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Scaling molecular dynamics for large-scale simulation of biological systems on AMD CPU/GPU supercomputers: Lessons from LUMI: Optimizing GENESIS for maximizing the computational efficiency of CPU and GPU kernels on the LUMI supercomputer 25

Scaling molecular dynamics for large-scale simulation of bio...

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8th International Conference on High Performance Computing in Asia-Pacific Region, HPC Asia 2025

作者： Ugarte La Torre, Diego Jung, Jaewoon Sugita, Yuji Computational Biophysics Research Team Riken R-CCS Kobe Japan Theoretical Molecular Science Laboratory Riken Cpr Wako Japan Laboratory for Biomolecular Function Simulation Riken Bdr Kobe Japan

ISBN: (纸本)9798400713354

This paper presents optimizations of the GENESIS molecular dynamics (MD) software for LUMI. GENESIS is a state-of-the-art MD program capable of simulating large-scale biological systems, yet it requires significant optimizations and investigations to fully utilize the computational resources of the LUMI-G hardware partition of LUMI, a hybrid architecture featuring AMD EPYC processors and AMD Instinct GPUs. Our work focuses on (1) addressing CPU-GPU communication bottlenecks, (2) tuning electrostatic interaction calculations using the Particle Mesh Ewald (PME) method, and (3) adapting GENESIS kernels for the AMD GPUs. A significant improvement in the MD performance is achieved through the NUMA mapping on each LUMI-G node. This improvement is shown in benchmark results for different molecular systems comprising from 2×104 to 1.6×107 atoms. The reciprocal-space calculation in the PME method on LUMI-G is faster than that on FUGAKU. Since the reciprocal-space calculation is carried out using only CPUs on both LUMI-G and FUGAKU, the results highlight the superior network performances on the former. The overall performance of a large system containing 1.6×107 atoms shows 200.8 ns/days when using 1024 nodes on LUMI-G, which is a better performance than previously reported results using general-purpose supercomputers. We conclude by providing recommendations for the optimal configurations of GENESIS on LUMI-G, including guidelines for selecting PME schemes for different system sizes and computational requirements. This optimization allows us to study cellular systems' stability, dynamics, and function relationships using atomistic MD simulations on a large scale. © 2025 Copyright held by the owner/author(s).

关键词： Supercomputers

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High-Performance Data Analysis on the Big Trajectory Data of Cellular Scale All-atom Molecular Dynamics simulations

High-Performance Data Analysis on the Big Trajectory Data of...

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International Meeting on High-Dimensional Data-Driven Science, HD3 2017

作者： Yu, Isseki Feig, Michael Sugita, Yuji ITHES Research Group RIKEN Saitama Japan Theoretical Molecular Science Laboratory RIKEN Saitama Japan Laboratory for Biomolecular Function Simulation RIKEN Quantitative Biology Center Kobe Japan Computational Biophysics Research Team RIKEN Advanced Institute for Computational Science Kobe Japan Department of Biochemistry and Molecular Biology Michigan State University East Lansing United States

The inside of a cell is highly crowded with a large number of macromolecules together with solvents and metabolites. To know the molecular-level behaviour of biomolecules in such dense crowding environment, we constructed full atomistic model of the cytoplasm of bacteria, and performed massive all-atom molecular dynamics (MD) simulations. On the other hand, to analyse such big MD data, we need significant computational power and efficient calculation methodology. Here, we introduce what and how we analyse the biomolecule properties from the big trajectory data produced by cellular scale all-atom MD simulations. © Published under licence by IOP Publishing Ltd.

关键词： Molecular dynamics

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Allosteric changes in the conformational landscape of Src kinase upon substrate binding

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Journal of Molecular Biology 2024年 168871页

作者： Chong, Song-Ho Oshima, Hiraku Sugita, Yuji Laboratory for Biomolecular Function Simulation RIKEN Center for Biosystems Dynamics Research Kobe Japan Global Center for Natural Resources Sciences Faculty of Life Sciences Kumamoto University Kumamoto Japan Graduate School of Science University of Hyogo Hyogo Japan Computational Biophysics Research Team RIKEN Center for Computational Science Kobe Japan Theoretical Molecular Science Laboratory Center for Pioneering Research Saitama Japan

Precise regulation of protein kinase activity is crucial in cell functions, and its loss is implicated in various diseases. The kinase activity is regulated by interconverting active and inactive states in the conformational landscape. However, how protein kinases switch conformations in response to different signals such as the binding at distinct sites remains incompletely understood. Here, we predict the binding mode for the peptide substrate to Src tyrosine kinase using enhanced conformational sampling simulations (totaling 24 μs) and then investigate changes in the conformational landscape upon substrate binding by conducting unbiased molecular dynamics simulations (totaling 50 μs) initiated from the apo and substrate-bound forms. Unexpectedly, the peptide substrate binding significantly facilitates the transitions from active to inactive conformations in which the αC helix is directed outward, the regulatory spine is broken, and the ATP-binding domain is perturbed. We also explore an underlying residue-contact network responsible for the allosteric conformational changes. Our results are in accord with the recent experiments reporting the negative cooperativity between the peptide substrate and ATP binding to tyrosine kinases and will contribute to advancing our understanding of the regulation mechanisms for kinase activity. © 2024 The Author(s)

