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13C-based metabolic flux analysis (13C-MFA) is a cornerstone of quantitative systems biology, yet its increasing data complexity and methodological diversity place high demands on simulation software. We introduce 13CFLUX(v3), a…

Quantitative Methods · Quantitative Biology 2025-09-30 Anton Stratmann , Martin Beyß , Johann F. Jadebeck , Wolfgang Wiechert , Katharina Nöh

Energetic particle (EP) driven instabilities will be of strongly increased relevance in future burning plasmas as the EP pressure will be very large compared to the thermal plasma. Understanding the interaction of EPs and bulk plasma is…

Plasma Physics · Physics 2022-12-14 T. J. Bogaarts , M. Hoelzl , G. T. A. Huijsmans , X. Wang

The method of using neural networks (NNs) for turbulent transport prediction in a simplified model of tokamak plasmas is explored. The NNs are trained on a database obtained via test-particle simulations of a transport model in the…

Plasma Physics · Physics 2023-12-18 L. M. Pomârjanschi

We present a novel hybrid incompressible flow/material point method solver for simulating the combustion of flammable solids. Our approach utilizes a sparse grid representation of solid materials in the material point method portion of the…

Graphics · Computer Science 2024-08-15 Victoria Kala , Jingyu Chen , David Hyde , Alexey Stomakhin , Joseph Teran

We introduce PULSEDYN, a particle dynamics program in $C++$, to solve many-body nonlinear systems in one dimension. PULSEDYN is designed to make computing accessible to non-specialists in the field of nonlinear dynamics of many-body systems…

Computational Physics · Physics 2017-10-27 Rahul Kashyap , Surajit Sen

Reduction of the peak heat loads on the plasma facing components is essential for the success of the next generation of high fusion power tokamaks such as the International Thermonuclear Experimental Reactor (ITER) 1 . Many present concepts…

plasm-ph · Physics 2009-10-28 D. Post , J. Abdallah , R. E. H. Clark , N. Putvinskaya

We present the VECMA toolkit (VECMAtk), a flexible software environment for single and multiscale simulations that introduces directly applicable and reusable procedures for verification, validation (V&V), sensitivity analysis (SA) and…

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…

Plasma Physics · Physics 2014-12-09 Mierk Schwabe , David B. Graves

We have developed URDME, a general software for simulation of stochastic reaction-diffusion processes on unstructured meshes. This allows for a more flexible handling of complicated geometries and curved boundaries compared to simulations…

Molecular Networks · Quantitative Biology 2026-02-27 Stefan Engblom

The document describes a numerical algorithm to simulate plasmas and fluids in the 3 dimensional space by the Euler method, in which the spatial meshes are fixed to the space. The plasmas and fluids move through the spacial Euler mesh…

Plasma Physics · Physics 2020-04-09 Hiroki Nakamura , Shigeo Kawata , Ken Uchibori , Takahiro Karino

This study investigates the feasibility of reconstructing the last closed flux surface (LCFS) in the DIII-D tokamak using neural network models trained on reduced input feature sets, addressing an ill-posed task. Two models are compared:…

A new parallel equilibrium reconstruction code for tokamak plasmas is presented. GPEC allows to compute equilibrium flux distributions sufficiently accurate to derive parameters for plasma control within 1 ms of runtime which enables…

Plasma Physics · Physics 2016-07-08 Markus Rampp , Roland Preuss , Rainer Fischer , the ASDEX Upgrade Team

The role of turbulence in setting boundary plasma conditions is presently a key uncertainty in projecting to fusion energy reactors. To robustly diagnose edge turbulence, we develop and demonstrate a technique to translate brightness…

We propose a neural physics system for real-time, interactive fluid simulations. Traditional physics-based methods, while accurate, are computationally intensive and suffer from latency issues. Recent machine-learning methods reduce…

Machine Learning · Computer Science 2025-05-27 Jingxuan Xu , Hong Huang , Chuhang Zou , Manolis Savva , Yunchao Wei , Wuyang Chen

This work introduces ChemPlasKin, a freely accessible solver optimized for zero-dimensional (0D) simulations of chemical kinetics of neutral gas in non-equilibrium plasma environments. By integrating the electron Boltzmann equation solver,…

Plasma Physics · Physics 2024-08-06 Xiao Shao , Deanna A. Lacoste , Hong G. Im

Turbulence in fluids, gases, and plasmas remains an open problem of both practical and fundamental importance. Its irreducible complexity usually cannot be tackled computationally in a brute-force style. Here, we combine Large Eddy…

Computational Physics · Physics 2023-09-29 Robin Greif , Frank Jenko , Nils Thuerey

It is proposed a dimensional Lattice Boltzmann Method (LBM) of wide application for simulating fluid flow and heat transfer problems. The proposed LBM consists in the numerical solution of the discrete lattice Boltzmann equation (LBE) using…

Fluid Dynamics · Physics 2024-05-14 Ivan Talão Martins , Pablo Fariñas Alvariño , Luben Cabezas-Gómez

We introduce a novel mesoscopic computational model based on a multiphase-multicomponent lattice Boltzmann method for the simulation of self-phoretic particles in the presence of liquid-liquid interfaces. Our model features fully resolved…

Soft Condensed Matter · Physics 2022-06-22 Lucas Palacios , Andrea Scagliarini , Ignacio Pagonabarraga

In tokamak experiments, sufficiently strong $E\times B$ flow shear reduces turbulent transport, thereby improving the prospects for fusion power plants. It is therefore of great importance to efficiently explore parameter space to find…

Plasma Physics · Physics 2024-01-30 Haomin Sun , Justin Ball , Stephan Brunner , Arnas Volčokas

This article presents the development and validation of a hybrid multi-sphere discrete element framework - Rigid3D, for the simulation of granular systems with arbitrarily shaped particles in 3D space. In this DEM framework, a non-spherical…

Computational Engineering, Finance, and Science · Computer Science 2023-06-27 Fei-Liang Yuan , Martin Sommerfeld , Pradeep Muramulla , Srikanth Gopireddy , Lars Pasternak , Nora Urbanetz , Thomas Profitlich