Search Results - "102009 Computer simulation"

Transferable Neural Network Potentials and Condensed Phase Properties

Authors: Anna Katharina Picha Marcus Wieder Stefan Boresch

Source: Journal of Chemical Information and Modeling. 65:9483-9496

Subject Terms: 104027 Computational chemistry, 102009 Computer simulation, Computer, Neural Networks, 104027 Computational Chemistry, 102009 Computersimulation, Solvents/chemistry

Access URL: https://ucrisportal.univie.ac.at/de/publications/05080cdd-8ee7-42eb-a3c8-88becd52e2c6
https://doi.org/10.1021/acs.jcim.5c01355

Forty-Year Time Series of Anthropogenic Uranium in Fucus vesiculosus from Kattegat: Validating 236U Releases from European Nuclear Reprocessing Plants

Authors: Jixin Qiao Yiyao Cao Mu Lin et al.

Source: Environmental Science & Technology. 59:2675-2685

Subject Terms: releases, Water Pollutants, Radioactive, overestimation, 103014 Kernphysik, SDG 14 – Leben unter Wasser, Europe, 102009 Computer simulation, Sellafield reprocessing plant, Radiation Monitoring, Fucus, Uranium, SDG 14 - Life Below Water, 103014 Nuclear physics, 102009 Computersimulation

Access URL: https://pubmed.ncbi.nlm.nih.gov/39887320
https://ucrisportal.univie.ac.at/de/publications/1ff5771b-a87d-4a17-8b92-7fe03d5992f0
https://doi.org/10.1021/acs.est.4c07622

Patchy charge distribution affects the pH in protein solutions during dialysis

Authors: Sebastian P. Pineda Pablo M. Blanco Roman Staňo et al.

Source: Langmuir

Subject Terms: 104010 Makromolekulare Chemie, 102009 Computer simulation, 104010 Macromolecular chemistry, 103015 Kondensierte Materie, 103015 Condensed matter, 102009 Computersimulation

Access URL: https://pubmed.ncbi.nlm.nih.gov/39964136

Learning Collective Variables with Synthetic Data Augmentation through Physics-Inspired Geodesic Interpolation

Authors: Soojung Yang Juno Nam Johannes C. B. Dietschreit et al.

Source: Journal of Chemical Theory and Computation. 20:6559-6568

Subject Terms: 104027 Computational chemistry, Chemical Physics (physics.chem-ph), FOS: Computer and information sciences, Computer Science - Machine Learning, FOS: Physical sciences, Biomolecules (q-bio.BM), 01 natural sciences, 104027 Computational Chemistry, 0104 chemical sciences, Machine Learning (cs.LG), 102009 Computer simulation, Quantitative Biology - Biomolecules, Physics - Chemical Physics, FOS: Biological sciences, 0103 physical sciences, 102009 Computersimulation

Access URL: https://pubmed.ncbi.nlm.nih.gov/39073442
http://arxiv.org/abs/2402.01542

Inverse-design topology optimization of magnonic devices using level-set method

Authors: Voronov, Andrei Cuervo Santos, Marcos Bruckner, Florian et al.

Source: Npj Spintron
npj Spintronics, Vol 3, Iss 1, Pp 1-8 (2025)

Subject Terms: TK7800-8360, FOS: Physical sciences, 102019 Machine learning, Computational Physics (physics.comp-ph), 103017 Magnetismus, Article, Condensed Matter - Other Condensed Matter, 102009 Computer simulation, 102019 Machine Learning, T1-995, Electronics, Physics - Computational Physics, Technology (General), 103017 Magnetism, 102009 Computersimulation, Other Condensed Matter (cond-mat.other)

Access URL: http://arxiv.org/abs/2411.19109
https://doaj.org/article/f8eeee1b94824ca386833eb4830b82d0
https://ucrisportal.univie.ac.at/de/publications/bc2c9651-41aa-475f-a53c-41e50f9566b7
https://doi.org/10.1038/s44306-025-00082-3

Phylogenetic and Chemical Probing Information as Soft Constraints in RNA Secondary Structure Prediction

Authors: Sarah von Löhneysen Thomas Spicher Yuliia Varenyk et al.

