Jean-Philip Piquemal
@jppiquem • 7,173 subscribers
Professor of Theoretical Chemistry at Sorbonne Université & Director @ LCT (UMR 7616 @CNRS)| Co-founder & CSO @qubit_pharma (My Views)
Videos
#compchem Second preprint linked to the FeNNix-Bio1 #machinelearning foundation model. FeNNix-Bio1's inference is pretty fast already with a few GPUs but, "what if", we were able to push it at the #Exascale? Let's have a glimpse into the future (1/3): "Pushing the Accuracy Limit of Foundation Neural Network Models with Quantum Monte Carlo Forces and Path Integrals" Check it out 💫: We propose an end-to-end integrated strategy to produce highly accurate quantum chemistry synthetic datasets (energies and forces) aimed at deriving Foundation Machine Learning models for molecular simulation. Starting from Density Functional Theory (DFT), a "Jacob's Ladder" approach leverages computationally-optimized layers of massively #GPU-accelerated software with increasing accuracy. Thanks to Exascale, this is the first time that the computationally intensive calculation of Quantum Monte Carlo forces (QMC), and the combination of multi-determinant QMC energies and forces with selected-Configuration Interaction wavefunctions, are computed at such scale at the complete basis-set limit. To bridge the gap between accurate QC and condensed-phase Molecular Dynamics, we leverage transfer learning to improve the DFT-based FeNNix-Bio1 foundation model. 🚀The resulting approach is coupled to path integrals adaptive sampling quantum dynamics to perform nanosecond reactive simulations at unprecedented accuracy on a full Satellite Tobacco Mosaic Virus (STMV) 1M, all-atom, complete solvated model (see the video produced using VTX, Maxime MARIA Matthieu Montes ). These results demonstrate the promise of Exascale to deepen our understanding of the inner machinery of complex biosystems. Immense thanks to all co-authors at Qubit Pharmaceuticals, Laboratoire de Chimie Théorique (Sorbonne Université /CNRS 🌍 ), The University of Chicago, Sandia National Labs, Oak Ridge Lab and Argonne National Lab for this collaborative efforts. Some are on X: Anouar Benali Thomas Plé ADJOUA Olivier Evgeny Posenitskiy Margaret Blazhynska Thomas Applencourt Jeongnim Kim #HPC This work was made possible thanks to #INCITE projects enabling the use of Argonne's Aurora exascale system and of the Polaris machine, to Genci (Jean Zay @ Idris) and EuroHPC Joint Undertaking (Leonardo CINECA). #supercomputing
Jean-Philip Piquemal15,131 Aufrufe • vor 1 Jahr
#compchem Just published in Chemical Science: Water-Glycan Interactions Drive the SARS-CoV-2 Spike Dynamics: Insights into Glycan-Gate Control and Camouflage Mechanism. Towards developing therapeutic strategies against #COVID19, we performed μs-long all-atom AMOEBA high-resolution polarizable adaptive sampling molecular dynamics simulations and zoomed in on the #SARSCoV2 interaction layers in open and closed states. Simulations reveal a protein-solvent-glycan polarization network supporting the open state. Besides, we showed that the glycan shield maintains viral camouflage in both states. Amazing work by @blazhynska. Kudos to L. Lagardère and ADJOUA Olivier. Another epic collaboration with Chengwen Liu and Pengyu Ren. This research was funded by European Research Council (ERC) (project EMC2). We thank Amazon Web Services for supporting this research and providing extensive #GPU-accelerated cloud computational ressources as well as Genci for #supercomputing time. #HPC Laboratoire de Chimie Théorique Qubit Pharmaceuticals Sorbonne Université CNRS Chimie Texas BME TINKERtools
Jean-Philip Piquemal17,899 Aufrufe • vor 1 Jahr
#compchem The long time overdue "polarizable" Spike protein preprint: "Water-Glycan Interactions Drive the SARS-CoV-2 Spike Dynamics: Insights into Glycan-Gate Control and Camouflage Mechanism" 👉: Full AMOEBA adaptive sampling simulations on the open and closed states and discussions around the solvent/glycan/protein interfaces. Amazing work by @blazhynska. A huge thank to the great L. Lagardère and ADJOUA Olivier and another fun collab with Chengwen Liu & Pengyu Ren. This work was made possible thanks to the funding European Research Council (ERC) (project EMC2) and Amazon Web Services which granted us "a lot" of #GPUs time... Thanks also to Genci for "more" #supercomputing time...😅🤣😇#HPC #SARSCoV2 TINKERtools Qubit Pharmaceuticals Laboratoire de Chimie Théorique
Jean-Philip Piquemal12,535 Aufrufe • vor 2 Jahren
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