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田中 成典大学院システム情報学研究科 システム情報学専攻教授
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■ 論文- 2025年04月, Chemical Physics Letters研究論文（学術雑誌）
- 2025年03月, Dynamics研究論文（学術雑誌）
- 2024年11月, Entropy研究論文（学術雑誌）
- 2024年08月, The Journal of Chemical Physics研究論文（学術雑誌）
- Abstract Proteins play a variety of roles in biological phenomena in cells. Proteins are synthesized by a ribosome, which is a large molecular complex composed of proteins and nucleic acids. Among many molecules involved in the process of protein synthesis, transfer RNA (tRNA) is one of the essential molecules. In this study, coarse-grained molecular dynamics simulations were performed to understand how the tRNA molecule is stabilized in the ribosome, and the free energy along the dissociation path of the tRNA was calculated. We found that some ribosomal proteins, which are components of the ribosome, are involved in the stabilization of the tRNA. The positively charged amino acid residues in the C-terminal region of the ribosomal proteins are particularly important for the stabilization. These findings contribute to our understanding of the molecular evolution of protein synthesis in terms of the ribosome, which is a universal component of life. TOC GraphicCold Spring Harbor Laboratory, 2024年07月
- Ultra-large virtual chemical spaces have emerged as a valuable resource for drug discovery, providing access to billions of make-on-demand compounds with high synthetic success rates. Chemical language models can potentially accelerate the exploration of these vast spaces through direct compound generation. However, existing models are not designed to navigate specific virtual chemical spaces and often overlook synthetic accessibility. To address this gap, we introduce product-of-experts (PoE) chemical language models, a modular and scalable approach to navigating ultra-large virtual chemical spaces. This method allows for controlled compound generation within a desired chemical space by combining a prior model pre-trained on the target space with expert and anti-expert models fine-tuned using external property-specific datasets. We demonstrate that the PoE chemical language model can generate compounds with desirable properties, such as those that favorably dock to the dopamine receptor D2 (DRD2) and are predicted to cross the blood-brain barrier (BBB), while ensuring that the majority of generated compounds are present within the target chemical space. Our results highlight the potential of chemical language models for navigating ultra-large virtual chemical spaces, and we anticipate that this study will motivate further research in this direction. The source code and data are freely available at https://github.com/shuyana/poeclm/.American Chemical Society (ACS), 2024年07月
- 2024年06月, Foundations研究論文（学術雑誌）
- The PAX8/PPARγ rearrangement, producing the PAX8–PPARγ fusion protein (PPFP), is thought to play an essential role in the oncogenesis of thyroid follicular tumors. To identify PPFP-targeted drug candidates and establish an early standard of care for thyroid tumors, we performed ensemble-docking-based compound screening. Specifically, we investigated the pocket structure that should be adopted to search for a promising ligand compound for the PPFP; the position of the ligand-binding pocket on the PPARγ side of the PPFP is similar to that of PPARγ; however, the shape is slightly different between them due to environmental factors. We developed a method for selecting a PPFP structure with a relevant pocket and high prediction accuracy for ligand binding. This method was validated using PPARγ, whose structure and activity values are known for many compounds. Then, we performed docking calculations to the PPFP for 97 drug or drug-like compounds registered in the DrugBank database with a thiazolidine backbone, which is one of the characteristics of ligands that bind well to PPARγ. Furthermore, the binding affinities of promising ligand candidates were estimated more reliably using the molecular mechanics Poisson–Boltzmann surface area method. Thus, we propose promising drug candidates for the PPFP with a thiazolidine backbone.MDPI AG, 2024年05月, International Journal of Molecular Sciences, 25(10) (10), 5347 - 5347研究論文（学術雑誌）
- We investigate Quantum Electrodynamics corresponding to the holographic brain theory introduced by Pribram to describe memory in the human brain. First, we derive a super-radiance solution in Quantum Electrodynamics with non-relativistic charged bosons (a model of molecular conformational states of water) for coherent light sources of holograms. Next, we estimate memory capacity of a brain neocortex, and adopt binary holograms to manipulate optical information. Finally, we introduce a control theory to manipulate holograms involving biological water’s molecular conformational states. We show how a desired waveform in holography is achieved in a hierarchical model using numerical simulations.MDPI AG, 2024年02月, International Journal of Molecular Sciences, 25(4) (4), 2399 - 2399研究論文（学術雑誌）
- Uncovering the mystery of efficient and directional energy transfer in photosynthetic organisms remains a critical challenge in quantum biology. Recent experimental evidence and quantum theory developments indicate the significance of quantum features of molecular vibrations in assisting photosynthetic energy transfer, which provides the possibility of manipulating the process by controlling molecular vibrations. Here, we propose and theoretically demonstrate efficient manipulation of photosynthetic energy transfer by using vibrational strong coupling between the vibrational state of a Fenna–Matthews–Olson (FMO) complex and the vacuum state of an optical cavity. Specifically, based on a full-quantum analytical model to describe the strong coupling effect between the optical cavity and molecular vibration, we realize efficient manipulation of energy transfer efficiency (from 58% to 92%) and energy transfer time (from 20 to 500 ps) in one branch of FMO complex by actively controlling the coupling strength and the quality factor of the optical cavity under both near-resonant and off-resonant conditions, respectively. Our work provides a practical scenario to manipulate photosynthetic energy transfer by externally interfering molecular vibrations via an optical cavity and a comprehensible conceptual framework for researching other similar systems.AIP Publishing, 2024年01月, The Journal of Chemical Physics, 160(4) (4)研究論文（学術雑誌）
- The Japan Association for Philosophy of Science, 2024年, Journal of the Japan Association for Philosophy of Science, 51(1-2) (1-2), 57 - 73研究論文（学術雑誌）
- 2023年11月, The Journal of Physical Chemistry Letters研究論文（学術雑誌）
- COVID-19 remains a global pandemic, necessitating the urgent development of more effective therapeutics. By combining molecular docking, molecular dynamics (MD), and fragment molecular orbital (FMO) calculations, the binding structure and properties with Mpro were predicted for Nelfinavir (NLF), which was identified as a candidate compound through drug repositioning targeting the Main Protease (Mpro) produced by the causative virus, SARS-CoV-2. For the four docking poses selected by scoring using FMO energy, 100 structures each from the MD trajectory were sampled, and FMO calculations were performed and ranked based on binding energy. Besides the interaction between NLF and each Mpro residue, the desolvation effect of the pocket affected the ranking order. Furthermore, we identified several residues important in ligand recognition, including Glu47, Asp48, Glu166, Asp187, and Gln189, all of which interacted strongly with NLF. Asn142 was mentioned as a residue with hydrogen bonds or CH/π interaction with NLF; however, it was considered a transient interacting residue because of its unstable structure. Moreover, the tert-butyl group of NLF had no interaction with Mpro. Identifying weak interactions provides candidates for substituting ligand functional groups and important suggestions for drug discovery using drug repositioning. Our approach provides a new guideline for structure-based drug design starting from a candidate compound whose complex crystal structure has not been obtained.American Chemical Society (ACS), 2023年07月
- American Chemical Society (ACS), 2023年07月, The Journal of Physical Chemistry B, 127(28) (28), 6306 - 6315[査読有り]研究論文（学術雑誌）
- Abstract Background Three-dimensional structures of protein–ligand complexes provide valuable insights into their interactions and are crucial for molecular biological studies and drug design. However, their high-dimensional and multimodal nature hinders end-to-end modeling, and earlier approaches depend inherently on existing protein structures. To overcome these limitations and expand the range of complexes that can be accurately modeled, it is necessary to develop efficient end-to-end methods. Results We introduce an equivariant diffusion-based generative model that learns the joint distribution of ligand and protein conformations conditioned on the molecular graph of a ligand and the sequence representation of a protein extracted from a pre-trained protein language model. Benchmark results show that this protein structure-free model is capable of generating diverse structures of protein–ligand complexes, including those with correct binding poses. Further analyses indicate that the proposed end-to-end approach is particularly effective when the ligand-bound protein structure is not available. Conclusion The present results demonstrate the effectiveness and generative capability of our end-to-end complex structure modeling framework with diffusion-based generative models. We suppose that this framework will lead to better modeling of protein–ligand complexes, and we expect further improvements and wide applications.Springer Science and Business Media LLC, 2023年06月, BMC Bioinformatics, 24(1) (1)[査読有り]研究論文（学術雑誌）
- American Chemical Society (ACS), 2023年04月, The Journal of Physical Chemistry Letters, 3609 - 3620[査読有り]研究論文（学術雑誌）
- We show renormalization in Quantum Brain Dynamics (QBD) in 3+1 dimensions, namely Quantum Electrodynamics with water rotational dipole fields. First, we introduce the Lagrangian density for QBD involving terms of water rotational dipole fields, photon fields and their interactions. Next, we show Feynman diagrams with 1-loop self-energy and vertex function in dipole coupling expansion in QBD. The counter-terms are derived from the coupling expansion of the water dipole moment. Our approach will be applied to numerical simulations of Kadanoff–Baym equations for water dipoles and photons to describe the breakdown of the rotational symmetry of dipoles, namely memory formation processes. It will also be extended to the renormalization group method for QBD with running parameters in multi-scales.MDPI AG, 2023年02月, AppliedMath, 3(1) (1), 117 - 146[査読有り]研究論文（学術雑誌）
- We describe non-equilibrium ϕ4 theory in a hierarchical manner to develop a method for manipulating coherent fields as a toy model of introducing control into Quantum Field Theory (QFT) of the brain, which is called Quantum Brain Dynamics (QBD). We begin with the Lagrangian density of ϕ4 model, where we adopt 2-Particle-Irreducible (2PI) effective action, and derive the Klein–Gordon equation of coherent fields with a damping term as an input–output equation proposed in areas of morphological computation or reservoir computing. Our analysis is extended to QFT in a hierarchy representing multiple layers covering cortex in a brain. We find that the desired target function is achieved via time-evolution in the Klein–Gordon Eqs. in a hierarchy of numerical simulations when a signal in both the input and output prevails over noise in the intermediate layers. Our approach will be applied to control coherent fields in the systems (in a hierarchy) described in the QFT framework, with potential applications allowing the manipulation of quantum fields, especially holograms in QBD. We could then provide realistic physical degrees of freedom of a light–matter system in the contexts of quantum cognition and the associated free-energy principle.MDPI AG, 2023年01月, Dynamics, 3(1) (1), 1 - 17[査読有り]研究論文（学術雑誌）
- Wiley, 2022年12月, Journal of Computational Chemistry, 44(7) (7), 857 - 868[査読有り]研究論文（学術雑誌）
- Pubtexto, 2022年12月, JOURNAL OF PHYSICS AND CHEMISTRY RESEARCH, 4(3) (3), 1 - 2[査読有り]研究論文（学術雑誌）
- Elsevier BV, 2022年11月, Physica A: Statistical Mechanics and its Applications, 605, 127979 - 127979[査読有り]研究論文（学術雑誌）
- Ribulose 1,5-bisphosphate carboxylase/oxygenase (RuBisCO) functions as the initial enzyme in the dark reactions of photosynthesis, catalyzing reactions that extract CO2 from the atmosphere and fix CO2 into organic compounds. RuBisCO is classified into four types (isoforms I–IV) according to sequence-based phylogenetic trees. Given its size, the computational cost of accurate quantum-chemical calculations for functional analysis of RuBisCO is high; however, recent advances in hardware performance and the use of the fragment molecular orbital (FMO) method have enabled the ab initio analyses of RuBisCO. Here, we performed FMO calculations on multiple structural datasets for various complexes with the 2′-carboxylarabinitol 1,5-bisphosphate (2CABP) ligand as a substrate analog and investigated whether phylogenetic relationships based on sequence information are physicochemically relevant as well as whether novel information unobtainable from sequence information can be revealed. We extracted features similar to the phylogenetic relationships found in sequence analysis, and in terms of singular value decomposition, we identified residues that strongly interacted with the ligand and the characteristics of the isoforms for each principal component. These results identified a strong correlation between phylogenetic relationships obtained by sequence analysis and residue interaction energies with the ligand. Notably, some important residues were located far from the ligand, making comparisons among species using only residues proximal to the ligand insufficient.MDPI AG, 2022年09月, International Journal of Molecular Sciences, 23(19) (19), 11347 - 11347[査読有り]研究論文（学術雑誌）
- Chem-Bio Informatics Society, 2022年09月, Chem-Bio Informatics Journal, 22, 55 - 62[査読有り]研究論文（学術雑誌）
- American Chemical Society (ACS), 2022年08月, The Journal of Physical Chemistry B, 126(31) (31), 5793 - 5802[査読有り]研究論文（学術雑誌）
- Wiley, 2022年07月, Journal of Computational Chemistry, 43(20) (20), 1362 - 1371[査読有り]研究論文（学術雑誌）
- By employing numerical simulations we describe non-equilibrium processes leading towards the breakdown of symmetry within Quantum Brain Dynamics (QBD) in 2+1 dimensions. We adopt time evolution equations for coherent electric fields, dipole moment density and the time derivative of dipole moment density, and the Kadanoff–Baym equations for incoherent dipoles and photons. We show that the Bose–Einstein distributions apply to incoherent dipoles and photons in the time evolution. Triggered by nonzero initial electric field, the system's dipoles are aligned in the same direction. We argue that these results can be applied as representative for memory formations in QBD.2022年07月, Physica A: Statistical Mechanics and its Applications, 598[査読有り]研究論文（学術雑誌）
- Wiley, 2022年07月, Proteins: Structure, Function, and Bioinformatics[査読有り]研究論文（学術雑誌）
- {MDPI} {AG}, 2022年06月, Dynamics, 2(2) (2), 187 - 218[査読有り]研究論文（学術雑誌）
- Elsevier {BV}, 2022年02月, Current Opinion in Structural Biology, 72, 127 - 134[査読有り]研究論文（学術雑誌）
- The physicochemical entity of biological phenomenon in the cell is a network of biochemical reactions and the activity of such a network is regulated by multimeric protein complexes. Mass spectroscopy (MS) experiments and multimeric protein docking simulations based on structural bioinformatics techniques have revealed the molecular-level stoichiometry and static configuration of subcomplexes in their bound forms, then revealing the subcomplex populations and formation orders. Meanwhile, these methodologies are not designed to straightforwardly examine temporal dynamics of multimeric protein assembly and disassembly, essential physicochemical properties to understand functional expression mechanisms of proteins in the biological environment. To address the problem, we had developed an atomistic simulation in the framework of the hybrid Monte Carlo/Molecular Dynamics (hMC/MD) method and succeeded in observing disassembly of homomeric pentamer of the serum amyloid P component protein in experimentally consistent order. In this study, we improved the hMC/MD method to examine disassembly processes of the tryptophan synthase tetramer, a paradigmatic heteromeric protein complex in MS studies. We employed the likelihood-based selection scheme to determine a dissociation-prone subunit pair at each hMC/MD simulation cycle and achieved highly reliable predictions of the disassembly orders with the success rate over 0.9 withoutRoyal Society of Chemistry ({RSC}), 2022年01月, Physical Chemistry Chemical Physics
a priori knowledge of the MS experiments and structural bioinformatics simulations. We similarly succeeded in reliable predictions for the other three tetrameric protein complexes. These achievements indicate the potential availability of our hMC/MD approach as the general purpose methodology to obtain microscopic and physicochemical insights into multimeric protein complex formation.[査読有り]研究論文（学術雑誌） - Biophysical Society of Japan, 2022年, Seibutsu Butsuri, 62(4) (4), 215 - 218[査読有り]研究論文（学術雑誌）
- {IOP} Publishing, 2022年01月, Applied Physics Express, 15(1) (1), 017001 - 017001
Abstract In large biomolecular systems such as protein complexes, there are huge numbers of combinations of inter-residue interactions whose comprehensive analyses are often beyond the intuitive processing by researchers. Here we propose a computational method to allow for a systematic analysis of these interactions based on the fragment molecular orbital calculations, in which the inter-fragment interaction energies are comprehensively processed by the singular value decomposition. For a trimer complex of SARS-CoV-2 spike protein, three-body interactions among residues belonging to three chains are analyzed to elicit a small number of essential interaction modes or networks crucial for the structural stability of the complex.[査読有り]研究論文（学術雑誌） - While the construction of a dependable force field for performing classical molecular dynamics (MD) simulation is crucial for elucidating the structure and function of biomolecular systems, the attempts to do this for glycans are relatively sparse compared to those for proteins and nucleic acids. Currently, the use of GLYCAM06 force field is the most popular, but there have been a number of concerns about its accuracy in the systematic description of structural changes. In the present work, we focus on the improvement of the GLYCAM06 force field for β-d-glucose, a simple and the most abundant monosaccharide molecule, with the aid of machine learning techniques implemented with the TensorFlow library. Following the pre-sampling over a wide range of configuration space generated by MD simulation, the atomic charge and dihedral angle parameters in the GLYCAM06 force field were re-optimized to accurately reproduce the relative energies of β-d-glucose obtained by the density functional theory (DFT) calculations according to the structural changes. The validation for the newly proposed force-field parameters was then carried out by verifying that the relative energy errors compared to the DFT value were significantly reduced and that some inconsistencies with experimental (e.g., NMR) results observed in the GLYCAM06 force field were resolved relevantly.2021年11月, Molecules, 26(21) (21), 英語, 国際誌[査読有り]研究論文（学術雑誌）
- The SARS-CoV-2 virus initiates infection of human cells by recognizing the human angiotensin-converting enzyme 2 (ACE2) with the receptor binding domain (RBD) of the viral spike protein. Thus, the variant of concern (VOC) with mutations on RBD is of special interest. Here, we present a series of interaction analyses for the RBD-ACE2 complex of the wild-type (PDB ID: 6M0J) and those of B.1.1.7 (alpha), B.1.351 (beta) and P.1 (gamma) VOCs, based on the fragment molecular orbital (FMO) calculations. The results revealed that the RBD variants have a higher affinity for ACE2 than the wild type does.IOP Publishing Ltd, 2021年09月, JAPANESE JOURNAL OF APPLIED PHYSICS, 60(9) (9), 090901 - 090901, 英語[査読有り]研究論文（学術雑誌）
- By the splendid advance in computation power realized with Fugaku supercomputer, it has become possible to perform ab initio fragment molecular orbital (FMO) calculations for thousands of dynamical structures of a protein-ligand complex in a parallelized way. We have thus carried out the electron-correlated FMO calculations for a complex of the 3C-like (3CL) main protease (Mpro) of the new coronavirus (SARS-CoV-2) and its inhibitor N3 incorporating the structural fluctuations sampled by classical molecular dynamics (MD) simulation in hydrated condition. Along with a statistical evaluation of inter-fragment interaction energies (IFIEs) between the N3 ligand and surrounding amino-acid residues for a thousand of dynamical structure samples, we have applied in this study a novel approach based on the principal component analysis (PCA) and the singular value decomposition (SVD) to the analysis of IFIE data in order to extract the dynamically cooperative interactions between the ligand and residues. We have found that the relative importance of each residue is modified via the structural fluctuations and that the ligand is bound in the pharmacophore in a dynamical manner through collective interactions formed by multiple residues, thus providing a new insight into structure-based drug discoveryAmerican Chemical Society ({ACS}), 2021年06月, The Journal of Physical Chemistry B, 125(24) (24), 6501 - 6512[査読有り]研究論文（学術雑誌）
- Physical Society of Japan, 2021年06月, Journal of the Physical Society of Japan, 90(6) (6), 064301 - 064301[査読有り]研究論文（学術雑誌）
- Springer Science and Business Media {LLC}, 2021年05月, Journal of Computer-Aided Molecular Design, 35(5) (5), 629 - 642[査読有り]研究論文（学術雑誌）
- Elsevier {BV}, 2021年04月, Physica A: Statistical Mechanics and its Applications, 567, 125706 - 125706[査読有り]研究論文（学術雑誌）
- Springer Science and Business Media {LLC}, 2021年04月, Foundations of Physics, 51(2) (2)[査読有り]研究論文（学術雑誌）
- (公社)日本薬学会, 2021年03月, 日本薬学会年会要旨集, 141年会, 27V04 - am12S, 日本語分子動力学計算とFMO計算を用いたSARS-CoV-2メインプロテアーゼと既存薬との結合性予測
- American Chemical Society ({ACS}), 2021年02月, ACS Omega, 6(7) (7), 4749 - 4758
Abstract Physicochemical characterization of multimeric biomacromolecule assembly and disassembly processes is a milestone to understand the mechanisms for biological phenomena at molecular level. Mass spectroscopy (MS) and structural bioinformatics (SB) approaches have become feasible to identify subcomplexes involved in assembly and disassembly, while they cannot provide atomic information sufficient for free energy calculation to characterize transition mechanism between two different sets of subcomplexes. To combine observations derived from MS and SB approaches with conventional free energy calculation protocols, we here designed a new reaction pathway sampling method with employing hybrid configuration bias Monte Carlo/Molecular Dynamics (hcbMC/MD) scheme and applied it to simulate disassembly process of serum amyloid P component (SAP) pentamer. The results we obtained are consistent with those of the earlier MS and SB studies with respect to SAP subcomplex species and the initial stage of SAP disassembly processes. Furthermore, we observed a novel dissociation event, ring-opening reaction of SAP pentamer. Employing free energy calculation combined with the hcbMC/MD reaction pathway trajectories, we moreover obtained experimentally testable observations on (1) reaction time of the ring-opening reaction and (2) importance of Asp42 and Lys117 for stable formation of SAP oligomer.TOC graphics [査読有り]研究論文（学術雑誌） - Multimeric protein complexes are molecular apparatuses to regulate biological systems and often determine their fate. Among proteins forming such molecular assemblies, amyloid proteins have drawn attention over a half century, since amyloid fibril formation of these proteins is supposed to be common pathogenic causes for neurodegenerative diseases. This process is triggered by accumulation of fibril-like aggregates, while the minimum size of such aggregate cores still remains to be elucidated. We addressed this problem with employing atomistic molecular dynamics simulations for the paradigmatic amyloid protein, amyloid-β (1-42) (Aβ42). Seven different dimeric forms of oligomeric Aβ42 fibril-like aggregate in aqueous solution, ranging from tetramer to decamer, were considered. We found effects of the size of these fibril-like aggregates on their thermodynamic stability and have clarified kinetic suppression of protomer-protomer dissociation reactions even at the point of pentamer dimer formation, where the theoretically estimated reaction time exceeds lifetime of human beings. Recalling that Aβ42 pentamer is found in the range of size of experimentally-observed Aβ42 aggregates, we could suppose that stable formation of fibril-like Aβ42 pentamer species is involved in a turning point where rapid growth of Aβ42 amyloid fibrils is triggered. Similar relationship between the oligomer size and the thermodynamic stability may be found in other amyloid fibril formations and also for multimeric protein assemblies via nuclei formation as seen in actin and tubulin filaments, for instance.Cold Spring Harbor Laboratory, 2021年02月[査読有り]
- {IOP} Publishing, 2021年02月, Applied Physics Express, 14(2) (2), 027003 - 027003[査読有り]研究論文（学術雑誌）
- We developed the world's first web-based public database for the storage, management, and sharing of fragment molecular orbital (FMO) calculation data sets describing the complex interactions between biomacromolecules, named FMO Database (https://drugdesign.riken.jp/FMODB/). Each entry in the database contains relevant background information on how the data was compiled as well as the total energy of each molecular system and interfragment interaction energy (IFIE) and pair interaction energy decomposition analysis (PIEDA) values. Currently, the database contains more than 13 600 FMO calculation data sets, and a comprehensive search function implemented at the front-end. The procedure for selecting target proteins, preprocessing the experimental structures, construction of the database, and details of the database front-end were described. Then, we demonstrated a use of the FMODB by comparing IFIE value distributions of hydrogen bond, ion-pair, and XH/π interactions obtained by FMO method to those by molecular mechanics approach. From the comparison, the statistical analysis of the data provided standard reference values for the three types of interactions that will be useful for determining whether each interaction in a given system is relatively strong or weak compared to the interactions contained within the data in the FMODB. In the final part, we demonstrate the use of the database to examine the contribution of halogen atoms to the binding affinity between human cathepsin L and its inhibitors. We found that the electrostatic term derived by PIEDA greatly correlated with the binding affinities of the halogen containing cathepsin L inhibitors, indicating the importance of QM calculation for quantitative analysis of halogen interactions. Thus, the FMO calculation data in FMODB will be useful for conducting statistical analyses to drug discovery, for conducting molecular recognition studies in structural biology, and for other studies involving quantum mechanics-based interactions.2021年01月, Journal of chemical information and modeling, 61(2) (2), 777 - 794, 英語, 国際誌[査読有り]研究論文（学術雑誌）
- GTP hydrolysis reaction by Rat Sarcoma protein (Ras) was examined by semi-reactive molecular dynamics simulations. The chemical energy generated by the hydrolysis reaction is stored in the phosphate-binding loop (P-loop) as mechanical one.Royal Society of Chemistry (RSC), 2021年, Physical Chemistry Chemical Physics, 23(46) (46), 26151 - 26164[査読有り]研究論文（学術雑誌）
- Springer Singapore, 2021年, Recent Advances of the Fragment Molecular Orbital Method, 53 - 67論文集(書籍)内論文
- Royal Society of Chemistry (RSC), 2021年, RSC Advances, 11(6) (6), 3272 - 3279
Visualized IFIE results seen from chain-B of spike protein.