Source: Journal of Computational Biology. 31:549-563

Subject Terms: 104027 Computational chemistry, 0301 basic medicine, RNA Folding, Base Sequence, 0206 medical engineering, Computational Biology, 02 engineering and technology, RNA secondary structure, 104027 Computational Chemistry, pseudo-energies, 102009 Computer simulation, 03 medical and health sciences, 106005 Bioinformatik, Nucleic Acid Conformation, RNA, Thermodynamics, consensus structure, 106005 Bioinformatics, Base Pairing, Algorithms, Phylogeny, 102009 Computersimulation, RNA structure probing

Access URL: https://pubmed.ncbi.nlm.nih.gov/38935442
https://ucrisportal.univie.ac.at/de/publications/2b043c16-60d4-4b49-ba80-298a01fd0b94
https://doi.org/10.1089/cmb.2024.0519

Updates to Protex for Simulating Proton Transfers in an Ionic Liquid

Authors: Gődény, Márta Joerg, Florian Kovar, Maximilian P.-P. et al.

Source: J Phys Chem B

Subject Terms: 104027 Computational chemistry, 102009 Computer simulation, 0103 physical sciences, 104017 Physical chemistry, 01 natural sciences, 104017 Physikalische Chemie, 104027 Computational Chemistry, 102009 Computersimulation, 0104 chemical sciences

File Description: application/pdf

Access URL: https://pubmed.ncbi.nlm.nih.gov/38557106

Drug design on quantum computers

Authors: Raffaele Santagati Alan Aspuru-Guzik Ryan Babbush et al.

Source: Nature Physics. 20:549-557

Subject Terms: 0301 basic medicine, 102009 Computer simulation, Quantum Physics, 0303 health sciences, 03 medical and health sciences, 104022 Theoretical chemistry, 104022 Theoretische Chemie, 0103 physical sciences, FOS: Physical sciences, Quantum Physics (quant-ph), 01 natural sciences, 102009 Computersimulation

Access URL: http://arxiv.org/abs/2301.04114
https://ucrisportal.univie.ac.at/de/publications/b9f9b7d8-c619-4dbc-8612-4a9c980d0dbd
https://doi.org/10.1038/s41567-024-02411-5

Resolution criteria to avoid artificial clumping in Lagrangian hydrodynamic simulations with a multiphase interstellar medium

Authors: Ploeckinger, Sylvia Nobels, Folkert S J Schaller, Matthieu et al.

Source: Monthly Notices of the Royal Astronomical Society. 528:2930-2951

Subject Terms: Galaxies: general, Methods: numerical, FOS: Physical sciences, Galaxies: formation, 103004 Astrophysik, galaxies: general, Astrophysics - Astrophysics of Galaxies, methods: numerical, Galaxies: ISM, 102009 Computer simulation, instabilities, Instabilities, Astrophysics of Galaxies (astro-ph.GA), hydrodynamics, Hydrodynamics, galaxies: formation, 103004 Astrophysics, Astrophysics - Instrumentation and Methods for Astrophysics, Instrumentation and Methods for Astrophysics (astro-ph.IM), galaxies: ISM, 102009 Computersimulation

File Description: application/pdf

Access URL: http://arxiv.org/abs/2310.10721
https://hdl.handle.net/1887/4209126
https://hdl.handle.net/1887/3719120

On analytical corrections for restraints in absolute binding free energy calculations

Authors: Boresch, Stefan

Source: J Chem Inf Model

Subject Terms: 104027 Computational chemistry, Models, Molecular, 0301 basic medicine, Proteins, Molecular Dynamics Simulation, Ligands, 01 natural sciences, 104027 Computational Chemistry, Chemical calculations, Oscillation, 102009 Computer simulation, 03 medical and health sciences, 0103 physical sciences, Thermodynamics, Free energy, Approximation, 102009 Computersimulation, Protein Binding

File Description: application/pdf

Access URL: https://pubmed.ncbi.nlm.nih.gov/38640478
https://phaidra.univie.ac.at/o:2085894
https://hdl.handle.net/11353/10.2085894
https://doi.org/10.1021/acs.jcim.4c00442

LVC/MM: A Hybrid Linear Vibronic Coupling/Molecular Mechanics Model with Distributed Multipole-Based Electrostatic Embedding for Highly Efficient Surface Hopping Dynamics in Solution

Authors: Polonius, Severin Zhuravel, Oleksandra Bachmair, Brigitta et al.

Source: J Chem Theory Comput

Subject Terms: Chemical calculations, Computational chemistry, 102009 Computer simulation, Electrostatics, 104022 Theoretical chemistry, 104022 Theoretische Chemie, Molecules, 7. Clean energy, Electron density, 102009 Computersimulation

File Description: application/pdf

Access URL: https://pubmed.ncbi.nlm.nih.gov/37788824

Insights from the Absorption Coefficient for the Development of Polarizable (Multipole) Force Fields

Authors: Marion Sappl András Szabadi Philipp Honegger et al.

