Tristan Bereau
@tristanbereau
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Interested in biomolecular simulations and machine learning of soft matter and biomolecules. Prof at Heidelberg University
Heidelberg, DE
Joined August 2012
Martignac: Computational Workflows for Reproducible, Traceable, and Composable Coarse-Grained Martini Simulations #MolecularDynamics
https://t.co/lXsxWSIVCw
@tristanbereau
#JCIM Vol64 Issue24 #compchem
pubs.acs.org
Despite their wide use and far-reaching implications, molecular dynamics (MD) simulations suffer from a lack of both traceability and reproducibility. We introduce Martignac: computational workflows...
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Solvation free energies with NeuralTI!
new preprint on solvation free energies: tl;dr: We define an interpolating density by its sampling process, and learn the corresponding equilibrium potential with score matching. https://t.co/sO0EI4sy5r with @francoisfleuret and @tristanbereau (1/n)
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Many thanks, @nicoli_kim, for having me! I had a great time in Bonn
Delighted to have had the pleasure of hosting @tristanbereau today, talking about Neural Thermodynamic Integration in a b2b talk with @balintmt 👏🏻👀 Work in collaboration with @francoisfleuret
#ML4PhysChem #BCTP #BetheForum #UniBonn
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I had a great time in Montpellier at this wonderful CECAM workshop. Many thanks to @RS_Chemist, Romain Dupuis, and Jorge Dolado!
We had an awesome @cecamEvents workshop on Bridging modeling scales at Montpellier! Thanks to all speakers, including @sven_rogge @vl_deringer @tristanbereau @CelineM35 @MarbachSophie @EdoBoek @SouzaPauloCT and to Romain Dupuis and Jorge Dolado for being the best co-organizers
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We also provide a Streamlit app https://t.co/bkvlYFfu5a to discover all Martignac calculations stored on NOMAD. The app can fetch and display custom properties, such as free energies. Try it out!
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Martignac is a great tool for reproducibility, where we can systematically vary simulation parameters to study changes in thermodynamic properties, such as free energies
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We implement several worfklows for system generation: solute, solvent, solute in solvent, lipid bilayer, and solute in bilayer. We also implement free-energy calculations for solvation and drug-membrane interactions
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Martignac connects to the @FAIRmat_NFDI's NOMAD research data management platform. NOMAD parses MD simulations to extract the metadata and store them permanently. Martignac automatically pulls existing sims and pushes new ones
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Martignac builds on @signacdata, a Python-based workflow library. We build a scientific workflow as a directed acyclic graph, where each node is a computational operation (e.g., an MD simulation). This enables traceability.
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MD simulations remain poorly shared, deficiently reproducible, and devoid of history. Together with Luis Walter and @JFRudzinski, we built Martignac: a computational workflow manager for CG Martini https://t.co/lAp8mr0H8C 🧵
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JCIM @JCIM_JCTC has a new special issue about Chemical Compound Space Exploration by Multiscale High-Throughput Screening and #MachineLearning. Check the editorial by @grynova_CCC @tristanbereau @Rebecca_Wade_C @kmerz1, me, others for more info! #compchem
https://t.co/lV1r3olPZq
pubs.acs.org
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Universität Heidelberg Establishes AI Board: Interdisciplinary committee advises Rectorate on issues of artificial intelligence
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It's been a blast working with @balintmate_ and @francoisfleuret on generative ML for thermodynamic integration. Bálint accurately computes extremely large free-energy differences from a _single_ reference simulation 🔥
New preprint on performing thermodynamic integration along the trajectories of a denoising diffusion model: https://t.co/DxTbYxVb4X. With @francoisfleuret and @tristanbereau (1/n)
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Check out the #openaccess accepted manuscript for 'Roadmap on Data-Centric Materials Science' published now in MSMSE. Learn more 👉 https://t.co/B0ZyciyzGf
@fhi_aims, @Kokookster, Bluesky: @fhi-aims.bsky.social @tristanbereau @a_logsdail, @CCI_Cardiff, and @ChemistryCU.
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I'm very grateful to be working together with @grynova_CCC, @cmueller_chemie, Stefan Chmiela, and @ProfvLilienfeld as part of the organization team 🌠
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... @TapaviczaEnrico Pascal Friedrich, Julia Zavadlav, Milica Todoroviç, Klaus Robert Müller, Paul Popelier, Yousung Jung, Markus Meuwly, and many others
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