[査読有り]研究論文（学術雑誌） - American Physical Society (APS), 2020年12月, Physical Review Letters, 125(23) (23)[査読有り]研究論文（学術雑誌）
- Quantum chemical calculations investigated molecular recognition of SARS-CoV-2 spike glycoproteins including its N501Y variant for ACE2 and antibody. Hot spot and epitope analyses revealed key residues to design drugs and antibodies against COVID-19.American Chemical Society ({ACS}), 2020年11月, Chemical Science, 12(13) (13), 4722 - 4739[査読有り]研究論文（学術雑誌）
- A theoretical scheme to systematically describe correlated (network-like) interactions between molecular fragments is proposed within the framework of the fragment molecular orbital (FMO) method. The method is mathematically based on the singular value decomposition (SVD) of the inter-fragment interaction energy (IFIE) matrix obtained by the FMO calculation, and can be applied to a comprehensive description of protein-protein interactions in the context of molecular recognition. In the present study we apply the proposed method to a complex of measles virus hemagglutinin and human SLAM receptor, thus finding a usefulness for efficiently eliciting the correlated interactions among the aminoacid residues involved in the two proteins. Additionally, collective interaction networks by amino-acid residues important for mutation experiments can be clearly visualized. (C) 2020 Elsevier Inc. All rights reserved.Elsevier BV, 2020年11月, Journal of Molecular Graphics and Modelling, 100, 107650 - 107650, 英語[査読有り]研究論文（学術雑誌）
- Elsevier BV, 2020年11月, Chemical Physics, 539, 110903 - 110903[査読有り]研究論文（学術雑誌）
- Inter-Fragment Interaction Energies (IFIEs) obtained by Fragment Molecular Orbital (FMO) method can quantitatively measure the effective interactions between ligand and residues in protein, which are therefore useful for drug discovery. However, it has not been clarified whether the IFIEs can be reproduced using only geometrical (e.g., interatomic distances) information of biomolecular complex without resort to explicit FMO calculations. In this study, through machine learning technique, we propose a highly accurate reproduction or prediction scheme for ligand-protein IFIEs using only the distance information as descriptors, thereby drastically saving the computational cost in FMO analysis for a variety of conformations.Elsevier {BV}, 2020年10月, Chemical Physics Letters, 757, 137883 - 137883, 英語[査読有り]研究論文（学術雑誌）
- Computational schemes to describe the temperature relaxation in the binary hard-sphere mixture system are given on the basis of molecular dynamics (MD) simulation and renormalized kinetic theory. Event-driven MD simulations are carried out for three model systems in which the initial temperatures and the ratios of diameter and mass of two components are different to study the temporal evolution of each component temperature in nanoscale molecular conditions mimicking those in living cells. On the other hand, the temperature changes of the two components are also described in terms of a mean-field kinetic theory with the correlation functions calculated in the Percus-Yevick approximation. The calculated results by both the computational approaches have shown fair agreement with each other, whereas slight deviations have been found in the temporal range of femto- to picoseconds when the initial temperatures of the two components are significantly different, such as 300 K vs 1000 K. This discrepancy can be ascribed to the fast intra-component temperature relaxation assumed in the kinetic theory, and its violation in the MD simulations can be evaluated in terms of the Kullback-Leibler divergence between the equilibrated Maxwell-Boltzmann distribution at each temperature and the actual non-equilibrium velocity distribution realized in the MD. Thus, the present analysis provides a quantitative basis for addressing the temperature inhomogeneities experimentally observed in nanoscale crowding conditions.AIP Publishing, 2020年07月, The Journal of Chemical Physics, 153(3) (3), 034114 - 034114, 英語[査読有り]研究論文（学術雑誌）
- The worldwide spread of COVID-19 (new coronavirus found in 2019) is an emergent issue to be tackled. In fact, a great amount of works in various fields have been made in a rather short period. Here, we report a fragment molecular orbital (FMO) based interaction analysis on a complex between the SARS-CoV-2 main protease (Mpro) and its peptide-like inhibitor N3 (PDB ID: 6LU7). The target inhibitor molecule was segmented into five fragments in order to capture site specific interactions with amino acid residues of the protease. The interaction energies were decomposed into several contributions, and then the characteristics of hydrogen bonding and dispersion stabilization were made clear. Furthermore, the hydration effect was incorporated by the Poisson-Boltzmann (PB) scheme. From the present FMO study, His41, His163, His164, and Glu166 were found to be the most important amino acid residues of Mpro in interacting with the inhibitor, mainly due to hydrogen bonding. A guideline for optimizations of the inhibitor molecule was suggested as well based on the FMO analysis.American Chemical Society (ACS), 2020年06月, Journal of chemical information and modeling, 60(7) (7), 3593 - 3602, 英語, 国際誌[査読有り]研究論文（学術雑誌）
- We have derived the fundamental formula of phonon transport in water for the evaluation of quantum thermal conductance by using a one-dimensional phonon model based on the nonequilibrium Green’s function method. In our model, phonons are excited as quantum waves from the left or right reservoir and propagate from left to right of H 2 O layer or vice versa. We have assumed these reservoirs as being of periodic structures, whereas we can also model the H 2 O sandwiched between these reservoirs as having aperiodic structures of liquid containing N water molecules. We have extracted the dispersion curves from the experimental absorption spectra of the OH stretching and intermolecular modes of water molecules, and calculated phonon transmission function and quantum thermal conductance. In addition, we have simplified the formulation of the transmission function by employing a case of one water molecule (N=1). From this calculation, we have obtained the characteristic that the transmission probability is almost unity at the frequency bands of acoustic and optical modes, and the transmission probability vanishes by the phonon attenuation reflecting the quantum tunnel effect outside the bands of these two modes. The classical limit of the thermal conductance calculated by our formula agreed with the literature value (order of 10 − 10 W/K) in high temperature regime (>300 K). The present approach is powerful enough to be applicable to molecular systems containing proteins as well, and to evaluate their thermal conductive characteristics.{MDPI} {AG}, 2020年03月, Molecules, 25(5) (5), 1185 - 1185[査読有り]研究論文（学術雑誌）
- (公社)日本薬学会, 2020年03月, 日本薬学会年会要旨集, 140年会, 27P - am095, 日本語ERβ選択的リガンドの設計に向けたFMO創薬の取り組み
- Methods for stabilizing G-quadruplex formation is a promising therapeutic approach for cancer treatment and other biomedical applications because stable G-quadruplexes efficiently inhibit biological reactions. Oligo and polyethylene glycols are promising biocompatible compounds, and we have shown that linear oligoethylene glycols can stabilize G-quadruplexes. Here, we developed a new modified deoxythymine with dibranched or tribranched tetraethylene glycol (TEG) and incorporated these TEG-modified deoxythymines into a loop region that forms an antiparallel G-quadruplex. We analyzed the stability of the modified G-quadruplexes, and the results showed that the tribranched TEG destabilized G-quadruplexes through entropic contributions, likely through steric hindrance. Interestingly, the dibranched TEG modification increased G-quadruplex stability relative to the unmodified DNA structures due to favorable enthalpic contributions. Molecular dynamics calculations suggested that dibranched TEG interacts with the G-quadruplex through hydrogen bonding and CH-π interactions. Moreover, these branched TEG-modified deoxythymine protected the DNA oligonucleotides from degradation by various nucleases in human serum. By taking advantage of the unique interactions between DNA and branched TEG, advanced DNA materials can be developed that affect the regulation of DNA structure.2020年02月, Molecules (Basel, Switzerland), 25(3) (3), 705 - 715, 英語, 国際誌[査読有り]研究論文（学術雑誌）
- We provide an overview of our recent studies on nonequilibrium quantum brain dynamics (QBD). QBD is essentially the application of quantum electrodynamics to a system that is immersed in water molecules containing dynamically coupled electric dipoles associated with essential biomolecules within the structure of the brain: phospholipids and proteins. We adopt a model of memory storage due to the breakdown of rotational symmetry of dipolar modes in QBD. Furthermore, we describe the dynamics of the QBD system using the Schrodinger-like equations for coherent electric dipole fields, the Klein-Gordon equations for coherent electric fields, and the Kadanoff-Baym equations for incoherent dipoles and photons. Nontrivial results are obtained by adopting quantum field theory to describe open quantum systems including networks. Nonequilibrium properties of the model of QBD are described by the use of numerical simulations to obtain time-dependent solutions.ELSEVIER ACADEMIC PRESS INC, 2020年, QUANTUM BOUNDARIES OF LIFE, 82, 159 - 180, 英語論文集(書籍)内論文
- The strongly coupled electron liquid provides a unique opportunity to study the complex interplay of strong coupling with quantum degeneracy effects and thermal excitations. To this end, we carry out extensive ab initio path integral Monte Carlo (PIMC) simulations to compute the static structure factor, interaction energy, density response function, and the corresponding static local field correction in the range of 20 <= r(s) <= 100 and 0.5 <= theta <= 4. We subsequently compare these data to several dielectric approximations and find that different schemes are capable to reproduce different features of the PIMC results at certain parameters. Moreover, we provide a comprehensive data table of interaction energies and compare those to two recent parametrizations of the exchange-correlation free energy, where they are available. Finally, we briefly touch upon the possibility of a charge-density wave. The present study is complementary to previous investigations of the uniform electron gas in the warm dense matter regime and, thus, further completes our current picture of this fundamental model system at finite temperature. All PIMC data are available online.AMER PHYSICAL SOC, 2020年01月, PHYSICAL REVIEW B, 101(4) (4), 英語[査読有り]研究論文（学術雑誌）
- We derive time evolution equations, namely the Klein–Gordon equations for coherent fields and the Kadanoff–Baym equations in quantum electrodynamics (QED) for open systems (with a central region and two reservoirs) as a practical model of quantum field theory of the brain. Next, we introduce a kinetic entropy current and show the H-theorem in the Hartree–Fock approximation with the leading-order (LO) tunneling variable expansion in the 1st order approximation for the gradient expansion. Finally, we find the total conserved energy and the potential energy for time evolution equations in a spatially homogeneous system. We derive the Josephson current due to quantum tunneling between neighbouring regions by starting with the two-particle irreducible effective action technique. As an example of potential applications, we can analyze microtubules coupled to a water battery surrounded by a biochemical energy supply. Our approach can be also applied to the information transfer between two coherent regions via microtubules or that in networks (the central region and the N res reservoirs) with the presence of quantum tunneling.{MDPI} {AG}, 2019年12月, Entropy, 22(1) (1), 43 - 43[査読有り]研究論文（学術雑誌）
- Adenosine triphosphate (ATP) is newly expected to be involved in the clearance of amyloid beta 1-42 (A beta(42)) fibril and its precursors, A beta(42 )oligomer. Meanwhile, the microscopic mechanism of the role in dissolving the protein aggregate still remains elusive. Aiming to elucidate the mechanism, we examined effects of ATP on the conformational change and thermodynamic stability of the protomer dimer of A beta(42) pentamer and tetramer, A beta(42) (9), by employing all-atom molecular dynamics simulations. We observed interprotomer twisting and intraprotomer peeling of A beta(42) (9). These conformational changes remarkably accelerate dissociation of the protomer dimer. However, the presence of ATP itself has no positive effect on dissociation processes of the protomer dimer and a monomer from the dimer, indicating its irrelevance to decomposition of the A beta(42) oligomer. Rather, it could be supposed that ATP prevents additional binding and rebinding of A beta(42) monomers to the A beta(42) oligomer and it then converts A beta(42) oligomer into an offpathway species which is excluded from A beta(42) fibril growth processes. Interestingly, hydrophobic adenosine in ATP makes contact with A beta(42)(9) on its backbone atoms, with respect to both A beta(42) monomers on the edge of A beta(42)(9) and dissociated Afi 42 monomers in A beta(42)(9). These roles of ATP would be applied without regard to the structural polymorphism of the A beta(42) fibril.AMER CHEMICAL SOC, 2019年11月, JOURNAL OF PHYSICAL CHEMISTRY B, 123(46) (46), 9922 - 9933, 英語[査読有り]研究論文（学術雑誌）
- We derive time evolution equations, namely the Schrödinger-like equations and the Klein–Gordon equations for coherent fields and the Kadanoff–Baym (KB) equations for quantum fluctuations, in quantum electrodynamics (QED) with electric dipoles in 2 + 1 dimensions. Next we introduce a kinetic entropy current based on the KB equations in the first order of the gradient expansion. We show the H-theorem for the leading-order self-energy in the coupling expansion (the Hartree–Fock approximation). We show conserved energy in the spatially homogeneous systems in the time evolution. We derive aspects of the super-radiance and the equilibration in our single Lagrangian. Our analysis can be applied to quantum brain dynamics, that is QED, with water electric dipoles. The total energy consumption to maintain super-radiant states in microtubules seems to be within the energy consumption to maintain the ordered systems in a brain.MDPI AG, 2019年10月, Entropy, 21(11) (11), 1066 - 1066[査読有り]研究論文（学術雑誌）
- First-principles molecular dynamics (FPMD) simulations are highly accurate, but due to their high calculation cost, the computational scale is often limited to hundreds of atoms and few picoseconds under specific temperature and pressure conditions. We present here the guidelines for creating artificial neural network empirical interatomic potential (ANN potential) trained with such a limited FPMD data, which can perform long time scale MD simulations at least under the same conditions. The FPMD data for training are prepared on the basis of the convergence of radial distribution function [g(r)]. While training the ANN using total energy and atomic forces of the FPMD data, the error of pressure is also monitored and minimized. To create further robust potential, we add a small amount of FPMD data to reproduce the interaction between two atoms that are close to each other. ANN potentials for alpha-Ag2Se were created as an application example, and it has been confirmed that not only g(r) and mean square displacements but also the specific heat requiring a long time scale simulation matched the FPMD and the experimental values. In addition, the MD simulation using the ANN potential achieved over 10(4) acceleration over the FPMD one. The guidelines proposed here mitigate the creation difficulty of the ANN potential, and a lot of FPMD data sleeping on the hard disk after the research may be put on the front stage again. Published under license by AIP Publishing.AIP Publishing, 2019年09月, The Journal of Chemical Physics, 151(12) (12), 124303 - 124303, 英語[査読有り]研究論文（学術雑誌）
- (公社)日本薬学会, 2019年03月, 日本薬学会年会要旨集, 139年会(2) (2), 96 - 96, 日本語エストロゲン様化合物におけるサブタイプ選択性の理論的解析[査読有り]
- Chem-Bio Informatics Society, 2019年03月, Chem-Bio Informatics Journal, 19(0) (0), 5 - 18, 英語[査読有り]研究論文（学術雑誌）
- American Chemical Society ({ACS}), 2019年02月, The Journal of Physical Chemistry B, 123(5) (5), 957 - 973[査読有り]研究論文（学術雑誌）
- Wiley, 2019年01月, Journal of Computational Chemistry, 40(2) (2), 349 - 359[査読有り]研究論文（学術雑誌）
- We developed an automated FMO calculation protocol (Auto-FMO protocol) to calculate huge numbers of protein and ligand complexes, such as drug discovery targets, by an <i>ab initio</i> FMO method. The protocol performs not only FMO calculations but also pre-processing of input structures by homology modeling of missing atoms and subsequent MM-based optimization, as well as post-processing of calculation results. In addition, QM/MM optimization of complex structures, conformational searches of ligand structures in solvent, and MM-PBSA/GBSA calculations can be optionally carried out. In this paper, FMO calculations for 149 X-ray complex structures of estrogen receptor α and p38 MAP kinase were performed at the K computer and in-house PC cluster server by using the Auto-FMO protocol. To demonstrate the usefulness of the Auto-FMO protocol, we compared the ligand binding interaction energies by the Auto-FMO protocol with those of manually prepared data. In most cases, the data calculated by the Auto-FMO protocol showed reasonable agreement with the manually prepared data. Further improvement of the protocol is necessary for the treatment of ionization and tautomerization at the structure preparation stage, because some outlier data were observed due to these issues. The Auto-FMO protocol provides a powerful tool to deal with huge numbers of complexes for drug design, as well as for the construction of the FMO database (http://drugdesign.riken.jp/FMODB/) released in 2019.情報計算化学生物学会(CBI学会), 2019年, Chem-Bio Informatics Journal, 19(0) (0), 5 - 18, 英語[査読有り]研究論文（学術雑誌）
- 2019年, 日本神経回路学会誌, 26(4) (4), 1 - 11, 日本語人工ニューラルネットワーク原子間相互作用ポテンシャルの分子動力学法への応用と課題[査読有り]
- 神戸から配信する遠隔インタラクティブ講義「計算生命科学の基礎」の2017年度報告計算生命科学は，生命の理解に向けて，近年急速に進展している計算科学と医農工理学分野が融合した学際的研究領域である．様々な研究分野や産業界等への研究の拡がりが期待されており，包括的な基礎知識を習得する機会が求められている．神戸大学計算科学教育センターは，関係諸機関と協力して，遠隔インタラクティブ講義「計算生命科学の基礎」シリーズを2014年から全国に配信を開始し，昨年度は600名の受講登録を受け付けた．本稿では，2017年度に実施した「計算生命科学の基礎IV」と，最近注目されているAIやディープラーニングに焦点を当て特別編として実施したディープラーニングチュートリアルの開催結果について報告する．年々受講者が増え続けており，アンケートでも高評価を得ている．．2018年11月, 大学ICT推進協議会2018年度年次大会論文集, 1 - 4, 日本語研究論文（研究会，シンポジウム資料等）
- Elsevier {BV}, 2018年10月, Computational and Structural Biotechnology Journal, 16, 421 - 434, 英語[査読有り]研究論文（学術雑誌）
- We evaluated the binding affinity between p38 MAP kinase and various inhibitors through use of the fragment molecular orbital (FMO) method at MP2/6-31G∗ level in comparison to experimental values of half maximal inhibitory concentration (IC50). Initially, the calculated results of the FMO-IFIE (inter-fragment interaction energy) sums for 60 complex structures registered in the Protein Data Bank were not well correlated with the IC50 activity data. Therefore, we performed the singular value decomposition (SVD) for the calculated results of the IFIE matrix (amino acid residues × various ligands) to improve the correlation and determine the cause of the initial poor results. In SVD, the original matrix is divided into multiple vectors that are orthogonal to each other. Through this method, we improved the correlation by removing some particular vectors that involved noise components and impaired the correlation. In addition, the correlation between the IC50 and FMO-IFIE for 22 complex structures of estrogen receptor α (ERα) was also improved in this way. We analyzed the amino acid residues of receptors that were mainly involved in the removed vectors and found an overestimation of the strength of the hydrogen bond between glutamic acid and the ligand.Elsevier B.V., 2018年05月, Computational and Theoretical Chemistry, 1132, 23 - 34, 英語[査読有り]研究論文（学術雑誌）
- Molecular crowding conditions provided by high concentration of cosolutes are utilized for characterization of biomolecules in cell-mimicking environment and development of drug-delivery systems. In this context, (poly)ethylene glycols are often used for studying non-canonical DNA structures termed G-quadruplexes, which came into focus by emerging structural biology findings and new therapeutic drug design approaches. Recently, several reports were made arguing against using (poly)ethylene glycols in role of molecular crowding agents due to their direct impact on DNA G-quadruplex stability and topology. However, the available data on structural details underlying DNA interaction is very scarce and thus limits in-depth comprehension. Herein, structural and thermodynamic analyses were strategically combined to assess G-quadruplex-cosolute interactions and address previously reported variances regarding the driving forces of G-rich DNA structural transformations under molecular crowding conditions. With the use of complementary (CD, NMR and UV) spectroscopic methods and model approach we characterized DNA G-quadruplex in the presence of the smallest and one of the largest typically used (poly)ethylene glycols. Dehydration effect is the key contributor to ethylene-glycol-induced increased stability of the G-quadruplex, which is in the case of the large cosolute mainly guided by the subtle direct interactions between PEG 8000 and the outer G-quartet regions.2018年05月, Nucleic acids research, 46(8) (8), 4301 - 4315, 英語, 国際誌[査読有り]研究論文（学術雑誌）
- Measles virus (MV) causes an acute and highly devastating contagious disease in humans. Employing the crystal structures of three human receptors, signaling lymphocyte-activation molecule (SLAM), CD46, and Nectin-4, in complex with the measles virus hemagglutinin (MVH), we elucidated computationally the details of binding energies between the amino acid residues of MVH and those of the receptors with an ab initio fragment molecular orbital (FMO) method. The calculated inter-fragment interaction energies (IFIEs) revealed a number of significantly interacting amino acid residues of MVH that played essential roles in binding to the receptors. As predicted from previously reported experiments, some important amino-acid residues of MVH were shown to be common but others were specific to interactions with the three receptors. Particularly, some of the (non-polar) hydrophobic residues of MVH were found to be attractively interacting with multiple receptors, thus indicating the importance of the hydrophobic pocket for intermolecular interactions (especially in the case of Nectin-4). In contrast, the electrostatic interactions tended to be used for specific molecular recognition. Furthermore, we carried out FMO calculations for in silico experiments of amino acid mutations, finding reasonable agreements with virological experiments concerning the substitution effect of residues. Thus, the present study demonstrates that the electron-correlated FMO method is a powerful tool to search exhaustively for amino acid residues that contribute to interactions with receptor molecules. It is also applicable for designing inhibitors of MVH and engineered MVs for cancer therapy.MDPI AG, 2018年05月, Viruses, 10(5) (5), 18, 英語[査読有り]研究論文（学術雑誌）
- American Chemical Society (ACS), 2018年04月, The Journal of Physical Chemistry B, 122(16) (16), 4457 - 4471[査読有り]研究論文（学術雑誌）
- 2018年, 日本核酸化学会誌, 2, 3 - 10テトラエチレングリコールで修飾されたグアニン四重鎖の安定性の分子動力学計算による解析
- The Onsager-Machlup (OM) relaxation process, which provides a prototypical example of linear nonequilibrium thermodynamics, is characterized in terms of information geometry over the two-dimensional temperature-time parameter space. After deriving the probability distribution function for the OM process under the harmonic potential within a theoretical framework based on a transformation into imaginary-time quantum mechanics, the Fisher information metric is explicitly obtained. Differential geometry in the temperature-time space then gives the scalar curvature R = -1, thus specifying the OM process in a topological manner. (C) 2017 Elsevier B.V. All rights reserved.ELSEVIER SCIENCE BV, 2017年12月, CHEMICAL PHYSICS LETTERS, 689, 152 - 155, 英語[査読有り]研究論文（学術雑誌）
- The state transitions of solvated H-Ras protein with GTP were theoretically analyzed through molecular dynamics (MD) simulations. To accelerate the structural changes associated with the locations of two switch regions (I and II), the Parallel Cascade Selection MD (PaCS-MD) method was employed in this study. The interconversions between the State 1 and State 2 were thus studied in atomic details, leading to a reasonable agreement with experimental observations and consequent scenarios concerning the transition mechanism that would be essential for the development of Ras inhibitors as anti-cancer agents. Furthermore, the state-transition-based local network entropy (SNE) was calculated for the transition process from State 1 to State 2, by which the temporal evolution of information entropy associated with the dynamical behavior of hydrogen bond network composed of hydration water molecules was described. The calculated results of SNE thus proved to provide a good indicator to detect the dynamical state transition of solvated Ras protein system (and probably more general systems) from a viewpoint of nonequilibrium statistical thermodynamics. (C) 2017 Elsevier Inc. All rights reserved.ELSEVIER SCIENCE INC, 2017年10月, JOURNAL OF MOLECULAR GRAPHICS & MODELLING, 77, 51 - 63, 英語[査読有り]研究論文（学術雑誌）
- Oligoethylene glycols are used as crowding agents in experiments that aim to understand the effects of intracellular environments on DNAs. Moreover, DNAs with covalently attached oligoethylene glycols are used as cargo carriers for drug delivery systems. To investigate how oligoethylene glycols interact with DNAs, we incorporated deoxythymidine modified with oligoethylene glycols of different lengths, such as tetraethylene glycol (TEG), into DNAs that form antiparallel G-quadruplex or hairpin structures such that the modified residues were incorporated into loop regions. Thermodynamic analysis showed that because of enthalpic differences, the modified G-quadruplexes were stable and the hairpin structures were slightly unstable relative to unmodified DNA. The stability of G-quadruplexes increased with increasing length of the ethylene oxides and the number of deoxythymidines modified with ethylene glycols in the G-quadruplex. Nuclear magnetic resonance analyses and molecular dynamics calculations suggest that TEG interacts with bases in the G-quartet and loop via CH-pi and lone pair-pi interactions, although it was previously assumed that oligoethylene glycols do not directly interact with DNAs. The results suggest that numerous cellular co-solutes likely affect DNA function through these CH-pi and lone pair-pi interactions.OXFORD UNIV PRESS, 2017年07月, Nuc. Acids Res., 45(12) (12), 7021 - 7030, 英語[査読有り]研究論文（学術雑誌）
- A recent series of shock experiments by Nakazawa et al. starting in 2005 (e.g. [Nakazawa et al., Earth Planet. Sci. Lett., 2005, 235, 356]) suggested that meteorite impacts on ancient oceans would have yielded a considerable amount of NH3 to the early Earth from atmospheric N-2 and oceanic H2O through reduction by meteoritic iron. To clarify the mechanisms, we imitated the impact events by performing multi-scale shock technique-based ab initio molecular dynamics in the framework of density functional theory in combination with multi-scale shock technique (MSST) simulations. Our previous simulations with impact energies close to that of the experiments revealed picosecond-order rapid NH3 production during shock compression [Shimamura et al., Sci. Rep., 2016, 6, 38952]. It was also shown that the reduction of N-2 took place with an associative mechanism as seen in the catalysis of nitrogenase enzymes. In this study, we performed an MSST-AIMD simulation to investigate the production by meteorite impacts with higher energies, which are closer to the expected values on the early Earth. It was found that the amount of NH3 produced further increased. We also found that the increased NH3 production is due to the emergence of multiple reaction mechanisms at increased impact energies. We elucidated that the reduction of N-2 was not only attributed to the associative mechanism but also to a dissociative mechanism as seen in the Haber-Bosch process and to a mechanism through a hydrazinium ion. The emergence of these multiple production mechanisms capable of providing a large amount of NH3 would support the suggestions from recent experiments much more strongly than was previously believed, i.e., shock-induced NH3 production played a key role in the origin of life on Earth.ROYAL SOC CHEMISTRY, 2017年05月, PHYSICAL CHEMISTRY CHEMICAL PHYSICS, 19(18) (18), 11655 - 11667, 英語[査読有り]研究論文（学術雑誌）
- Protein flexibility is a major hurdle in current structure-based virtual screening (VS). In spite of the recent advances in high-performance computing, protein-liganddocking methods still demand tremendous computational cost to take into account the full degree of protein flexibility. In this context, ensemble docking has proven its utility and efficiency for VS studies, but it still needs a rational and efficient method to select and/or generate multiple protein conformations. Molecular dynamics (MD) simulations are useful to produce distinct protein conformations without abundant experimental structures. In this study, we present a novel strategy that makes use of cosolvent-based molecular dynamics (CMD) simulations for ensemble docking. By mixing small organic molecules into a solvent, CMD can stimulate dynamic protein motions and induce partial conformational changes of binding pocket residues appropriate for the binding of diverse ligands. The present method has been applied to six diverse target proteins and assessed by VS experiments using many actives and decoys of DEKOIS 2.0. The simulation results have revealed that the CMD is beneficial for ensemble docking. Utilizing cosolvent simulation allows the generation of druggable protein conformations, improving, the VS performance compared with the use of a single experimental structure or ensemble docking by standard MD with pure water as the solvent.AMER CHEMICAL SOC, 2017年04月, JOURNAL OF CHEMICAL INFORMATION AND MODELING, 57(4) (4), 742 - 756, 英語[査読有り]研究論文（学術雑誌）
- An accurate expression for the exchange-correlation free energy f(xc) of homogeneous electron fluids at finite temperatures is presented on the basis of Singwi-Tosi-Land-Sjolander (STLS) approximation. In addition to the derivation for the paramagnetic state, that for the ferromagnetic state is carried out afresh in which a correction in the strong Coulomb coupling regime is incorporated into the construction of the analytic expression as a function of the coupling constant and Fermi degeneracy. The fitting formula for f xc is then extended over any degree of spin polarization with the aid of available interpolation scheme. The proposed equation of state, called the iSTLS formula, shows reasonable agreement with the existing quantum Monte Carlo evaluations at finite temperatures in the paramagnetic state, thus giving a consensus for the thermodynamic functions between many-body theories and computer simulations. On the other hand, the current status for the agreement between various evaluations of f(xc) is relatively unsatisfactory in the ferromagnetic state, suggesting the necessity for further investigations.WILEY-V C H VERLAG GMBH, 2017年03月, CONTRIBUTIONS TO PLASMA PHYSICS, 57(3) (3), 126 - 136, 英語[査読有り]研究論文（学術雑誌）
- Society of Computer Chemistry Japan, 2017年, Journal of Computer Chemistry, Japan, 16(5) (5), 119 - 122[査読有り]研究論文（学術雑誌）
- 2017年, 大学ICT推進協議会2017年度年次大会論文集, TF1-2, 1 - 5, 日本語神戸から配信する遠隔インタラクティブ講義「計算生命科学の基礎」研究論文（研究会，シンポジウム資料等）
- American Chemical Society ({ACS}), 2017年, Journal of Chemical Information and Modeling, 57(12) (12), 2996 - 3010, 英語[査読有り]研究論文（学術雑誌）
- 2017年, J. Environ. Health Sci., 3(1) (1), 1 - 5, 英語[査読有り]研究論文（学術雑誌）
- NH3 is an essential molecule as a nitrogen source for prebiotic amino acid syntheses such as the Strecker reaction. Previous shock experiments demonstrated that meteorite impacts on ancient oceans would have provided a considerable amount of NH3 from atmospheric N-2 and oceanic H2O through reduction by meteoritic iron. However, specific production mechanisms remain unclear, and impact velocities employed in the experiments were substantially lower than typical impact velocities of meteorites on the early Earth. Here, to investigate the issues from the atomistic viewpoint, we performed multiscale shock technique-based ab initio molecular dynamics simulations. The results revealed a rapid production of NH3 within several picoseconds after the shock, indicating that shocks with greater impact velocities would provide further increase in the yield of NH3. Meanwhile, the picosecond-order production makes one expect that the important nitrogen source precursors of amino acids were obtained immediately after the impact. It was also observed that the reduction of N-2 proceeded according to an associative mechanism, rather than a dissociative mechanism as in the Haber-Bosch process.NATURE PUBLISHING GROUP, 2016年12月, SCIENTIFIC REPORTS, 6(38953) (38953), 10, 英語[査読有り]研究論文（学術雑誌）
