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We present RKappa, a framework for the development and analysis of rule-based models within a mature, statistically empowered R environment. The infrastructure allows model editing, modification, parameter sampling, simulation, statistical…

Molecular Networks · Quantitative Biology 2014-12-16 Anatoly Sorokin , Oksana Sorokina , J. Douglas Armstrong

The propagation and absorption of electromagnetic waves in plasma is one of the fundamental issues in plasma physics. The electromagnetic particle-in-cell method with the finite-difference time-domain solver plus Monte Carlo collision model…

Plasma Physics · Physics 2025-08-15 Fei Du , Yize Yan , Jingfeng Tang , Daren Yu , Yinjian Zhao

A computational procedure is developed for determining the conversion probability for reaction-diffusion systems in which a first-order catalytic reaction is performed over active particles. We apply this general method to systems on metric…

Soft Condensed Matter · Physics 2020-03-19 Renato Feres , Matthew Wallace , Ari Stern , Gregory Yablonsky

State-space models are used to describe and analyse dynamical systems. They are ubiquitously used in many scientific fields such as signal processing, finance and ecology to name a few. Particle filters are popular inferential methods used…

Computation · Statistics 2024-12-20 Alaa Amri

The problem of electromagnetic emission generation in plasma with electron beams is relevant both for practical applications and for interpretation of radio emission processes in astrophysical systems. In this work, we consider the case of…

Plasma Physics · Physics 2023-08-08 Vladimir Annenkov , Evgeniia Volchok , Igor Timofeev

A method for generating random $U(1)$ variables with Boltzmann distribution is presented. It is based on the rejection method with transformation of variables. High efficiency is achieved for all range of temparatures or coupling…

High Energy Physics - Lattice · Physics 2009-10-22 Tetsuya Hattori , Hideo Nakajima

We present a detailed strong and weak scaling analysis of PICCANTE, an open source, massively parallel, fully-relativistic Particle-In-Cell (PIC) code. PIC codes are widely used in plasma physics and astrophysics to study the cases where…

Distributed, Parallel, and Cluster Computing · Computer Science 2015-03-27 Andrea Sgattoni , Luca Fedeli , Stefano Sinigardi , Alberto Marocchino , Andrea Macchi , Volker Weinberg , Anupam Karmakar

There are many interesting physical processes which involve the generation of high density plasmas in large volumes. However, when modeling these systems numerically, the large densities and volumes present a significant computational…

Computational Physics · Physics 2007-05-23 A. E. Schulz , A. D. Greenwood , K. L. Cartwright , P. J. Mardahl

We simulate decaying turbulence in electron-positron pair plasmas using a fully- kinetic particle-in-cell (PIC) code. We run two simulations with moderate-to-low plasma beta. The energy decay rate is found to be similar in both the cases.…

Plasma Physics · Physics 2016-08-30 Kirit Makwana , Hui Li , Fan Guo , Xiaocan Li

A method to approximate transmission probabilities for a nonseparable multidimensional barrier is applied to a waveguide model. The method uses complex barrier-crossing orbits to represent reaction probabilities in phase space and is…

Chaotic Dynamics · Physics 2009-11-11 Christopher S. Drew , Stephen C. Creagh , Richard H. Tew

Metastability is a common obstacle to performing long molecular dynamics simulations. Many numerical methods have been proposed to overcome it. One method is parallel replica dynamics, which relies on the rapid convergence of the underlying…

Numerical Analysis · Mathematics 2015-05-20 Andrew Binder , Tony Lelièvre , Gideon Simpson

Compared with conventional accelerators, laser plasma accelerators can generate high energy ions at a greatly reduced scale, due to their TV/m acceleration gradient. A compact laser plasma accelerator (CLAPA) has been built at the Institute…

Accelerator Physics · Physics 2017-10-17 J. G. Zhu , K. Zhu , L. Tao , X. H. Xu , C. Lin , W. J. Ma , H. Y. Lu , Y. Y. Zhao , Y. R. Lu , J. E. Chen , X. Q. Yan

Particle-in-Cell (PIC) methods are widely used computational tools for fluid and kinetic plasma modeling. While both the fluid and kinetic PIC approaches have been successfully used to target either kinetic or fluid simulations, little was…

A new spectral particle-in-cell (PIC) method for plasma modeling is presented and discussed. In the proposed scheme, the Fourier-Bessel transform is used to translate the Maxwell equations to the quasi-cylindrical spectral domain. In this…

Plasma Physics · Physics 2019-08-17 Igor A. Andriyash , Remi Lehe , Agustin Lifschitz

First-principles particle-in-cell (PIC) simulation is a powerful tool for understanding plasma behavior, but this power often comes at great computational expense. Artificially reducing the ion/electron mass ratio is a time-honored practice…

Plasma Physics · Physics 2022-01-14 Gregory R. Werner , Scott Robertson , Thomas G. Jenkins , Andrew M. Chap , John R. Cary

The Particle-In-Cell (PIC) method is a computational technique widely used in plasma physics to model plasmas at the kinetic level. In this work, we present our effort to prepare the semi-implicit energy-conserving PIC code ECsim for…

Probabilistic error cancellation (PEC) is a leading quantum error mitigation method that provides an unbiased estimate, although it is known to have a large sampling overhead. In this work, we propose a new method to perform PEC, which…

Quantum Physics · Physics 2025-06-06 Yi-Hsiang Chen

We propose a spectral Particle-In-Cell (PIC) algorithm that is based on the combination of a Hankel transform and a Fourier transform. For physical problems that have close-to-cylindrical symmetry, this algorithm can be much faster than…

Plasma Physics · Physics 2016-05-04 Remi Lehe , Manuel Kirchen , Igor A. Andriyash , Brendan B. Godfrey , Jean-Luc Vay

In this paper we combine the Alias method with the concept of systematic sampling, a method commonly used in particle filters for efficient low-variance resampling. The proposed method allows very fast sampling from a discrete distribution:…

Data Structures and Algorithms · Computer Science 2025-09-30 Ilari Vallivaara , Katja Poikselkä , Pauli Rikula , Juha Röning

Room-temperature metals and semi-metals which consist of a gas of bound electrons in a near-continuum band structure can be classified as cold quantum plasmas. This insight suggests that Particle-in-Cell (PIC) simulations, traditionally…

Plasma Physics · Physics 2025-01-14 Gregory K. Ngirmang , Hue T. B. Do , Guangxin Liu , Michel Bosman , Lin Wu
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