physics - Phenomenology · Physics 2010-04-12 S. Ovyn , X. Rouby , V. Lemaitre

This paper introduces ChemGen, a software package that uses code generation to integrate multispecies thermodynamics and chemical kinetics into C+-based computational physics codes. ChemGen aims to make chemical kinetics more accessible in…

Computational Physics · Physics 2025-12-11 Ryan F. Johnson , Eric J. Ching , Ethan S. Genter , Joshua E. Lipman , Andrew D. Kercher , Jay Arcities , Hai Wang

MCViNE (Monte-Carlo VIrtual Neutron Experiment) is a versatile Monte Carlo (MC) neutron ray-tracing program that provides researchers with tools for performing computer modeling and simulations that mirror real neutron scattering…

Simulations with high accuracy are an essential part of scientific research to accelerate the innovation process. They are especially useful for finding novel approaches or optimizing existing methods. Today, powerful software tools are…

Medical Physics · Physics 2022-08-31 Patrick Vogel , Martin A. Rückert , Thomas Kampf , Volker C. Behr

We present simulations of star forming filaments incorporating - to our knowledge - the largest chemical network used to date on-the-fly in a 3D-MHD simulation. The network contains 37 chemical species and about 300 selected reaction rates.…

Astrophysics of Galaxies · Physics 2016-06-01 D. Seifried , S. Walch

Non-linear wave-driven processes in plasmas are normally described by either a monochromatic pump wave that couples to other monochromatic waves, or as a random phase wave coupling to other random phase waves. An alternative approach…

Plasma Physics · Physics 2014-02-27 R. M. G. M. Trines , L. O. Silva , J. T. Mendonça , W. B. Mori , P. A. Norreys , R. Bingham

Molecular circuits capable of autonomous learning could unlock novel applications in fields such as bioengineering and synthetic biology. To this end, existing chemical implementations of neural computing have mainly relied on emulating…

Machine Learning · Computer Science 2025-09-23 Rajiv Teja Nagipogu , John H. Reif

We present a software framework called CARAVAN, which was developed for comprehensive simulations on massive parallel computers. The framework runs user-developed simulators with various input parameters in parallel without requiring the…

Distributed, Parallel, and Cluster Computing · Computer Science 2019-08-20 Yohsuke Murase , Hiroyasu Matsushima , Itsuki Noda , Tomio Kamada

Simulating chemical reaction networks is often computationally demanding, in particular due to stiffness. We propose a novel simulation scheme where long runs are not simulated as a whole but assembled from shorter precomputed segments of…

Logic in Computer Science · Computer Science 2022-06-22 Martin Helfrich , Milan Češka , Jan Křetínský , Štefan Martiček

Motivation: Complex computational pipelines are becoming a staple of modern scientific research. Often these pipelines are resource intensive and require days of computing time. In such cases, it makes sense to run them over distributed…

Software Engineering · Computer Science 2015-01-28 David K. Brown , Thommas M. Musyoka , David L. Penkler , Özlem Tastan Bishop

Simulations of hadronic and nuclear interactions are essential in both collider and astroparticle physics. The Chromo package provides a unified Python interface to multiple widely used hadronic event generators, including EPOS, DPMJet,…

Computational Physics · Physics 2025-07-30 Anatoli Fedynitch , Hans Dembinski , Anton Prosekin