- Correlational and thermodynamic properties of homogeneous electron liquids at finite temperatures are theoretically analyzed in terms of dielectric response formalism with the hypernetted-chain (HNC) approximation and its modified version. The static structure factor and the local-field correction to describe the strong Coulomb-coupling effects beyond the random-phase approximation are self-consistently calculated through solution to integral equations in the paramagnetic (spin unpolarized) and ferromagnetic (spin polarized) states. In the ground state with the normalized temperature theta = 0, the present HNC scheme well reproduces the exchange-correlation energies obtained by quantum Monte Carlo (QMC) simulations over the whole fluid phase (the coupling constant r(s) <= 100), i.e., within 1% and 2% deviations from putative best QMC values in the paramagnetic and ferromagnetic states, respectively. As compared with earlier studies based on the Singwi-Tosi-Land-Sjolander and modified convolution approximations, some improvements on the correlation energies and the correlation functions including the compressibility sum rule are found in the intermediate to strong coupling regimes. When applied to the electron fluids at intermediate Fermi degeneracies (theta approximate to 1), the static structure factors calculated in the HNC scheme show good agreements with the results obtained by the path integral Monte Carlo (PIMC) simulation, while a small negative region in the radial distribution function is observed near the origin, which may be associated with a slight overestimation for the exchange-correlation hole in the HNC approximation. The interaction energies are calculated for various combinations of density and temperature parameters ranging from strong to weak degeneracy and from weak to strong coupling, and the HNC values are then parametrized as functions of rs and theta. The HNC exchange-correlation free energies obtained through the coupling-constant integration show reasonable agreements with earlier results including the PIMC-based fitting over the whole fluid region at finite degeneracies in the paramagnetic state. In contrast, a systematic difference between the HNC and PIMC results is observed in the ferromagnetic state, which suggests a necessity of further studies on the exchange-correlation free energies from both aspects of analytical theory and simulation. Published by AIP Publishing.AMER INST PHYSICS, 2016年12月, JOURNAL OF CHEMICAL PHYSICS, 145(21) (21), 11, 英語[査読有り]研究論文（学術雑誌）
- Water plays a significant role in the binding process between protein and ligand. However, the thermodynamics of water molecules are often underestimated, or even ignored, in protein-ligand docking. Usually, the free energies of active-site water molecules are substantially different from those of waters in the bulk region. The binding of a ligand to a protein causes a displacement of these waters from an active site to bulk, and this displacement process substantially contributes to the free energy change of protein-ligand binding. The free energy of active-site water molecules can be calculated by grid inhomogeneous solvation theory (GIST), using molecular dynamics (MD) and the trajectory of a target protein and water molecules. Here, we show a case study of the combination of GIST and a docking program and discuss the effectiveness of the displacing gain of unfavorable water in protein-ligand docking. We combined the GIST-based desolvation function with the scoring function of AutoDock4, which is called AutoDock-GIST. The proposed scoring function was assessed employing 51 ligands of coagulation factor Xa (FXa), and results showed that both scoring accuracy and docking success rate were improved. We also evaluated virtual screening performance of AutoDock-GIST using FXa ligands in the directory of useful decoys-enhanced (DUD-E), thus finding that the displacing gain of unfavorable water is effective for a successful docking campaign.MDPI AG, 2016年11月, MOLECULES, 21(11) (11), 21, 英語[査読有り]研究論文（学術雑誌）
- Thermodynamic properties of water molecules around single- and double-stranded DNAs (ssDNAs and dsDNAs) with different sequences were investigated using grid inhomogeneous solvation theory. Free energies of water molecules solvating the minor groove of dsDNAs are lower than those near ssDNAs, while water molecules should be released during the formation of dsDNA. Free energies of water molecules around dsDNA are lower than those around ssDNA even in the second and third hydration shells. Our findings will help to clarify the role of water molecules in the formation of dsDNA from ssDNAs, thus facilitating the designs of drugs or nanomaterials using DNA. (C) 2016 Elsevier B.V. All rights reserved.ELSEVIER SCIENCE BV, 2016年09月, CHEMICAL PHYSICS LETTERS, 660, 250 - 255, 英語[査読有り]研究論文（学術雑誌）
- A computational scheme to describe the coherent dynamics of excitation energy transfer (EET) in molecular systems is proposed on the basis of generalized master equations with memory kernels. This formalism takes into account those physical effects in electron-bath coupling system such as the spin symmetry of excitons, the inelastic electron tunneling and the quantum features of nuclear motions, thus providing a theoretical framework to perform an ab initio description of EET through molecular simulations for evaluating the spectral density and the temporal correlation function of electronic coupling. Some test calculations have then been carried out to investigate the dependence of exciton population dynamics on coherence memory, inelastic tunneling correlation time, magnitude of electronic coupling, quantum correction to temporal correlation function, reorganization energy and energy gap. (C) 2016 Elsevier B.V. All rights reserved.ELSEVIER SCIENCE BV, 2016年08月, CHEMICAL PHYSICS, 474, 18 - 24, 英語[査読有り]研究論文（学術雑誌）
- Photosystem I (PS I) is one of the most important protein complexes for photosynthesis, which is present in plants, algae and cyanobacteria. A variety of mechanisms for environmental response in and around PS I have been elucidated experimentally and theoretically. During the photosynthetic induction time, the congestion of electron occurs in PSI and then the over-reduced PS I states are realized. This means that the degree of freedom of the redox states of PSI becomes large and thus the understanding of phenomena based on the model describing PSI in the state space becomes difficult. To understand the phenomena intuitively, we have reduced the complicated PS I model which has the multi-timescale property for electron and excitation-energy transfer processes into a simple one which has only the mono-timescale property through the use of hierarchical coarse-graining (HCG) method. The coarse-grained model describes the state of PS I by seven variable states, while the original model describes the PS I by 3 x 2(7) (=384) states. Based on the derived model, the I-820 (820 nm transmittance signal) curve in photosynthetic induction term, which indicates the accumulations of P-700(+) and Pc+, is simulated and analyzed in comparison with experiment With respect to this signal curve, it is revealed that the initial increase up to the shoulder at 10(-3) s, the increase from that point to the peak at 2 x10(-2) s, and the decay after that peak reflect the accumulations of P-700(+), Pc+ and P700FA-FB- (PSI state in which P-700,F-A(-) and F-B(-) are observed.), respectively. Besides, the important role of the charge recombination processes from P(700)(+)A(0A)(-) and P(700)(+)A(1A)(-) states for the dissipation of the extra absorbed energy in photosynthetic induction period is confirmed. (C) 2016 Elsevier B.V. All rights reserved.ELSEVIER SCIENCE SA, 2016年07月, JOURNAL OF PHOTOCHEMISTRY AND PHOTOBIOLOGY B-BIOLOGY, 160, 364 - 375, 英語[査読有り]研究論文（学術雑誌）
- A computational scheme to describe the temporal evolution of thermodynamic functions in stochastic nonequilibrium processes of isothermal classical systems is proposed on the basis of overdamped Langevin equation under given potential and temperature. In this scheme the associated Fokker-Planck-Smoluchowski equation for the probability density function is transformed into the imaginary-time Schrodinger equation with an effective Hamiltonian. The propagator for the time-dependent wave function is expressed in the framework of the path integral formalism, which can thus represent the dynamical behaviors of nonequilibrium molecular systems such as those conformational changes observed in protein folding and ligand docking. The present study then employs the diffusion Monte Carlo method to efficiently simulate the relaxation dynamics of wave function in terms of random walker distribution, which in the long-time limit reduces to the ground-state eigenfunction corresponding to the equilibrium Boltzmann distribution. Utilizing this classical-quantum correspondence, we can describe the relaxation processes of thermodynamic functions as an approach to the equilibrium state with the lowest free energy. Performing illustrative calculations for some prototypical model potentials, the temporal evolutions of enthalpy, entropy, and free energy of the classical systems are explicitly demonstrated. When the walkers initially start from a localized configuration in one- or two-dimensional harmonic or double well potential, the increase of entropy usually dominates the relaxation dynamics toward the equilibrium state. However, when they start from a broadened initial distribution or go into a steep valley of potential, the dynamics are driven by the decrease of enthalpy, thus causing the decrease of entropy associated with the spatial localization. In the cases of one- and two-dimensional asymmetric double well potentials with two minimal points and an energy barrier between them, we observe a nonequilibrium behavior that the system entropy first increases with the broadening of the initially localized walker distribution and then it begins to decrease along with the trapping at the global minimum of the potential, thus leading to the minimization of the free energy. (C) 2016 AIP Publishing LLC.AMER INST PHYSICS, 2016年03月, JOURNAL OF CHEMICAL PHYSICS, 144(9) (9), 14, 英語[査読有り]研究論文（学術雑誌）
- 一般社団法人日本物理学会, 2016年, 日本物理学会講演概要集, 71, 3156 - 3156, 日本語
- タンパク質とリガンドの結合において水分子が重要な役割を果たすことはよく知られているが，これらの水分子の効果をドッキング計算に取り入れるのは容易ではない．水和したタンパク質の活性部位に存在する水分子の自由エネルギーは様々だが，通常そのプロファイルはバルクの水分子とは大きく異なる．リガンドはタンパク質に結合するとき，元々タンパク質の活性部位を満たしてたいた水分子をバルクへと放出する．従って排除される水分子の自由エネルギー変化はタンパク質ーリガンド結合における結合自由エネルギーに大きく寄与する．例えば，タンパク質の疎水性部位に存在する水分子は水素結合を適切に形成できないためバルクの水分子と比較して不安定である．つまり，リガンドがこのような水分子をバルクへと放出することはリガンドの結合自由エネルギーにおける大きな利得となる．本研究では，分子動力学法を用いて得た水分子の自由エネルギーを取り入れることによってドッキング計算の精度向上を試みた．公益社団法人 日本化学会・情報化学部会, 2016年, ケモインフォマティクス討論会予稿集, 2016, Y2, 日本語
- 公益社団法人 日本化学会・情報化学部会, 2016年, CICSJ Bull., 34(No. 1) (No. 1), 10 - 16, 日本語[査読有り]研究論文（研究会，シンポジウム資料等）
- 2016年, ACS Symposium Series 1234, 173, 英語[招待有り]研究論文（国際会議プロシーディングス）
- In conditions that mimic those of the living cell, where various biomolecules and other components are present, DNA strands can adopt many structures in addition to the canonical B-form duplex. Previous studies in the presence of cosolutes that induce molecular crowding showed that thermal stabilities of DNA structures are associated with the properties of the water molecules around the DNAs. To understand how cosolutes, such as ethylene glycol, affect the thermal stability of DNA structures, we investigated the thermodynamic properties of water molecules around a hairpin duplex and a G-quadruplex using grid inhomogeneous solvation theory (GIST) with or without cosolutes. Our analysis indicated that (i) cosolutes increased the free energy of water molecules around DNA by disrupting water-water interactions, (ii) ethylene glycol more effectively disrupted water-water interactions around Watson-Crick base pairs than those around G-quartets or non-paired bases, (iii) due to the negative electrostatic potential there was a thicker hydration shell around G-quartets than around Watson-Crick-paired bases. Our findings suggest that the thermal stability of the hydration shell around DNAs is one factor that affects the thermal stabilities of DNA structures under the crowding conditions.OXFORD UNIV PRESS, 2015年12月, NUCLEIC ACIDS RESEARCH, 43(21) (21), 10114 - 10125, 英語[査読有り]研究論文（学術雑誌）
- 日本放射線影響学会, 2015年10月, 第1回放射線ワークショップ 講演論文集, 2015, 84, 日本語細胞生存率とDNA損傷を考慮した指標による急性被ばく影響の解析研究論文（研究会，シンポジウム資料等）
- Photosystem II (PS II) is a protein complex which evolves oxygen and drives charge separation for photosynthesis employing electron and excitation-energy transfer processes over a wide timescale range from picoseconds to milliseconds. While the fluorescence emitted by the antenna pigments of this complex is known as an important indicator of the activity of photosynthesis, its interpretation was difficult because of the complexity of PS II. In this study, an extensive kinetic model which describes the complex and multi-timescale characteristics of PS II is analyzed through the use of the hierarchical coarse-graining method proposed in the authors' earlier work. In this coarse-grained analysis, the reaction center (RC) is described by two states, open and closed RCs, both of which consist of oxidized and neutral special pairs being in quasi-equilibrium states. Besides, the PS II model at millisecond scale with three-state RC, which was studied previously, could be derived by suitably adjusting the kinetic parameters of electron transfer between tyrosine and RC. Our novel coarse-grained model of PS II can appropriately explain the light-intensity dependent change of the characteristic patterns of fluorescence induction kinetics from O-J-I-P, which shows two inflection points, J and I, between initial point O and peak point P, to O-J-D-I-P, which shows a dip D between J and I inflection points. (C) 2015 Elsevier Ltd. All rights reserved.ACADEMIC PRESS LTD- ELSEVIER SCIENCE LTD, 2015年09月, JOURNAL OF THEORETICAL BIOLOGY, 380, 220 - 237, 英語[査読有り]研究論文（学術雑誌）
- We propose a novel method for virtual ligand screening to explore drug candidates binding to target proteins. Employing both information on the ligand-residue interactions calculated by the fragment molecular orbital method and the molecular properties represented by the MDL MACCS keys, a couple of advanced clustering analyses on the basis of the self-organizing map and the multi-dimensional scaling are carried out. In comparison to earlier, similar approaches, the present method can provide higher-dimensional, wider viewpoints to look for better inhibitors and to improve them with reducing the possibilities of false-positives and false-negatives for hit or lead compounds, thus accelerating drug designs. The feasibility and usefulness of the proposed methodology are then demonstrated through the application to the complex systems of estrogen receptor and its ligand molecules, in which a molecular modification to improve the binding property of drug candidates is also suggested. (C) 2015 Elsevier B.V. All rights reserved.ELSEVIER SCIENCE BV, 2015年06月, COMPUTATIONAL AND THEORETICAL CHEMISTRY, 1061, 12 - 22, 英語[査読有り]研究論文（学術雑誌）
- In this report the radial distribution functions (RDFs) of liquid water are calculated on the basis of the classical density functional theory combined with the reference interaction site model for molecular liquids. The bridge functions, which are neglected in the hypernetted-chain (HNC) approximation, are taken into account through the density expansion for the Helmholtz free energy functional up to the third order. A factorization approximation to the ternary direct correlation functions in terms of the site-site pair correlation functions is then employed in the expression of the bridge functions, thus leading to a closed set of integral equations for the determination of the RDFs. It is confirmed through numerical calculations that incorporation of the oxygen-oxygen bridge function substantially improves the poor descriptions by the HNC approximation at room temperature, e.g., for the second peak of the oxygen-oxygen RDF.SPRINGER HEIDELBERG, 2015年06月, INTERDISCIPLINARY SCIENCES-COMPUTATIONAL LIFE SCIENCES, 7(2) (2), 152 - 156, 英語[査読有り]研究論文（学術雑誌）
- L-2-Haloacid dehalogenase (L-DEX YL) is a member of a family of enzymes that decontaminate a variety of environmental pollutants such as L-2-chloropropionate (L-2-CPA). This enzyme specifically catalyzes the hydrolytic dehalogenation of L-2-haloacid to produce D-2-hydroxy acid, and does not catalyze that of D-2-haloacid. Here, using the quantum-mechanical/molecular-mechanical and the fragment molecular orbital calculations, the enzymatic reaction of L-DEX YL to D-2-CPA was compared with that to L-2-CPA. As a result, Tyrl 2, Leu45 and Phe60 were predicted to affect the enantioselectivity. We then performed the site-directed-mutagenesis experiments and the activity measurement of these mutants, thus finding that the F60Y mutant had the enzymatic activity with D-2-CPA. (C) 2015 Elsevier B.V. All rights reserved.ELSEVIER SCIENCE BV, 2015年03月, CHEMICAL PHYSICS LETTERS, 623, 101 - 107, 英語[査読有り]研究論文（学術雑誌）
- Elsevier {BV}, 2015年02月, Computational and Theoretical Chemistry, 1054, 29 - 37, 英語[査読有り]研究論文（学術雑誌）
- Protein-ligand docking is an optimization problem, which aims to identify the binding pose of a ligand with the lowest energy in the active site of a target protein. In this study, we employed a novel optimization algorithm called fitness learning-based artificial bee colony with proximity stimuli (FlABCps) for docking. Simulation results revealed that FlABCps improved the success rate of docking, compared to four state-of-the-art algorithms. The present results also showed superior docking performance of FlABCps, in particular for dealing with highly flexible ligands and proteins with a wide and shallow binding pocket.ROYAL SOC CHEMISTRY, 2015年, PHYSICAL CHEMISTRY CHEMICAL PHYSICS, 17(25) (25), 16412 - 16417, 英語[査読有り]研究論文（学術雑誌）
- Thermodynamic analyses and molecular dynamics calculations demonstrated that i-motifs in a hydrated ionic liquid of choline dihydrogen phosphate (choline dhp) were more stable than G-quadruplexes due to choline ion binding to loop regions in the i-motifs. Interestingly, the i-motifs formed even at physiological pH in the choline dhp-containing solution.ROYAL SOC CHEMISTRY, 2015年, CHEMICAL COMMUNICATIONS, 51(32) (32), 6909 - 6912, 英語[査読有り]研究論文（学術雑誌）
- 2015年, JPS Conf. Proc., 5, 011008, 英語Choline Ions Stabilize A-T Base Pairs by Fitting into Minor Groove[査読有り]研究論文（国際会議プロシーディングス）
- L-2-Haloacid dehalogenase (L-DEX) is one of a family of enzymes that decompose a variety of environmental pollutants such as L-2-chloropropionate (L-2-CPA). This enzyme specifically produces a D-2-hydroxy acid from a L-2-haloacid, and, to date, some residues have been suggested as important in this enzymatic reaction. Here, quantum-mechanical (QM)/molecular-mechanical (MM) calculations for the L-DEX from Pseudomonas sp. YL (L-DEX YL) 2-CPA complex were performed to elucidate the structure of transition state and the energy profile in this enzymatic reaction. QM/MM simulations using the ONIOM (PM3:Amber) method revealed that the activation energy of dehalogenation reaction was around 9.0 kcal/mol and that one of the most important residues in the ester intermediate formation step was Arg41, which was found to decrease the activation energy by about 40 kcal/mol compared to the case of its absence. On the other hand, this stabilization effect by Arg41 was significantly counterbalanced by the presence of Asnl 77. Simulations of enzymes mutated at Arg41 indicated that mutants possessing a positive charge near the Arg41 position would allow the dehalogenation reaction as well. Specifically, it was suggested by our simulations that homolysine (homK) mutant of Arg41, which contains one more methylene group in the side chain compared to lysine, could be active as well as the wild-type enzyme. The distance from the chloride ion to the position of the positive charge of the acceptor seems to dictate the activation energy. (C) 2014 Elsevier B.V. All rights reserved.ELSEVIER SCIENCE BV, 2014年12月, JOURNAL OF MOLECULAR CATALYSIS B-ENZYMATIC, 110, 23 - 31, 英語[査読有り]研究論文（学術雑誌）
- On the basis of available molecular structures registered in Protein Data Bank, we have theoretically carried out the interaction energy analysis for the complexes of influenza virus hemagglutinin (HA) proteins and sialosaccharide receptor analogs of host cells. Employing the fragment molecular orbital method for quantum-chemical calculations, the differences in magnitude and pattern of the interactions between the amino acid residues of avian-type (H7N3) or human-type (H7N9) HA and each saccharide part of avian or human receptor were studied in order to elucidate the molecular mechanism of avian-to-human infectious transmission of influenza virus. We have thus confirmed quantitatively that the mutations from the avian HA to the human HA significantly strengthened the binding affinity of human HA to human receptor, while retaining the affinity to avian receptor. In addition to direct effects regarding the changes of interactions between the altered residues and the receptors, we have also found the importance of indirect effects in which structural changes caused by the mutations play vital roles to modify the intermolecular interactions. (C) 2014 Elsevier Inc. All rights reserved.ELSEVIER SCIENCE INC, 2014年09月, JOURNAL OF MOLECULAR GRAPHICS & MODELLING, 53, 48 - 58, 英語[査読有り]研究論文（学術雑誌）
- It is considered that Hoogsteen base pairs and DNA triplex structures play important roles in cellular processes even though these structures are less than duplexes of Watson Crick base pairs. Molecular ions clearly affect the stability of DNA structures in vivo; however, the mechanisms are unknown. Here, we investigated the effects of sodium ions, choline ions, and tetramethylammonium ions on DNA triplexes using molecular dynamics simulations. We found that nonpolar interactions, which are associated with van der Waals interactions, and solvent-accessible surface area were more important than polar or electrostatic interactions in determining the affinity of a molecular cation for the DNA groove areas. The free energy gain due to a cation that fit optimally within a DNA groove was larger than the free energy loss due to the effect of dehydration. Cations with shapes complementary to that of a particular DNA groove configuration stabilized triplex formation, but cations that disturbed hydrogen bonds between DNA bases were destabilizing. These stabilizing and destabilizing mechanisms of molecular cations were also applicable to a DNA duplex composed of Watson Crick base pairs. The molecular-level view of cation interactions with DNA structures will guide the design of DNA devices, DNA-based drugs, and genetic therapies.AMER CHEMICAL SOC, 2014年08月, JOURNAL OF PHYSICAL CHEMISTRY B, 118(32) (32), 9583 - 9594, 英語[査読有り]研究論文（学術雑誌）
- The mechanism to fix helix 12 (H12) in the agonist/antagonist position, which is involved in controlling transcriptional activation, of the human estrogen receptor a ligand binding domain (hER alpha LBD) is studied by using fragment molecular orbital calculations at the Moller-Plesset second-order perturbation levels to analyze inter-fragment interaction energies (IFIEs), electrostatic potentials (ESPs), and atomic charges. The mutually attractive and complementary relationships between H12 and highly conserved Lys529/Lys362 are shown through the IFIEs and ESPs. The highly conserved Lys529 and Lys362 are found to have strong attractive interactions with the anionic residues of H12 in the agonist and antagonist positions, respectively, thus playing roles of charge clamps to fix H12. Additionally, intramolecular interactions between the neutral residues of H12 including the LXXML motif and the other part of hER alpha are strengthened by the hydrogen bonds and polarization. It is noted that the highly conserved Asp351 forms a hydrogen bond with Leu540 of H12 in the hER alpha agonist complex, while it is also involved in stabilization of ligand binding in the hER alpha antagonist complex. The charges of residues at the interface between H12 and the other part of hER alpha approach approximately neutral upon forming the agonist/antagonist binding conformation so as to relax the electrostatic repulsion caused by the negative charges of H12 and the other part of hER alpha. Our observations would thus provide useful information to control the H12 position for regulation of transcription in hER alpha and other nuclear receptors.AMER CHEMICAL SOC, 2014年05月, J. Phys. Chem. B, 118(19) (19), 4993 - 5008, 英語[査読有り]研究論文（学術雑誌）
- The fragment molecular orbital (FMO) method can calculate the electronic structure of macromolecules such as DNA by dividing them into several fragments and introducing suitable approximations. To establish guiding principles for FMO calculation of DNA, benchmark tests were performed for several small DNA models consisting of one or two bases or two base pairs. The effects of several factors on the accuracy of FMO calculations were investigated, including the methods used to fragment the nucleotide units, approximations for the electrostatic potential, charge neutralization, and electron correlation. It was found that charge neutralization is indispensable for the reliable calculation of energies and spatial distribution of molecular orbitals, but not necessarily so for inter-fragment interaction energy analyses, such as calculation of the base-base interaction. The electrostatic approximations were shown to have only an insignificant effect on the qualitative nature of the calculations. It was also confirmed that the base-base stacking energy can be reproduced semi-quantitatively by the Moller-Plesset second-order perturbation (MP2) method though with some overestimation, and that the overestimation can be alleviated by the spin-component-scaled MP2 method. (C) 2014 Elsevier B.V. All rightsELSEVIER SCIENCE BV, 2014年04月, COMPUTATIONAL AND THEORETICAL CHEMISTRY, 1034, 7 - 16, 英語[査読有り]研究論文（学術雑誌）
- We have calculated the radial distribution functions (RDFs) of liquid water on the basis of the classical density functional theory combined with the reference interaction site model for molecular liquids. The density expansion for the Helmholtz free energy functional is retained up to the third order in order to take into account the effects of the bridge functions beyond the hypernetted-chain (HNC) approximation. The ternary direct correlation functions in the expression of the bridge functions are then given by a factorization approximation in terms of the site-site pair correlation functions, thus leading to a closed set of integral equations for the determination of the RDFs. We have obtained a numerical result in which a poor description by the HNC approximation for the second peak of the oxygen-oxygen RDF at room temperature has been improved to some extent by incorporating the oxygen-oxygen bridge function. Some directions toward more satisfactory agreement with computer simulation results are addressed as well. (C) 2013 Elsevier B.V. All rights reserved.ELSEVIER SCIENCE BV, 2014年02月, CHEMICAL PHYSICS, 430, 18 - 22, 英語[査読有り]研究論文（学術雑誌）
- 2014年, J. Comput. Chem. Jpn., 13, 163 - 164, 日本語人工蜂コロニーアルゴリズムを用いたタンパク質―リガンドの結合予測と評価[査読有り]研究論文（学術雑誌）
- 2014年, CBI学会誌, 2(No.4) (No.4), 17 - 25, 日本語フラグメント分子軌道法を用いたspin-component-scaled MP2法に基づくタンパク－リガンド相互作用クラスター解析[査読有り]研究論文（学術雑誌）
- We propose a hierarchical reduction scheme to cope with coupled rate equations that describe the dynamics of multi-time-scale photosynthetic reactions. To numerically solve nonlinear dynamical equations containing a wide temporal range of rate constants, we first study a prototypical three-variable model. Using a separation of the time scale of rate constants combined with identified slow variables as (quasi-)conserved quantities in the fast process, we achieve a coarse-graining of the dynamical equations reduced to those at a slower time scale. By iteratively employing this reduction method, the coarse-graining of broadly multi-scale dynamical equations can be performed in a hierarchical manner. We then apply this scheme to the reaction dynamics analysis of a simplified model for an illuminated photosystem II, which involves many processes of electron and excitation-energy transfers with a wide range of rate constants. We thus confirm a good agreement between the coarse-grained and fully (finely) integrated results for the population dynamics. © 2014 Elsevier Ireland Ltd.2014年, BioSystems, 117(1) (1), 15 - 29, 英語[査読有り]研究論文（学術雑誌）
- Under physiological conditions, G C base pairs are more stable than A T base pairs. In a previous study, we showed that in the hydrated ionic liquid of choline dihydrogen phosphate, the stabilities of these base pairs are reversed. In the present study, we elucidated the unique binding interactions of choline ions with DNA atoms from a microscopic viewpoint using molecular dynamics simulations. Three times more choline ions bind to the DNA duplex than sodium ions. Sodium ions bind closely but not stably; in contrast, the choline ions bind through multiple hydrogen bonding networks with DNA atoms stably. The affinity of choline ion for the minor groove of A-T base pairs is more than 2 times that for other groove areas. In the narrow A-T minor groove, choline ion has high affinity for the ribose atoms of thymine. Choline ions also destabilize the formation of hydrogen bonds between G C base pairs by binding to base atoms preferentially for both of duplex and single-strand DNA, which are associated with the bonds between G-C base pairs. Our new finding will not only lead to better control of DNA stability for use in DNA nanodevices, but also provide new insight into the stability of DNA duplexes under crowding conditions found in living cells.AMER CHEMICAL SOC, 2014年01月, JOURNAL OF PHYSICAL CHEMISTRY B, 118(2) (2), 379 - 389, 英語[査読有り]研究論文（学術雑誌）
- PHYSICAL SOC JAPAN, 2013年07月, JOURNAL OF THE PHYSICAL SOCIETY OF JAPAN, 82(7) (7), 075001, 英語[査読有り]
- Density functional theory for molecular fluids developed by Donley et al. (J. Chem. Phys. 101 (1994) 3205) is extended to include the effects of orientation-dependent bridge functions associated with the interparticle, triplet correlations. Resultant integral equations for the pair and direct correlation functions are solved for water, where the three-body direct correlation functions are approximated in terms of two-body functions. A test calculation employing a simple Gaussian form for the two-body function between the oxygen sites then provides a promising result to improve the description of the oxygen-oxygen correlations in liquid water at room temperature. (C) 2013 Elsevier B.V. All rights reserved.ELSEVIER SCIENCE BV, 2013年05月, CHEMICAL PHYSICS LETTERS, 572, 38 - 43, 英語[査読有り]研究論文（学術雑誌）
- We develop an inter-fragment interaction energy (IFIE) analysis based on the three- and four-body corrected fragment molecular orbital (FMO3 and FMO4) method to evaluate the interactions of functional group units in structure-based drug design context. The novel subdividing fragmentation method for a ligand (in units of their functional groups) and amino acid residues (in units of their main and side chains) enables us to understand the ligand-binding mechanism in more detail without sacrificing chemical accuracy of the total energy and IFIEs by using the FMO4 method. We perform FMO4 calculations with the second order Møller-Plesset perturbation theory for an estrogen receptor (ER) and the 17β-estradiol (EST) complex using the proposed fragmentation method and assess the interaction for each ligand-binding site by the FMO4-IFIE analysis. When the steroidal EST is divided into two functional units including "A ring" and "D ring", respectively, the FMO4-IFIE analysis reveals their binding affinity with surrounding fragments of the amino acid residues; the "A ring" of EST has polarization interaction with the main chain of Thr347 and two hydrogen bonds with the side chains of Glu353 and Arg394; the "D ring" of EST has a hydrogen bond with the side chain of His524. In particular, the CH/π interactions of the "A ring" of EST with the side chains of Leu387 and Phe404 are easily identified in cooperation with the CHPI program. The FMO4-IFIE analysis using our novel subdividing fragmentation method, which provides higher resolution than the conventional IFIE analysis in units of ligand and each amino acid reside in the framework of two-body approximation, is a useful tool for revealing ligand-binding mechanism and would be applicable to rational drug design such as structure-based drug design and fragment-based drug design. © 2013 Elsevier Inc. All rights reserved.Elsevier {BV}, 2013年04月, Journal of Molecular Graphics and Modelling, 41, 31 - 42, 英語[査読有り]研究論文（学術雑誌）
- Polyglutamine (polyQ, a peptide) with an abnormal repeat length is the causative agent of polyQ diseases, such as Huntington's disease. Although glutamine is a polar residue, polyQ peptides form insoluble aggregates in water, and the mechanism for this aggregation is still unclear. To elucidate the detailed mechanism for the nucleation and aggregation of polyQ peptides, replica exchange molecular dynamics simulations were performed for monomers and dimers of polyQ peptides with several chain lengths. Furthermore, to determine how the aggregation mechanism of polyQ differs from those of other peptides, we compared the results for polyQ with those of polyasparagine and polyleucine. The energy barrier between the monomeric and dimeric states of polyQ was found to be relatively low, and it was observed that polyQ dimers strongly favor the formation of antiparallel beta-sheet structures. We also found a characteristic behavior of the monomeric polyQ peptide: a turn at the eighth residue is always present, even when the chain length is varied. We previously showed that a structure including more than two sets of beta-turns is stable, so a long monomeric polyQ chain can act as an aggregation nucleus by forming several pairs of antiparallel beta-sheet structures within a single chain. Since the aggregation of polyQ peptides has some features in common with an amyloid fibril, our results shed light on the mechanism for the aggregation of polyQ peptides as well as the mechanism for the formation of general amyloid fibrils, which cause the onset of amyloid diseases.SPRINGER, 2013年04月, JOURNAL OF MOLECULAR MODELING, 19(4) (4), 1627 - 1639, 英語[査読有り]研究論文（学術雑誌）
