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Papers matching “molecular dynamics simulation” 102

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Influence of Sara Fractions on the Bitumen Property Using Molecular Dynamics Simulation
2023 SSRN Electronic Journal preprint Engineering Asphalt Pavement Performance Evaluation Open access

Quan Liu, Wenhao Cha, Jiantao Wu, Pengfei Liu

0

citations
Tuning the H 2 Production Activity of ToHydA by Molecular Simulation-Informed Protein Engineering
2025 bioRxiv (Cold Spring Harbor Laboratory) preprint Energy Metalloenzymes and iron-sulfur proteins Open access

Chandan Kumar Das, Subhasri Ghosh, Shuvankar Naskar, Thomas Happe, Lars V. Schäfer

0

citations
Molecular Dynamics and Structural Studies of Zinc Chloroquine Complexes
2022 ChemRxiv preprint Medicine Metal complexes synthesis and properties Open access

Mirko Paulikat, Daniele Vitone, Florian Karl Schackert, Nils Schuth, Alessandra Barbanente, GiovanniMaria Piccini, +11 more

2

citations
Molecular Dynamics and Structural Studies of Zinc Chloroquine Complexes
2022 ChemRxiv preprint Medicine Metal complexes synthesis and properties Open access

Mirko Paulikat, Daniele Vitone, Florian Karl Schackert, Nils Schuth, Alessandra Barbanente, GiovanniMaria Piccini, +11 more

0

citations
Impact of Cholesterol on the Stability of Monomeric and Dimeric Forms of the Translocator Protein TSPO: a Molecular Simulation Study
2020 Preprints.org preprint Biochemistry, Genetics and Molecular Biology Lipid Membrane Structure and Behavior Open access

Zeineb Si Chaib, Alessandro Marchetto, Klevia Dishnica, Paolo Carloni, Alejandro Giorgetti, Giulia Rossetti

4

citations
Correction to “From setup to analysis: a compact guide to performing Molecular Dynamics simulations of ion transport in solids”
2025 SSRN Electronic Journal preprint Engineering Nanopore and Nanochannel Transport Studies Open access

0

citations
Long timescale ensemble methods in molecular dynamics: Ligand-protein interactions and allostery in SARS-CoV-2 targets
2023 ChemRxiv preprint Computer Science Computational Drug Discovery Methods Open access

Agastya P. Bhati, Art Hoti, Andrew Potterton, M. Bieniek, Peter V. Coveney

0

citations
Long timescale ensemble methods in molecular dynamics: Ligand-protein interactions and allostery in SARS-CoV-2 targets
2022 ChemRxiv preprint Computer Science Computational Drug Discovery Methods Open access

Agastya P. Bhati, Art Hoti, Andrew Potterton, Peter V. Coveney

1

citations
Heating of CeO₂ surfaces under microwave irradiation using non-equilibrium molecular dynamics
2025 ChemRxiv preprint Chemistry Microwave-Assisted Synthesis and Applications Open access

Sahar Koritisani, Kazem Zhour, Gunjana Yadav, Abhishek Khetan

1

citations
Heating of CeO₂ surfaces under microwave irradiation using non-equilibrium molecular dynamics
2025 ChemRxiv preprint Chemistry Microwave-Assisted Synthesis and Applications Open access

Sahar Koritisani, Gunjana Yadav, Abhishek Khetan

0

citations
Understanding the heating of ceria surfaces under microwave irradiation using non-equilibrium molecular dynamics
2025 ChemRxiv preprint Chemistry Microwave-Assisted Synthesis and Applications Open access

Sahar Koritisani, Gunjana Yadav, Abhishek Khetan

0

citations
Heating of CeO₂ surfaces under microwave irradiation using non-equilibrium molecular dynamics
2025 ChemRxiv preprint Chemistry Microwave-Assisted Synthesis and Applications Open access

Sahar Koritisani, Gunjana Yadav, Abhishek Khetan

0

citations
Implementation of quantum-classical mapping approaches for nonadiabatic molecular dynamics in the PySurf package
2025 ChemRxiv preprint Physics and Astronomy Spectroscopy and Quantum Chemical Studies Open access

