Language：Japanese   Publishing type：Research paper (scientific journal)  

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Authorship：Lead author,　Corresponding author   Publishing type：Research paper (scientific journal)   Publisher：Physical Society of Japan  

DOI： 10.7566/jpsj.93.084805

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Language：English   Publishing type：Research paper (scientific journal)   Publisher：Elsevier BV  

DOI： 10.1016/j.molliq.2023.123197

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Publishing type：Research paper (scientific journal)   Publisher：The Electrochemical Society of Japan  

DOI： 10.5796/electrochemistry.23-00086

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Language：English   Publishing type：Research paper (scientific journal)   Publisher：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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Language：English   Publishing type：Research paper (scientific journal)   Publisher：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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Other Link： https://onlinelibrary.wiley.com/doi/full-xml/10.1002/jcc.26975

Authorship：Lead author   Publishing type：Research paper (scientific journal)  

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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Authorship：Lead author   Language：English   Publishing type：Research paper (scientific journal)  

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

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DOI： 10.1063/5.0075969

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Language：English   Publishing type：Research paper (scientific journal)  

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

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Authorship：Lead author   Publishing type：Research paper (scientific journal)   Publisher：Wiley  

DOI： 10.1002/jcc.26742

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Other Link： https://onlinelibrary.wiley.com/doi/full-xml/10.1002/jcc.26742

Authorship：Lead author   Language：English   Publishing type：Research paper (scientific journal)  

DOI： 10.1021/acs.jctc.0c00448

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Language：English   Publishing type：Research paper (scientific journal)  

DOI： 10.1063/1.5091450

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Authorship：Lead author   Language：English   Publishing type：Research paper (scientific journal)  

Cryo-cooling is routinely performed before x-ray diffraction image collection to reduce the damage to crystals due to ionizing radiation. It has been suggested that although backbone structures are usually very similar between room temperature and cryo-temperature, cryo-cooling may hamper biologically relevant dynamics. In this study, the crystal of Escherichia coli dihydrofolate reductase is studied with replica-exchange molecular dynamics simulation, and the results are compared with the crystal structure determined at cryo-temperature and room temperature with the time-averaged ensemble method. Although temperature dependence of unit cell compaction and root mean-square fluctuation of Cα is found in accord with experiment, it is found that the protein structure at low temperature can be more heterogeneous than the ensemble of structures reported by using the time-averaged ensemble method, encouraging further development of the time-averaged ensemble method and indicating that data should be examined carefully to avoid overinterpretation of one average structure.

DOI： 10.1016/j.bpj.2018.11.3139

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Language：English   Publishing type：Research paper (scientific journal)  

Protein structural biology came a long way since the determination of the first three-dimensional structure of myoglobin about six decades ago. Across this period, X-ray crystallography was the most important experimental method for gaining atomic-resolution insight into protein structures. However, as the role of dynamics gained importance in the function of proteins, the limitations of X-ray crystallography in not being able to capture dynamics came to the forefront. Computational methods proved to be immensely successful in understanding protein dynamics in solution, and they continue to improve in terms of both the scale and the types of systems that can be studied. In this review, we briefly discuss the limitations of X-ray crystallography in studying protein dynamics, and then provide an overview of different computational methods that are instrumental in understanding the dynamics of proteins and biomacromolecular complexes.

DOI： 10.3390/ijms19113401

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Authorship：Lead author   Language：English   Publishing type：Research paper (scientific journal)  

We explore the advantage of Gaussian mixture model (GMM) for interpretation of single particle diffraction patterns from X-ray free electron laser (XFEL) experiments. GMM approximates a biomolecular shape by the superposition of Gaussian distributions. As the Fourier transformation of GMM can be quickly performed, we can efficiently simulate XFEL diffraction patterns from approximated structure models. We report that the resolution that GMM can accurately reproduce is proportional to the cubic root of the number of Gaussians used in the modeling. This behavior can be attributed to the correspondence between the number of adjustable parameters in GMM and the amount of sampling points in diffraction space. Furthermore, GMMs can successfully be used to perform angular assignment and to detect conformational variation. These results demonstrate that GMMs serve as useful coarse-grained models for hybrid approach in XFEL single particle experiments.

DOI： 10.1364/OE.26.026734

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Language：English   Publishing type：Research paper (scientific journal)  

DOI： 10.1063/1.4999709

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Authorship：Lead author,　Last author,　Corresponding author   Language：English   Publishing type：Research paper (scientific journal)  

DOI： 10.7566/JPSJ.86.014003

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Authorship：Lead author,　Corresponding author   Language：English   Publishing type：Research paper (scientific journal)  

DOI： 10.1002/jcc.24430

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Authorship：Lead author,　Corresponding author   Language：English   Publishing type：Research paper (international conference proceedings)  

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Authorship：Lead author,　Corresponding author   Language：English   Publishing type：Research paper (scientific journal)  

DOI： 10.1063/1.4895510

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Authorship：Lead author   Language：English   Publishing type：Research paper (scientific journal)  

DOI： 10.1088/1742-5468/2013/02/P02039

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Authorship：Lead author   Language：English   Publishing type：Research paper (scientific journal)  

DOI： 10.5488/CMP.16.23605

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Authorship：Lead author   Language：English   Publishing type：Research paper (scientific journal)  

DOI： 10.1103/PhysRevE.86.056705

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Authorship：Lead author   Language：English   Publishing type：Research paper (scientific journal)  

DOI： 10.1143/JPSJ.81.024002

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Authorship：Lead author   Language：English   Publishing type：Research paper (scientific journal)  

DOI： 10.1080/08927022.2011.564172

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Authorship：Lead author   Language：English   Publishing type：Research paper (international conference proceedings)  

DOI： 10.1016/j.phpro.2012.05.016

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Language：Japanese  

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Other Link： https://ndlsearch.ndl.go.jp/books/R000000004-I033277556