- We have applied the four-body corrected fragment molecular orbital (FMO4) method to the investigation of the interaction between an artificially designed peptide, with sequence of Arg1-Lys2-Leu3-Pro4-Asp5-Ala6 [Sano et al., Langmuir, 21 (2005) 3090], and the silica surface modeled by a large cluster model including 257 silicon atoms. The second-order Møller-Plesset perturbation calculation was accelerated by the Cholesky decomposition with adaptive metric technique (CDAM-MP2). Systematic analyses were made for inter-fragment interaction energies (IFIEs) with and without a statistical correction for screening. As the result, the importance of three charged residues (Arg1, Lys2 and Asp5) in the peptide-silica interaction was illuminated. © 2013 Elsevier B.V. All rights reserved.Elsevier {BV}, 2013年04月, Chemical Physics Letters, 566, 25 - 31, 英語[査読有り]研究論文（学術雑誌）
- 公益社団法人 日本化学会・情報化学部会, 2013年, 日本化学会情報化学部会誌, 31(3) (3), 54 - 54, 日本語
- 一般社団法人 日本生物物理学会, 2013年, 生物物理, 53(1) (1), S253, 英語
- A theoretical scheme to evaluate effective, screened interactions between fragments is proposed within the framework of the fragment molecular orbital (FMO) method. In this theory, the presence of implicit, dielectric continuum solvent is not assumed, but only the information on bare, inter-fragment interaction energies obtained through the FMO calculation for explicit, molecular system is employed. The effective interactions with inclusion of entropic effect are then described and optimized as a consequence of inter-fragment correlations on the basis of classical-mechanical many-body theories. Test calculations for a simple model system and a realistic protein system are performed, and their implications are discussed. © 2012 Elsevier B.V. All rights reserved.Elsevier {BV}, 2013年01月, Chemical Physics Letters, 556, 272 - 277, 英語[査読有り]研究論文（学術雑誌）
- We have performed ab initio path integral Monte Carlo simulations for water trimer (H2O)(3) system. The electron correlation effects have been taken into account up to the level of third-order Moller-Plesset (MP3) perturbation theory. Through comparisons of calculated geometrical properties of water trimer such as O-O distance, O-H-O angle, and torsional angle between O-H and O-O-O plane, the interplays among the nuclear quantum, thermal and electron correlation effects are analyzed quantitatively. (c) 2012 Elsevier B.V. All rights reserved.ELSEVIER, 2012年10月, COMPUTATIONAL AND THEORETICAL CHEMISTRY, 997, 7 - 13, 英語[査読有り]研究論文（学術雑誌）
- We have developed a theoretical formulation for excitation energy transfer between structurally fluctuating dimer molecules in surrounding environments. On the basis of a generalized master equation in which a memory function plays a vital role, the temporal evolutions of the population densities of exciton at the donor and acceptor sites are described. By employing an ansatz form for the memory function, the competitive effects of dimeric coupling and bath modes are analyzed quantitatively, where the roles of oscillating electronic coupling are highlighted.AMER PHYSICAL SOC, 2012年08月, PHYSICAL REVIEW E, 86(2) (2), 021914, 英語[査読有り]研究論文（学術雑誌）
- Vibrational energy transfer in protein molecule is studied by a renormalization-group inspired approach. An effective Lagrangian and associated equations of motion to describe the resonant energy transfer are first analyzed in terms of the lowest-order perturbative renormalization group theory as a unified tool for global asymptotic analysis. After the elimination of singular terms associated with the Fermi resonance, amplitude equations to describe the slow dynamics of vibrational energy transfer in protein are derived, which can be reformulated by a method of variation of parameters and reproduce simulation results quantitatively.PHYSICAL SOC JAPAN, 2012年03月, JOURNAL OF THE PHYSICAL SOCIETY OF JAPAN, 81(3) (3), 033801, 英語[査読有り]研究論文（学術雑誌）
- The multiparticle distribution functions and density matrices for ideal Fermi gas system in the ground state are calculated for any spatial dimension. The results are expressed as determinant forms, in which a correlation kernel plays a vital role. The expression obtained for the one-dimensional Fermi gas is essentially equivalent to that observed for the eigenvalue distribution of random unitary matrices, and thus to that conjectured for the distribution of the non-trivial zeros of the Riemann zeta function. Their implications are discussed briefly.SPRINGER, 2012年, ADVANCES IN THE THEORY OF QUANTUM SYSTEMS IN CHEMISTRY AND PHYSICS, 22, 249 - 266, 英語[査読有り]研究論文（国際会議プロシーディングス）
- The four-body corrected fragment molecular orbital (FMO4) method was implemented at the second-order Møller-Plesset perturbation (MP2) level. A series of accuracy tests relative to the previous two-body and three-body treatments were performed. As expected, FMO4 provided better accuracy in total energies in comparison with the reference values by regular MO calculations. A nonconventional fragmentation by separating main and side chains in amino acid residues was examined for Ala-pentamer and Chignolin, where the four-body corrections were shown to be substantial. A large complex of HIV-1 protease (total 198 residues) with lopinavir was calculated as well. Furthermore, this new FMO scheme was successfully applied to adamantane-shaped clusters with three-dimensional bonding framework. © 2011 Elsevier B.V. All rights reserved.Elsevier {BV}, 2012年01月, Chemical Physics Letters, 523, 128 - 133, 英語[査読有り]研究論文（学術雑誌）
- Division of Chemical Information and Computer Sciences, 2012年, J. Comput. Aided Chem., 13(0) (0), 44 - 50, 日本語[査読有り]研究論文（学術雑誌）
- We have performed ab initio path integral molecular dynamics and Monte Carlo simulations for water trimer and oligopeptide. In the first part, we illustrate the path integral molecular dynamics method based on fragment molecular orbital (FMO-PIMD) method. The FMO-PIMD method is applied to water trimer and glycine pentamer to investigate nuclear quantum effects on the structure and molecular interactions. In the second part, we employ the Moller-Plesset perturbation theory and discuss interplay of nuclear quantum effects and electron correlations. (C) 2012 American Chemical SocietyAMER CHEMICAL SOC, 2012年, ADVANCES IN QUANTUM MONTE CARLO, 1094, 187 - +, 英語[査読有り]研究論文（国際会議プロシーディングス）
- Effective interactions between amino acid residues in antigen-antibody complex of influenza virus hemagglutinin (HA) protein can be evaluated in terms of the inter-fragment interaction energy (IFIE) analysis with the fragment molecular orbital (FMO) method, in which each fragment contains the side chain of corresponding amino acid residue. We have carried out the FMO-MP2 (second-order Moeller-Plesset) calculation for the complex of HA antigen and Fab antibody of influenza virus H3N2 A/Aichi/2/68 and obtained the IFIE values between each amino acid residue in HA and the whole antibody as the sums over the residues contained in the latter. Combining this IFIE data with experimental data for hemadsorption activity of HA mutants, we succeeded in theoretically explaining the mutations in HA observed after the emergence of influenza virus H3N2 A/Aichi/2/68 in an earlier study, except for those of THR83. In the present study, we employ an alternative way of fragment division in the FMO calculation at the carbonyl C site of the peptide bond instead of the C(alpha) site used in the previous work, which provides revised IFIE values consistent with all the historical mutation data in the antigenic region E of HA including the case of THR83 in the present prediction scheme for probable mutations in HA.SPRINGER, 2011年12月, THEORETICAL CHEMISTRY ACCOUNTS, 130(4-6) (4-6), 1197 - 1202, 英語[査読有り]研究論文（学術雑誌）
- We have developed a new module for higher-order correlated methods up to coupled-cluster singles and doubles with perturbative triples (CCSD(T)). The matrix-matrix operations through the DGEMM routine were pursued for a number of contractions. This code was then incorporated into the ABINIT-MPX program for the fragment molecular orbital (FMO) calculations. Intra-fragment processings were parallelized with OpenMP in a node-wise fashion, whereas the message passing interface (MPI) was used for the fragment-wise parallelization over nodes. Our new implementation made the FMO-based higher-order calculations applicable to realistic proteins. We have performed several benchmark tests on the Earth Simulator (ES2), a massively parallel computer. For example, the FMO-CCSD(T)/6-31G job for the HIV-1 protease (198 amino acid residues)-lopinavir complex was completed in 9.8 h with 512 processors (or 64 nodes). Another example was the influenza neuraminidase (386 residues) with oseltamivir calculated at the full fourth-order Moller-Plesset perturbation level (MP4), of which job timing was 10.3 h with 1024 processors. The applicability of the methods to commodity cluster computers was tested as well.SPRINGER, 2011年10月, THEORETICAL CHEMISTRY ACCOUNTS, 130(2-3) (2-3), 515 - 530, 英語[査読有り]研究論文（学術雑誌）
- Ab initio electronic-state calculations for influenza virus hemagglutinin (HA) trimer complexed with Fab antibody were performed on the basis of the fragment molecular orbital (FMO) method at the second and third-order Møller-Plesset (MP2 and MP3) perturbation levels. For the protein complex containing 2351 residues and 36,160 atoms, the inter-fragment interaction energies (IFIEs) were evaluated to illustrate the effective interactions between all the pairs of amino acid residues. By analyzing the calculated data on the IFIEs, we first discussed the interactions and their fluctuations between multiple domains contained in the trimer complex. Next, by combining the IFIE data between the Fab antibody and each residue in the HA antigen with experimental data on the hemadsorption activity of HA mutants, we proposed a protocol to predict probable mutations in HA. The proposed protocol based on the FMO-MP2.5 calculation can explain the historical facts concerning the actual mutations after the emergence of A/Hong Kong/1/68 influenza virus with subtype H3N2, and thus provides a useful methodology to enumerate those residue sites likely to mutate in the future. © 2011 Elsevier Inc. All rights reserved.Elsevier {BV}, 2011年09月, Journal of Molecular Graphics and Modelling, 30, 110 - 119, 英語[査読有り]研究論文（学術雑誌）
- Basis set superposition error (BSSE) correction with counterpoise (CP) procedure under the environmental electrostatic potential is newly introduced to interfragment interaction energy (IFIE), which is important for interaction analysis in the fragment molecular orbital method. The CP correction for IFIE is applied to a stacked dimer of base pair and a protein-ligand complex of estrogen receptor and 17β-estradiol with scaled third-order Møller-Plesset perturbation theory. The BSSEs amount to about quarter of IFIE for hydrogen-bonding and electrostatic interactions and half or even more for dispersion interactions. Estimation of IFIE with the CP correction is therefore preferred for the quantitative discussion. © 2011 Elsevier B.V. All rights reserved.Elsevier {BV}, 2011年06月, Chemical Physics Letters, 509(1-3) (1-3), 67 - 71, 英語[査読有り]研究論文（学術雑誌）
- Quantum mechanical fragment molecular orbital calculations have been performed for receptor binding of the hemagglutinin protein of the recently pandemic influenza 2009 H1N1 (2009/HIN1pdm), A/swine/Iowa/1930, and A/Puerto Rico/8/1934 viruses to alpha 2-6 linked sialyloligosaccharides, as analogs of human receptors. The strongest receptor binding affinity was observed for the 2009/H1N1pdm. The inter-fragment interaction energy analysis revealed that the amino acid mutation of 2009/H1N1pdm, Ser145Lys, was a major cause of such strong binding affinity. Strong ionic pair interaction between the sialic acid and Lys145 was observed only in the 2009/H1N1pdm, in addition to the hydrogen bond between the sialic acid and Gln226 observed in all the HAs. Therefore, pandemic 2009/H1N1pdm has been found to recognize the alpha 2-6 receptor much stronger than the 1930-swine and 1934-human.BENTHAM SCIENCE PUBL LTD, 2011年05月, PROTEIN AND PEPTIDE LETTERS, 18(5) (5), 530 - 539, 英語[査読有り]研究論文（学術雑誌）
- Excitation energy transfer in a symmetric dimer embedded in biomolecular environment is theoretically analyzed. The present study especially focuses on the role played by conformational oscillation of surrounding environment, which may cause the oscillation of electronic coupling relevant to energy transfer. A generalized master equation describing the temporal evolution of population densities of exciton is derived from the quantum Liouville equation for density matrix, and solved with a memory function representing the relaxational and oscillatory features of temporal correlation of electronic coupling. Modulations of the coherent dynamics of excitation energy transfer are thus discussed analytically and numerically. (C) 2011 Elsevier B.V. All rights reserved.ELSEVIER SCIENCE BV, 2011年05月, CHEMICAL PHYSICS LETTERS, 508(1-3) (1-3), 139 - 143, 英語[査読有り]研究論文（学術雑誌）
- The periodic boundary condition (PBC) is incorporated in the fragment molecular orbital (FMO) method to appropriately describe systems with aqueous solutions. We present benchmark calculations for (H(2)O)(64) and show that this PBC-FMO method can eliminate artificial surface effects. An application to molecular dynamics simulation for liquid water is also shown, and calculated radial distribution functions are in reasonable agreement with those obtained from experiments. It is thus confirmed that the present PBC-FMO method is useful for ab initio simulations in aqueous solution. (C) 2011 Elsevier B.V. All rights reserved.ELSEVIER SCIENCE BV, 2011年04月, CHEMICAL PHYSICS LETTERS, 506(1-3) (1-3), 112 - 116, 英語[査読有り]研究論文（学術雑誌）
- The multiparticle distribution functions for ideal Fermi gas system in the ground state are calculated for any spatial dimension. The n-particle distribution function is expressed in terms of a determinant form in which a correlation kernel plays a vital role. The expression obtained for the one-dimensional Fermi gas is essentially equivalent to that known for the distribution of the eigenvalues of random unitary matrices, which, in turn, has a mathematical structure analogous to the distribution of non-trivial zeros of the Riemann zeta function. Thus, these analogies may provide deeper insights into the understanding of the individual theories.PHYSICAL SOC JAPAN, 2011年03月, JOURNAL OF THE PHYSICAL SOCIETY OF JAPAN, 80(3) (3), 英語[査読有り]研究論文（学術雑誌）
- Electron-ion collisions were studied for various protonated peptide monocations with disulfide bonds, using an electrostatic storage-ring equipped with a merged-electron-beam device. Resonant neutral particle emissions at the energies of 6-7 eV were observed, as well as a rise towards zero-energy, which are typical electron-capture dissociation profiles. The presence of disulfide (S-S) bonds tends to enhance the resonant bump heights. Chemical nature of the amino-acid residues adjacent to cysteines appears to correlate with the bump strength. Molecular-dynamical simulations help clarify the role of molecular vibration modes in the electron-capture dissociation process. (C) 2011 Elsevier B. V. All rights reserved.ELSEVIER SCIENCE BV, 2011年02月, CHEMICAL PHYSICS LETTERS, 504(1-3) (1-3), 83 - 87, 英語[査読有り]研究論文（学術雑誌）
- We propose a novel concept associated with the relationship between structure and function in biomolecular systems. We performed a 75 nanoseconds molecular dynamics (MD) simulation for an RNA-binding protein, neurooncological ventral antigen (NOVA), and examined its physico-chemical properties. NOVA dissociated from the NOVA-RNA complex showed a large conformational change: formation of intra-molecular hydrogen bonds between the C-terminal region and the loop structure located at the middle of amino acid sequence. The free energy analysis suggests that the deformed structure is more stabilized in macromolecular crowding environment where the dielectric constant is smaller than 5. The solvent accessible surface area (SASA) analysis indicates that NOVA enhances the efficiency of association with RNA by changing the relative SASA for the target sequence in RNA molecules. Based on the obtained results, we propose a novel concept of spontaneous adjustment mechanism to explain the structural and energetic changes observed for NOVA in the free state.BENTHAM SCIENCE PUBL LTD, 2010年12月, PROTEIN AND PEPTIDE LETTERS, 17(12) (12), 1547 - 1552, 英語[査読有り]研究論文（学術雑誌）
- We report the molecular mechanism of protein-RNA complex stabilization based on the electronic state calculation Fragment molecular orbital (FMO) method based quantum mechanical calculations were performed for neuro-oncological ventral antigen (NOVA)-RNA complex system The inter-molecular interactions and their effects on the electronic state of NOVA were examined in the framework of ab initio quantum calculation The strength of inter molecular interactions was evaluated using inter-fragment interaction energies (IFIEs) associated with residue-RNA base and residue-RNA backbone interactions Under the influence of Inter-molecular interactions the change of electronic state of NOVA upon the complex formation was examined based on IFIE values associated with ultra-NOVA residue-residue interactions and the change of atomic charges by each residue The results indicated that non-specifically recognized bases contributed to the stability of the complex as well as specifically recognized bases and that the secondary structure of NOVA was remarkably associated with the change of electronic state upon the complex formation (C) 2010 Elsevier B V All rights reservedELSEVIER SCIENCE BV, 2010年12月, JOURNAL OF MOLECULAR STRUCTURE-THEOCHEM, 962(1-3) (1-3), 45 - 55, 英語[査読有り]研究論文（学術雑誌）
- We developed FMO-PB method, which incorporates solvation effects into the Fragment Molecular Orbital calculation with the Poisson-Boltzmann equation. This method retains good accuracy in energy calculations with reduced computational time. We calculated the solvation free energies for polyalanines, Alpha-1 peptide, tryptophan cage, and complex of estrogen receptor and 17β-estradiol to show the applicability of this method for practical systems. From the calculated results, it has been confirmed that the FMO-PB method is useful for large biomolecules in solution. We also discussed the electric charges which are used in solving the Poisson-Boltzmann equation. © 2010 Elsevier B.V. All rights reserved.Elsevier {BV}, 2010年11月, Chemical Physics Letters, 500(1-3) (1-3), 116 - 119, 英語[査読有り]研究論文（学術雑誌）
- Positional displacement of helix12 (H12) in the estrogen receptor a, which belongs to the nuclear receptor (NR) superfamily, is studied by the molecular dynamics (MD) simulation and the linear response theory. Tendency of the H12 to swing up upon ligand binding, which is consistent with X-ray structures and earlier MD simulations, is reproduced by the calculation of the conformational fluctuation in apo state and the response to the external perturbation. Our study thus provides an interpretation of the positional change of the H12 such that it is derived by the preexistent swing-up motion where the ligand binding works only as a trigger. Our finding, which illustrates underlying mechanism of the H12 motion, would contribute to finding a way to regulate the transcriptional activity by synthesized ligands because the transcriptional activity of the NR is governed by the position of the H12. (C) 2010 Elsevier B.V. All rights reserved.ELSEVIER SCIENCE BV, 2010年09月, BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS, 1804(9) (9), 1832 - 1840, 英語[査読有り]研究論文（学術雑誌）
- 2010年09月, 日本科学教育学会年会論文集, 34, 271-274, 日本語兵庫県における持続可能な社会に向けた市民科学活動支援の取組と事例紹介研究論文（学術雑誌）
- Two proteins on the influenza virus surface have been well known. One is hemagglutinin (HA) associated with the infection to cells. The fragment molecular orbital (FMO) calculations were performed on a complex consisting of HA trimer and two Fab-fragments at the third-order Møller-Plesset perturbation (MP3) level. The numbers of residues and 6-31G basis functions were 2351 and 201276, and thus a massively parallel-vector computer was utilized to accelerate the processing. This FMO-MP3 job was completed in 5.8 h with 1024 processors. Another protein is neuraminidase (NA) involved in the escape from infected cells. The FMO-MP3 calculation was also applied to analyze the interactions between oseltamivir and surrounding residues in pharmacophore. © 2010 Elsevier B.V. All rights reserved.Elsevier {BV}, 2010年06月, Chemical Physics Letters, 493(4-6) (4-6), 346 - 352, 英語[査読有り]研究論文（学術雑誌）
- Polyglutamine (polyQ) diseases are caused by an abnormal expansion of CAG repeats. While their detailed structure remains unclear, polyQ peptides assume beta-sheet structures when they aggregate. To investigate the conformational ensemble of short, monomeric polyQ peptides, which consist of 15 glutamine residues (Q(15)), we performed replica exchange molecular dynamics (REMD) simulations. We found that Q(15) can assume multiple configurations due to all of the residues affecting the formation of side-chain hydrogen bonds. Analysis of the free energy landscape reveals that Q(15) has a basin for random-coil structures and another for a-helix or beta-turn structures. To investigate properties of aggregated polyQ peptides, we performed multiple molecular dynamics (MMD) simulations for monomeric and oligomeric Q(15). MMD revealed that the formation of oligomers stabilizes the beta-turn structure by increasing the number of hydrogen bonds between the main chains.AMER CHEMICAL SOC, 2010年05月, JOURNAL OF PHYSICAL CHEMISTRY B, 114(20) (20), 7056 - 7061, 英語[査読有り]研究論文（学術雑誌）
- A novel method, Cholesky decomposition with adaptive metric (CDAM), is applied to the two-electron integral calculations in the fragment molecular orbital (FMO) method. We thus accelerate the Hartree-Fock and the second-order Møller-Plesset perturbation (MP2) energy calculations substantially. Especially, the MP2 part for fragment dimers, which is computationally expensive, is accelerated by a factor of about 10. The CDAM approximations would enable FMO-MP2 calculations to easily process multiple structure samples even including dynamics of large molecular systems and lead to next-generation high-performance computations where statistical samplings or free energy estimates would be important. © 2010 Elsevier B.V. All rights reserved.Elsevier {BV}, 2010年04月, Chemical Physics Letters, 490(1-3) (1-3), 84 - 89, 英語[査読有り]研究論文（学術雑誌）
- We perform potential energy calculations on mutant polyglutamine peptides that were studied experimentally, and found to aggregate with varying efficiencies. Low-energy structures were generated for each peptide by simulated annealing molecular dynamics, and were analyzed by molecular mechanics and by all-electron fragment molecular orbital energy calculations. In order to make a comparison between the two sets of potential energies, we devised a means of computing molecular-mechanical analogues of the quantum-mechanical energies. Our results suggest that in accordance with a previous paper (VanSchouwen et al., submitted for publication [16]) the experimentally-observed inhibition of aggregation is due to localized, geometry-based effects on peptide structure, with little appreciable perturbation from longer-range non-bonded effects. (C) 2009 Elsevier B.V. All rights reserved.ELSEVIER SCIENCE BV, 2010年03月, JOURNAL OF MOLECULAR STRUCTURE-THEOCHEM, 944(1-3) (1-3), 12 - 20, 英語[査読有り]研究論文（学術雑誌）
- We have developed a theoretical formulation for evaluating the nonadiabatic electron-transfer (ET) rate constant in condensed medium which takes into account both inelastic electron tunneling and nuclear quantum effects. The derived formula allows us to calculate the ET rate as a function of the free-energy gap between the ET donor and acceptor states using the information on the spectral density associated with environmental polarization fluctuation and the temporal correlation function of electronic tunneling matrix element. Model calculations have been performed illustratively.AMER PHYSICAL SOC, 2010年02月, PHYSICAL REVIEW E, 81(2) (2), 英語[査読有り]研究論文（学術雑誌）
- CELL PRESS, 2010年01月, BIOPHYSICAL JOURNAL, 98(3) (3), 74A - 74A, 英語Theoretical Analysis of the Molecular Mechanism of Stabilization of Nova-RNA Complex System: Fragment Molecular Orbital Method Based Quantum Chemical Calculation For the Effect of the Complex Formation on the Electronic State of Biomacromolecular System[査読有り]
- We compared binding affinity evaluations for 10 FKBP ligands with such state-of-the-art computational methods as FMO, QM/MM, MM-PB/SA, and MP-CAFEE. For the FKBP ligands, we confirmed that each method could provide good correlations between the experimental and computational binding affinities. From the calculated results, we discussed the importance of solvation effect and structural sampling for these methods in detail. In addition, we addressed the issues of computational time and present arguments on the future perspective of the computational binding affinity evaluations. © 2010 Chem-Bio Informatics Society.Chem-Bio Informatics Society, 2010年, Chem-Bio Informatics Journal, 10(1) (1), 32 - 45, 英語[査読有り]研究論文（学術雑誌）
- L-2-haloacid dehalogenase (L-DEX) catalyzes the hydrolytic dehalogenation of L-2-haloalkanoic acids to produce the corresponding D-2-hydroxyalkanoic acids. This enzyme is expected to be applicable to the bioremediation of environments contaminated with halogenated organic compounds. We analyzed the reaction mechanism of L-DEX from Pseudomonas sp. YL (L-DEX YL) by using molecular modeling. The complexes of wild-type L-DEX YL and its K151A and D180A mutants with its typical substrate, L-2-chloropropionate, were constructed by docking simulation. Subsequently, molecular dynamics (MD) and ab initio fragment molecular orbital (FMO) calculations of the complexes were performed. The ab initio FMO method was applied at the MP2/6-31G level to estimate inter-fragment interaction energies. K151 and D180, which are experimentally shown to be important for enzyme activity, interact particularly strongly with L-2-chloropropionate, catalytic water, nucleophile (1310), and with each other. Our calculations Suggest that K151 stabilizes substrate orientation and balances the charge around the active site, while 13180 stabilizes the rotation Of the nucleophile D10, fixes catalytic water around 1310, and prevents K151 from approaching D10. Further, D180 may activate catalytic water on its own or with K151, S175, and N177. These roles are consistent with the previous results. Thus, MD and ab initio FMO calculations are powerful tools for the elucidation of the mechanism of enzymatic reaction at the molecular level and can be applied to other catalytically important residues. The results obtained here will play an important role in elucidating the reaction mechanism and rational design of L-DEX YL with improved enzymatic activity or Substrate specificity. (C) 2009 Wiley Periodicals, Inc. J Comput Chem 30: 2625-2634, 2009JOHN WILEY & SONS INC, 2009年12月, JOURNAL OF COMPUTATIONAL CHEMISTRY, 30(16) (16), 2625 - 2634, 英語[査読有り]研究論文（学術雑誌）
- We have developed an ab initio path integral molecular dynamics method based on the fragment molecular orbital method. This "FMO-PIMD" method can treat both nuclei and electrons quantum mechanically, and is useful to simulate large hydrogen-bonded systems with high accuracy. After a benchmark calculation for water monomer, water trimer and glycine pentamer have been studied using the FMO-PIMD method to investigate nuclear quantum effects on structure and molecular interactions. The applicability of the present approach is demonstrated through a number of test calculations.PHYSICAL SOC JAPAN, 2009年10月, JOURNAL OF THE PHYSICAL SOCIETY OF JAPAN, 78(10) (10), 英語[査読有り]研究論文（学術雑誌）
- We discuss the accuracy of fragmentation in fragment molecular orbital (FMO) calculations for the hydrated sodium ion. Two-body expansion shows a considerable error in total energy even if water molecules in the second hydration shell are included in the same fragment as the sodium ion. Inclusion of the three-body term significantly improves both the total energy and the charge distributions. We also illustrate the dependence of the net charge of sodium ion on solvent size and the interfacial property of water molecules. The present study will thus provide fundamental information about hydrated ion to facilitate further theoretical and experimental studies. (C) 2009 Elsevier B. V. All rights reserved.ELSEVIER SCIENCE BV, 2009年08月, CHEMICAL PHYSICS LETTERS, 478(4-6) (4-6), 295 - 300, 英語[査読有り]研究論文（学術雑誌）
- Singlet electronic excitations of DNA duplex trimers and tetramers with regular homogeneous base-pair sequences ((dA)(n) . (dT)(n) and (dG)(n) . (dC)(n), with n = 3, 4) have been investigated in vacuo using semiempirical quantum chemistry in a Zerner's Intermediate Neglect of Differential Overlap (ZINDO) approximation. Frequencies, oscillator strengths, and single-electron assignments of many-electron transitions have been calculated as functions of all 12 possible conformational modes of DNA duplexes. Specific DNA conformational modes responsible for significant changes in the exciton parentage (onset or arrest of the charge-transfer excitons' involvement into observable electronic transition spectra) are revealed. These computational results are thoroughly discussed in connection with numerous data of the most recent relevant experiments.AMER CHEMICAL SOC, 2009年07月, JOURNAL OF PHYSICAL CHEMISTRY B, 113(30) (30), 10428 - 10435, 英語[査読有り]研究論文（学術雑誌）
- We have performed a quantum-chemical MP2/6-31G* calculation for the hemagglutinin (HA) antigen-antibody system of the H3N2 influenza virus with the fragment molecular orbital method, which provides one of the world's largest ab initio electron-correlated calculations for biomolecular systems. On the basis of the calculated interfragment interaction energies (IFIEs) representing the molecular interactions between the amino acid residues in the antigen-antibody complex, we have identified those residues in the antigenic region E of HA protein that are significantly recognized by the Fab fragment of antibody with strongly attractive interactions. Combining these IFIE results with those of hemadsorption experiments by which the mutation-prohibited sites are specified has enabled us to explain most of the historical mutation data (five of six residues), which would thus provide a promising method for predicting the HA residues that have a high probability of forthcoming mutation.AMER CHEMICAL SOC, 2009年04月, JOURNAL OF PHYSICAL CHEMISTRY B, 113(15) (15), 4991 - 4994, 英語[査読有り]研究論文（学術雑誌）
- Bioluminescence spectra of firefly Luciola cruciata were theoretically analyzed on the basis of the fragment molecular orbital (FMO) method. The CIS(D) and PR-CIS(Ds) methods were employed for the calculations of emission energies of wild-type and mutant luciferase-oxyluciferin systems, and various multilayer FMO calculations were performed changing the sizes of the luciferase protein and of the chromophore to which the excited-state calculations were applied. We have thus reproduced the experimental emission energies of wild-type and mutant luciferase systems with good accuracy, which provides useful information concerning the roles of protein environment for the color tuning of the bioluminescence spectra of firefly. (C) 2009 Elsevier B.V. All rights reserved.ELSEVIER SCIENCE BV, 2009年04月, CHEMICAL PHYSICS LETTERS, 472(1-3) (1-3), 118 - 123, 英語[査読有り]研究論文（学術雑誌）
- 一般社団法人 日本生物物理学会, 2009年, 生物物理, 49, S71 - S72, 英語
- 一般社団法人 日本生物物理学会, 2009年, 生物物理, 49, S161, 英語
- The application of quantum chemical methods to large molecules such as proteins and DNAs remains a great challenge in computational chemistry. The calculations of electronic structures for biomolecules are usually difficult due to their huge size, and some models are needed to realize quantum mechanical calculations on such systems.CRC Press: Boca Raton, FL, 2009年, The Fragment Molecular Orbital Method: Practical Applications to Large Molecular Systems, 37 - 62[査読有り]論文集(書籍)内論文
- 2009年, Annual Report of the Earth Simulator Center April, 2010[査読有り]
- In structural biology, molecular simulations have played an important role in elucidating functions of the biological system. The understanding of biological phenomena at the molecular level is expected to lead the modeling of disease, drug discovery, and various applications. A variety of life phenomena occur through the combination of site-specific molecular recognition of biomacromolecules. Computer simulations thus provide a promising approach to elucidate these molecular interactions in detail. However, most calculations carried out to date have employed classical mechanical methods based on empirical force fields. Such methods remain limited for performing an accurate analysis of intermolecular interactions such as charge redistribution and charge-transfer (CT) interactions. In contrast to the limitations of classical approaches to molecular simulation, quantum mechanical simulations have been used to successfully characterize weak intermolecular interactions and CT processes. Because several different types of interactions are involved in the interactions of biomolecules, quantum mechanical treatment is necessary to obtain an accurate and systematic understanding of these interactions. The fragment molecular orbital (FMO) method1-4 is one of the most reasonable tools with which to analyze the electronic structure of biomacromolecules.CRC Press, 2009年, The Fragment Molecular Orbital Method: Practical Applications to Large Molecular Systems, 133 - 169[査読有り]論文集(書籍)内論文
