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Tree-Code Based Improvement of Computational Performance of the X-ray-Matter-Interaction Simulation Tool XMDYN

In this work, we report on incorporating for the first time tree-algorithm based solvers into the molecular dynamics code, XMDYN. XMDYN was developed to describe the interaction of ultrafast X-ray pulses with atomic assemblies. It is also a part of the simulation platform, SIMEX, developed for compu...

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Detalles Bibliográficos
Autores principales: Stransky, Michal, Jurek, Zoltan, Santra, Robin, Mancuso, Adrian P., Ziaja, Beata
Formato: Online Artículo Texto
Lenguaje:English
Publicado: MDPI 2022
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9267930/
https://www.ncbi.nlm.nih.gov/pubmed/35807452
http://dx.doi.org/10.3390/molecules27134206
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author Stransky, Michal
Jurek, Zoltan
Santra, Robin
Mancuso, Adrian P.
Ziaja, Beata
author_facet Stransky, Michal
Jurek, Zoltan
Santra, Robin
Mancuso, Adrian P.
Ziaja, Beata
author_sort Stransky, Michal
collection PubMed
description In this work, we report on incorporating for the first time tree-algorithm based solvers into the molecular dynamics code, XMDYN. XMDYN was developed to describe the interaction of ultrafast X-ray pulses with atomic assemblies. It is also a part of the simulation platform, SIMEX, developed for computational single-particle imaging studies at the SPB/SFX instrument of the European XFEL facility. In order to improve the XMDYN performance, we incorporated the existing tree-algorithm based Coulomb solver, PEPC, into the code, and developed a dedicated tree-algorithm based secondary ionization solver, now also included in the XMDYN code. These extensions enable computationally efficient simulations of X-ray irradiated large atomic assemblies, e.g., large protein systems or viruses that are of strong interest for ultrafast X-ray science. The XMDYN-based preparatory simulations can now guide future single-particle-imaging experiments at the free-electron-laser facility, EuXFEL.
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spelling pubmed-92679302022-07-09 Tree-Code Based Improvement of Computational Performance of the X-ray-Matter-Interaction Simulation Tool XMDYN Stransky, Michal Jurek, Zoltan Santra, Robin Mancuso, Adrian P. Ziaja, Beata Molecules Article In this work, we report on incorporating for the first time tree-algorithm based solvers into the molecular dynamics code, XMDYN. XMDYN was developed to describe the interaction of ultrafast X-ray pulses with atomic assemblies. It is also a part of the simulation platform, SIMEX, developed for computational single-particle imaging studies at the SPB/SFX instrument of the European XFEL facility. In order to improve the XMDYN performance, we incorporated the existing tree-algorithm based Coulomb solver, PEPC, into the code, and developed a dedicated tree-algorithm based secondary ionization solver, now also included in the XMDYN code. These extensions enable computationally efficient simulations of X-ray irradiated large atomic assemblies, e.g., large protein systems or viruses that are of strong interest for ultrafast X-ray science. The XMDYN-based preparatory simulations can now guide future single-particle-imaging experiments at the free-electron-laser facility, EuXFEL. MDPI 2022-06-30 /pmc/articles/PMC9267930/ /pubmed/35807452 http://dx.doi.org/10.3390/molecules27134206 Text en © 2022 by the authors. https://creativecommons.org/licenses/by/4.0/Licensee MDPI, Basel, Switzerland. This article is an open access article distributed under the terms and conditions of the Creative Commons Attribution (CC BY) license (https://creativecommons.org/licenses/by/4.0/).
spellingShingle Article
Stransky, Michal
Jurek, Zoltan
Santra, Robin
Mancuso, Adrian P.
Ziaja, Beata
Tree-Code Based Improvement of Computational Performance of the X-ray-Matter-Interaction Simulation Tool XMDYN
title Tree-Code Based Improvement of Computational Performance of the X-ray-Matter-Interaction Simulation Tool XMDYN
title_full Tree-Code Based Improvement of Computational Performance of the X-ray-Matter-Interaction Simulation Tool XMDYN
title_fullStr Tree-Code Based Improvement of Computational Performance of the X-ray-Matter-Interaction Simulation Tool XMDYN
title_full_unstemmed Tree-Code Based Improvement of Computational Performance of the X-ray-Matter-Interaction Simulation Tool XMDYN
title_short Tree-Code Based Improvement of Computational Performance of the X-ray-Matter-Interaction Simulation Tool XMDYN
title_sort tree-code based improvement of computational performance of the x-ray-matter-interaction simulation tool xmdyn
topic Article
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9267930/
https://www.ncbi.nlm.nih.gov/pubmed/35807452
http://dx.doi.org/10.3390/molecules27134206
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