MDAnalysis

@mdanalysis.bsky.social

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Working with data in the molecular sciences. https://www.mdanalysis.org

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In-person participants at the MDAnalysis 2025 User Group Meeting (online participants not shown).
Lillian Chong in front of her opening slide.
Matthias Heyden of Arizona State University presenting in front of a screen with multiple protein structures where dynamics are indicated by arrows.
Dr. Matthias Heyden, Associate Professor, Arizona State University. Prof. Heyden's research group studies the dynamics and function of biomolecules with molecular simulations and Monte Carlo simulations. A special interest of his is anharmonic low-frequency vibrations, which are easily excitable by molecular collisions and can exhibit large deviations from harmonic approximations.
Dr. Lillian Chong, Professor, University of Pittsburgh. Prof. Chong's research focuses on developing and applying advanced simulation methods to investigate rare but biologically important events, with an emphasis on capturing rigorous kinetics. Her group leads the development of the open-source WESTPA software, which implements weighted ensemble path sampling strategies for efficient simulation of rare events. She also works on the development of implicitly polarized force fields and rational design of protein conformational switches.
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Visualization of part of a protein with MDAnalysis and Blender/MolecularNodes together with Python code to generate the image.
MDAnalysis UGM 2024
group photo from the MDAnalysis/MolSSI Workshop at ASU, June 24-25, 2024
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MDAnalysis Workshop June 24-25th 2024, Arizona State University. Stylized saguaro cactus with flowers shaped like the MDAnalysis logo.
MDAnalysis Workshop June 24-25th 2024 at Arizona State University. A Saguaro cactus in the desert with flowers shaped like the MDAnalysis logo.
Dr. Francesca Stanzione, Senior Scientist, Sosei Heptares. Francesca is a computational chemist with over a decade expertise in target assessment, hit identification and lead optimisation. After obtaining a Ph.D. in Biotechnology, Francesca embarked on a distinguished career path. With five years of postdoctoral fellowships Francesca’s work centered on characterising the structural and dynamical properties of complex biological systems, including proteins and protein-ligand complexes, biological membranes and biomaterials. In 2023, Francesca joined Sosei Heptares, a renowned player in the pharmaceutical industry, where she now provides invaluable computational support to a variety of drug discovery campaigns. Prior to her role at Sosei Heptares, Francesca was at the Cambridge Crystallographic Data Centre (CCDC), working closely with software developers to help the development and enhancement of computational tools for drug discovery.
Dr. Antonia Mey, Chancellor's Fellow, University of Edinburgh School of Chemistry. Antonia has worked on Markov State models with Frank Noe and alchemical free energy calculations with Julien Michel before starting her own research group in 2020. Her group works on computational biophysics problems using machine learning and simulations to understand protein function. She is an advocate for open-source software and diamond open access publishing models. She has contributed to pyEmma, BioSimSpace and she and her group (https://mey-research.org) are avid users of MDAnalysis.