記述言語：日本語   掲載種別：研究論文（学術雑誌）  

Web of Science

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担当区分：筆頭著者,　責任著者   掲載種別：研究論文（学術雑誌）   出版者・発行元：Physical Society of Japan  

DOI： 10.7566/jpsj.93.084805

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記述言語：英語   掲載種別：研究論文（学術雑誌）   出版者・発行元：Elsevier BV  

DOI： 10.1016/j.molliq.2023.123197

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掲載種別：研究論文（学術雑誌）   出版者・発行元：The Electrochemical Society of Japan  

DOI： 10.5796/electrochemistry.23-00086

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記述言語：英語   掲載種別：研究論文（学術雑誌）   出版者・発行元：AIP Publishing  

A new version of the highly parallelized general-purpose molecular dynamics (MD) simulation program MODYLAS with high performance on the Fugaku computer was developed. A benchmark test using Fugaku indicated highly efficient communication, single instruction, multiple data (SIMD) processing, and on-cache arithmetic operations. The system’s performance deteriorated only slightly, even under high parallelization. In particular, a newly developed minimum transferred data method, requiring a significantly lower amount of data transfer compared to conventional communications, showed significantly high performance. The coordinates and forces of 101 810 176 atoms and the multipole coefficients of the subcells could be distributed to the 32 768 nodes (1 572 864 cores) in 2.3 ms during one MD step calculation. The SIMD effective instruction rates for floating-point arithmetic operations in direct force and fast multipole method (FMM) calculations measured on Fugaku were 78.7% and 31.5%, respectively. The development of a data reuse algorithm enhanced the on-cache processing; the cache miss rate for direct force and FMM calculations was only 2.74% and 1.43%, respectively, on the L1 cache and 0.08% and 0.60%, respectively, on the L2 cache. The modified MODYLAS could complete one MD single time-step calculation within 8.5 ms for the aforementioned large system. Additionally, the program contains numerous functions for material research that enable free energy calculations, along with the generation of various ensembles and molecular constraints.

DOI： 10.1063/5.0144361

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記述言語：英語   掲載種別：研究論文（学術雑誌）   出版者・発行元：Wiley  

Abstract

Molecular self‐diffusion coefficients underlie various kinetic properties of the liquids involved in chemistry, physics, and pharmaceutics. In this study, 547 self‐diffusion coefficients are calculated based on all‐atom molecular dynamics (MD) simulations of 152 diverse pure liquids at various temperatures employing the OPLS4 force field. The calculated coefficients are compared with experimental data (424 extracted from the literature and 123 newly measured by pulsed‐field gradient nuclear magnetic resonance). The calculations well agree with the experimental values. The determination coefficient and root mean square error between the observed and calculated logarithmic self‐diffusion coefficients of the 547 entries are 0.931 and 0.213, respectively, demonstrating that the MD calculation can be an excellent industrial tool for predicting, for example, molecular transportation in liquids such as the diffusion of active ingredients in biological and pharmaceutical liquids. The self‐diffusion coefficients collected in this study are compiled into a database for broad researches including artificial intelligence calculations.

DOI： 10.1002/jcc.26975

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その他リンク： https://onlinelibrary.wiley.com/doi/full-xml/10.1002/jcc.26975

担当区分：筆頭著者   掲載種別：研究論文（学術雑誌）  

Using our recently developed dynamic Monte Carlo (MC) method [Nagai et al., J. Chem. Phys. 156, 154506 (2022)], we investigated the global diffusion of hydrogen molecules over structural heterogeneities of polymer electrolyte membranes in fuel cells. The three-dimensional position-dependent free energies and the diffusion constants of the hydrogen molecules, required by the present dynamic MC calculations, were taken from our previous study [Nagai et al., J. Chem. Phys. 156, 044507 (2022)] and newly evaluated in this work, respectively. The calculations enabled evaluating the hydrogen dynamics over long-time scales, including global diffusion constants. Based on the calculated global diffusion constants and free energies, the permeability of hydrogen molecules was estimated via the solubility-diffusion model. The estimated values were in good agreement with the reported experimental data, thus validating the present methodology. The analysis of the Monte Carlo trajectories indicated that the main permeation paths are located in the polymer and interfacial phases, although the water phase may make a non-negligible contribution to mass transport.

DOI： 10.1063/5.0096574

PubMed

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担当区分：筆頭著者   記述言語：英語   掲載種別：研究論文（学術雑誌）  

A series of new Monte Carlo (MC) transition probabilities was investigated that could produce molecular trajectories statistically satisfying the diffusion equation with a position-dependent diffusion coefficient and potential energy. The MC trajectories were compared with the numerical solution of the diffusion equation by calculating the time evolution of the probability distribution and the mean first passage time, which exhibited excellent agreement. The method is powerful when investigating, for example, the long-distance and long-time global transportation of a molecule in heterogeneous systems by coarse-graining them into one-particle diffusive molecular motion with a position-dependent diffusion coefficient and free energy. The method can also be applied to many-particle dynamics.