- A number of biochemical systems are photoactive in the visible region through electronic transitions. The rhodopsin protein in vertebrate eyes is a representative case of such photoabsorptions. As for emissions, the green fluorescent protein (GFP)1 and related derivatives are useful marker labels in the field of biotechnology. The central region in photoactive proteins is known as the chromophore, and it consists of the crucial pigment part and some neighboring residues that should provide the electrostatic or hydrogen-bonding interactions with the pigment. Surrounding residues also put some electrostatic potentials on the chromophore system. These environmental.CRC Press, 2009年, The Fragment Molecular Orbital Method: Practical Applications to Large Molecular Systems, 63 - 89[査読有り]論文集(書籍)内論文
- The Biophysical Society of Japan General Incorporated Association, 2009年, Seibutsu Butsuri, 49(supplement) (supplement), S161[査読有り]
- The Biophysical Society of Japan General Incorporated Association, 2009年, Seibutsu Butsuri, 49(supplement) (supplement), S15[査読有り]
- 2009年, J. Comput. Chem. Jpn., 8 (2009) pp. 41-50, 日本語計算機シミュレーションを用いたRNA結合タンパク質PumilioのRNA結合様式の研究[査読有り]研究論文（学術雑誌）
- We have improved a modified charge equilibration (MQEq) method for calculating the geometry-dependent distribution of atomic charges. In this paper, Ohno-Klopman, Ohno and DasGupta-Huzinaga equations are adopted to express the shielding effect, and the calculated atomic charges with these MQEq methods are in good agreement with those by the HF/6-31G(d,p) calculations for several organic molecules. These MQEq methods would be useful to estimate the charge distribution for large molecules. © 2009 Chem-Bio Informatics Society.Chem-Bio Informatics Society, 2009年, Chem-Bio Informatics Journal, 9(1) (1), 30 - 40, 英語[査読有り]研究論文（学術雑誌）
- We have performed a series of fragment molecular orbital (FMO) calculations for a family of red fluorescent proteins, DsRed and mFruits. The electronic transition energies were evaluated by the method of configuration interaction singles with perturbative doubles [CIS(D)] including higher-order corrections. The calculated values were in good agreement with the corresponding experimental peak values of spectra. Additionally, the chromophore environment was systematically analyzed in terms of the interaction energies between the pigment moiety and neighboring residues. It was' theoretically revealed that the electrostatic interactions play a dominant role in the DsRed chromophore, whereas the color tunings in mFruits are controlled in a more delicate fashion.AMER CHEMICAL SOC, 2009年01月, JOURNAL OF PHYSICAL CHEMISTRY B, 113(4) (4), 1153 - 1161, 英語[査読有り]研究論文（学術雑誌）
- Fragment molecular orbital (FMO) and FMO-MO (MOs of the FMO) calculations with three typical fragmentations were performed for DNA molecules with various lengths up to 40 base pairs (bps) to validate the accuracy of the total energy and the interfragment interaction energy (IFIE). The respective accuracies of the FMO energies are 5.8 × 10-5, 1.3 × 10-4, and 5.0 × 10-3 hartree/bp for large, medium, and small fragmentations with HF/STO-3G, all sufficiently satisfying chemical accuracy. Two iterative calculations of the FMO-MO methods gave sufficient accuracy as less than 6.6 × 10-5 hartree/bp even with small fragmentation. The IFIE validations showed that IFIE, even with small fragmentation, has sufficient accuracy for chemical analyses. Small fragmentation is useful for the interaction analysis, not only for the hydrogen bonding interaction of base pairs but also for the stacking interaction of bases. For analyses of DNA molecules, IFIE analysis with small fragmentation is expected to be a powerful tool. Some frontier MOs of the largest model DNA examined in this study were delocalized over multiple base pairs, which well reflected the conductivity of DNA by a coherent mechanism. Such delocalized MO cannot be obtained in terms of the usual FMO calculation. This is a typical demonstration of the advantages of the FMO-MO calculation. These fundamental data for validation of the total energy and IFIE are expected to promote FMO and FMO-MO applications to biosystems related to DNA molecules. Copyright © 2009 American Scientific Publishers.2009年01月, J. Comput. Theor. Nanosci., 6 (2009) pp. 1328-1337.(6) (6), 1328 - 1337, 英語[査読有り]研究論文（学術雑誌）
- The restrained electrostatic potential (RESP) fitting method with a harmonic restraint toward target values is applied to determination of atomic charges on polypeptides on the basis of the fragment molecular orbital method. The present RESP charges are determined to be confined around the targeted Amber 94 charges with high-fitting quality, including structural specificity; an optimal value of restraint weight makes the fitted charges reliable and stable. We employ the optimally-weighted RESP charges for an improvement of force fields in molecular dynamics simulation and show that the charges keep good reproducibility of the electrostatic properties during the simulation. © 2008 Elsevier B.V. All rights reserved.Elsevier {BV}, 2009年01月, Chemical Physics Letters, 467(4-6) (4-6), 417 - 423, 英語[査読有り]研究論文（学術雑誌）
- We have developed a method named 'fragment interaction analysis based on local MP2' (abbreviated as FILM). This method enables us to decompose the interaction energy associated with dispersion interactions into contributions of localized occupied orbitals. In this study, the basis set dependence of the results derived from FILM was examined. The results suggested that the individual ratio of pair correlation energies of selected orbital pairs to the total dispersion interaction was almost independent of the basis set size. As an illustrative example, detailed analysis was performed on the human immunodeficiency virus type 1 protease complexed with lopinavir molecule. (c) 2008 Elsevier B. V. All rights reserved.ELSEVIER SCIENCE BV, 2008年09月, CHEMICAL PHYSICS LETTERS, 463(1-3) (1-3), 189 - 194, 英語[査読有り]研究論文（学術雑誌）
- The ab initio fragment molecular orbital calculations were performed for the (x-subtype of the human retinoid X receptor (hRXR alpha) complex with its natural ligand 9-cis retinoic acid (9cRA) to quantitatively specify the key residues with important roles for the ligand inducible information transmission of RXR. In the RXR-9cRA complex, the transactivation helix 12 (H12) adopts a canonical agonist conformation, which just corresponds to the transcriptional activation function 2 activating domain core (AF2C). Through the analyses of molecular interactions by the second-order Moller-Plesset perturbation (MP2) method, it was proved that Trp305 and Leu436 of the AF2C binding pocket would be important for the stabilization of the H12 canonical agonist conformation, and, at the same time, for the recognition of the 9cRA molecule. Besides, through the analyses of orbital interactions by the local MP2 (LMP2) method, it was found that Trp305 and Leu436 would recognize the 9cRA molecule especially at its C 19 methyl group, which has been most notably targeted to modify for agonist and antagonist design. Moreover, on the basis of the relationships of molecular interactions, it was suggested that the interactions of Trp305 and Leu436 with AF2C residues would be significantly influenced by the interactions of Trp305 and Leu436 with 9cRA. Taken together, our findings quantitatively demonstrated that Trp305 and Leu436 would be the possible key residues for the information transmission in liganded RXR, accounting for their importance suggested by experiments. Altogether, these results substantiated that our approach is useful for the understanding of the detailed molecular mechanism underlying the transcriptional regulation of RXR and related nuclear receptors at the quantum mechanical level.AMER CHEMICAL SOC, 2008年09月, JOURNAL OF PHYSICAL CHEMISTRY B, 112(38) (38), 12081 - 12094, 英語[査読有り]研究論文（学術雑誌）
- AMER CHEMICAL SOC, 2008年08月, ABSTRACTS OF PAPERS OF THE AMERICAN CHEMICAL SOCIETY, 236, 英語COMP 246-Simulation study of RNA-binding protein by fragment molecular orbital (FMO) method[査読有り]
- The hemagglutinin (HA) protein of the influenza virus binds to the host cell receptor in the early stage of viral infection. A change in binding specificity from avian alpha 2-3 to human alpha 2-6 receptor is essential for optimal human-to-human transmission and pandemics. Therefore, it is important to reveal the key factors governing the binding affinity of HA-receptor complex at the molecular level for the understanding and prediction of influenza pandemics. In this work, on the basis of ab initio fragment molecular orbital (FMO) method, we have carried out the interaction energy analysis of HA-receptor complexes to quantitatively elucidate the binding specificity of HAs to avian and human receptors. To discuss the binding property of influenza HA comprehensively, a number of HAs from human H1, swine H1, avian H3 and avian H5 viruses were analyzed. We performed detailed investigations about the interaction patterns of complexes of various HAs and receptor analogues, and revealed that intra-molecular interactions between conserved residues in HA play an important role for HA-receptor binding. These results may provide a hint to understand the role of conserved acidic residues at the receptor binding site which are destabilized by the electrostatic repulsion with sialic acid. The calculated binding energies and interaction patterns between receptor and HAs are consistent with the binding specificities of each HA and thus explain the receptor binding mechanism. The calculated results in the present analysis have provided a number of viewpoints regarding the models for the HA-receptor binding specificity associated with mutated residues. Examples include the role of Glu190 and Gln226 for the binding specificity of H5 HA. Since H5 HA has not yet been adapted to human receptor and the mechanism of the specificity change is unknown, this result is helpful for the prediction of the change in receptor specificity associated with forthcoming possible pandemics. (C) 2008 Elsevier Ltd. All rights reserved.ELSEVIER SCI LTD, 2008年06月, COMPUTATIONAL BIOLOGY AND CHEMISTRY, 32(3) (3), 198 - 211, 英語[査読有り]研究論文（学術雑誌）
- The fragment molecular orbital (FMO) calculations have been successfully applied to a variety of realistic biochemical problems, by using our original ABINIT-MP program. In these applications, the inclusion of electron correlation through the second-order Moller-Plesset perturbation (MP2) was demonstrated to be essential to obtain qualitatively correct descriptions. Recently, the FMO calculations in ABINIT-MP were tuned for a massively parallel-vector processing. A series of FMO-MP2/6-31G calculations were performed on the Earth Simulator by which up to 4096 vector processors are available. The largest FMO-MP2 computation was carried out for an influenza hemagglutinin antigen-antibody system consisting of 921 residues, which was completed within one hour with 4096 processors. (c) 2008 Elsevier B. V. All rights reserved.ELSEVIER SCIENCE BV, 2008年05月, CHEMICAL PHYSICS LETTERS, 457(4-6) (4-6), 396 - 403, 英語[査読有り]研究論文（学術雑誌）
- Background: Benign familial neonatal convulsion (BFNC) is an autosomal-dominantly inherited epilepsy of neonates. The KCNQ2 and KCNQ3 genes have been cloned as the responsible genes for BFNC. Detection of mutations in these genes is helpful for confirmation of BFNC or differential diagnosis of convulsive disorders in the neonatal period. Methods: A Japanese family with BFNC was investigated. Two siblings were clinically diagnosed as having BFNC. KCNQ2 and KCNQ3 were screened for mutations using a combination of polymerase chain reaction and denaturing high-performance liquid chromatography. Nucleotide substitutions were confirmed by direct sequencing. Results: In the affected siblings a C-to-T heterozygous substitution was detected at nucleotide 683 (c.683C > T) in KCNQ2, leading to substitution of arginine with tryptophan at amino acid position 213 (p.R213W) in the S4 voltage-sensing domain of the KCNQ2 protein. The detected mutation may disrupt this highly conserved region among potassium channel proteins. The c.683C > T substitution in KCNQ2 was not present in the parents. KCNQ3 was also analyzed and a single nucleotide polymorphism, c.1241A > G (National Center for Biotechnology Information (NCBI), SNP ID: rs2303995), was detected in the index family. Conclusions: Two siblings with BFNC had a novel heterozygous missense mutation, p.R213W, in KCNQ2. This mutation may affect potassium gating, leading to neuronal excitability or convulsions in the patients. Furthermore, neither of the parents had the p.R213W mutation, indicating that it was a germ-line mutation. The possibility of recurrence of such a germ-line mutation in the next siblings should be explained during genetic counseling.BLACKWELL PUBLISHING, 2008年04月, PEDIATRICS INTERNATIONAL, 50(2) (2), 167 - 171, 英語[査読有り]研究論文（学術雑誌）
- It is a mysterious fact that protein systems often show an extremely slow dynamics of their molecular motions with time scales much longer than nanosecond order, although their characteristic frequencies obtained by the normal mode analysis fall in much shorter temporal regions. This Letter provides a heuristic account for why and how such extremely slow modes of protein motions naturally emerge from fast molecular modes on the basis of an idea of entropy invariance in the principal component analysis. (C) 2007 Elsevier B.V. All rights reserved.ELSEVIER SCIENCE BV, 2008年02月, PHYSICS LETTERS A, 372(8) (8), 1280 - 1282, 英語[査読有り]研究論文（学術雑誌）
- 日本生物物理学会, 2008年, 生物物理, 48, S91, 英語
- 2008年, J. Comput. Aided Chem., 9 (2008) pp. 47-54., 日本語フラグメント分子軌道法によるホタルルシフェラーゼの発光特性に関する理論的研究[査読有り]研究論文（学術雑誌）
- Huntington's disease patients commonly have glutamine (Q) repeats longer than 37 residues in the Huntingtin protein. This unusual protein will misfold and aggregate to form insoluble amyloid-like fibrils. Although the determination of polyQ structure is very important for elucidation of the aggregation mechanism, this has not yet been accomplished due to the experimental difficulties. In this study, we performed in silico mutation analysis to examine the stability of polyQ peptide on the basis of the β-helix structure which is known as a possible model. From the results of molecular dynamics simulations for 10ns, some mutant models were found to be unstable, and their stabilities were largely dependent on the position of replaced residues. Besides, to examine the relationship between the aggregation mechanism of polyQ and the stability of the corresponding monomer, we constructed trimer models. Through the trimer studies, we confirmed that the stability of the monomer contributes significantly to that of the oligomer, and found that some mutant polyQs have the ability to inhibit polyQ aggregation. Furthermore, we estimated the free energies in solution and the conformational entropic contributions with normal mode analysis. The entropic contributions were not exhibiting remarkable differences between the models under study compared to the differences in the free energies in solution. Supposing that the stability of monomer is associated with aggregation process, the β-helix structure has been found to be somewhat inconsistent with the experimental results in this study. Our results thus indicate the necessity for the revalidation of the β-helix model. © 2009 International Association of Scientists in the Interdisciplinary Areas and Springer-Verlag GmbH.2008年, Interdiscip. Sci. Comput. Life Sci., 1 (2009) pp. 21-29(1) (1), 21 - 29, 英語[査読有り]研究論文（学術雑誌）
- The cyclic AMP receptor protein (CRP) of Escherichia coli binds preferentially to DNA sequences possessing a T:A base pair at position 6 (at which the DNA becomes kinked), but with which it does not form any direct interactions. It has been proposed that indirect readout is involved in CRP-DNA binding, in which specificity for this base pair is primarily related to sequence effects on the energetic susceptibility of the DNA to kink formation. In the current study, the possibility of contributions to indirect readout by water-mediated hydrogen bonding of CRP with the T:A base pair was investigated. A 1.0 ns molecular dynamics simulation of the CRP-cAMP-DNA complex in explicit solvent was performed, and assessed for water-mediated CRP-DNA hydrogen bonds; results were compared to several X-ray crystal structures of comparable complexes. While several water-mediated CRP-DNA hydrogen bonds were identified, none of these involved the T:A base pair at position 6. Therefore, the sequence specificity for this base pair is not likely enhanced by water-mediated hydrogen bonding with the CRP. © 2008 Elsevier Ltd. All rights reserved.2008年01月, Comput. Biol. Chem., 32 (2008) pp. 149-158(3) (3), 149 - 158, 英語[査読有り]研究論文（学術雑誌）
- We have developed a fragment interaction analysis based on local MP2 (FILM) in the context of the fragment molecular orbital (FMO) scheme. The primary purpose of this work is to provide a tool for analyzing inter-fragment interaction associated with dispersion interactions in a large molecule such as protein and DNA. Our implementation of local MP2 (LMP2) is based on the algorithm developed by Pulay and Werner. A potential of FILM was demonstrated using the human immunodeficiency virus type 1 protease (HIV-1 PR) complexed with lopinavir (LPV). The total energy, binding affinity, and inter-fragment interaction energy (IFIE) by the FMO method using LMP2 were compared with those obtained by canonical MP2 and the site-specific information in dispersion interaction was obtained. It turned out that the FILM is a useful tool for analyzing the dispersion interaction between an amino acid residue and a specific site of a ligand.SPRINGER, 2007年12月, THEORETICAL CHEMISTRY ACCOUNTS, 118(5-6) (5-6), 937 - 945, 英語[査読有り]研究論文（学術雑誌）
- JOHN WILEY & SONS INC, 2007年10月, JOURNAL OF COMPUTATIONAL CHEMISTRY, 28(13) (13), 2237 - 2239, 英語[査読有り]
- A visualization method for inter-fragment interaction energies (IFIEs) of biopolymers is presented on the basis of the fragment molecular orbital (FMO) method. The IFIEs appropriately illustrate the information about the interaction energies between the fragments consisting of amino acids, nucleotides and other molecules. The IFTEs are usually analyzed in a matrix form called an IFTE matrix. Analyzing the IFIE matrix, we detect important fragments for the function of biomolecular systems and quantify the strength of interaction energies based on quantum chemistry, including the effects of charge transfer, electronic polarization and dispersion force. In this study, by analyzing a protein-DNA complex, we report a visual representation of the IFTE matrix, a so-called IFTE map. We comprehensively examine what information the THE map contains concerning structures and stabilities of the protein-DNA complex. (c) 2007 Elsevier B.V. All rights reserved.ELSEVIER SCIENCE BV, 2007年10月, BIOPHYSICAL CHEMISTRY, 130(1-2) (1-2), 1 - 9, 英語[査読有り]研究論文（学術雑誌）
- Molecular orbital calculations of the complex between DNA-ERE (estrogen response element) and ER (estrogen receptor)-DBD (DNA-binding domain) were performed using the fragment molecular orbital (FMO) method, which enables large-scale MO (molecular orbital) calculations by reducing the computational cost and by significantly increasing efficiency for parallel computation. Such a large system, which contains 3354 atoms, is impractical via conventional MO methods due to the immense computational cost. Details of the interaction between DNA-ERE and ER-DBD were revealed in this study as follows by using the FMO calculations to analyze the interfragment interaction energies (IFIEs) and the electrostatic potentials (ESPs). An area with a high positive ESP is identified on the DNA-binding side of ER-DBD and is the main driving force behind access to the DNA. The position of the ER-DBD monomer can be fixed on a phosphate group of DNA-ERE by the strong electrostatic interactions, whereas the rotation cannot be fixed. In contrast, both the position and rotation of the ER-DBD dimer can be fixed and can therefore form the stable (ER-DBD)(2)center dot center dot center dot DNA-ERE complex. Dimerization of the ER-DBD monomers, each of which have a charge of +5 , is mainly due to large attractive interaction energies of the second Zn fragments. The base pairs in the consensus sequence of DNA-ERE interact only with the recognition helix located in the major groove due to the large shielding effect of the phosphate groups of DNA. The recognition helix has weaker interactions with the base pairs than the electrostatic interactions with the phosphate groups. Thus, the DNA-binding machinery of the ER-DBD dimer, which can secure the recognition helix in the major groove of DNA, is crucial for interactions between the recognition helix and base pairs.AMER CHEMICAL SOC, 2007年08月, JOURNAL OF PHYSICAL CHEMISTRY B, 111(32) (32), 9621 - 9627, 英語[査読有り]研究論文（学術雑誌）
- The total energy of a small polypeptide system is calculated by combining the quantum Monte Carlo (QMC) and fragment molecular orbital (FMO) methods. Electronic correlation is taken into account using Slater-Jastrow wave functions and the variational quantum Monte Carlo (VMC) method. We calculate the energy of the whole system directly and by using the FMO method, finding that the combined QMC-FMO approach works very well.PHYSICAL SOC JAPAN, 2007年06月, JOURNAL OF THE PHYSICAL SOCIETY OF JAPAN, 76(6) (6), 英語[査読有り]研究論文（学術雑誌）
- BLACKWELL PUBLISHING, 2007年06月, JOURNAL OF NEUROCHEMISTRY, 101, 65 - 66, 英語Determination of the tertiary structure of exon 1 Huntingtin[査読有り]研究論文（国際会議プロシーディングス）
- On the basis of the fragment molecular orbital method we addressed molecular interactions of liganded retinoid X receptor (RXR) with steroid receptor co-activating factor-1 (SRC1) coactivator to examine the contribution of helix 12 (H12), which contains the core of the transcriptional activation function 2 activating domain, to the coactivator binding of RXR. The interaction between H12 and SRC1 was proved to be the main cause for the stabilization of the coactivator binding. In particular, highly conserved charged (Glu453) and hydrophobic (Phe450) residues in H12 were found to have stronger electrostatic and dispersion interactions with SRC1 than the other charged and hydrophobic residues in H12, respectively. In addition, the charge transfer (CT) from RXR to SRC1 was found to occur mainly by the changes in charges of H12 residues. Large positive and negative charge changes were observed especially for Glu453 and for Lys631 and Ile632 in SRC1, respectively, indicating that Glu453 is an electron donor for Lys631 and Ile632 in this CT. Taken together, our findings quantitatively demonstrated that H12 and its highly conserved residues significantly contribute to the coactivator binding not only by the Coulomb and dispersion interactions but also by the CT described with the quantum-mechanical framework.AMER CHEMICAL SOC, 2007年04月, JOURNAL OF PHYSICAL CHEMISTRY B, 111(13) (13), 3525 - 3533, 英語[査読有り]研究論文（学術雑誌）
- 2007年, Journal of Computational Chemistry, 28(13) (13), 2237 - 2239[査読有り]研究論文（学術雑誌）
- The Biophysical Society of Japan General Incorporated Association, 2007年, Seibutsu Butsuri, 47(supplement) (supplement), S127, 英語[査読有り]
- 2007年, J. Comput. Chem. Jpn., 6, No. 3 (2007) pp. 173-184., 英語フラグメント分子軌道法に基づいた生体巨大分子の電子状態計算の現状と今後の展望研究論文（学術雑誌）
- 2007年, 戦略的創造研究推進事業（JST-CREST）「シミュレーション技術の革新と実用化基盤の構築」第2回シンポジウム講演要旨集, pp. 121-127., 日本語フラグメント分子軌道法による生体分子計算システムの開発研究論文（国際会議プロシーディングス）
- 2007年, J. Comput. Chem. Jpn. 6,, 6, No. 3 (2007) pp. 185-198., 英語フラグメント分子軌道法による生体高分子の応用計算[査読有り]研究論文（学術雑誌）
- エストロゲン受容体とエストラジオールとの結合に関する分子メカニズムを解明することを目的とし、エストロゲン受容体にコンピュータ上でアミノ酸変異を導入して、エストラジオールとの結合能をフラグメント分子軌道法を用いて評価した。アミノ酸変異の導入方法の妥当性を検討するために、実験で用いられたのと同じアミノ酸変異を導入して、結合エネルギーを評価し、実験データと比較した。その結果、6種類のアミノ酸変異のうち、3つは定性的に一致し、残り3つは不一致となった。それらの結果の原因を検討した。Society of Computer Chemistry, Japan, 2007年, J. Comput. Chem. Jpn., 6 (2007) pp. 33-46(1) (1), 33 - 46, 日本語[査読有り]研究論文（学術雑誌）
- In spite of the numerous experimental and theoretical studies on green fluorescent protein and its modifications, there is still no definitive answer to the central question: why such systems exhibit enhanced fluorescence. Based upon detailed quantum-chemical estimations, we advocate the following hypothesis. In the green fluorescent protein ground electronic state, the protein surrounding strains the chromophore with respect to its native intramolecular conformational preference in vacuo or in solution. Absorbing a photon of the proper wavelength not only causes a joint proton-electron transfer in and around the chromophore, but also increases the intrinsic strain of the latter. Since conformational relaxation of such a structure will not require any additional energy input, the energy gained by the chromophore cannot be dissipated into the chromophore's internal non-radiative degrees of freedom, and thus it returns as a fluorescence emission. © 2007 World Scientific Publishing Company.2007年, Biophys. Rev. Lett., 2, Nos. 3&4 (2007) pp. 221-227(3-4) (3-4), 221 - 227, 英語[査読有り]研究論文（学術雑誌）
- It is known that Huntington's disease patients commonly have glutamine (Q) repeat sequences longer than a critical length in the coding area of Huntingtin protein in their genes. As the polyglutamine (polyQ) region becomes longer than the critical length, the disease occurs and Huntingtin protein aggregates, both in vitro and in vivo, as suggested by experimental and clinical data. The determination of polyglutamine structure is thus very important for elucidation of the aggregation and disease mechanisms. Here, we perform molecular dynamics calculations on the stability of the structure based on the β-helix structure suggested by Perutz et al. (2002) [Perutz, M.F., Finch, J.T., Berriman, J., Lesk, A., 2002. Amyloid fibers are water-filled nanotubes. Proc. Natl. Acad. Sci. USA 99, 5591]. We ensure that perfect hydrogen bonds are present between main chains of the β-helix based on the previous studies, and perform simulations of stretches with 20, 25, 30, 37 and 40 glutamine residues (20Q, 25Q, 30Q, 37Q and 40Q) for the Perutz models with 18.5 and 20 residues per turn (one coil). Our results indicate that the structure becomes more stable with the increase of repeated number of Q, and there is a critical Q number of around 30, above which the structure of the Perutz model is kept stable. In contrast to previous studies, we started molecular dynamics simulations from conformations in which the hydrogen bonds are firmly formed between stacked main chains. This has rendered the initial β-helix structures of polyQ much more stable for longer time, as compared to those proposed previously. Model calculations for the initial structures of polyQ dimer and tetramer have also been carried out to study a possible mechanism for aggregation. © 2007 Elsevier Ltd. All rights reserved.2007年, Comput. Biol. Chem., 32 (2008) pp. 102-110(2) (2), 102 - 110, 英語[査読有り]研究論文（学術雑誌）
- We have performed the calculations of configuration interaction singles with perturbative doubles correction (CIS(D)) in conjunction with the multilayer fragment molecular orbital (MLFMO) scheme for a red fluorescent protein isolated from Discosoma coral (known as DsRed). The pigment geometry of DsRed was first examined by employing several model molecules whose spectra in gas-phase were actually observed, and an adequacy was confirmed. The excitation energy was then calculated to be 2.28 eV at the MLFMO-CIS(D)/6-31G* level. The emission energy was also estimated to be 2.21 eV similarly. These theoretical values were in good agreement with the corresponding experimental values of 2.22 eV and 2.13 eV. (c) 2006 Elsevier B.V. All rights reserved.ELSEVIER SCIENCE BV, 2007年01月, CHEMICAL PHYSICS LETTERS, 433(4-6) (4-6), 360 - 367, 英語[査読有り]研究論文（学術雑誌）
- Starting with nine plaques of influenza A/Kamata/14/91(H3N2) virus, we selected mutants in the presence of monoclonal antibody 203 (mAb203). In total, amino acid substitutions were found at nine positions (77, 80, 131, 135, 141, 142, 143, 144 and 146), which localized in the antigenic site A of the hemagglutinin (HA). The escape mutants differed in the extent to which they had lost binding to mAb203. HA protein with substitutions of some amino acid residues created by site-directed mutagenesis in the escape mutants retained the ability to bind to mAb203. Changes in the amino acid character affecting charge or hydrophobicity accounted for the binding capacity to the antibody of the HA with most of the substitutions in the escape mutants and binding-positive mutants. However, the effect of some amino acid substitutions remained unexplained. A three-dimensional model of the 1991 HA was constructed and used to analyze substituted amino acids in these mutants for the accessible surface hydrophobic and hydrophilic characters. One amino acid substitution in an escape mutant and another amino acid substitution in a binding-positive mutant seemed to be explained by the changes noted on this model.BLACKWELL PUBLISHING, 2007年, MICROBIOLOGY AND IMMUNOLOGY, 51(12) (12), 1179 - 1187, 英語[査読有り]研究論文（学術雑誌）
- The electrostatic potential fitting methods for the determination of atomic charges are applied to polypeptides on the basis of the fragment molecular orbital (FMO) method. We show that the charges determined in the pair-approximation stage agree with those determined from the conventional molecular orbital method within an error of 1%. Analyzing the dependency of charges on the structural variation of glycine trimer and the reproducibility of electrostatic potential on the surface of the ligand-binding pocket of estrogen receptor, we also show the applicability of the FMO method for atomic charge determination using the electrostatic potential fitting. © 2007 Elsevier B.V. All rights reserved.Elsevier {BV}, 2007年, Chemical Physics Letters, 449(4-6) (4-6), 329 - 335, 英語[査読有り]研究論文（学術雑誌）
- Ribulose bisphosphate carboxylase/oxygenase (Rubisco) from one of the thermophilic red algae Galdieria partita with a high specificity factor shows a characteristic difference from higher plant Rubisco in structural change. We investigate such a difference by evaluating the inter-fragment interaction energy (IFIE) value with fragment molecular orbital (FMO) method in comparison to experimental structural studies. We found some important residues which determine the loop6 stability or which make difference in the structure between higher plant and G. partita Rubiscos. We found that amino acid change of LYS18 to ILE18 is important for the difference in location at which anion binding site is occupied, P1α or P1β, when inorganic anions are bound to the enzyme. Occupation of P2 anion binding site makes the stabilizing interaction between LYS128 and the loop6 stronger. Amino acid change of HIS386 to GLN386 contributed to the difference in the loop6 stability, while amino acid change of MET472 to THR472 did not contribute to it. It is confirmed that the patterns of interactions among THR65, THR67, and THR462 are consistent with previous experimental discussions. However, we found a case that THR65 was not stabilized with anion at P1α binding site in a closed-state structure of G. partita Rubisco. © 2007 Elsevier Inc. All rights reserved.2007年, Biochem. Biophys. Res. Commun., 361 (2007) pp. 367-372(2) (2), 367 - 372, 英語[査読有り]研究論文（学術雑誌）
- The ab initio fragment molecular orbital (FMO) calculations were performed for retinoid X receptor (RXR) complexes with its ligand 9-cis retinoic acid (9cRA) and steroid receptor coactivator-1 (SRC1) to examine the influence of mutations in transcriptional activation function 2 activating domain core (AF2C) of RXR on molecular interactions between 9cRA liganded RXR and SRC1 coactivator. The RXR-SRC1 interactions in three types of RXR-9cRA-SRC1 complexes, namely, a wild type (WT), a mutant whose Glu453 of AF2C was substituted by Lys (E453K), and another mutant whose Glu456 of AF2C was substituted by Lys (E456K), were compared. Through the comparison of WT, E453K, and E456K, possible causes for a marked decrease in the transcriptional activity of RXR by the mutation of Glu453, which is known as a highly conserved charged residue of AF2C, were discussed. It was quantitatively demonstrated that the strength of the RXR-SRC1 interaction correlates with the degree of the transcriptional activation (WT > E456K > E453K). In E453K, the RXR-SRC1 interaction was substantially reduced by the AF2C-SRC1 repulsive interaction, and the charge transfer (CT) from RXR to SRC1 was also inhibited by the decreased electron donation from AF2C to SRC1. Our findings suggest that the inhibitions of the local RXR-SRC1 interaction via AF2C and of the local CT from RXR to SRC1 via AF2C would be the possible causes for the marked decrease in the transcriptional activity of RXR. © 2008 American Chemical Society.2007年, J. Phys. Chem. A, 112 (2008) pp. 1986-1998(10) (10), 1986 - 1998, 英語[査読有り]研究論文（学術雑誌）
- Ab Initio Biomolecular Calculations Using Quantum Monte Carlo Combined with the Fragment Molecular Orbital MethodA novel computational scheme for the electronic states of biomolecules is proposed on the basis of the quantum Monte Carlo (QMC) method combined with the fragment molecular orbital (FMO) method. The latter provides an accurate and very efficient framework for calculating the molecular orbitals of huge systems through parallel computations for divided subsystems, thus enabling the applications to realistic proteins and nucleic acids with chemical accuracies. The feasibility of the proposed method is illustrated for a small polypeptide, the glycine trimer, as a benchmark test. © 2007 American Chemical Society.2007年, “Advances in Quantum Monte Carlo”, pp. 141-146., 141 - 146, 英語研究論文（学術雑誌）