Source: Molecules
Molecules, Vol 30, Iss 14, p 2941 (2025)

Subject Terms: 104027 Computational chemistry, 104022 Theoretical chemistry, water, Organic chemistry, terahertz spectroscopy, 104027 Computational Chemistry, 104017 Physikalische Chemie, Article, 102009 Computer simulation, QD241-441, 104022 Theoretische Chemie, 104017 Physical chemistry, induced dipoles, computational spectroscopy, 102009 Computersimulation

Access URL: https://doaj.org/article/c9ef2a4baf624864b4a23e28314b9408

Prototypical – A Framework for Board Game Creation

Authors: Campisi, Vincente Hlavacs, Helmut Pazour, Patrick et al.

Source: Lecture Notes in Computer Science ISBN: 9783031743528

Subject Terms: 102009 Computer simulation, 102007 Computer animation, 102007 Computeranimation, 102009 Computersimulation

Access URL: https://ucrisportal.univie.ac.at/de/publications/828d6f64-808d-4d4b-9ff6-ff6114d49ecd
https://doi.org/10.1007/978-3-031-74353-5_4

Stochastic Super-resolution of Cosmological Simulations with Denoising Diffusion Models

Authors: Schanz, Andreas List, Florian Hahn, Oliver

Source: The Open Journal of Astrophysics, Vol 7 (2024)

Subject Terms: FOS: Computer and information sciences, Computer Science - Machine Learning, Cosmology and Nongalactic Astrophysics (astro-ph.CO), Astronomy, 103044 Cosmology, FOS: Physical sciences, QB1-991, 103004 Astrophysik, Astrophysics, Machine Learning (cs.LG), QB460-466, 102009 Computer simulation, 103043 Computational physics, 103044 Kosmologie, 103004 Astrophysics, Astrophysics - Instrumentation and Methods for Astrophysics, Instrumentation and Methods for Astrophysics (astro-ph.IM), 103043 Computational Physics, 102009 Computersimulation, Astrophysics - Cosmology and Nongalactic Astrophysics

Access URL: http://arxiv.org/abs/2310.06929
https://doaj.org/article/f342843937b34bfc9c9b76e85160bc03
https://ucrisportal.univie.ac.at/de/publications/fafbc627-9ea8-4cb6-977b-a87edcfad7b7
https://doi.org/10.33232/001c.125902

The adsorption of drugs on nanoplastics has severe biological impact

Authors: Dick, Leonard Batista, Patrick R. Zaby, Paul et al.

Source: Sci Rep
Scientific Reports, Vol 14, Iss 1, Pp 1-17 (2024)

Subject Terms: Polystyrenes Chemistry, Polymers, Science, Microplastics, Anti-Bacterial Agents/chemistry, Molecular Dynamics Simulation, Polypropylenes/chemistry, Polypropylenes, Article, 102009 Computer simulation, Polystyrenes/chemistry, Polymers/chemistry, Microplastics Chemistry, Humans, Polypropylenes Chemistry, Anti-Bacterial Agents Pharmacology, Polymer Technologies, Tetracycline Pharmacology, Microplastics/chemistry, Tetracycline chemistry, Polymers Chemistry, Tetracycline/chemistry, Tetracycline, Polymerteknologi, Anti-Bacterial Agents, Anti-Bacterial Agents Chemistry, Medicine, Polystyrenes, Adsorption, 102009 Computersimulation

File Description: application/pdf

Access URL: https://pubmed.ncbi.nlm.nih.gov/39468142
https://doaj.org/article/5ed80949df9b448bb7086154eeed61ad
https://phaidra.vetmeduni.ac.at/o:3771
https://doi.org/10.1038/s41598-024-75785-4
http://urn.kb.se/resolve?urn=urn:nbn:se:umu:diva-231630

The impact of stochastic modelling on the predictive power of galaxy formation simulations

Authors: Josh Borrow Matthieu Schaller Yannick M Bahé et al.

Source: Borrow, J, Schaller, M, Bahe, Y M, Schaye, J, Ludlow, A D, Ploeckinger, S, Nobels, F S J & Altamura, E 2022 'The impact of stochastic modeling on the predictive power of galaxy formation simulations'.

