Browsing by Author "Takamoto, Makoto"

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    Research data management in simulation science : infrastructure, tools, and applications
    (2024) Flemisch, Bernd; Hermann, Sibylle; Herschel, Melanie; Pflüger, Dirk; Pleiss, Jürgen; Range, Jan; Roy, Sarbani; Takamoto, Makoto; Uekermann, Benjamin
    Research Data Management (RDM) has gained significant traction in recent years, being essential to allowing research data to be, e.g., findable, accessible, interoperable, and reproducible (FAIR), thereby fostering collaboration or accelerating scientific findings. We present solutions for RDM developed within the DFG-Funded Cluster of Excellence EXC2075 Data-Integrated Simulation Science (SimTech). After an introduction to the scientific context and challenges faced by simulation scientists, we outline the general data management infrastructure and present tools that address these challenges. Exemplary domain applications demonstrate the use and benefits of the proposed data management software solutions. These are complemented by additional measures for enablement and dissemination to foster the adoption of these techniques.
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    Uncertainty-biased molecular dynamics for learning uniformly accurate interatomic potentials
    (2024) Zaverkin, Viktor; Holzmüller, David; Christiansen, Henrik; Errica, Federico; Alesiani, Francesco; Takamoto, Makoto; Niepert, Mathias; Kästner, Johannes
    Efficiently creating a concise but comprehensive data set for training machine-learned interatomic potentials (MLIPs) is an under-explored problem. Active learning, which uses biased or unbiased molecular dynamics (MD) to generate candidate pools, aims to address this objective. Existing biased and unbiased MD-simulation methods, however, are prone to miss either rare events or extrapolative regions-areas of the configurational space where unreliable predictions are made. This work demonstrates that MD, when biased by the MLIP’s energy uncertainty, simultaneously captures extrapolative regions and rare events, which is crucial for developing uniformly accurate MLIPs. Furthermore, exploiting automatic differentiation, we enhance bias-forces-driven MD with the concept of bias stress. We employ calibrated gradient-based uncertainties to yield MLIPs with similar or, sometimes, better accuracy than ensemble-based methods at a lower computational cost. Finally, we apply uncertainty-biased MD to alanine dipeptide and MIL-53(Al), generating MLIPs that represent both configurational spaces more accurately than models trained with conventional MD.