- A performance simulation model of dye-sensitized solar cells including a "bulk" electrolyte layer separated from a TiO2, layer has been presented. The calculation results with this novel model agree well with experimental results, which indicates the importance of considering the bulk electrolyte layer in theoretical models. The model allows us to specify the diffusion coefficients of ionic species in nano-pores of the TiO2 layer and in the bulk electrolyte layer separately, and the importance of ionic diffusions in each layer is discussed. We further clarify the difference between ionic liquid-type cells and acetonitrile type cells, and discuss the important issues for increasing the efficiencies in cells containing ionic liquid-based electrolytes. (c) 2006 Elsevier B.V. All rights reserved.ELSEVIER SCIENCE BV, 2006年10月, SOLAR ENERGY MATERIALS AND SOLAR CELLS, 90(16) (16), 2696 - 2709, 英語[査読有り]研究論文（学術雑誌）
- The fragment molecular orbital (FMO) scheme has been successfully used for a variety of large-scale molecules such as proteins and nucleic acids so far. We have applied the FMO calculations to the silicon-containing systems like polysilanes. The error caused by the fragmentation was examined by the Hartree-Fock method and the second-order Moller-Plesset (MP2) perturbation method for the ground state energy. The dynamic polarizability as a linear response property was also evaluated with and without the fragmentation. A series of numerical comparisons showed that the FMO scheme is applicable to silicon-based molecules with reasonable accuracy. This implied a potential availability of FMO calculations for the issues relevant to nanoscience and nanotechnology. (c) 2006 Elsevier B.V. All rights reserved.ELSEVIER SCIENCE BV, 2006年10月, CHEMICAL PHYSICS LETTERS, 430(4-6) (4-6), 361 - 366, 英語[査読有り]研究論文（学術雑誌）
- We have realized a fully quantum mechanical treatment of large scale systems containing heavy metal atom, by introducing the model core potential (MCP) technique into the fragment molecular orbital (FMO) scheme. The scalar relativistic effects are incorporated by the use of MCP. This FMO/MCP method was applied to the divalent mercury ion hydrated, with 256 water molecules at the second-order Moller-Plesset (MP2) perturbation level. The complex between cisplatin and DNA was also calculated with MP2, where about a thousand of water molecules and dozens of sodium ions were employed for the explicit treatment of hydration. (c) 2006 Elsevier B.V. All rights reserved.ELSEVIER SCIENCE BV, 2006年08月, CHEMICAL PHYSICS LETTERS, 427(1-3) (1-3), 159 - 165, 英語[査読有り]研究論文（学術雑誌）
- We investigate the influence of molecular motion on DNA conductance and charge transfer in the ballistic transport regime. We evaluate the conductance/charge transfer properties for ensembles of conformations representative of the molecular fluctuations in an explicit all-atom representation. We generate such ensembles by classical molecular dynamics (MD) and investigate the influence of conformational change on the charge transfer properties of the system. Using this approach, we can qualitatively explain the influence of base-pair mismatches on DNA electrical properties.TAYLOR & FRANCIS LTD, 2006年08月, MOLECULAR SIMULATION, 32(9) (9), 759 - 764, 英語[査読有り]研究論文（学術雑誌）
- 「市民の科学に対する大学の支援に関する実践的研究」(略称「市民の科学」)プロジェクトの一環として、「サイエンスカフェ神戸」を創始した。このプロジェクトは、科学技術的課題に対する市民のエンパワーメント・システム構築をめざすもので、サイエンスカフェ開催はその第一段階として位置づけられる。2005年10月から2006年6月までに16回を開催し、科学コミュニケーションの新しいスタイルとして高い可能性を確認した。サイエンスカフェは現在各地に広がりつつあるが、「サイエンスカフェ神戸」では、文化としての科学を地域社会に根づかせることを大きな目的とし、運営に市民が主体的に参加し、様々な場で頻繁に開催されるようなあり方をゴールとして設定している点で特徴をもっている。「市民の科学」プロジェクトでは、次のステップとして、サイエンスカフェを通じて形成された緩やかなネットワークも利用しつつ、大学の支援のもとでの、環境などに関わる課題の市民による調査・研究の展開可能性を探ってゆく。一般社団法人 日本科学教育学会, 2006年08月, 日本科学教育学会研究会研究報告, Vol. 21, No. 1, pp. 37-42(1) (1), 37 - 42, 日本語研究論文（学術雑誌）
- The ab initio fragment molecular orbital (FMO) calculations were performed for the cAMP receptor protein (CRP) complexed with a cAMP and DNA duplex to elucidate their sequence-specific binding and the stability of the DNA duplex, as determined by analysis of their inter- and intramolecular interactions. Calculations were performed with the AMBER94 force field and at the HF and MP2 levels with several basis sets. The interfragment interaction energies (IFIEs) were analyzed for interactions of CRP-cAMP with each base pair, DNA duplex with each amino acid residue, and each base pair with each residue. In addition, base-base interactions were analyzed including hydrogen bonding and stacking of DNA. In the interaction between DNA and CRP-cAMP, there was a significant charge transfer (CT) from the DNA to CRP. and this CT interaction played an important role as well as the electrostatic interactions. It is necessary to apply a quantum mechanical approach beyond the "classical" force-field approach to describe the sequence specificity. In the DNA intramolecular interaction, the dispersion interactions dominated the stabilization of the base-pair stacking interactions. Strong, attractive 1,2-stacking interactions and weak, repulsive 1,3-stacking interactions were observed. Comparison of the intramolecular interactions of free and complexed DNA revealed that the base-pairing interactions were stronger, and the stacking interactions were weaker, in the complexed structure. Therefore, the DNA duplex stability appears to change due to both the electrostatic and the CT interactions that take place under conditions of DNA-CRP binding. (c) 2006 Wiley Periodicals, Inc.WILEY-BLACKWELL, 2006年06月, JOURNAL OF COMPUTATIONAL CHEMISTRY, 27(8) (8), 948 - 960, 英語[査読有り]研究論文（学術雑誌）
- Factors determining the photovoltaic performance of cells containing ionic liquid based electrolytes are compared with those of cells containing acetonitrile based electrolytes. The difference is made clear by using a Simulation model having a bulk electrolyte layer. In the former case, ionic diffusions in bulk electrolytes determine photocurrents. In contrast, in the latter case, electron diffusion in nano-porous TiO2 layers determines the photovoltaic performances. The increase in photocurrents for the former cells would be made most effectively by increasing ionic diffusions in electrolytes.INST PURE APPLIED PHYSICS, 2006年04月, JAPANESE JOURNAL OF APPLIED PHYSICS PART 1-REGULAR PAPERS BRIEF COMMUNICATIONS & REVIEW PAPERS, 45(4A) (4A), 2780 - 2787, 英語[査読有り]研究論文（学術雑誌）
- We have developed a linear response module to evaluate the dynamic polarizability, by accepting the fragment molecular orbital (FMO) scheme proposed by Kitaura. The module is parallelized in an integral-driven fashion with atomic-orbital indices in a local version Of ABINIT-MP program. The error caused by fragmentation was checked through test calculations on the water pentamer and the glycine pentamer. The error is shown to be small even under nonzero frequency, indicating the potential applicability of the FMO-based polarizability evaluation for large molecules. (c) 2005 Elsevier B.V. All rights reserved.ELSEVIER SCIENCE BV, 2006年02月, CHEMICAL PHYSICS LETTERS, 418(4-6) (4-6), 418 - 422, 英語[査読有り]研究論文（学術雑誌）
- Gel electrolytes for quasi-solid dye-sensitized solar cells (QDSC) are reported. The gel electrolyte consists of ionic liquids and nanoparticles modified with imidazolium cations. Ionic liquid-type gel electrolytes containing nanoparticles are well-known. The difference between previous reports and this report is that imidazolium cations are bonded to nanoparticles through Ti-O-CO bonds and long alkyl chains. The role of the long alkyl chains turns out to be critical for high performances. When unmodified nanoparticles are added into ionic liquids until the gel becomes of clay-like hardness, the photovoltaic performances decrease with an increase in the bare nanoparticle content. However, the decreases in photovoltaic performances are retarded when surface-modified nanoparticles are added. Photovoltaic performances increase with an increase in the chain lengths connecting nanoparticles and imidazolium cations. When the chain length becomes 12 and counter anion is I-, solidification occurs without losing the performance of DSCs having the parent liquid electrolytes. The photocurrents of QDSCs do not decrease even when the ratio (nanoparticles/ionic liquids) increases to 0.9 and the feature looks like hard clay. Ionic paths between nanoparticles are discussed. (c) 2006 The Electrochemical Society.ELECTROCHEMICAL SOC INC, 2006年, JOURNAL OF THE ELECTROCHEMICAL SOCIETY, 153(3) (3), A626 - A630, 英語[査読有り]研究論文（学術雑誌）
- Solidification of dye sensitized solar cells (DSC) is carried out in two methods. One is a method to use soft gels containing less than 10 % of chemically crosslinkable gelators. The soft gel is characterized with the latent property. The other is a method to use hard gels containing 100 % of surface modified TiO2 nanoparticles as gelators. In both cases, electrolytes are solidified without decreasing photovoltaic performances even after solidification by fabricating ion-paths in the solidified electrolytes associated with self-organization of long alkyl groups. copyright The Electrochemical Society.2006年, ECS Transactions, 1(32) (32), 23 - 30研究論文（国際会議プロシーディングス）
- The Drug discovery on grid project is aimed at developing a platform for drug discovery, on which various calculations and simulations are effectively executed at high speed. For storing and retrieving calculated and experimental information, the drug, markup language database is an extension of the chemical markup language database with appropriate figures as indicated. Before the docking of a drug molecule with its target receptor, an extensive conformational search of the drug molecule is carried out for defining the bioactive conformation. The conformational search is carried out for a series of molecules selected from the database, where information on the two-dimensional structure of molecules is stored. Then all the low energy conformers obtained in the previous procedure are subjected to the docking analysis. There are three methods for evaluating the docking energy; the fragment molecular orbital , the replica exchange molecular dynamics , and the empirical scoring function based on the energy obtained from the force field calculation and indexes of three-dimensional complementary structure between a drug and its target protein. The chapter studies CONFLEX that has been recognized as one of the most efficient conformational space search programs. The types of CONFLEX and its application to peptide folding are studied along with flowcharts. Hence, computational techniques, such as parallel computing and grid will enable to probe the drug-receptor mediated phenomenon directly. © 2006 Elsevier B.V. All rights reserved.2006年, Modern Methods for Theoretical Physical Chemistry of Biopolymers, 227 - 248論文集(書籍)内論文
- This chapter presents and discusses DNA conductance based upon the Kubo formula. Using this approach, the effects of base pair mismatches, different conformational changes, and base pair sequence on DNA electrical properties can be investigated. This makes possible the very fast estimation of conductance spectra for oligonucleotides with hundreds of base pairs and can be used to treat the arbitrary chemical modifications of DNA. This novel formulation estimates the ballistic transport through finite atomically resolved DNA fragments within the framework of the Kubo formalism, recast in its Green function representation. Such an approach permits the extremely fast evaluation of DNA conductance, with the computation time scaling linearly versus DNA duplex length. The chapter presents the method of calculation step by step. Results suggest that isolated DNA itself is at best a kind of poor semiconductor. Chemically, one could still select some special charge donor and/or acceptor moieties, which being properly attached to a DNA duplex, would use its specific channels to facilitate the charge transfer between them. The results clearly demonstrate the presence of such channels in different DNA duplexes. External effects, as well as internal structural alterations, should play a significant role in tuning the effectiveness of the DNA charge transfer channels. The application of the approach presented in the chapter would result in a noticeably faster estimation of the DNA conductance spectrum than the already available methods of the same class. This should enable to efficiently estimate conductance spectra for the DNA duplexes of arbitrary length as well as their complexes with diverse organic/inorganic molecular or polymeric agents. © 2006 Elsevier B.V. All rights reserved.Elsevier, 2006年, Modern Methods for Theoretical Physical Chemistry of Biopolymers, 535 - 546, 英語[査読有り]論文集(書籍)内論文
- The fragment molecular orbit (FMO) method relies on the division of a large molecular system into a collection of small fragments and on the molecular orbital (MO) calculations for the fragments (monomers) and their pairs (dimers) performed to obtain the total energy and other molecular properties. The ABINIT-MP software is a program code freely available on the web to perform the FMO calculations for biopolymers, such as proteins and nucleic acids. The chapter focuses on the recent developments of the ABINIT-MP software and some examples of its application to the MO calculations for proteins. The FMO calculations in the Hartree-Fock , the second-order Møller-Plesset perturbation , and the configuration interaction with singles approximations are now available in an efficiently parallelized fashion. The application examples are demonstrated for the virtual screening of ligand molecules for estrogen receptor and the evaluation of the excitation energy of photoactive yellow protein. ABINIT-MP software is developed to make ab initio calculations for biomolecules more efficient. © 2006 Elsevier B.V. All rights reserved.Elsevier, 2006年, Modern Methods for Theoretical Physical Chemistry of Biopolymers, 39 - 52, 英語[査読有り]論文集(書籍)内論文
- The ab initio fragment molecular orbital calculations were performed for molecular interactions of the whole estrogen receptor (ER) ligand-binding domain with a natural ligand, 17β-estradiol (EST). The interaction energies of the ligand at the residue level were calculated using HF and MP2 methods with several basis sets. The charge-transfer (CT) interactions were also analyzed based on configuration analysis for fragment interaction. Strong electrostatic interactions were observed between the EST and surrounding charged/polarized residues, Glu353, Arg394, His524, and Thr347. Weak electrostatic and significant van der Waals dispersion interactions were observed between the EST and the many surrounding hydrophobic residues. Together with the experimental interpretations, both interactions equally contributed to the total binding energies, and it was found that the inclusion of electron correlation was essential to obtain an appropriate picture of the interaction. The strongest interaction energy was observed between Glu353 and the EST, and the CT interactions from the lone-pair orbital of the carbonyl oxygen of Glu353 to the σ*OH orbital of the hydroxyl group of EST were found to be important. The CT interactions from the lone-pair orbital of EST to the σ*NH of Arg394 and from the lone-pair orbital of EST to the σ*NH of His524 were also observed. These CT interactions occurred through the hydrogen-bond networks between the ER and EST. Therefore, electron donations from the ER to the EST and electron back-donations from EST to the ER were characteristic of ER-ligand binding. Our approach provides a powerful tool to understanding detailed molecular interactions at the quantum mechanical level. © 2006 American Chemical Society.2006年, J. Phys. Chem. B, 110 (2006) 16102-16110(47) (47), 24276 - 16110, 英語[査読有り]研究論文（学術雑誌）
- 2006年, Chem. Phys. Lett., 433 (2007) 360, 英語Fragment molecular orbital calculations on red fluorescent protein (DsRed)[査読有り]研究論文（学術雑誌）
- A novel approach to estimate DNA conductance based upon Kubo formula is presented and discussed. Using this approach, the effects of base pair mismatches, different conformational changes and base pair sequence on DNA electrical properties were investigated. The results were compared with the data from other methods. The new approach makes possible very fast estimation of conductance spectra for oligonucleotides with hundreds of base pairs and can easily be extended to treat arbitrary chemical modifications of DNA.SPRINGER, 2005年12月, EUROPEAN PHYSICAL JOURNAL E, 18(4) (4), 437 - 445, 英語[査読有り]研究論文（学術雑誌）
- 科学・技術が高度に発達した社会において、(a)環境問題等の解決手段として、(b)知的探求活動として、市民の科学・技術にかかわる問題の調査・研究能力を高めてゆくこと(エンパワーメント)が大きな意味を持つ。我々は、神戸大学大学院総合人間科学研究科に設置された発達支援インスティテュート/ヒューマン・コミュニティ創成研究センターの研究プロジェクトとして「市民科学に対する大学の支援に関する実践的研究」の取り組みを始めた。本プロジェクトは、神戸を主なフィールドとして、幅広い年齢や素養をもつ市民が、大学の支援のもとに、科学リテラシーを高めるとともに、自らが調査・研究能力を獲得してゆく持続可能なシステムとそれを担う組織、人材のあり方を実践的に探り、日本の社会に適したモデルを構築することを目指す。一般社団法人 日本科学教育学会, 2005年09月, 科教研報, 20・2, 47-51(2) (2), 47 - 51, 日本語研究論文（学術雑誌）
- We propose a modified version of configuration analysis (CA) for the fragment interaction in conjunction with Kitaura's fragment molecular orbital (FMO) scheme. The proposal is abbreviated as CAFI. The MO sets of fragments are merged and then orthonormalized by the use of a weighted Lowdin orthonormalization. The energy calculation is performed with the concurrent electron relaxation functional (CERF). The relaxation energy is obtained in an orbital-wise fashion and is distinguished as the charge-transfer and the polarization. The utility of CAM is demonstrated through test calculations on hydrogen-bonding systems. (c) 2005 Elsevier B.V. All rights reserved.ELSEVIER SCIENCE BV, 2005年07月, CHEMICAL PHYSICS LETTERS, 410(4-6) (4-6), 247 - 253, 英語[査読有り]研究論文（学術雑誌）
- To elucidate the effect of DNA base-mismatch on the charge transfer through DNA, we investigated stable structures and electronic properties of double-strand DNA and its base-mismatched ones by semiempirical molecular orbital calculations. Based on these electronic properties, we analyzed the charge transfer by using an I-V simulator based on the Landauer formula. The results indicate that the base-pair mismatches (A-C and G-A) affect the electronic properties around the Fermi level, so that the hole conductivity through double strand DNA is significantly reduced by these mismatches. (c) 2005 Elsevier B.V. All rights reserved.ELSEVIER SCIENCE BV, 2005年06月, CHEMICAL PHYSICS LETTERS, 408(4-6) (4-6), 381 - 388, 英語[査読有り]研究論文（学術雑誌）
- The specific interaction between catabolite activator protein (CAP) and cyclic adenosine monophosphate (cAMP) was investigated using the fragment molecular orbital method based on density functional theory (FMO-DFT). One of the efficient tools of FMO-DFT is the analysis of effective pair interactions, which are the pairwise fragment interactions under the influence of electrostatic potentials from surrounding fragments. We investigated the specific interaction between CAP/mutated-CAP and cAMP/cGMP to elucidate the effect of amino-acid mutations in CAP on the CAP-cAMP as well as CAP-cGMP interactions.WORLD SCIENTIFIC PUBL CO PTE LTD, 2005年03月, JOURNAL OF THEORETICAL & COMPUTATIONAL CHEMISTRY, 4(1) (1), 183 - 195, 英語[査読有り]研究論文（学術雑誌）
- Functionally relevant motion of proteins has been associated with a number of atoms moving in a concerted fashion alone, so-called "collective coordinates." We present an approach to extract collective coordinates from conformations obtained from molecular dynamics simulations. The power of this technique for differentiating local structural fuctuations between classes of conformers obtained by clustering is illustrated by analyzing nanosecond-long trajectories for the response regulator protein Spo0F of Bacillus subtilis, generated both in vacuo and using an implicit-solvent representation. Conformational clustering is performed using automated histogram filtering of the inter-C-alpha distances. Orthogonal (varimax) rotation of the vectors obtained by principal component analysis of these interresidue distances for the members of individual clusters is key to the interpretation of collective coordinates dominating each conformational class. The rotated loadings plots isolate significant variation in interresidue distances, and these are associated with entire mobile secondary structure elements. From this we infer concerted motions of these structural elements. For the Spo0F simulations employing an implicit-solvent representation, collective coordinates obtained in this fashion are consistent with the location of the protein's known active sites and experimentally determined mobile regions. (C) 2005 American Institute of Physics.AMER INST PHYSICS, 2005年01月, JOURNAL OF CHEMICAL PHYSICS, 122(3) (3), 英語[査読有り]研究論文（学術雑誌）
- 2005年, Proceedings of 7th Congress of the World Association of Theoretically Oriented Chemists (WATOC) (Cape Town, South Africa), ES-P23,Fragment Molecular Orbital Study on Molecular Interaction between Estrogen Receptor and Their Ligands研究論文（国際会議プロシーディングス）
- The atomic parameters in consistent charge equilibration (CQEq) method were optimized to reproduce electrostatic potentials around the 20 standard amino acid molecules. The introduction of two atom types for hydrogen improves significantly partial charges on hydrogen atoms. Geometry optimizations of a crambin protein were performed using force fields combined with the CQEq. The CQEq charges were found to be more comparable to the Mulliken charges obtained by the ab initio molecular orbital calculation than the fixed charges used in the AMBER force field. Furthermore, the CQEq charges give more realistic charge redistribution between amino acids in the crambin. (C) 2004 Elsevier B.V. All rights reserved.ELSEVIER SCIENCE BV, 2004年10月, CHEMICAL PHYSICS LETTERS, 397(4-6) (4-6), 382 - 387, 英語[査読有り]研究論文（学術雑誌）
- A recent experimental report on the suppression of the oxidative decomposition of guanines in deoxyribonucleic acid (DNA) double helices due to the attachment of a phenyl group to a guanine [Nakatani, K.; Dohno, C.; Saito, I. J. Am. Chem. Soc. 2002, 124, 6802] is examined by semiempirical Hartree-Fock (HF) molecular orbital (MO) calculations and ab initio HF MO calculations with the STO-3G basis set. Because of this attachment, the energy level of MO localized on the guanine shifts to lower energy in a vacuum, whereas it shifts to higher energy in water. This is mainly because the energy reduction of MO levels by the water solvent becomes smaller when the solvent molecules are excluded by the phenyl group. Consequently, a hole trap is enhanced at the phenylated guanine base in water. The observed suppression of the oxidative decomposition of guanines around the phenylated guanine is thus explained by considering the solvent effects. In addition, we have observed that energy shifts due to a benzyl group or a tert-butyl group are similar to those due to the phenyl group in our calculation.AMER CHEMICAL SOC, 2004年06月, JOURNAL OF PHYSICAL CHEMISTRY B, 108(22) (22), 7500 - 7505, 英語[査読有り]研究論文（学術雑誌）
- AMER CHEMICAL SOC, 2004年03月, ABSTRACTS OF PAPERS OF THE AMERICAN CHEMICAL SOCIETY, 227, U685 - U685, 英語Drug discovery using grid technologies and DrugML.研究論文（国際会議プロシーディングス）
- 2004年, J. Comput. Aided Chem., 5, 52p-61p１重鎖及び２重鎖DNAの電流電圧特性の理論的解析[査読有り]研究論文（学術雑誌）
- 2004年, J. Comput. Aided Chem., 5, 1p-8p密度汎関数法に基づくフラグメント分子軌道法を用いたDNA電子状態計算[査読有り]研究論文（学術雑誌）
- 2004年, J. Comput. Aided Chem., 5, 19p-25pカタボライト活性化タンパク質と環状AMP複合体の構造解析[査読有り]研究論文（学術雑誌）
- DNA and estrogen receptor interaction revealed by the fragment molecular orbital method - Implementation of SCF convergenceThe fragment molecular orbital (FMO) method was applied to evaluate the interaction between estrogen response element (ERE) in DNA and DNA binding domain (DBD) of estrogen receptor (ER). In order to calculate the whole electronic state of DNA-ERE and ER-DBD, we developed the SCC-DIIS method and the field scaling method. The SCC-DIIS method is for acceleration of the self-consistent charge (SCC) convergence, and the field scaling method changes the field effect from other fragments for stable convergence. Hybridization of these two methods made it possible to calculate the whole electronic state of DNA-ERE and ER-DBD.NANO SCIENCE & TECHNOLOGY INST, 2004年, NSTI NANOTECH 2004, VOL 1, TECHNICAL PROCEEDINGS, Vol. 1, 176p-179p, 176 - 179, 英語研究論文（国際会議プロシーディングス）
- 2004年, Proceedings of 3rd International Conference “Computational Modeling and Simulation of Materials” (Acireale, Sicily, Italy), ,Ab Initio Approach to Nanoscale Dynamics of DNA研究論文（国際会議プロシーディングス）
- 2004年, Abstr. Joint Meeting of “International Conference on Molecular Simulation (ICMS)” and “Computational Science Workshop 2004 (CSW2004)” (Tsukuba, Japan), , 12p-13pAb Initio Approach to Nanoscale Dynamics of DNA研究論文（国際会議プロシーディングス）
- 日本表面科学会, 2003年11月, 表面科学, 24, 664-670(11) (11), 664 - 670, 日本語
- AMER CHEMICAL SOC, 2003年09月, ABSTRACTS OF PAPERS OF THE AMERICAN CHEMICAL SOCIETY, 226, U302 - U302, 英語Quantum Monte Carlo descriptions of molecular interactions relevant to biopolymers.研究論文（国際会議プロシーディングス）
- A theory for charge transfer between the electrode and the donor/acceptor molecule coupled through a DNA bridge in solution is developed. We explore the crossover between the coherent tunneling and the incoherent sequential transfer regimes by varying the electrode potential and discuss the effects of single-base mismatches in DNA duplex in both regimes. In the former regime a single-base mismatch in DNA duplex causes a reduction in the charge transfer rate simply by decreasing the electron tunneling matrix element, however, in the latter regime the effects are rather complicated. (C) 2003 Elsevier Science B.V. All rights reserved.ELSEVIER SCIENCE BV, 2003年07月, JOURNAL OF MOLECULAR STRUCTURE-THEOCHEM, 630(1-3) (1-3), 283 - 290, 英語[査読有り]研究論文（学術雑誌）
- By combining the consistent charge equilibration (CQEq) method with universal force field (UFF), we developed the CQEq with UFF (CUFF) method and confirmed its efficiency for investigating the hydrogen bonding of DNA base pairs. By using the new parameters together with reduced van der Waals radii for hydrogen atoms, the CUFF method was capable of yielding hydrogen-bonding lengths and energies comparable with those by correlated ab initio MP2 calculations. (C) 2003 Elsevier Science B.V. All rights reserved.ELSEVIER SCIENCE BV, 2003年06月, CHEMICAL PHYSICS LETTERS, 374(3-4) (3-4), 271 - 278, 英語[査読有り]研究論文（学術雑誌）
- .公益社団法人 日本化学会・情報化学部会, 2003年, 日本化学会情報化学部会誌, 21(5) (5), 95 - 95, 日本語
- INT INST INFORMATICS & SYSTEMICS, 2003年, 7TH WORLD MULTICONFERENCE ON SYSTEMICS, CYBERNETICS AND INFORMATICS, VOL VIII, PROCEEDINGS, Vol. VIII, 318p, 318 - 318, 英語Theoretical modeling for electron transfer and transport in DNA研究論文（国際会議プロシーディングス）
- 2003年, Abstr. International Symposium on Fusion of Nano and Bio Technologies (FNB 2003) (Tsukuba International Congress Center, Tsukuba), , 14pElectrochemical DNA Chip: Simulations and Applications研究論文（国際会議プロシーディングス）
- 電荷平衡法(QEq)は、固定電荷を用いる標準的な分子力場とは異なり、分子の構造や環境に依存して原子上の部分電荷を決定し、静電エネルギーを求める方法である。我々は、部分電荷を決定するときと、その部分電荷を用いて構造最適化や分子動力学計算を行うときとで、矛盾無く一貫した取り扱いを行うCQEq法を提案してきた。今回、分子力場のひとつであるUniversal Force Field(UFF)とCQEqとを組み合わせたCUFF力場の精度を確認するために、一連のアミノ酸分子の構造最適化計算を行った。CUFFによって最適化した構造を、HF/6-31G**計算で最適化した構造と比較すると、一部の二面角を除いて、比較的よく一致していることがわかった。さらに、最適化した構造における各原子上のCUFF法による部分電荷と、HF/6-31G**レベルのRESP法によって求めた部分電荷との比較を行った。その結果、CUFF法では、炭素原子と結合した水素原子上の部分電荷は過大評価され、酸素原子や窒素原子と結合した水素原子上の部分電荷は過小評価される傾向があることなどが明らかになった。このことから、電荷平衡法の精度向上のためには、少なくとも２種類の水素原子を考慮する必要があり、各元素の電気陰性度や硬さなどのパラメータも改善する必要があることが示された。Chem-Bio Informatics Society, 2003年, Chem-Bio Informatics J., 3, No. 2, 78p-85p, 78 - 85, 英語[査読有り]研究論文（学術雑誌）
- 2003年, International Workshop on Radiation Risk and its Origin at Molecular and Cellular Level (Japan Atomic Energy Research Institute, Tokai, Ibaraki), , 13pAb Initio Approach to Nanoscale Dynamics of DNA, Abstr研究論文（国際会議プロシーディングス）
- The driving force dependence of photoinduced electron transfer rate constant in synthetic DNA hairpins in aqueous solutions has been analyzed by means of molecular dynamics simulations. The quantum energy gap law has thus been investigated from a fully atomistic point of view, well reproducing the experimental results with reduced ambiguities in the parameter fitting. Although the contribution from the high-frequency vibrational modes of DNA and water solvent to the reorganization energy is fairly small, their quantum effect on the electron transfer rate constant is significant, well accounting for the deviation from the Marcus parabola observed in the experiments. © 2003 The American Physical Society.2003年, Physical Review E - Statistical Physics, Plasmas, Fluids, and Related Interdisciplinary Topics, 68(3) (3), 5 - 319055, 英語[査読有り]研究論文（学術雑誌）
- The nonequilibrium dynamics of intramolecular vibrational energy relaxation in cis-azobenzene after the excitation of each normal mode has been studied through the dynamic reaction coordinate analysis based on the PM3 molecular orbital method. With a high-excitation energy injected into a specific normal mode, a cis-to-trans isomerization reaction has been induced before the intramolecular vibrational energy redistribution is completed. This is a first finding (though in silico) of a nonequilibrium isomerization reaction of azobenzene triggered by the vibrational excitation, which is different from the usual optical and thermal isomerizations. A relevant model for describing this nonequilibrium, reaction is addressed. (C) 2002 Elsevier Science B.V. All rights reserved.ELSEVIER SCIENCE BV, 2002年08月, CHEMICAL PHYSICS LETTERS, 362(5-6) (5-6), 467 - 475, 英語[査読有り]研究論文（学術雑誌）
- Dynamics of intramolecular vibrational energy relaxation in a third-generation aryl ether azodendrimer and an azobenzene after the excitation of stretching modes of aromatic rings is analyzed using the dynamic reaction coordinate method in which the electronic state is described semiempirically on the basis of the PM3 scheme. It is found that the behavior of the vibrational relaxation depends sensitively on the magnitude of the excitation energy and on the species of the excited mode so that the relaxation time ranges over several orders of magnitude from picoseconds to nano-seconds. The vibrational energy transfer begins to take place when a threshold for the excitation energy or the elapsed time is exceeded, and this behavior of relaxation is not temporally homogeneous but is triggered by the resonant energy transfer to some specific modes satisfying the frequency matching condition. With the aid of a phenomenological, nonlinear coupled oscillator model, we also discuss the relation of the present analysis to a unique cis-to-trans isomerization reaction of azodendrimers induced by weak infrared irradiation. © 2001 Elsevier Science B.V. All rights reserved.2001年10月, Chemical Physics, 272(2-3) (2-3), 171 - 184[査読有り]研究論文（学術雑誌）
- We have carried out performance simulations for the dye-sensitized solar cells which consist of a mesoporous TiO2 semiconductor film coated with photosensitizing dyes and a charge transport layer which is either a liquid electrolyte or a solid hole conductor. The calculations for the current-voltage characteristics and the energy conversion efficiency have been made, and the dependence of the efficiency on the material parameters has been discussed. In the case of liquid-state cells, the improvement in the sunlight absorption ability through the enhancement of molar extinction coefficient of the dye sensitizer or of roughness factor of the nanocrystalline TiO2 is essential for achieving very high efficiencies. The effects on the efficiency caused by other factors such as the resistance of transparent conducting oxide electrode, the cell area and the diffusion constants of redox ions are also investigated. In the case of solid-state cells, some specific factors such as the detachment of the hole transport layer from the TiO2 electrode and the decrease of the shunt resistance associated with internal leakages are suggested as possible causes of the significant suppression of the efficiency.2001年01月, Japanese Journal of Applied Physics, Part 1: Regular Papers and Short Notes and Review Papers, 40(1) (1), 97 - 107研究論文（学術雑誌）
- The structure of trans-azobenzene (TAB) has been a subject of controversy in experimental and theoretical studies. To provide the theoretical basis for stable structures and vibrational properties of TAB and cis-azobenzene (CAB), we performed ab initio molecular orbital calculations based on the second-order Møller - Plesset (MP2) method and density functional theory (DFT). Only the MP2 calculation accounting for the diffuse basis set (6-31+G*) leads to the distorted structure of TAB, which is consistent with the gas-phase electron diffraction experiment. The Hartree - Fock and DFT (PW91PW91, MPW91, BP86, and B3LYP) calculations, on the other hand, result in the almost planar structure of TAB. The frequencies of normal modes of TAB and CAB are calculated most accurately by the PW91PW91/6-31+G* method followed by the BP86/6-31G* method. These results are expected to provide useful benchmark data on the accuracy of MP2 and DFT methods for describing the structural and vibrational properties of azobenzene-like molecules, which consist of weakly interacting phenyl rings. © 2000 American Chemical Society.2000年08月, Journal of Physical Chemistry A, 104(34) (34), 8114 - 8120研究論文（学術雑誌）