Subject Terms: Methods: numerical, 103003 Astronomie, Galaxies: evolution, software: simulations, FOS: Physical sciences, Software: simulations, Galaxies: formation, 103004 Astrophysik, Astrophysics - Astrophysics of Galaxies, methods: numerical, 103003 Astronomy, 102009 Computer simulation, Astrophysics of Galaxies (astro-ph.GA), galaxies: formation, 103004 Astrophysics, galaxies: evolution, 102009 Computersimulation

File Description: application/pdf

Access URL: http://arxiv.org/abs/2211.08442
https://ucrisportal.univie.ac.at/de/publications/804771dd-e1cc-41e6-b614-4f25f876ecf0
https://doi.org/10.1093/mnras/stad2928
https://research.manchester.ac.uk/en/publications/61688a58-3a5e-4efe-af56-f43b1d09377e
https://hdl.handle.net/1887/3717428

Calculations of Absolute Solvation Free Energies with Transformato─Application to the FreeSolv Database Using the CGenFF Force Field

Authors: Johannes Karwounopoulos Åsmund Kaupang Marcus Wieder et al.

Source: J Chem Theory Comput

Subject Terms: 102009 Computer simulation, 104022 Theoretical chemistry, 104022 Theoretische Chemie, 104017 Physical chemistry, 104017 Physikalische Chemie, 102009 Computersimulation

Access URL: https://pubmed.ncbi.nlm.nih.gov/37616333

The FLAMINGO project: cosmological hydrodynamical simulations for large-scale structure and galaxy cluster surveys: cosmological hydrodynamical simulations for large-scale structure and galaxy cluster surveys

Authors: Joop Schaye Roi Kugel Matthieu Schaller et al.

Source: Monthly Notices of the Royal Astronomical Society

Subject Terms: Cosmology and Nongalactic Astrophysics (astro-ph.CO), Methods: numerical, Large-scale structure of Universe, 103044 Cosmology, FOS: Physical sciences, Galaxies: formation, 103004 Astrophysik, 7. Clean energy, Astrophysics - Astrophysics of Galaxies, 102009 Computer simulation, Astrophysics of Galaxies (astro-ph.GA), 103043 Computational physics, Galaxies: clusters: general, Cosmology: theory, 103044 Kosmologie, 103004 Astrophysics, 103043 Computational Physics, 102009 Computersimulation, Astrophysics - Cosmology and Nongalactic Astrophysics

File Description: application/pdf

Access URL: http://arxiv.org/abs/2306.04024
https://ucrisportal.univie.ac.at/de/publications/2f55a60e-c0ca-4ff6-ac22-061db276292e
https://hdl.handle.net/1887/3719156

Catching a wave: on the suitability of traveling-wave solutions in epidemiological modeling

Authors: Anna M. Langmüller Joachim Hermisson Courtney C. Murdock et al.

Source: Langmüller, A M, Hermisson, J, Murdock, C & Messer, P W 2025, 'Catching a wave : On the suitability of traveling-wave solutions in epidemiological modeling', Theoretical Population Biology, vol. 162, pp. 1-12. https://doi.org/10.1016/j.tpb.2024.12.004
bioRxiv

Subject Terms: SI/SIS/SIR model, Spatial disease modeling, 303007 Epidemiologie, Diffusion theory, 101004 Biomathematics, Communicable Diseases, 3. Good health, Individual-based simulations, 102009 Computer simulation, 101004 Biomathematik, SDG 3 - Good Health and Well-being, 303007 Epidemiology, SDG 3 – Gesundheit und Wohlergehen, Humans, Epidemiological Models, Computer Simulation, Epidemics, Ordinary differential equations, 102009 Computersimulation

Access URL: https://pubmed.ncbi.nlm.nih.gov/39733976
https://ucrisportal.univie.ac.at/de/publications/c0206470-ea9c-48a7-8aa9-918eb295becc
https://doi.org/10.1101/2023.06.23.546298
https://pure.au.dk/portal/en/publications/97c1db8a-9346-47ff-affa-f22a80b85a0c
http://www.scopus.com/inward/record.url?scp=85215088838&partnerID=8YFLogxK
https://doi.org/10.1016/j.tpb.2024.12.004

Proton Transport in Perfluorinated Ionomer Simulated by Machine-Learned Interatomic Potential

Authors: Ryosuke Jinnouchi Saori Minami Ferenc Karsai et al.

Source: The Journal of Physical Chemistry Letters. 14:3581-3588

Subject Terms: 102009 Computer simulation, 103018 Materialphysik, 103018 Materials physics, 102009 Computersimulation

Access URL: https://pubmed.ncbi.nlm.nih.gov/37018477
https://ucrisportal.univie.ac.at/de/publications/a8e15aec-10c2-47ec-b590-393396a0ceb0
https://doi.org/10.1021/acs.jpclett.3c00293