Jonathan Barnoud

12 papers Journal 8Unranked 4
YearRankTypeTitle / Venue / Authors
2025 J jnl
AI-Guided Molecular Simulations in VR: Exploring Strategies for Imitation Learning in Hyperdimensional Molecular Systems.
SN Comput. Sci.
Mohamed Dhouioui, Jonathan Barnoud, Rhoslyn Roebuck Williams, Harry J. Stroud, Phil Bates, David R. Glowacki
2025 J jnl
NanoVer Server: A Python Package for Serving Real-Time Multi-User Interactive Molecular Dynamics in Virtual Reality.
J. Open Source Softw.
Harry J. Stroud, Mark D. Wonnacott, Jonathan Barnoud, Rhoslyn Roebuck Williams, Mohamed Dhouioui, Adam McSloy, Ludovica Aisa, Luis E. Toledo, Phil Bates, Adrian J. Mulholland, David R. Glowacki
2024 J jnl
A Perspective on AI-Guided Molecular Simulations in VR: Exploring Strategies for Imitation Learning in Hyperdimensional Molecular Systems.
CoRR
Mohamed Dhouioui, Jonathan Barnoud, Rhoslyn Roebuck Williams, Harry J. Stroud, Phil Bates, David R. Glowacki
2024 — conf
Measuring the Limit of Perception of Bond Stiffness of Interactive Molecules in VR via a Gamified Psychophysics Experiment.
XR (1)
Rhoslyn Roebuck Williams, Jonathan Barnoud, Luis Toledo, Till Holzapfel, David R. Glowacki
2024 J jnl
Measuring the limit of perception of bond stiffness of interactive molecules in VR via a gamified psychophysics experiment.
CoRR
Rhoslyn Roebuck Williams, Jonathan Barnoud, Luis Toledo, Till Holzapfel, David R. Glowacki
2023 — conf
MDAKits: A Framework for FAIR-Compliant Molecular Simulation Analysis.
SciPy
Irfan Alibay, Lily Wang, Fiona Naughton, Ian M. Kenney, Jonathan Barnoud, Richard J. Gowers, Oliver Beckstein
2022 J jnl
Martinize2 and Vermouth: Unified Framework for Topology Generation.
CoRR
Peter C. Kroon, Fabian Grünewald, Jonathan Barnoud, Marco van Tilburg, Paulo C. T. Souza, Tsjerk A. Wassenaar, Siewert-Jan Marrink
2020 J jnl
Interactive Molecular Dynamics in Virtual Reality Is an Effective Tool for Flexible Substrate and Inhibitor Docking to the SARS-CoV-2 Main Protease.
J. Chem. Inf. Model.
Helen M. Deeks, Rebecca Walters, Jonathan Barnoud, David R. Glowacki, Adrian J. Mulholland
2020 — conf
Narupa iMD: A VR-Enabled Multiplayer Framework for Streaming Interactive Molecular Simulations.
SIGGRAPH Immersive Pavilion
Alexander D. Jamieson-Binnie, Michael B. O'Connor, Jonathan Barnoud, Mark D. Wonnacott, Simon J. Bennie, David R. Glowacki
2019 J jnl
Sharing Data from Molecular Simulations.
J. Chem. Inf. Model.
Mark James Abraham, Rossen Apostolov, Jonathan Barnoud, Paul Bauer, Christian Blau, Alexandre M. J. J. Bonvin, Matthieu Chavent, John D. Chodera, Karmen Condic-Jurkic, Lucie Delemotte, Helmut Grubmüller, Rebecca J. Howard, E. Joseph Jordan, Erik Lindahl, Samuli Ollila, Jana Selent, Daniel G. A. Smith, Phillip J. Stansfeld, Johanna K. S. Tiemann, Mikaël Trellet, Christopher J. Woods, Artem A. Zhmurov
2016 — conf
MDAnalysis: A Python Package for the Rapid Analysis of Molecular Dynamics Simulations.
SciPy
Richard J. Gowers, Max Linke, Jonathan Barnoud, Tyler J. E. Reddy, Manuel N. Melo, Sean L. Seyler, Jan J. Domanski, David L. Dotson, Sébastien Buchoux, Ian M. Kenney, Oliver Beckstein
2014 J jnl
Hydrophobic Compounds Reshape Membrane Domains.
PLoS Comput. Biol.
Jonathan Barnoud, Giulia Rossi, Siewert J. Marrink, Luca Monticelli