- The structural optimization and normal-mode analysis are performed for the aryl ether azodendrimers on the basis of the semi-empirical molecular orbital methods. Through the geometrical characterization for the stable structures, the fractal dimension and the degree of azo core wrapping are found to provide key parameters related to the unique photoinduced isomerization. We also find that the normal-mode frequency distribution is virtually invariable irrespective of the molecular structure and generation of azodendrimers. The importance of normal-mode distribution gap in the range of 700-900 cm(-1) is suggested regarding the efficient vibrational energy transfer to the azo core region. (C) 2000 Elsevier Science B.V. All rights reserved.ELSEVIER SCIENCE BV, 2000年06月, CHEMICAL PHYSICS LETTERS, 323(5-6) (5-6), 407 - 415, 英語[査読有り]研究論文（学術雑誌）
- The electron transfer rate constant at electrode/liquid interfaces is theoretically described on the basis of the Anderson-Newns-Schmickler model. A compact formula for the rate constant is derived in the nonadiabatic limit, which is expressed in terms of the spectral density of surrounding media, the density of states of electrons in the electrode, and the weighted electronic coupling constant between the electrode and the redox couple in the liquid. The outer-sphere spectral density is then related to the experimentally accessible data on the frequency-dependent dielectric response functions of the solvent and the electrode with the aid of the dielectric continuum approximation. The derived formula provides a quantum-mechanical extension of the conventional nonadiabatic expression for the heterogeneous electron transfer reactions at electrode/liquid interfaces, taking into account the quantum effects associated with the high-frequency modes of both outer and inner spheres. On this basis, the quantum correction for the electron-transfer rate constant is numerically analyzed for some metal or semiconductor electrodes in contact with the Fe2+/3+ redox couple dissolved in water solvent at room temperature. In the case of zero energy gap, the quantum correction is found to be a factor of 4-5 for a typical configuration of the redox couple regardless of the species of electrode, while the rate constant itself is significantly affected by the dielectric property of the electrode. The energy gap dependence of the quantum correction is also discussed. © 1999 American Institute of Physics.1999年12月, Journal of Chemical Physics, 111(24) (24), 11117 - 11137研究論文（学術雑誌）
- 1999年12月, 分子シミュレーション討論会講演要旨集, 13th, 21 - 22, 日本語アゾデンドリマーの構造シミュレーションと振動解析
- The effect of an electric field on a photoinduced charge separation process is treated theoretically. The system considered is a reaction center (RC) of photosynthetic bacteria, involving an electron transfer (ET) from the electronically excited singlet state of the bacteriochlorophyll dimer (P) to the bacteriopheophytin (H) and quinone (Q). In contrast to formulations which focus only on the forward steps and do not explain the major effect on the quantum yield of P+Q- or, in Q-depleted samples, of P+H-, the present study includes the effect on the back reactions, an effect which we find to be large. The low-frequency medium and high-frequency intramolecular vibrational modes are included in the calculation of the various ET rates. Recent experimental results on the ET energetics, including the estimated effect of static heterogeneity in RCs, are incorporated. The rate equations for the population densities of distinct states are solved for both oriented and randomly oriented (isotropic) RC samples, and the results are compared with experimental data for the field-induced reduction of the quantum yield of formation of charge-separated state P+Q-. A simple (quasiequilibrium) model calculation illustrates the essential features of this analysis of the electric field effect and compares reasonably well with these numerical results of the more detailed model. The question of the electric field effect on the fluorescence quantum yield is also addressed, and a suggestion is made for consistency with the data on the formation of P+Q-.1997年06月, Journal of Physical Chemistry B, 101(25) (25), 5031 - 5045研究論文（学術雑誌）
- Strained lattice organic thin film which possessed distinct lattice structure from the bulk crystal was formed by molecular beam epitaxy (MBE). In situ infrared (IR) spectroscopic characterization was carried out to clarify the as-grown film structure under several growth conditions. The growth condition for parallel orientation of the flat molecules was discussed under the interrelation between the molecule-substrate interactions and the intermolecular interactions.1996年, Molecular Crystals and Liquid Crystals Science and Technology Section A: Molecular Crystals and Liquid Crystals, 276-277, 267 - 271研究論文（学術雑誌）
- We have carried out an evaluation of cation valences in Y1-xPrxBa2Cu3O7 (YPBCO) on the basis of the fractional-valency ionic crystal model to investigate the causes of Tc suppression with Pr doping. Through comparison with the case of YBa2Cu3O7-x, we have quantitatively estimated the extent to which the Tc depression can be accounted for in terms of the decrease in hole concentration in the CuO2 planes, paying special attention to the difference in the fourth ionization potential between Y and Pr. We have found that the valency of Pr is higher than that of Y by about 0.3 in YPBCO, thus reducing the Cu valency in the CuO2 planes with the Pr substitution, but that this effect can quantitatively explain no more than about one-third of the Tc depression. Accordingly, it is suggested that those effects neglected in the present model, such as a further decrease in mobile hole concentration due to the Pr-O hybridization, the localization of carriers due to disorder, and the magnetic pair breaking due to Pr spin, must play an important role in the mechanism of Tc suppression in YPBCO. © 1995 The American Physical Society.1995年, Physical Review B, 52(1) (1), 85 - 88研究論文（学術雑誌）
- The electronic structure of NiO solid with the fee type-II antiferromagnetic structure has been studied using a variational quantum Monte Carlo approach. The Jastrow-Slater many-body wave function has been used for valence electrons, and the pseudopotentials have been evaluated with the aid of a local approximation. The calculated results for the binding energy and the structural properties are in good agreement with experiment. Reasonable evaluations have also been made for the charge and spin density distributions and the electron-electron radial distribution functions. Although the results for the one-particle energy distribution and the charge-transfer excitation energy gap are encouraging, further increase in Monte Carlo steps and improvements in computational methods would be required for the detailed comparison with experiments and the most dependable density-functional band calculations. © 1995, THE PHYSICAL SOCIETY OF JAPAN. All rights reserved.1995年, Journal of the Physical Society of Japan, 64(11) (11), 4270 - 4277研究論文（学術雑誌）
- We have studied the effects of an external electric field on the phase properties of mixed-stack organic charge-transfer complexes through illustrative calculations based on the ionic crystal model, paying special attention to the roles of electrostatic energy. The ground-state charge configurations of tetrathiafulvalene-p-chloranil (TTF-CA) under electric fields have been explored mainly by the Monte Carlo simulated annealing method in the cases of one-dimensional chain, three-dimensional bulk crystal, and thin film. It has been found for TTF-CA bulk crystals at room temperature and ambient pressure that the applied electric field beyond approximately 106 V/cm would induce a transition from the neutral phase to the charge-separated phase in which positively and negatively charged donor-acceptor pairs, D+A0 and D0A-, separately appear near both ends of DA stack chains. Investigating the phase structure of charge-transfer complexes through the variations in ionization energy, Madelung energy, and external field, we have also found that the applied field can cause a neutral-ionic transition of mixed-stack organic charge-transfer compounds in the close vicinity of neutral-ionic phase boundary. We then discuss the feasibility of this electric-field-induced neutral-ionic transition in actual organic-complex systems in terms of employing compounds other than TTF-CA or of varying temperature, pressure, and film thickness to approach the systems to the neutral-ionic phase boundary. © 1995 The American Physical Society.1995年, Physical Review B, 52(3) (3), 1549 - 1565研究論文（学術雑誌）
- We develop a semiempirical computational scheme for analyzing the charge distribution and the carrier doping in multinary transition-metal oxides on the basis of the fractional-valency ionic crystal model, in which the optimization of charge partitioning is efficiently carried out with the simplex method. The adequacy and limitation of linear and nonlinear interpolation schemes for the atomic energy of fractionally-charged ions are comparatively assessed through a benchmark application to NiO. The proposed models are then applied to the analysis of the charge transfer in La2 - xSrxNiO4 compared with La2 - xSrxCuO4. In the two systems, the behaviors of the hole doping into the conduction plane are quantitatively similar, which is consistent with the experimental suggestion that the remarkable difference in the properties of the insulator-to-metal transition between them should be ascribed to the difference in the mobility of the holes doped in the plane. © 1994.1994年12月, Physica C: Superconductivity and its applications, 234(3-4) (3-4), 355 - 360研究論文（学術雑誌）
- A semiempirical method for the calculation of the bond ionicity, which is applicable even to extremely anisotropic systems such as copper-oxide superconductors, is proposed as a generalization of the Phillips-Van Vechten-Levine scheme. The value of the ionicity calculated for oxides generally tends to increase as the crystal strain becomes more tensile. It is characteristic of cuprate superconductors that the values of the ionicity are high compared with other 3d transition-metal oxides. Also significant are the extremely high ionicities in the direction normal to the CuO2 planes and the relatively high covalencies of the intraplanar bonds. These crystal-chemical characteristics may be intimately related to the remarkable insulator-to-metal transition and the associated high-Tc superconductivity in the layered copper-oxide systems. © 1994.1994年02月, Physica C: Superconductivity and its applications, 220(3-4) (3-4), 341 - 346研究論文（学術雑誌）
- High-Tccopper-oxide superconductors are characterized from the viewpoint of crystal chemistry through com-parative analyses of Cu-O bond lengths, Madelung site potentials and bond valence sums. The interrelationships among these structural and electronic parameters are investigated in detail for the elucidation of the crystal- chemical factors governing Tcand the species of doped carriers. Two characteristics, the strain parameter for CuO2planes calculated on the basis of bond valence sums and the Madelung-potential difference between in-plane O and Cu sites, are shown to represent an essentially equivalent physical content. The ability of the present analysis to predict the maximum value of Tcof (possible candidates for) cuprate superconductors is also discussed. © 1994 The Japanese Journal of Applied Physics.1994年02月, Japanese Journal of Applied Physics, 33(2 R) (2 R), 1004 - 1011研究論文（学術雑誌）
- A new computational scheme to simultaneously optimize the electronic and ionic configurations in solids and molecules is presented in the framework of variational quantum Monte Carlo method. This scheme, in which a fictitious Lagrangian to describe the dynamics of electronic variational parameters and ionic coordinates is introduced, is formulated virtually in parallel with the Car-Parrinello method for density-functional theory. The feasibility and usefulness of the proposed scheme are demonstrated by carrying out a structural optimization for water molecule with the aid of steepest-descents technique. © 1994 American Institute of Physics.1994年, The Journal of Chemical Physics, 100(10) (10), 7416 - 7420研究論文（学術雑誌）
- NMR measurements have been made to study the electron correlation effect in metallic layered perovskite compounds Srn+1VnO3n+1(n =2, 3 and ∞). It has been found that the exchange enhancement of the spin susceptibil ity increases with decreasing n from ∞ to 2 within the random phase approximation. © 1993.1993年05月, Physica B: Physics of Condensed Matter, 186-188(C) (C), 1062 - 1064, 英語[査読有り]研究論文（学術雑誌）
- A new layered perovskite vanadium oxide S^VsOs-^ was synthesized and its crystal structure and magnetic properties were studied. Sr4V308-6 has a novel crystal structure, containing a V-0 octahedron and a two-fold V- O fence in a unit cell. It exhibits negative magnetization below 30 K, when cooled in a magnetic field. This magnetism was explained based upon a N-type parasitic ferrimagnetism model. © 1993 IOP Publishing Ltd.1993年02月, Japanese Journal of Applied Physics, 32(2 A) (2 A), 190 - 192研究論文（学術雑誌）
- The variational quantum Monte Carlo method has been applied to the first-principles calculation of the cohesive energy of NiO with the fee type-II antiferromagnetic structure. The trial wave functions used for the calculations for O and Ni atoms and solid NiO have been chosen to be of the form of a Jastrow exponential factor multiplying a Slater determinant. The pseudopotentials introduced to avoid the large fluctuations of energy in the core region have been evaluated with the aid of a local approximation whose utility and accuracy were assessed through comparison with the nonlocal method in the calculation for isolated atom. By appropriate choice for the form of the trial functions, a promising result has been obtained for the calculated value of cohesive energy, which is consistent with experiment. © 1993, THE PHYSICAL SOCIETY OF JAPAN. All rights reserved.1993年, Journal of the Physical Society of Japan, 62(6) (6), 2112 - 2119研究論文（学術雑誌）
- A phenomenological two-carrier model for high-Tc oxide superconductors is proposed on the basis of experimental results for optical conductivity. A dielectric response function is formulated for the system consisting of Drude and hopping carriers, in which relaxation and strong-correlation effects are taken into account. Given an appropriate choices for the values of effective masses, carrier concentrations and relaxation times, this dielectric function can well reproduce the experimental results for optical conductivity in La2-xSrxCuO4 and YBa2Cu3O7-δ. The superconducting transition temperature Tc is then estimated, regarding the hopping component as a dielectric medium producing an attractive pairing force between the Drude carriers. This model can consistently account for a number of experimental facts, such as (i) optical anomalies in the mid-infrared region, (ii) high transition temperature, (iii) correlations between Tc and a number of physical parameters, (iv) the significance of low dimensionality. © 1992.1992年03月, Physica C: Superconductivity and its applications, 192(3-4) (3-4), 315 - 327研究論文（学術雑誌）
- The electronic structures of layered-perovskite oxides Srn+1VnO3n+1(n=l, 2, 3) have been analyzed through ab initio molecular-orbital calculations for VO6 clusters, using the Hartree-Fock method followed by Moller-Plesset perturbation and configuration-interaction corrections. Comparisons of the electronic states have been made among VO6, CuO6 and CuO4 clusters to study the possibility of realizing vanadate superconductors on the analogy of the high-Tc cuprate superconductors. Hole- and electron-doped states have also been investigated as well as the undoped state. We thus clarify a number of similarities and differences between the vanadates and the cuprates. It is also suggested that some of these differences may prevent the layered vanadium oxides from becoming high-Tc superconductors. © 1992, THE PHYSICAL SOCIETY OF JAPAN. All rights reserved.1992年03月, Journal of the Physical Society of Japan, 61(7) (7), 2399 - 2411研究論文（学術雑誌）
- The electronic structure of layered-perovskite oxides Srn+1VnO3n+1 (n = 1, 2, 3) is investigated through ab initio molecular-orbital calculations for VO6 model clusters. The results are compared with those for the CuO6 clusters in high-Tc cuprate superconductors. A number of causes, which may suppress superconductivity in the layered vanadium oxides, are suggested. © 1991.1991年12月, Physica C: Superconductivity and its applications, 185-189(PART 1) (PART 1), 709 - 710研究論文（学術雑誌）
- Two types of metal-insulator transitions in Sr3V2O7 have been observed. A transition from the metallic state to the insulating state took place by substituting Cr for V, and this transition was interpreted as the result of the band splitting from the XPS data. The other transition occured when the oxygen content was decreased in Sr3V2O7-d, and the insulator exibits variable range hopping conduction and spin freezing properties, which denotes that this transition is considered as the disorder-induced Anderson localization. © 1991.1991年12月, Physica C: Superconductivity and its applications, 185-189(PART 1) (PART 1), 715 - 716研究論文（学術雑誌）
- We have found a metal-insulator transition in the layered-perovskite vanadate Sr 3 V 207. The transition from the metallic state to the insulating state took place by substituting Cr for V. Magnetization measurements did not indicate the drastic change between metallic and insulating states. The possibility of high-Z, superconductivity was also discussed in comparison with the layered-cuprate and other oxide superconductors. © 1990 The Japan Society of Applied Physics.1990年12月, Japanese Journal of Applied Physics, 29(12) (12), 2190 - 2192研究論文（学術雑誌）
- We have analyzed relationships between crystal structures and electronic states of layered transition-metal oxides in the light of bond valence sums. We introduce parameters representing excess charge and internal strain in the central MO2planes (M = 3d transition metal) and thereby characterize the electronic states of those oxides. Correlations between the superconducting transition temperature and those bond-valence-sum parameters are investigated for the high-Tccuprate compounds and the possibility of making nonsuperconducting oxides superconducting is discussed. © 1990 IOP Publishing Ltd.1990年11月, Japanese Journal of Applied Physics, 29(11) (11), 1987 - 1990研究論文（学術雑誌）
- To account for the anomalies observed in the optical experiments for the normal state of the high-Tc oxide superconductors, we analyzed the optical properties of two-dimensional charged Fermi liquids on the basis of the Lindhard dielectric function in the relaxation-time approximation. We can reproduce the non-Drude behavior in optical conductivity in the mid-infrared region through inclusion of the frequency-dependent damping effects of quasi-particles. In order to quantitatively explain the anomalously large Raman scattering amplitude ranging over the far- and mid-infrared regions, however, we need to take account of the contributions made by fluctuations other than those arising from charged Fermi liquids. © 1990.1990年08月, Physica C: Superconductivity and its applications, 169(3-4) (3-4), 271 - 274研究論文（学術雑誌）
- Strong correlations between electrons and ions in hydrogen plasmas near metal-insulator boundaries are analyzed through an integral equation approach, which adopts the hypernetted-chain (HNC) approximation for the classical ion-ion correlation and the modified convolution approximation (MCA) for the quantum-mechanical electron-electron and electron-ion correlations. The resulting HNC MCA equations are solved self-consistently. The correlation functions and the equation of state thus calculated reveal the emergence of Rydberg states in the metallic phase near the metal-insulator boundaries, which acts to reduce the electric and thermal conductivities. Parametrized formulas for the equation of state and the conductivities are presented. © 1990 The American Physical Society.1990年, Physical Review A, 41(10) (10), 5616 - 5625研究論文（学術雑誌）
- Screening action of the s-d hybridized electrons in PdHx and TiHx is analyzed in the Fermi-Thomas approximation. The resulting interaction between hydrogen exhibits an attractive part arising from interference between the H-induced s-electrons and the valence electrons. The screening potentials due to many-body effects between the electron-screened protons are examined through solution to the hypernetted-chain equations. The nuclear reaction rates between hydrogen isotopes are calculated at various temperatures by taking account of statistical-mechanical enhancement arising from the increment in the Coulombic chemical potential of a reacting pair before and after nuclear reaction. Remarkable isotopic and temperature-dependent effects are predicted. © 1990, THE PHYSICAL SOCIETY OF JAPAN. All rights reserved.1990年, Journal of the Physical Society of Japan, 59(4) (4), 1333 - 1340研究論文（学術雑誌）
- We solve a set of coupled integral equations obtained in the modified-convolution approximation scheme, to calculate the spin-dependent correlation functions and interaction energies for electron liquids at arbitrary degrees of Fermi degeneracy and spin polarization. Analytic expressions for the free energies are obtained through parametrization of the numerical results over a wide range of density, temperature, and spin polarization in the fluid state; Fermi-liquid properties are thereby investigated. Phase boundary curves, arising from divergence of the isothermal compressibility and of the spin susceptibility, are drawn on the density-temperature plane for the metallic electrons. In particular, it is pointed out that the signs and magnitudes of the spin-dependent or phonon-induced electron interactions exhibit remarkable changes across the phase boundaries; strong attractive interaction between electrons with parallel spins appears near the spin-susceptibility anomaly, where the spin-density fluctuations are enormously enhanced. © 1989 The American Physical Society.1989年, Physical Review B, 39(2) (2), 1036 - 1051研究論文（学術雑誌）
- A new theory of dynamic correlations in a strongly coupled, classical one-component plasma (OCP) is developed within the generalized viscoelastic formalism. Fully convergent kinetic equations for the strongly coupled OCP are thereby derived with the aid of a fluctuation-theoretic formulation of the collision integrals. The dynamic structure factor S(k,) and the coefficient of shear viscosity are calculated both in the ordinary fluid state and in the metastable supercooled state through a self-consistent solution to the kinetic equation. It is shown that the numerical results in the ordinary fluid state agree well with other theoretical and molecular-dynamics simulation results. A possibility of the dynamic glass transition is predicted in the supercooled OCP through the analyses of the variation in , the quasielastic peak in S(k,) and the behavior of the self-diffusion coefficient; the prediction is compared with those in the glass-transition theories for other systems. Relevance to laboratory experiment is examined in terms of the metastable-state lifetimes against homogeneous nucleation of the crystalline state. © 1987 The American Physical Society.1987年, Physical Review A, 35(11) (11), 4743 - 4754研究論文（学術雑誌）
- We carry out explicit calculations to determine the phase boundaries on the density-temperature plane associated with divergence of the isothermal compressibility and the spin susceptibility of the electron liquid in metallic substances. It is shown that the signs and magnitudes of the spin-dependent and phonon-induced electron interactions exhibit remarkable changes across the phase boundaries. We point out that the strong attractive interaction between electrons with parallel spins appears near the spin-susceptibility anomaly, which may take place at n2×1020 cm-3 for T150 K. © 1987 The American Physical Society.1987年, Physical Review B, 36(11) (11), 6182 - 6185研究論文（学術雑誌）
- The dielectric formulation is applied to the study of the static correlations in the electron liquids at finite temperatures. The strong coupling effects arising from the exchange and Coulomb correlations are taken into account through the local-field correction in the Singwi-Tosi-Land-Sjölander approximation. The resulting integral equations are solved self-consistently, and the thermodynamic quantities are evaluated at various combinations of the plasma parameters in the range of the intermediate Fermi degeneracy. The results are parametrized in the form of the analytic formulas, which satisfy a number of exact boundary conditions and limiting behaviors. © 1986, THE PHYSICAL SOCIETY OF JAPAN. All rights reserved.1986年07月, Journal of the Physical Society of Japan, 55(7) (7), 2278 - 2289研究論文（学術雑誌）
- We present a new theory of dynamic correlations for a classical one-component plasma in strong Coulomb coupling within the generalized viscoelastic formalism. The dynamic structure factor and the coefficient of shear viscosity for the one-component plasma in a metastable supercooled state are investigated and the possibility of a glass transition is predicted. Relevance to laboratory experiment is pointed out through analyses of the metastable-state lifetimes against homogeneous nucleation of the crystalline state. © 1986 The American Physical Society.1986年, Physical Review Letters, 56(26) (26), 2815 - 2818研究論文（学術雑誌）
- We derive a fully convergent collision term of the kinetic equation for charged particles obeying the classical statistics, within the static approximation to the local-field correction. The coefficient of the ionic shear viscosity is then calculated through a solution to the kinetic equation for dense, high-temperature plasmas appropriate to the inertial-confinement-fusion experiments and to the interior of the main-sequence stars. An analytic expression for the generalized Coulomb logarithm of the shear viscosity is obtained through parametrization of those numerical results. © 1986 The American Physical Society.1986年, Physical Review A, 34(5) (5), 4163 - 4170研究論文（学術雑誌）
- On the basis of the general formalism and the analysis of the correlation functions presented in the preceding two papers (I and II), we calculate in this paper (III) various thermodynamic functions with explicit inclusion of the varied degrees of the electron degeneracy and the local-field corrections describing the strong Coulomb-coupling effects. The physical implications of the computed results are investigated through comparison with other model calculations. Mindful of practical applications of the present theory, we derive the analytic interpolation formulas parametrizing the computed results accurately for the thermodynamic functions. © 1985 The American Physical Society.1985年, Physical Review A, 32(3) (3), 1779 - 1784研究論文（学術雑誌）
- The stopping power of a dense, two-component plasma is calculated in the dielectric formulation, where the static and dynamic local-field corrections (LFCs) describing strong Coulomb-coupling effects beyond the random-phase approximation are explicitly taken into account. We thus clarify the extent to which the LFCs and the presence of ions act to modify the rate of inelastic scattering. It is found that when the velocity v of the injected particle is smaller than the Fermi velocity vF of the electrons, LFCs enhance the stopping power; when vvF, the ionic contribution may predominate over the electronic contribution, which takes on a much reduced magnitude. © 1985 The American Physical Society.1985年, Physical Review A, 32(3) (3), 1785 - 1789研究論文（学術雑誌）
- On the basis of the quantum-statistical formulation of electronic transport, we calculate the electric and thermal conductivities of plasmas in a wide range of densities and temperatures where it is essential to take into account the varied degrees of electron degeneracy and local-field corrections describing the strong Coulomb-coupling effects. The physical implications of the results are investigated through comparison with other theories and experiments. For utility in the practical applications, we derive the analytic formulas parametrizing the computed results accurately for the generalized Coulomb logarithms appearing in those conductivities. © 1985 The American Physical Society.1985年, Physical Review A, 32(3) (3), 1790 - 1798研究論文（学術雑誌）
- We derive analytic formulas for the interaction and excess-free energies of dense hydrogenic plasmas, which accurately parametrize the numerical data calculated earlier in the hypernetted chain approximation at an intermediate Fermi degeneracy of the electrons and which exactly satisfy the known boundary conditions at complete degeneracy as well as in the weak- and strong-coupling regimes. The resulting equation of state is valid over a wide range of densities and temperatures, as long as the system is in a liquid-metallic state. © 1985 The American Physical Society.1985年, Physical Review A, 32(6) (6), 3756 - 3757研究論文（学術雑誌）
- We calculate the interaction and excess free energies of the electron system at finite temperatures on the basis of the Singwi-Tosi-Land- Sjölander approximation [Phys. Rev. 176, 589 (1968)]. The results are parametrized in the form of analytic formulas, which adequately describe the equation of state for homogeneous, paramagnetic electron liquids over a wide range of the density and temperature parameters. © 1985 The American Physical Society.1985年, Physical Review A, 32(3) (3), 1896 - 1899研究論文（学術雑誌）
- This is the first in a series of papers in which we carry out a systematic study of multiparticle correlation effects in the dense, high-temperature plasmas, appropriate to the inertially-confined-fusion experiments and the interior of the main-sequence stars. In this paper (paper I), we develop a general density-response formalism with inclusion of varied degrees of the electron degeneracy and the local-field corrections (LFCs) describing the strong Coulomb-coupling effects. An explicit theoretical scheme of calculating the static LFCs is developed on the basis of the hypernetted-chain approximation; useful expressions for the dynamic LFCs are proposed. © 1985 The American Physical Society.1985年, Physical Review A, 32(3) (3), 1768 - 1774研究論文（学術雑誌）
- We calculate the stopping power of the degenerate electron liquid at metallic densities in the dielectric formalism. The strong Coulomb-coupling effects beyond the random-phase approximation are taken into account through the static and dynamic local-field corrections. It is shown that those strong-coupling and dynamic effects act to enhance the stopping power substantially in the low-velocity regime, leading to an improved agreement with experimental data. © 1985, THE PHYSICAL SOCIETY OF JAPAN. All rights reserved.1985年, Journal of the Physical Society of Japan, 54(7) (7), 2537 - 2542研究論文（学術雑誌）
- On the basis of the general theoretical framework constructed in the preceding paper (paper I in the present series), we calculate in this paper various correlation functions in dense plasmas, taking account of local-field corrections and varied degrees of electron degeneracy; physical implications of the results are investigated. © 1985 The American Physical Society.1985年, Physical Review A, 32(3) (3), 1775 - 1778研究論文（学術雑誌）
- The inter-ionic density correlations and the associated screening potential are investigated for those dense, high-temperature plasmas with parameters appropriate to the inertially confined fusion experiments and the interior of main-sequence stars. The hypernetted chain scheme is used for the analysis of the correlations, where the screening effect of the electrons is taken into account via the dielectric function with inclusion of partial degeneracy and the local-field correction. We derive explicit analytic expressions for the enhancement rate of thermonuclear reactions applicable uniformly over the entire parameter domain of plasmas with the ionic charge Z= 1 and 2. © 1984, THE PHYSICAL SOCIETY OF JAPAN. All rights reserved.1984年, Journal of the Physical Society of Japan, 53(6) (6), 2039 - 2048研究論文（学術雑誌）
- We present the first quantitative study of the screening potential and the effective cross section for thermonuclear reaction in dense plasmas relevant to the inertially confined fusion experiments and the interior of main-sequence stars. It is shown that the enhancement of the thermonuclear reaction rate due to strong Coulomb correlations has a considerable effect in such a dense plasma. © 1984 The American Physical Society.1984年, Physical Review A, 29(4) (4), 2033 - 2035研究論文（学術雑誌）
- 1984年, Physical Review A, 30(3) (3), 1548研究論文（学術雑誌）
- 2023年, CBI学会大会(CD-ROM), 2023MDおよびFMO計算を用いたIL-10受容体複合体の相互作用解析【JST機械翻訳】
- 2023年, 日本物理学会講演概要集(CD-ROM), 78(1) (1)量子散逸系に対する準古典マッピング動力学法の精度検証
- 2022年, 日本化学会春季年会講演予稿集(Web), 102nd脱ワトソン・クリックの核酸化学(77):高圧環境がDNA非二重らせん構造に与える影響
- 2022年, 日本核酸医薬学会年会講演要旨集(CD-ROM), 7th核酸構造の定量的解析を基にしたC9orf72由来のリピートRNAとペプチドの相互作用制御法の開発
- 2022年, 日本物理学会講演概要集(CD-ROM), 77(1) (1)Symmetrical quasi-classical法の電子状態間・非断熱遷移過程への応用
- 2022年, 日本蛋白質科学会年会プログラム・要旨集, 22nd (Web)FMODBデータ収集:高分解能X線結晶構造データに対する量子化学計算
- 2022年, 構造活性相関シンポジウム講演要旨集, 50th (CD-ROM)FMO法を用いたSARS-CoV-2メインプロテアーゼ-阻害薬S-217622結合メカニズムの解明
- 2021年, 日本核酸医薬学会年会講演要旨集(CD-ROM), 6th神経変性疾患に関連するGGGGCCリピート配列から成るRNA四重鎖とジペプチドリピートの集積メカニズムの解析
- 2021年, 構造活性相関シンポジウム講演要旨集, 49th (CD-ROM)FMO法を用いたJAK2とイミダゾピロロピリジン系化合物の結合性および選択性評価
- 2021年, 構造活性相関シンポジウム講演要旨集, 49th (CD-ROM)SARS-CoV-2メインプロテアーゼと既存薬のFMO動的相互作用解析
- Springer Singapore, 2021年
- 2021年, 日本薬学会関東支部大会講演要旨集, 65th (CD-ROM)自己組織化写像によるフラグメント間相互作用解析手法の開発
- 2021年, 日本コンピュータ化学会年会講演予稿集, 2021FMO動的相互作用解析によるSARS-CoV-2メインプロテアーゼと既存薬のポーズ推定と結合性予測
- 2021年, 日本化学会春季年会講演予稿集(Web), 101st脱ワトソン・クリックの核酸化学(69):神経変性疾患に関連するRNA四重鎖とジペプチドリピートの分子シミュレーションによる相互作用の解析
- 2020年, 構造活性相関シンポジウム講演要旨集, 48th (CD-ROM)フラグメント分子軌道法によるSARS-CoV-2Mproと阻害剤の相互作用解析
- 2020年, 日本化学会春季年会講演予稿集(CD-ROM), 100th脱ワトソン・クリックの核酸化学(63):分子シミュレーションによるGGGGCCリピートのRNA四重鎖とジペプチドリピートの集積メカニズムの解析
- 2020年, CBI学会大会, 2020 (CD-ROM)分子動力学とフラグメント分子軌道計算を用いたSARS-CoV-2主要プロテアーゼへの既存薬物の結合の予測【JST・京大機械翻訳】