David Picconi, Maximilian F. S. J. Menger, Elisa Palacino‐González, Edison X. Salazar, Shirin Faraji

0

citations
Implementation of quasiclassical mapping approaches for nonadiabatic molecular dynamics in the PySurf package
2025 ChemRxiv preprint Physics and Astronomy Spectroscopy and Quantum Chemical Studies Open access

David Picconi, Maximilian F. S. J. Menger, Elisa Palacino‐González, Edison X. Salazar, Shirin Faraji

0

citations
Assessing the Potential of Zero Charge in Ab Initio Molecular Dynamics Simulations
2026 ChemRxiv preprint Physics and Astronomy Advanced Chemical Physics Studies Open access

Arthur Hagopian, Marc T. M. Koper, Katharina Doblhoff-Dier

0

citations
Assessing the Potential of Zero Charge in Ab Initio Molecular Dynamics Simulations
2026 ChemRxiv preprint Physics and Astronomy Advanced Chemical Physics Studies Open access

Arthur Hagopian, Marc T. M. Koper, Katharina Doblhoff-Dier

0

citations
Completely computational model setup for spectroscopic techniques: the ab initio molecular dynamics indirect hard modeling (AIMD-IHM) approach
2022 ChemRxiv preprint Chemistry Spectroscopy and Chemometric Analyses Open access

Justus Wöhl, Wassja A. Kopp, Iryna Yevlakhovych, Leo Bahr, Hans‐Jürgen Koß, Kai O. Leonhard

0

citations
Long timescale ensemble methods in molecular dynamics: Ligand-protein interactions and allostery in SARS-CoV-2 targets
2023 ChemRxiv preprint Computer Science Computational Drug Discovery Methods Open access

Agastya P. Bhati, Art Hoti, Andrew Potterton, M. Bieniek, Peter V. Coveney

1

citations
Different force fields give rise to different amyloid aggregation pathways in molecular dynamics simulations
2020 bioRxiv (Cold Spring Harbor Laboratory) preprint Medicine Alzheimer's disease research and treatments

Suman Samantray, Feng Yin, Batuhan Kav, Birgit Strodel

4

citations
KnowVolution of an efficient polyamidase through molecular dynamics simulations of incrementally docked oligomeric substrates
2024 bioRxiv (Cold Spring Harbor Laboratory) preprint Biochemistry, Genetics and Molecular Biology Enzyme Catalysis and Immobilization Open access

Hendrik Puetz, Alexander-Maurice Illig, Mariia Vorobii, Christoph Janknecht, Francisca Contreras, Fabian Flemig, +1 more

1

citations
Elucidation of SARS-Cov-2 Budding Mechanisms Through Molecular Dynamics Simulations of M and E Protein Complexes
2021 bioRxiv (Cold Spring Harbor Laboratory) preprint Medicine SARS-CoV-2 and COVID-19 Research Open access

3

citations
Insights on the effect of extracellular acidification on an HCN channel: a molecular dynamics study
2025 bioRxiv (Cold Spring Harbor Laboratory) preprint Biochemistry, Genetics and Molecular Biology Ion channel regulation and function Open access

Somayeh Asgharpour, Michalis Lazaratos, Marc Spehr, Paolo Carloni

0

citations
Time-resolved investigation of photocatalytic allene deracemization with kinetic modeling and force-field-based molecular dynamics
2026 ChemRxiv preprint Chemistry Photochemistry and Electron Transfer Studies Open access

Gereon Feldmann, Christoph Bannwarth

0

citations
Molecular mechanism of light-driven sodium pumping
2020 bioRxiv (Cold Spring Harbor Laboratory) preprint Neuroscience Photoreceptor and optogenetics research Open access

Kirill Kovalev, Roman Astashkin, Ivan Gushchin, Philipp S. Orekhov, D. Volkov, Egor V. Zinovev, +14 more

6

citations
Modeling neuron-astrocyte interactions in neural networks using distributed simulation
2024 bioRxiv (Cold Spring Harbor Laboratory) preprint Neuroscience Neural dynamics and brain function Open access

Han-Jia Jiang, Jugoslava Aćimović, Tiina Manninen, Iiro Ahokainen, Jonas Stapmanns, Mikko Lehtimäki, +4 more

4

citations