关键词： allostery binding cooperativity enhanced sampling molecular simulation molecular dynamics simulation Src tyrosine kinase

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High-Performance Data Analysis on the Big Trajectory Data of Cellular Scale All-atom Molecular Dynamics simulations

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Journal of physics. Conference series 2018年第1期1036卷 012009页

作者： Isseki Yu Michael Feig Yuji Sugita iTHES Research Group RIKEN Saitama Japan. Theoretical Molecular Science Laboratory RIKEN Saitama Japan. Department of Biochemistry and Molecular Biology Michigan State University East Lansing United States. Laboratory for Biomolecular Function Simulation RIKEN Quantitative Biology Center Kobe Japan. Computational Biophysics Research Team RIKEN Advanced Institute for Computational Science Kobe Japan.

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Innentitelbild: Molecular Basis for Two Stereoselective Diels–Alderases that Produce Decalin Skeletons (Angew. Chem. 41/2021)

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Angewandte Chemie 2021年第41期133卷

作者： Dr. Keisuke Fujiyama Dr. Naoki Kato Dr. Suyong Re Kiyomi Kinugasa Dr. Kohei Watanabe Dr. Ryo Takita Dr. Toshihiko Nogawa Dr. Tomoya Hino Dr. Hiroyuki Osada Dr. Yuji Sugita Dr. Shunji Takahashi Prof. Shingo Nagano Department of Chemistry and Biotechnology Graduate School of Engineering Tottori University 4-101 Koyama-cho Minami Tottori 680-8552 Japan Current address: Dormancy and Adaptation Research Unit RIKEN Center for Sustainable Resource Science 1-7-22 Suehiro Tsurumi Yokohama Kanagawa 230-0045 Japan Natural Product Biosynthesis Research Unit RIKEN Center for Sustainable Research Science 2-1 Hirosawa Wako Saitama 351-0198 Japan Faculty of Agriculture Setsunan University 45-1 Nagaotoge-cho Hirakata Osaka 573-0101 Japan Laboratory for Biomolecular Function Simulation RIKEN Center for Biosystems Dynamics Research 2-2-3 Minatojima-minami-machi Chuo-ku Kobe Hyogo 650-0047 Japan Artificial Intelligence Center for Health and Biomedical Research National Institutes of Biomedical Innovation Health and Nutrition 7-6-8 Saito-Asagi Ibaraki Osaka 567-0085 Japan Graduate School of Pharmaceutical Sciences The University of Tokyo 7-3-1 Hongo Bunkyo-ku Tokyo 113-0033 Japan Chemical Biology Research Group RIKEN Center for Sustainable Research Science 2-1 Hirosawa Wako Saitama 351-0198 Japan Center for Research on Green Sustainable Chemistry Tottori University 4-101 Koyama-cho Minami Tottori 680-8552 Japan Theoretical Molecular Science Laboratory RIKEN Cluster for Pioneering Research 2-1 Hirosawa Wako Saitama 351-0198 Japan Computational Biophysics Research Team RIKEN Center for Computational Science 7-1-26 Minatojima-minami-machi Chuo-ku Kobe Hyogo 650-0047 Japan

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Molecular Basis for Two Stereoselective Diels–Alderases that Produce Decalin Skeletons**

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Angewandte Chemie 2021年第41期133卷

Enzymes catalyzing [4+2] cycloaddition have attracted increasing attention because of their key roles in natural product biosynthesis. Here, we solved the X-ray crystal structures of a pair of decalin synthases, Fsa2 and Phm7, that catalyze intramolecular [4+2] cycloadditions to form enantiomeric decalin scaffolds during biosynthesis of the HIV-1 integrase inhibitor equisetin and its stereochemical opposite, phomasetin. Computational modeling, using molecular dynamics simulations as well as quantum chemical calculations, demonstrates that the reactions proceed through synergetic conformational constraints assuring transition state-like substrates folds and their stabilization by specific protein-substrate interactions. Site-directed mutagenesis experiments verified the binding models. Intriguingly, the flexibility of bound substrates is largely different in two enzymes, suggesting the distinctive mechanism of dynamics regulation behind these stereoselective reactions. The proposed reaction mechanism herein deepens the basic understanding how these enzymes work but also provides a guiding principle to create artificial enzymes.

关键词： [4+2] cycloaddition biosynthesis molecular dynamics natural products stereoselectivity

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Inside Cover: Molecular Basis for Two Stereoselective Diels–Alderases that Produce Decalin Skeletons (Angew. Chem. Int. Ed. 41/2021)

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Angewandte Chemie International Edition 2021年第41期60卷

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