DOI： 10.1063/5.0086949

PubMed

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担当区分：筆頭著者   掲載種別：研究論文（学術雑誌）  

DOI： 10.1063/5.0075969

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記述言語：英語   掲載種別：研究論文（学術雑誌）  

X-ray free-electron laser (XFEL) is the latest generation of the X-ray source that could become an invaluable technique in structural biology. XFEL has ultrashort pulse duration, extreme peak brilliance, and high spatial coherence, which could enable the observation of the biological molecules in near nature state at room temperature without crystallization. However, for biological systems, due to their low diffraction power and complexity of sample delivery, experiments and data analysis are not straightforward, making it extremely challenging to reconstruct three-dimensional (3D) structures from single particle XFEL data. Given the current limitations to the amount and resolution of the data from such XFEL experiments, we propose a new hybrid approach for characterizing biomolecular conformational transitions by using a single 2D low-resolution XFEL diffraction pattern in combination with another known conformation. In our method, we represent the molecular structure with a coarse-grained model, the Gaussian mixture model, to describe large conformational transitions from low-resolution XFEL data. We obtain plausible 3D structural models that are consistent with the XFEL diffraction pattern by deforming an initial structural model to maximize the similarity between the target pattern and the simulated diffraction patterns from the candidate models. We tested the proposed algorithm on two biomolecules of different sizes with different complexities of conformational transitions, adenylate kinase, and elongation factor 2, using synthetic XFEL data. The results show that, with the proposed algorithm, we can successfully describe the conformational transitions by flexibly fitting the coarse-grained model of one conformation to become consistent with an XFEL diffraction pattern simulated from another conformation. In addition, we showed that the incident beam orientation has some effect on the accuracy of the 3D structure modeling and discussed the reasons for the inaccuracies for certain orientations. The proposed method could serve as an alternative approach for retrieving information on 3D conformational transitions from the XFEL diffraction patterns to interpret experimental data. Since the molecules are represented by Gaussian kernels and no atomic structure is needed in principle, such a method could also be used as a tool to seek initial models for 3D reconstruction algorithms.

DOI： 10.3389/fmolb.2022.913860

PubMed

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担当区分：筆頭著者   掲載種別：研究論文（学術雑誌）   出版者・発行元：Wiley  

DOI： 10.1002/jcc.26742

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その他リンク： https://onlinelibrary.wiley.com/doi/full-xml/10.1002/jcc.26742

担当区分：筆頭著者   記述言語：英語   掲載種別：研究論文（学術雑誌）  

DOI： 10.1021/acs.jctc.0c00448

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記述言語：英語   掲載種別：研究論文（学術雑誌）  

DOI： 10.1063/1.5091450

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担当区分：筆頭著者   記述言語：英語   掲載種別：研究論文（学術雑誌）  

DOI： 10.1016/j.bpj.2018.11.3139

PubMed

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記述言語：英語   掲載種別：研究論文（学術雑誌）  

DOI： 10.3390/ijms19113401

PubMed

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担当区分：筆頭著者   記述言語：英語   掲載種別：研究論文（学術雑誌）  

DOI： 10.1364/OE.26.026734

PubMed

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記述言語：英語   掲載種別：研究論文（学術雑誌）  

DOI： 10.1063/1.4999709

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担当区分：筆頭著者,　最終著者,　責任著者   記述言語：英語   掲載種別：研究論文（学術雑誌）  

DOI： 10.7566/JPSJ.86.014003

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担当区分：筆頭著者,　責任著者   記述言語：英語   掲載種別：研究論文（学術雑誌）  

DOI： 10.1002/jcc.24430

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担当区分：筆頭著者,　責任著者   記述言語：英語   掲載種別：研究論文（国際会議プロシーディングス）  

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担当区分：筆頭著者,　責任著者   記述言語：英語   掲載種別：研究論文（学術雑誌）  

DOI： 10.1063/1.4895510

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担当区分：筆頭著者   記述言語：英語   掲載種別：研究論文（学術雑誌）  

DOI： 10.1088/1742-5468/2013/02/P02039

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担当区分：筆頭著者   記述言語：英語   掲載種別：研究論文（学術雑誌）  

DOI： 10.5488/CMP.16.23605

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担当区分：筆頭著者   記述言語：英語   掲載種別：研究論文（学術雑誌）  

DOI： 10.1103/PhysRevE.86.056705

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担当区分：筆頭著者   記述言語：英語   掲載種別：研究論文（学術雑誌）  

DOI： 10.1143/JPSJ.81.024002

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担当区分：筆頭著者   記述言語：英語   掲載種別：研究論文（学術雑誌）  

DOI： 10.1080/08927022.2011.564172

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担当区分：筆頭著者   記述言語：英語   掲載種別：研究論文（国際会議プロシーディングス）  

DOI： 10.1016/j.phpro.2012.05.016

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記述言語：日本語   出版者・発行元：[岡崎] : 理論化学会 = Japan Society of Theoretical Chemistry  

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その他リンク： https://ndlsearch.ndl.go.jp/books/R000000004-I033277556