- 2020年, 日本薬学会関東支部大会講演要旨集, 64thフラグメント分子軌道法による動的相互作用解析を用いたSARS-CoV-2メインプロテアーゼと既存薬との結合性予測
- This chapter describes the current status of development of the fragment molecular orbital (FMO) method for analyzing the electronic state and intermolecular interactions of biomolecular systems in solvent. The orbital energies and the inter-fragment interaction energies (IFIEs) for a specific molecular structure can be obtained directly by performing FMO calculations by exposing water molecules and counterions around biomolecular systems. Then, it is necessary to pay attention to the thickness of the water shell surrounding the biomolecules. The single-point calculation for snapshots from MD trajectory does not incorporate the effects of temperature and configurational fluctuation, but the SCIFIE (statistically corrected IFIE) method is proposed as a many-body correlated method that partially compensates for this deficiency. Furthermore, implicit continuous dielectric models have been developed as effective approaches to incorporating the screening effect of the solvent in thermal equilibrium, and we illustrate their usefulness for theoretical evaluation of IFIEs and ligand-binding free energy on the basis of the FMO-PBSA (Poisson-Boltzmann surface area) method and other computational methods.2020年, Methods in molecular biology (Clifton, N.J.), 2114, 105 - 122, 英語, 国際誌
- 2019年, 日本化学会春季年会講演予稿集(CD-ROM), 99th脱ワトソン・クリックの核酸化学(51):DNAとクラウディング分子の相互作用の分子動力学計算と電子状態計算による定量的解析
- 2019年, 日本コンピュータ化学会年会講演予稿集, 2019エストロゲン様化合物におけるサブタイプ選択性の解析
- 2019年, 日本コンピュータ化学会年会講演予稿集, 2019FMO計算を用いたJAK阻害剤のサブタイプ選択性の評価
- 2019年, Newton別冊「量子論のすべて：量子論の基本から量子コンピュータまで」, 106 - 107, 日本語「量子生物学」とは何か？
- 2019年, 大学ICT推進協議会2019年度年次大会論文集, 日本語計算生命科学の基礎
- 2018年03月, 日本化学会春季年会講演予稿集(CD-ROM), 98th, ROMBUNNO.4D5‐32, 日本語脱ワトソン・クリックの核酸化学(42):クラウディング分子により形成される分子ネットワークがDNA四重鎖の構造安定性に及ぼす影響の定量的解析
- 2018年, 日本薬学会関東支部大会講演要旨集, 62ndフラグメント分子軌道法によるエストロゲン受容体のサブタイプ特異性の解析
- 2017年11月29日, 分子シミュレーション討論会講演要旨集, 31st, 64‐65, 日本語共溶質存在下におけるDNA水和水の熱力学的性質の解析
- 2017年09月, 実験医学, Vol. 35(No. 14(9月号)) (No. 14(9月号)), 2423 - 2427, 日本語量子生命科学の展望[招待有り]記事・総説・解説・論説等（商業誌、新聞、ウェブメディア）
- 2017年07月01日, 日本核酸医薬学会年会講演要旨集, 3rd, 67, 日本語テトラエチレングリコール修飾核酸を活用した新しい逆転写制御法の開発
- 2017年03月03日, 日本化学会春季年会講演予稿集(CD-ROM), 97th, ROMBUNNO.2C4‐47, 日本語脱ワトソン・クリックの核酸化学(30):Cyclic naphthalene diimideによるDNA四重鎖の安定化メカニズムの解明
- 2017年, CICSJ Bull., 35(No. 3) (No. 3), 205 - 209, 日本語FMO創薬を加速する大規模データ解析記事・総説・解説・論説等（学術雑誌）
- We have been developing the ABINIT-MP program for the fragment molecular orbital (FMO) method. The list of inter-fragment interaction energies (IFIEs) is available from FMO calculations and is useful in analyzing the nature of interactions in a given target system. In this Letter, we summarize the current status of ABINIT-MP and also the machine-learning assisted analyses of IFIE data.日本コンピュータ化学会, 2017年, J. Comput. Chem. Jpn., 16(No. 5) (No. 5), 119 - 122, 日本語[査読有り]記事・総説・解説・論説等（学術雑誌）
- 2016年11月01日, 日本核酸医薬学会年会講演要旨集, 2nd, 93, 日本語テトラエチレングリコール修飾塩基をもつ四重鎖構造を用いた逆転写反応制御
- 2016年, 分子科学討論会講演プログラム&要旨(Web), 10thテトラエチレングリコール修飾によるDNA四重鎖の安定化機構の解明
- American Chemical Society, 2016年, ACS Symposium Series, 1234, ix, 英語その他
- Center for Earth Information Science and Technology, Japan Agency for Marine-Earth Science and Technology, 2016年, Annual Report of the Earth Simulator Center, April 2015 – March 2016, 251 - 257, 英語Analysis of Biological Interaction by Fragment Molecular Orbital (FMO) Method – Analyses of the Interactions between Measles Virus Hemagglutinin and Their Receptors –[招待有り]速報，短報，研究ノート等（大学，研究機関紀要）
- 2015年03月11日, 日本化学会講演予稿集, 95th(2) (2), 232, 日本語フラグメント分子軌道法のインシリコ創薬への応用
- Center for Earth Information Science and Technology, Japan Agency for Marine-Earth Science and Technology, 2015年, Annual Report of the Earth Simulator Center, April 2014 – March 2015, 131 - 135, 英語Analysis of Global Ecosystem Ecology by Fragment Molecular Orbital (FMO) Method: Analyses of the Interactions between Virus Hamagglutinins and Their Receptors[招待有り]速報，短報，研究ノート等（大学，研究機関紀要）
- 2014年05月26日, 日本蛋白質科学会年会プログラム・要旨集, 14th, 63, 日本語フラグメント分子軌道法に基づくタンパク質の理論計算
- 2014年03月12日, 日本化学会講演予稿集, 94th(2) (2), 300, 日本語ABINIT‐MPによる京でのフラグメント分子軌道計算
- 2014年03月12日, 日本化学会講演予稿集, 94th(2) (2), 300, 日本語FMO電子状態計算によるX線結晶構造の精密化の検討
- 2014年, CBI学会大会, 2014, 1, 英語Theorectical calculations on proteins with fragment molecular orbital method
- Recent developments in the fragment molecular orbital (FMO) method for theoretical formulation, implementation, and application to nano and biomolecular systems are reviewed. The FMO method has enabled ab initio quantum-mechanical calculations for large molecular systems such as protein-ligand complexes at a reasonable computational cost in a parallelized way. There have been a wealth of application outcomes from the FMO method in the fields of biochemistry, medicinal chemistry and nanotechnology, in which the electron correlation effects play vital roles. With the aid of the advances in high-performance computing, the FMO method promises larger, faster, and more accurate simulations of biomolecular and related systems, including the descriptions of dynamical behaviors in solvent environments. The current status and future prospects of the FMO scheme are addressed in these contexts. This journal is © the Partner Organisations 2014.Royal Society of Chemistry ({RSC}), 2014年, Phys. Chem. Chem. Phys., 16(22) (22), 10310 - 10344, 英語[招待有り]記事・総説・解説・論説等（学術雑誌）
- Earth Simulator Center, Japan Agency for Marine-Earth Science and Technology, 2014年, Annual Report of the Earth Simulator Center, April 2013 – March 2014, 155 - 160, 英語Analysis of Global Ecosystem Ecology by Fragment Molecular Orbital (FMO) Method: Analyses of the Interactions between Virus Hamagglutinins and Their Receptors[招待有り]速報，短報，研究ノート等（大学，研究機関紀要）
- 2013年08月31日, 応用物理学会秋季学術講演会講演予稿集(CD-ROM), 74th, ROMBUNNO.17A-C6-1, 日本語フラグメント分子軌道計算に基づくペプチド‐シリカの相互作用解析
- 2013年, 日本分子生物学会年会プログラム・要旨集(Web), 36th, 3P-0116 (WEB ONLY), 日本語京コンピュータを用いたFMO電子密度解析による生体分子構造の高精度化の検討
- 日本磁気学会, 2013年, 日本磁気学会第190回研究会「生体物質の物理」資料, 31 - 36, 日本語第一原理シミュレーションによる生体高分子の電子状態・ダイナミクス・輸送特性の解析記事・総説・解説・論説等（その他）
- 2013年, CICSJ Bull., 31(3) (3), 56 - 63, 日本語フラグメント分子軌道法による分子内・分子間相互作用解析記事・総説・解説・論説等（学術雑誌）
- 2013年, CBI学会誌, 1(1) (1), 25 - 31, 日本語フラグメント分子軌道法によるインフルエンザウイルス表面タンパク質の大規模量子化学計算記事・総説・解説・論説等（学術雑誌）
- 2013年, CBI学会誌, 1(1) (1), 32 - 41, 日本語Structure-based drug designを指向した新規フラグメント分割法に基づく4体補正フラグメント分子軌道（FMO4）計算記事・総説・解説・論説等（学術雑誌）
- The Earth Simulator Center, Japan Agency for Marine-Earth Science and Technology, 2013年, Annual Report of the Earth Simulator Center, 173 - 178, 英語Large-Scale Electronic Structure Calculations of Biomolecular and Related Systems by the Fragment Molecular Orbital Method記事・総説・解説・論説等（大学・研究所紀要）
- F402 フラグメント分子軌道(FMO)計算の現状と今後(F4.物質・材料と計算力学〜無機・有機・ナノ材料の新展開〜,フォーラム)生体分子に対する大規模電子状態計算を可能とする手法であるフラグメント分子軌道(FMO)法の最近の進展と将来の展望について述べる。Protein Data Bankに登録されているタンパク質の構造等を用い、比較的短時間で電子相関を考慮した精確な第一原理計算ができるソフトウェアが各種開発され、ユーザーフレンドリーな計算環境が整いつつある。今後はペタスケールのスーパーコンピュータなどの利用も視野に入れ、創薬や材料開発を加速する有用な分子計算システムの一翼を担うことが期待される。一般社団法人日本機械学会, 2012年10月06日, 計算力学講演会講演論文集, 2012(25) (25), "F - 61"-"F-62", 日本語
- 2012年03月09日, 日本化学会講演予稿集, 92nd(2) (2), 276, 日本語Fragment Based Drug Design(FBDD)を指向した新規フラグメント分割法に基づくFMO計算
- 2012年03月09日, 日本化学会講演予稿集, 92nd(2) (2), 275, 日本語フラグメント分子軌道法によるインフルエンザウイルスノイラミニダーゼと抗ウイルス薬との相互作用解析
- 一般社団法人日本物理学会, 2012年03月05日, 日本物理学会講演概要集, 67(1) (1), 392 - 392, 日本語24pAA-10 レプリカ交換分子動力学法によるポリグルタミンペプチドの凝集メカニズムの解明(24pAA 生物物理,領域12(ソフトマター物理,化学物理,生物物理))
- 2012年, ACS Symposium Series, 1094その他
- 2012年, 分子科学討論会講演プログラム&要旨(Web), 6th, ROMBUNNO.2E16 (WEB ONLY), 日本語ABINIT‐MP(X)によるFMO計算の最近の展開
- 2012年, 分子科学討論会講演プログラム&要旨(Web), 6th, ROMBUNNO.2E17 (WEB ONLY), 日本語ABINIT‐MP/BioStationによるFMO応用計算事例
- 2012年, 分子科学討論会講演プログラム&要旨(Web), 6th, ROMBUNNO.4P105 (WEB ONLY), 日本語ABINIT‐MP(X)による京でのFMO計算
- Earth Simulator Center, Japan Agency for Marine-Earth Science and Technology, 2012年, Annual Report of the Earth Simulator Center, April 2011 – March 2012, 185 - 190, 英語Large-Scale Electronic-State Calculations of Protein-Ligand Systems for Drug Design with Fragment Molecular Orbital Method機関テクニカルレポート，技術報告書，プレプリント等
- 2011年11月08日, 情報計算化学生物学会大会予稿集, 2011 (CD-ROM), ROMBUNNO.CBI-P1-13, 英語Fragment molecular orbital study for interaction between influenza virus neuraminidase and antiviral drug
- 2011年, 分子科学討論会講演プログラム&要旨(Web), 5th, ROMBUNNO.3P099 (WEB ONLY), 日本語Fragment‐based drug design(FBDD)を指向した新規分割法に基づくFMO計算
- 2011年, Proceedings of JSST 2011, International Conference on Modeling and Simulation Technology, 101 - 104Development of ABINIT-MP(X) program for processing fragment molecular orbital calculations[招待有り]記事・総説・解説・論説等（国際会議プロシーディングズ）
- 2011年, 信学技報 IEICE Technical Report 111, 255, 47 - 48, 日本語量子モンテカルロ法による分子系のシミュレーション記事・総説・解説・論説等（学術雑誌）
- 2011年, Annual Report of the Earth Simulator Center, April 2010 – March 2011, 187 - 191, 英語Large-Scale Electronic-State Calculations of Influenza Viral Proteins with Fragment Molecular Orbital Method and Applications to Mutation Prediction機関テクニカルレポート，技術報告書，プレプリント等
- 2010年09月15日, 情報計算化学生物学会大会予稿集, 2010, 89, 英語Molecular Interaction of Estrogen Receptor .ALPHA. in Fluctuating State Studied by Ab initio Fragment Molecular Orbital Method
- AMER CHEMICAL SOC, 2010年08月, JOURNAL OF PHYSICAL CHEMISTRY B, 114(31) (31), 10234 - 10234, 英語
- 2010年06月, Interdisciplinary Bio Central, 2(2) (2), 6.1 - 6.5, 英語[査読有り]記事・総説・解説・論説等（学術雑誌）
- 一般社団法人日本物理学会, 2010年03月01日, 日本物理学会講演概要集, 65(1) (1), 382 - 382, 日本語リガンドに依存した核内受容体の構造変化に対する線型応答理論による解析
- 一般社団法人日本物理学会, 2009年08月18日, 日本物理学会講演概要集, 64(2) (2), 589 - 589, 日本語26aQL-6 大規模シミュレーションによる生体反応の理解(第一原理電子状態計算のフロンティアと次世代計算機への期待,領域11,領域4,領域8,領域9,領域12合同シンポジウム,領域4,半導体,メゾスコピック系・局在)
- 一般社団法人日本物理学会, 2009年03月03日, 日本物理学会講演概要集, 64(1) (1), 366 - 366, 日本語28aVC-5 フラグメント分子軌道法を用いた経路積分分子動力学法の開発(28aVC 水・水溶液・水分子・その他溶液,領域12(ソフトマター物理,化学物理,生物物理))
- 一般社団法人日本物理学会, 2009年03月03日, 日本物理学会講演概要集, 64(1) (1), 373 - 373, 日本語核内受容体における揺らぎと構造変化の線形応答理論解析
- 2009年, 日本化学会講演予稿集, 89th(1) (1)フラグメント分子軌道法によるポリシラン類の物性に関する理論的研究
- 2008年10月22日, 情報計算化学生物学会大会予稿集, 2008, 77, 英語Relationship between Structural Fluctuation and Positions of Helix 12 in the Nuclear Receptors Studied by Molecular Dynamics Simulation
- 2008年, 分子科学討論会講演プログラム&要旨(Web), 2ndフラグメント分子軌道法によるポリシラン類の物性に関する理論的研究
- 2008年, 日本化学会講演予稿集, 88th(1) (1)フラグメント分子軌道法によるDsRed類縁種の励起状態に関する理論的研究
- エヌ・ティー・エス, 2008年, 未来材料, Vol. 8, No. 9(2008)pp. 40-45(9) (9), 40 - 45, 日本語分子動力学法でみる生体高分子の安定性とダイナミクス[査読有り]記事・総説・解説・論説等（学術雑誌）
- 一般社団法人日本物理学会, 2007年02月28日, 日本物理学会講演概要集, 62(1) (1), 380 - 380, 日本語19pRH-13 光合成における物質の移動と状態変化 : BOXモデルを用いた解析III(環境物理(地球システム・物質循環・生命系),領域13,物理教育,物理学史,環境物理)
- 一般社団法人日本物理学会, 2007年02月28日, 日本物理学会講演概要集, 62(1) (1), 376 - 376, 日本語21pTC-5 分子間力は振動電場の下で増大するか(化学物理一般(光応答・電子状態・シミュレーション),領域12,ソフトマター物理,化学物理,生物物理)
- To elucidate the difference in charge transfer through single- and double-strand DNAs, we performed simulations based on classical molecular dynamics (MD) and semiempirical molecular orbital (MO) methods. Stable structures of DNA strands in water were determined by MD simulations and their energy levels and distributions of frontier MOs that mediate charge transfer were analyzed by the MO calculations. The transfer integrals for a hole or an electron between the neighboring DNA bases were estimated from the energy levels of frontier MOs. We obtained the current-voltage characteristics for single- and double-strand DNAs that are qualitatively in agreement with the experimental results. (c) 2007 Elsevier B.V. All rights reserved.ELSEVIER SCIENCE BV, 2007年02月, CHEMICAL PHYSICS LETTERS, 436(1-3) (1-3), 244 - 251, 英語[査読有り]
- 2007年, 分子科学討論会講演要旨集(CD-ROM), 1stフラグメント分子軌道法を用いたポリペプチドのESP電荷の決定
- 2007年, 分子科学討論会講演要旨集(CD-ROM), 1stFMO-MD/MLFMO-CIS(D)法による水和分子の励起状態シミュレーション
- 2007年, 分子科学討論会講演要旨集(CD-ROM), 1stスピン適合並列化中間状態駆動CASCIプログラムと応用計算
- 2007年, 分子科学討論会講演要旨集(CD-ROM), 1stFMO法における局在化MP2法を用いた相互作用解析:FILMの開発と応用
- 2007年, 分子科学討論会講演要旨集(CD-ROM), 1stフラグメント分子軌道法における大規模Post-HF計算
- Effects of salt addition on strength and dynamics of hydrophobic interactions are investigated by molecular dynamics simulations for hydrophobic solutes in aqueous solution of various salts such as sodium chloride, ammonium chloride, and guanidinium chloride. Hydrophobic interaction is reduced by ammonium chloride, enhanced by sodium chloride, and strongly enhanced by guanidinium chloride. Addition of salts tends to delay the relaxations of hydrophobic associations by reducing water diffusivities and enhancing structuring of water. The underlying molecular mechanisms are discussed in detail. (c) 2006 Elsevier B.V. All rights reserved.ELSEVIER SCIENCE BV, 2007年01月, CHEMICAL PHYSICS LETTERS, 434(1-3) (1-3), 42 - 48, 英語[査読有り]
- 一般社団法人日本物理学会, 2006年08月18日, 日本物理学会講演概要集, 61(2) (2), 306 - 306, 日本語25pWA-11 振動電場下の分子間力の調和振動子モデルによる解析II(25pWA 環境物理(総論・地球システム・物質循環・環境評価・環境技術・環境政策・廃棄物・電磁波・その他),領域13(物理教育,物理学史,環境物理))
- 一般社団法人日本物理学会, 2006年08月18日, 日本物理学会講演概要集, 61(2) (2), 304 - 304, 日本語25aWA-2 光合成における物質の移動と状態変化 : BOXモデルを用いた解析II(25aWA 環境物理(物質循環・生命系・環境教育),領域13(物理教育,物理学史,環境物理))
- 一般社団法人日本物理学会, 2006年03月04日, 日本物理学会講演概要集, 61(1) (1), 409 - 409, 日本語30pZA-3 振動電場下の分子間力の調和振動子モデルによる解析(30pZA 環境物理(総論・電磁波・環境教育・地球システム),領域13(物理教育,物理学史,環境物理))
- 一般社団法人日本物理学会, 2006年03月04日, 日本物理学会講演概要集, 61(1) (1), 410 - 410, 日本語30pZA-7 光合成における物質の移動と状態変化 : BOXモデルを用いた解析(30pZA 環境物理(総論・電磁波・環境教育・地球システム),領域13(物理教育,物理学史,環境物理))
- 2006年, 分子構造総合討論会講演要旨集(CD-ROM), 2006FMO法へのMCPの導入と生体分子系への適用
- 2006年, 分子構造総合討論会講演要旨集(CD-ROM), 2006レチノイドXレセプターのヘリックス12に関する理論的研究
- シーエムシー出版, 2005年11月, 機能材料, 25(11) (11), 6 - 12, 日本語修正電荷平衡(MQEq)法の生体分子系への応用 (特集 電荷平衡法による機能材料設計)
- 一般社団法人日本物理学会, 2005年03月04日, 日本物理学会講演概要集, 60(1) (1), 385 - 385, 日本語25aWK-3 マイクロ波領域の放射場中における誘電体物体間の分散力増大説の検討(環境物理(地球システム,物質循環,エコマテリアル,電磁波),領域13(物理教育,物理学史,環境物理))
- AMER CHEMICAL SOC, 2005年03月, ABSTRACTS OF PAPERS OF THE AMERICAN CHEMICAL SOCIETY, 229, U779 - U779, 英語DNA and estrogen receptor interaction revealed by the fragment molecular orbital calculation.研究発表ペーパー・要旨（国際会議）
- 一般社団法人日本物理学会, 2004年08月25日, 日本物理学会講演概要集, 59(2) (2), 302 - 302, 日本語13pTH-7 Circular dichroism of glycine and polyglycines
- 2004年05月20日, 日本コンピュータ化学会年会講演予稿集, 2004, 86, 日本語フラグメントMO法によるDNAとエストロゲン受容体の相互作用解析
- 一般社団法人日本物理学会, 2003年03月06日, 日本物理学会講演概要集, 58(1) (1), 358 - 358, 日本語29pZD-11 DNA 塩基におけるエナジェティクス
- 一般社団法人日本物理学会, 2003年03月06日, 日本物理学会講演概要集, 58(1) (1), 357 - 357, 日本語29pZD-9 DNA 電子移動における溶媒効果
- 2002年07月03日, 日本コンピュータ化学会年会講演予稿集, 2002(1) (1), 2O02, 日本語分子動力学シミュレーションに基づくDNAの電子移動速度定数の解析
- 一般社団法人日本物理学会, 1993年03月16日, 日本物理学会講演概要集. 年会, 48(3) (3), 289 - 289, 日本語30p-PSA-2 NiOの電子状態
- 一般社団法人日本物理学会, 1992年03月12日, 年会講演予稿集, 47(3) (3), 307 - 307, 日本語28p-PS-78 酸化物超伝導体に対する2キャリア・モデル
- 1991年, Journal of the Physical Society of Japan, 60(7) (7), 2481 - 2482速報，短報，研究ノート等（学術雑誌）
- We review the current status of the theoretical developments in the study of the interparticle correlations in dense plasmas and the transport and elementary processes. The specific features considered are the strong Coulomb-coupling effects in the dense ion systems, the varied degrees of Fermi degeneracy in the electron systems and the mutual coupling between the ion and electron systems. The subjects covered are confined, more or less, to those areas where the authors were able to make some contributions and progress through theoretical studies since the previous review [1]. Relevant experimental works are also cited and are compared with the theoretical results. © 1987.1987年05月, Physics Reports, 149(2-3) (2-3), 91 - 205書評論文,書評,文献紹介等
- 現代思想（青土社）, 2020年02月量子と生命
- 現代化学 No. 579, 東京化学同人, 2019年生体分子夾雑系の理論計算化学：分子論から生命論へ
- Quantum Mechanics in Drug Discovery, Humana Press, 2019年Taking Water into Account with the Fragment Molecular Orbital Method
- 内田老鶴圃, 2018年12月, 日本語, ISBN: 9784753623136計算分子生物学 : 物質科学からのアプローチ
- その他, 東京出版, 2018年05月, 日本語大学への数学 巻頭言「価値を生み出す」一般書・啓蒙書
- 共著, 技術情報協会, 2018年, 日本語In silico創薬におけるスクリーニングの高速化・高精度化技術学術書
- 実験医学, 2017年09月量子生命科学の展望
- American Chemical Society,Distributed in print by Oxford University Press, 2016年, 英語, ISBN: 9780841231795Recent progress in quantum Monte Carlo
- 共著, ACS Symposium Series 1094, American Chemical Society, 2012年, 英語Advances in Quantum Monte Carlo学術書
- 単著, パリティ, 2011年, 日本語量子生物学の展開学術書
- 共編者(共編著者), サイエンスハウス, 2011年, 日本語Amberによる生体高分子シミュレーション入門学術書
- 共著, CRC Press, Boca Raton, U.S.A., 2009年, 英語Excited States of Photoactive Proteins by Configuration Interaction Studies, in "The Fragment Molecular Orbital Method: Practical Applications to Large Molecular Systems ",学術書
- 共著, CRC Press, 2009年, 英語Excited States of Photoactive Proteins by Configuration Interaction Studies, in "The Fragment Molecular Orbital Method: Practical Applications to Large Molecular Systems "学術書
- 共著, CRC Press, 2009年, 英語Developments of FMO Methodology and Graphical User Interface in ABINIT-MP, in "The Fragment Molecular Orbital Method: Practical Applications to Large Molecular Systems "学術書
- 共著, CRC Press, Boca Raton, U.S.A., 2009年, 英語Developments of FMO Methodology and Graphical User Interface in ABINIT-MP, in "The Fragment Molecular Orbital Method: Practical Applications to Large Molecular Systems "学術書
- 共著, CRC Press, Boca Raton, U.S.A., 2009年, 英語Application of FMO Method to Specific Molecular Recognition of Bio-Macromolecules, in "The Fragment Molecular Orbital Method: Practical Applications to Large Molecular Systems"学術書
- 単著, 「発達科学への招待」（かもがわ出版、2008）, 2008年, 日本語学問を学ぶということ―物理学者としての経験から―学術書
- 単著, 「フリーソフトウェアで学ぶ生体分子量子化学計算」（森北出版、2008）, 2008年, 日本語FMO法の今後の展開学術書
- 単著, 大学への数学, 2007年, 日本語対話＜知＞のクロスロード―「大数」読者だったわたし一般書・啓蒙書
- 単著, 大学への数学, 2007年, 日本語新しい「総合理学型」の人材求む！―神戸大学発達科学部人間環境学科へのお誘い一般書・啓蒙書
- 共著, 物性研究, 2007年, 日本語「生体電子物性と環境応答」学術書
- 共著, Elsevier B.V., Amsterdam, The Netherlands, 2006年, 英語Modern Methods for Theoretical Physical Chemistry of Biopolymers学術書
- 共著, Modern Methods for Theoretical Physical Chemistry for Biopolymers, 2006年, 英語Drug Discovery Using Grid Technology学術書
- 共著, Modern Methods for Theoretical Physical Chemistry of Biopolymers, 2006年, 英語Developments and Applications of ABINIT-MP Software Based on the Fragment Molecular Orbital Method学術書
- 共著, Modern Methods for Theoretical Physical Chemistry of Biopolymers, 2006年, 英語Ballistic Conductance for All-Atom Models of Native and Chemically Modified DNA: A Review of Kubo-Formula-Based Approach学術書
- 共著, Advances in Quantum Monte Carlo, 2006年, 英語Ab Initio Biomolecular Calculations Using Quantum Monte Carlo Combined with the Fragment Molecular Orbital Method学術書
- 共著, 機能材料, 2005年, 日本語修正電荷平衡（MQEｑ）法の生体高分子系への応用学術書
- 単著, 「デンドリティック高分子―多分岐構造が拡げる高機能化の世界―」（エヌ・ティー・エス、2005）, 2005年, 日本語デンドリティック高分子の量子化学的シミュレーション学術書
- 「新しい有機太陽電池のオールプラスチック化への課題と対応策」（技術情報協会）, 2004年効率シミュレーション技術とポイント－電流‐電圧特性、光電変換効率へ物性パラメータが及ぼす影響に関して－学術書
- 「色素増感太陽電池及び太陽電池の最前線と将来展望」（情報機構）, 2003年色素増感太陽電池の合理的設計と実用化への課題学術書
- 表面科学, 2003年DNA鎖の第一原理計算の現状と将来学術書
- CICSJ Bull., 2003年DNAを中心とする生体高分子のナノ領域ダイナミクスの解明を目指して学術書
- The 2nd Workshop on Quantum Cognition, 2019年12月, 英語Quantum Brain Dynamics from a Viewpoint of Field Theory[招待有り]口頭発表（招待・特別）
- AHeDD2019/IPAB2019 Joint Symposium, 2019年11月, 英語Perspectives of Computational Drug Discovery: AMED-BINDS Activities in Japan[招待有り]口頭発表（基調）
- 遠隔講義「計算生命科学の基礎VI」, 2019年11月, 日本語大規模分子系の第一原理計算と量子生命科学[招待有り]公開講演，セミナー，チュートリアル，講習，講義等
- 研究会「計算生命科学：多体問題から生命システムへ」, 2019年08月, 日本語多体問題と生命[招待有り]公開講演，セミナー，チュートリアル，講習，講義等
- JST-CREST「生命動態の理解と制御のための基盤技術の創出」研究領域・第12回数理デザイン道場, 2019年08月, 日本語生命と量子[招待有り]口頭発表（招待・特別）
- Himakajima Workshop 2019 Spring on “Multiscale Simulation and Data Science of Complex Molecular Systems, 2019年03月, 英語, Aichi, 国際会議Resonant Energy Transfer in Biological Systems[招待有り]シンポジウム・ワークショップパネル（指名）
- 日本薬学会第139年会シンポジウム「量子化学とAIでみる創薬の世界」, 2019年03月, 日本語, 千葉, 国内会議FMOデータベースの情報科学的な活用[招待有り]シンポジウム・ワークショップパネル（指名）
- 第25回バイオメディカル研究会「バイオテクノロジーの次世代技術」, 2018年10月, 日本語, 大阪, 国内会議ライフサイエンスと量子コンピューティング公開講演，セミナー，チュートリアル，講習，講義等
- CBI学会2018年大会シンポジウム「AMED/BINDSインシリコユニットにおける創薬支援研究」, 2018年10月, 日本語, 東京, 国内会議BINDSインシリコユニットの紹介[招待有り]シンポジウム・ワークショップパネル（指名）
- Chem-Bio Informatics Society(CBI) Annual Meeting 2018, 2018年10月, 英語, Chem-Bio Informatics Society, Tower Hall Funabori (4-1-1 Funabori, Edogawa-ku, Tokyo), Although there are several hypotheses attempting to interpret abiotic synthesis of organic molecules, such as formic acids and amino acid, in the early Earth, the most of them lack the consideration about sustainability of the reactions. We focus on the environment of alkaline hydrothermal vents, which is regarded as one of the most promising places as the origin of life. Membr, 国内会議Ab initio Molecular Dynamics Simulation of Continuous Production of Organic Molecules in Alkaline Hydrothermal Ventsポスター発表
- 第56回日本生物物理学会年会シンポジウム「Basis for Supporting Innovative Drug Discovery and Life Science Research (BINDS)」, 2018年09月, 日本語, 岡山, 国内会議インシリコ創薬の展望[招待有り]シンポジウム・ワークショップパネル（指名）
- 科研費新学術領域「分子夾雑の生命化学」第2回領域会議, 2018年05月, 日本語, 福岡, 国内会議リガンド分子ドッキング－様々な階層での理解－[招待有り]シンポジウム・ワークショップパネル（指名）
- USC-Kobe Bilateral Workshop on Computational Science, 2018年03月, 英語, USA, 国際会議Nonequilibrium Relaxation Processes in Biomolecular Systems[招待有り]シンポジウム・ワークショップパネル（指名）
- 第73回尾張コンプレックスセミナー, 2017年12月, 日本語, 名古屋, 国内会議生体分子系における非平衡緩和の記述公開講演，セミナー，チュートリアル，講習，講義等
- 科学基礎論学会2017年度秋の研究例会シンポジウム「生命科学および認知科学における量子論的アプローチ」, 2017年10月, 日本語, 東京, 国内会議量子生命科学の展望[招待有り]シンポジウム・ワークショップパネル（指名）
- 1st QST International Symposium “Quantum Life Science”, 2017年07月, 英語, Chiba, Japan, 国際会議Charge and Energy Transfer Dynamics in Biological Systems[招待有り]シンポジウム・ワークショップパネル（指名）
- 第1回量子生命科学研究会, 2017年04月, 日本語, 東京, 国内会議量子生命科学の展望[招待有り]口頭発表（招待・特別）
- 日本化学会第97春季年会・特別企画「分子夾雑の生命化学」, 2017年03月, 日本語, 横浜, 国内会議バイオシミュレーションにおける分子夾雑効果[招待有り]口頭発表（招待・特別）
- 公開シンポジウム「気候変動の中での（植物）生態系へのマクロ、ミクロからの考察：光合成、植物進化までを視座に置いて」, 2017年02月, 日本語, 国内会議水和生体分子系の熱力学公開講演，セミナー，チュートリアル，講習，講義等
- FIBER未来大学・第2回研究成果報告会, 2017年01月, 日本語, 神戸, 国内会議水溶液中の生体分子の構造変化に伴う自由エネルギー解析公開講演，セミナー，チュートリアル，講習，講義等
- Workshop on Multiscale Understanding of Nonequilibrium Processes, 2017年01月, 英語, 国際会議Entropic and Enthalpic Contributions to Thermodynamics of Biomolecular Systems公開講演，セミナー，チュートリアル，講習，講義等
- 生物学・光源・物性研究者による量子生物学合宿勉強会, 2016年07月, 日本語, 国内会議電子状態計算を基盤とした量子生物学公開講演，セミナー，チュートリアル，講習，講義等
- FIBER Future College: FIBER国際核酸サミット2016, 2016年07月, 英語, 国際会議Theoretical Study on Dynamics and Functions of Solvated Biomolecules公開講演，セミナー，チュートリアル，講習，講義等
- University of Southern California / Kobe University Joint Research Kick-off Symposium, 2016年03月, 英語, Kobe, 国際会議Possible Applications of Large-Scale Molecular Simulations toward the Understanding of Real World[招待有り]シンポジウム・ワークショップパネル（指名）
- Leipzig University, 2016年02月, 英語, Leipzig, Germany, 国際会議Multiscale Modeling of Photosynthetic Reactions公開講演，セミナー，チュートリアル，講習，講義等
- Karlsruhe Institute of Technology, 2016年02月, 英語, Karlsruhe, Germany, 国際会議Diffusion Monte Carlo Study on Temporal Evolution of Thermodynamic Functions in Nonequilibrium Biomolecular Systems公開講演，セミナー，チュートリアル，講習，講義等
- High Performance Computing Chemistry 2015ワークショップ, 2016年01月, 日本語, 神戸, 国内会議生体分子系のボトムアップ・マルチスケールシミュレーションに向けて[招待有り]シンポジウム・ワークショップパネル（指名）
- University of Bonn, 2016年01月, 英語, Bonn, Germany, 国際会議Fragment Molecular Orbital Approach to Computational Drug Design公開講演，セミナー，チュートリアル，講習，講義等
- バイオスーパーコンピューティング神戸2015, 2015年11月, 日本語, 神戸, 国内会議生体分子系における非平衡過程[招待有り]口頭発表（招待・特別）
- 広島大学地球惑星システム学セミナー, 2015年10月, 日本語, 東広島, 国内会議生命の起源分子生成に関する計算機シミュレーション公開講演，セミナー，チュートリアル，講習，講義等
- 第1回放射線ワークショップ, 2015年10月, 日本語, 富山大学五福キャンパス, 国内会議細胞生存とDNA 損傷を考慮した指標による急性被ばく影響の解析口頭発表（一般）
- CBI学会2015年大会, 2015年10月, 日本語, 東京, 国内会議フラグメント分子軌道法に基づくアカデミア創薬[招待有り]口頭発表（招待・特別）
- スパコン入門セミナー, 2015年09月, 日本語, 神戸, 国内会議物質工学のためのシミュレーション技術：生体分子を中心に公開講演，セミナー，チュートリアル，講習，講義等
- 研究セミナー「環境変動の生態・生理学に関する研究会」, 2015年09月, 日本語, 江別市, 国内会議生体分子系における非平衡過程公開講演，セミナー，チュートリアル，講習，講義等
- 第53回日本生物物理学会年会, 2015年09月, 英語, 日本生物物理学会, 金沢大学 角間キャンパス, Photosystem II (PSII) and Photosystem I (PSI) are the protein complexes which drive photosynthesis in tandem employing electron and excitation-energy transfer processes over a wide timescale range from picoseconds to milliseconds. While the fluorescence emitted by the antenna pigments of these complexes is known as an important indicator of the activity of photosynthesis, its i, 国内会議光合成のマルチ時間スケールダイナミクスに対するシステム解析ポスター発表
- Workshop on “Current Topics in Nano Simulations, 2015年09月, 英語, Tsukuba, 国際会議Nonequilibrium Processes in Biomolecular Systems[招待有り]シンポジウム・ワークショップパネル（指名）
- ワークショップ「量子構造生物学の現状と将来」、第15回日本蛋白質科学会年会, 2015年06月, 日本語, 徳島, 国内会議タンパク質の量子化学計算の現状[招待有り]口頭発表（招待・特別）
- Mini-Symposium on Functional and Biogenous Materials II, 2015年03月, 英語, Okayama University, Okayama, 国際会議Toward First-Principles Simulations for the Origin of Life[招待有り]口頭発表（招待・特別）
- 第56回日本植物生理学会年会, 2015年03月, 英語, 東京, 国内会議Systems Approach to Excitation-Energy and Electron Transfer Reaction Networks in Thylakoid Membrane: Model Studies for Chlorophyll a Fluorescence Inductionポスター発表
- Workshop on Innovation and Pioneering Technology – Innovation by Synergy of Computational & Synchrotron Radiation Sciences (WINTech 2015), 2015年03月, 英語, Kobe University, Kobe, 国際会議FMO Pharmaceutical Applications[招待有り]口頭発表（招待・特別）
- 神戸大学先端融合科学シンポジウム「生体分子のダイナミクスを眺める」, 2015年02月, 日本語, 神戸大学、神戸, 国内会議生体分子ダイナミクスにおける階層性と粗視化[招待有り]口頭発表（招待・特別）
- 第3回先進科学技術活用力養成講座：FMO計算法の創薬への活用, 2015年02月, 日本語, 神戸大学計算科学教育センター、神戸, 国内会議FMO法への期待[招待有り]口頭発表（招待・特別）
- 甲南大学先端生命工学研究所（FIBER）私立大学研究基盤形成支援事業第1回研究成果報告会（FIBER未来大学シリーズ Series 10）, 2015年01月, 日本語, 甲南大学、神戸, 国内会議大規模シミュレーションによる生体分子機能デザインの試み[招待有り]口頭発表（招待・特別）
- 第5回「咲いテク」情報交換会, 2014年10月, 日本語, 神戸高校、神戸, 国内会議高校生を軸に未来の社会を構想する[招待有り]口頭発表（招待・特別）
- 探索医療薬物研究会第2回合同シンポジウム「創薬と医療－基礎と臨床の架け橋」, 2014年09月, 日本語, 大阪薬科大学、高槻, 国内会議大規模分子シミュレーション技術の医療・創薬への応用[招待有り]口頭発表（招待・特別）
- 先進技術活用力養成講座・構造ベース創薬セミナー, 2014年03月, 日本語, 神戸, 国内会議精度の高い相互作用エネルギー解析公開講演，セミナー，チュートリアル，講習，講義等
- Workshop on Current Topics in Nano Simulations (CT-NanoSim2014), 2014年03月, 英語, Tsukuba, 国際会議Multi-Scale Simulations for Complex Biomolecular Systems[招待有り]口頭発表（招待・特別）
- International Workshop on Eigenvalue Problems: Algorithms, Software and Applications in Petascale Computing (EPASA2014), 2014年03月, 英語, Tsukuba, 国際会議Large-Scale Biomolecular Simulations on the Basis of Fragment Molecular Orbital Method[招待有り]口頭発表（招待・特別）
- The 5th JCS International Symposium on Theoretical Chemistry, 2013年12月, 英語, Nara, 国際会議Exploring Theoretical Models for Waterポスター発表
- VINAS Users Conference 2013, 2013年10月, 日本語, 国内会議大規模分子シミュレーションと創薬[招待有り]口頭発表（招待・特別）
- HPCIワークショップ2013, 2013年09月, 日本語, 国内会議第一原理シミュレーションと創薬[招待有り]口頭発表（招待・特別）
- 医薬基盤研究所セミナー, 2013年07月, 英語, 国内会議First-Principles Biomolecular Simulations for Drug Design公開講演，セミナー，チュートリアル，講習，講義等
- 科学基礎論学会2013年度講演会ワークショップ「High Performance Computingの哲学」, 2013年06月, 日本語, 国内会議大規模シミュレーションの意義[招待有り]口頭発表（招待・特別）
- 日本磁気学会第190回研究会「生体物質の物理」, 2013年05月, 日本語, 国内会議第一原理シミュレーションによる生体高分子の電子状態・ダイナミクス・輸送特性の解析[招待有り]口頭発表（招待・特別）
- University of Southern California / Kobe University Joint Research Kick-off Symposium, 2013年03月, 英語, Kobe, 国際会議Possible Applications of Large-Scale Molecular Simulations toward the Understanding of Real World[招待有り]シンポジウム・ワークショップパネル（指名）
- Workshop on Innovation and Pioneering Technology – Recent Development in Drug Discovery Sciences (WINPTech 2012), 2013年02月, 英語, Kobe, 国際会議Structure-Based Drug Design with the Fragment Molecular Orbital Method[招待有り]口頭発表（招待・特別）
- 平成24年度地球シミュレータ利用報告会, 2013年01月, 日本語, 横浜, 国内会議フラグメント分子軌道法を用いた薬剤耐性メカニズムの解析口頭発表（一般）
- Joint Dresden-Japan Workshop on Molecular Scale and Organic Electronic Materials, 2012年12月, 英語, Dresden, Germany, 国際会議Towards the First-Principles and Coarse-Grained Descriptions for Charge and Energy Transfers in Biomolecular Systems[招待有り]口頭発表（招待・特別）
- Indo-Japan Workshop on “Recent Advances in Spectroscopy and Microscopy: Fundamentals and Applications to Materials and Biology”, 2012年11月, 英語, Hyderabad, India, 国際会議Towards the First-Principles and Coarse-Grained Descriptions for Charge and Energy Transfers in Biomolecular Systems[招待有り]口頭発表（招待・特別）
- 日本機械学会第25回計算力学講演会, 2012年10月, 日本語, 神戸, 国内会議フラグメント分子軌道（FMO）計算の現状と今後[招待有り]口頭発表（招待・特別）
- KOBE工学サミットin Tokyoトライアル, 2012年10月, 日本語, 東京, 国内会議スーパーコンピュータによるドラッグデザイン[招待有り]口頭発表（招待・特別）
- 第4回「イノベーション基盤シミュレーションソフトウェアの研究開発」シンポジウム, 2012年07月, 日本語, 東京, 国内会議FMO計算の今後[招待有り]口頭発表（招待・特別）
- 2nd AICS International Symposium – Computer and Computational Sciences for Exascale Computing –, 2012年03月, 英語, 神戸, 国際会議Multi-Scale Simulations for Biomolecular Functions[招待有り]口頭発表（招待・特別）
- NRI-TUD Joint Workshop for Organic Nanomaterials 2012, 2012年03月, 英語, つくば, 国際会議Charge and Energy Transfers in Biomolecular Systems[招待有り]口頭発表（招待・特別）
- 先端融合科学シンポジウム「タンパク質アセンブリ－会合、超分子化、凝集－, 2012年02月, 日本語, 神戸, 国内会議ポリグルタミンペプチドの自由エネルギー地形と凝集機構口頭発表（一般）
- 平成23年度地球シミュレータ利用報告会, 2012年02月, 日本語, 横浜, 国内会議フラグメント分子軌道法を用いた薬剤耐性メカニズムの解析口頭発表（招待・特別）
- HPC産業利用スクール・ナノテクコース, 2012年02月, 日本語, 柏, 国内会議フラグメント分子軌道法のソフトウェア[招待有り]口頭発表（招待・特別）
- 洲本高校インスパイア・ハイスクール, 2012年02月, 日本語, 洲本, 国内会議コンピュータによる計算生命科学口頭発表（招待・特別）
- 先端融合科学シンポジウム タンパク質アセンブリ, 2012年01月, 日本語, 兵庫, 国内会議分子動力学シミュレーションによるポリグルタミンペプチド凝集機構の解明ポスター発表
- 大阪大学蛋白質研究所セミナー「タンパク質科学の未来を語る－実験・理論研究者の対話－」, 2011年11月, 日本語, 豊中, 国内会議タンパク質の電子状態計算から機能解析へ[招待有り]口頭発表（招待・特別）
- FIBER International Symposium, FIBER FORUM 2011, 2011年11月, 英語, 兵庫, 国際会議Aggregation mechanism of polyglutamine peptides in water by replicaポスター発表
- CBI/JSBi 2001合同大会, 2011年11月, 英語, 兵庫, 国際会議Aggregation mechanism of polyglutamine peptides in water by replicaポスター発表
- 日本生物物理学会年会, 2011年09月, 英語, 日本生物物理学会, 兵庫, 国際会議Comparison of Antigen-Antibody Binding by the Fragment Molecular Orbital Calculations for Swine-Origin Influenza Hemagglutinin Proteins口頭発表（一般）
- 第４回バイオナノシステムズ研究会, 2011年08月, 日本語, 神戸, 国内会議蛋白質の電子状態計算と医療・創薬・環境科学への応用[招待有り]口頭発表（招待・特別）
- 鳥取大学応用数理工学セミナー, 2011年06月, 日本語, 鳥取, 国内会議第一原理生体分子シミュレーションの展開[招待有り]口頭発表（招待・特別）
- 神戸大学統合研究拠点設置記念・システム情報学研究科１周年合同シンポジウム, 2011年06月, 日本語, 神戸, 国内会議創薬とシミュレーション口頭発表（招待・特別）
- 第11回日本蛋白質科学会年会, 2011年06月, 日本語, 大阪, 国内会議コンピューターシミュレーションによるポリグルミタミンペプチドの特性解析ポスター発表
- Technische Universitat Dresden, 2011年06月, 英語, Dresden, Germany, 国際会議Large-Scale Ab Initio Simulations for Biomolecular Systems[招待有り]口頭発表（招待・特別）
- Karlsruhe Institute of Technology, 2011年06月, 英語, Karlsruhe, Germany, 国際会議Large-Scale Ab Initio Simulations for Biomolecular Systems[招待有り]口頭発表（招待・特別）
- th JCS Symposium on Theoretical Chemistry,, 2011年05月, 英語, Liblice, Czech Republic, 国際会議Large-Scale Ab Initio Simulations for Biomolecular Systems[招待有り]口頭発表（招待・特別）
- Pacifichem2010, 2010年12月, 英語, Honolulu, 国際会議Ab initio path integral molecular dynamics and Monte Carlo simulations for water trimer and oligopeptide口頭発表（一般）
- サイエンスカフェ鳥取, 2010年11月, 日本語, 鳥取, 国内会議スーパーコンピュータが変える医療の未来!?口頭発表（招待・特別）
- 日本科学教育学会年会, 2010年09月, 日本語, 日本科学教育学会, 広島大学, 国内会議兵庫県における持続可能な社会に向けた市民科学活動支援の取組と事例紹介口頭発表（一般）
- 第4回分子科学討論会, 2010年09月, 日本語, 大阪, 国内会議周期境界条件フラグメント分子軌道法の開発ポスター発表
- CBI学会2010年大会, 2010年09月, 英語, 東京, 国際会議Energy analysis of polyglutamine peptides by MM-GB/SA methodポスター発表
- 第10回蛋白質科学会, 2010年06月, 日本語, 札幌, 国内会議レプリカ交換MDによるポリグルタミンペプチドの自由エネルギー地形解析ポスター発表
- 日本コンピュータ化学会2010春季年会, 2010年05月, 日本語, 東京, 国内会議分子動力学シミュレーションによるインフルエンザウイルスNS1タンパク質とdsRNAの結合解析ポスター発表
- 第13回理論化学討論会, 2010年05月, 日本語, 北海道, 国内会議周期境界条件フラグメント分子軌道法の開発ポスター発表
- 次世代ナノ統合シミュレーションソフトウェアの研究開発 第５回公開シンポジウム, 2010年02月, 日本語, 神戸, 国内会議レプリカ分子動力学法によるポリグルタミンペプチドの自由エネルギー地形解析ポスター発表
- 第23回KOBE工学サミット, 2010年, 英語, 第23回KOBE工学サミット, 神戸, 国際会議生体分子系の機能を探る第一原理ボトムアップ・シミュレーション口頭発表（招待・特別）
- 九州大学第10回化学・材料研究セミナー, 2010年, 日本語, 九州大学, 九州大学国際ホール, 国内会議生体高分子の第一原理計算：量子構造生物学の創成に向けて口頭発表（招待・特別）
- 平成22年度地球シミュレータ利用報告会, 2010年, 日本語, 海洋研究開発機構横浜研究所, 海洋研究開発機構横浜研究所三好記念講堂, 国内会議フラグメント分子軌道法を用いた薬剤耐性メカニズムの解析口頭発表（招待・特別）
- 地球シミュレータ産業利用シンポジウム2010, 2010年, 英語, 地球シミュレータ産業利用シンポジウム, 鳥取, 国内会議スーパーコンピュータでインフルエンザウイルスの変異の仕組みを探る口頭発表（招待・特別）
- 洲本高校インスパイア・ハイスクール, 2010年, 日本語, 兵庫県立洲本高校, 兵庫県立洲本高校, 国内会議コンピュータによる計算生命科学その他
- Indo-Japan Joint Workshop on “New Frontiers of Molecular Spectroscopy: From Gas Phase to Proteins, 2010年, 英語, Indo-Japan Joint Workshop on “New Frontiers of Molecular Spectroscopy: From Gas Phase to Proteins, 神戸, 国際会議Large-Scale Biomolecular Calculations on the Basis of Fragment Molecular Orbital Method口頭発表（招待・特別）
- Pacifichem 2010, 2010年, 英語, Symposium “Advances in Quantum Monte Carlo” in the 2010 International Chemical Congress of Pacific Basin Societies, Honolulu, Hawaii, 国際会議Ab Initio Path Integral Molecular Dynamics and Monte Carlo Simulations for Water Trimer and Oligopeptides” (Symposium “Advances in Quantum Monte Carlo”口頭発表（一般）
- Quantum Systems in Chemistry and Physics Workshop (QSCP-XV), 2010年, 英語, Quantum Systems in Chemistry and Physics Workshop (QSCP-XV), Magdalene College, Cambridge, England, 国際会議Ab Initio FMO Approach to Biomolecular Reactions口頭発表（招待・特別）
- 地球シミュレータ利用報告会, 2010年01月, 日本語, 海洋研究開発機構横浜研究所三好記念講堂, 国内会議フラグメント分子軌道法を用いた薬剤耐性メカニズムの解析口頭発表（招待・特別）
- 徳島大学創薬理論化学セミナー, 2010年01月, 日本語, 徳島大学, 国内会議フラグメント分子軌道法に基づく生体分子シミュレーション口頭発表（招待・特別）
- 第23回分子シミュレーション討論会, 2009年12月, 日本語, 名古屋市中小企業振興会館, 国内会議生体分子系の大規模第一原理シミュレーションに向けて口頭発表（招待・特別）
- 蛋白研セミナー 「分子科学を基盤とした生命活動への理論的アプローチ」, 2009年12月, 日本語, 大阪大学, 国内会議フラグメント分子軌道(FMO)法が明らかにする立体構造と電子状態の関係:複合体形成に伴うタンパク質内電子状態変化の解析口頭発表（招待・特別）
- International Symposium of Electronic Structure Calculations -Theory, Correlated and Large Scale Systems and Numerical Methods-, 2009年12月, 英語, The university Tokyo, 国際会議Possibility of the Prediction for Mutations of Influenza Hemagglutinin by a Combination of Ab initio Molecular Simulation and Hemadsorption Experimentポスター発表
- International Symposium of Electronic Structure Calculations -Theory, Correlated and Large Scale Systems and Numerical Methods-, 2009年12月, 英語, 東京大学, 国際会議Ab Initio Quantum Simulation Basedポスター発表
- International Symposium of Electronic Structure Calculations – Theory, Correlated and Large Scale Systems and Numerical Methods –, 2009年12月, 英語, The University of Tokyo, 国際会議Ab Initio Biomolecular Simulations Based on the Fragment Molecular Orbital Method口頭発表（招待・特別）
- 第７回地球シミュレータシンポジウム, 2009年11月, 日本語, 日本科学未来館, 国内会議タンパク質シミュレーションの拓く世界：インフルエンザウイルスの変異予測まで口頭発表（招待・特別）
- CBI KSBSB Joint Conference, BIOINFO 2009, 2009年11月, 英語, Busan, Korea, 国際会議Incorporation of solvation effect with Poisson-Boltzmann equation into FMO methodポスター発表
- CBI KSBSB Joint Conference, BIOINFO 2009, 2009年11月, 英語, Busan, 国際会議Fragment Molecular Orbital (FMO) Method: Application to Drug Discovery口頭発表（招待・特別）
- Institute of Chemistry, Academia Sinica, 2009年11月, 英語, Taipei, 国際会議Ab Initio Biomolecular Simulations Based on the Fragment Molecular Orbital Method口頭発表（招待・特別）
- 「シミュレーション技術の革新と実用化基盤の構築」第5回シンポジウム, 2009年10月, 日本語, 東京大学弥生講堂, 国内会議フラグメント分子軌道法による生体分子計算システムの開発口頭発表（招待・特別）
- 日本生物物理学会第47回年会, 2009年10月, 日本語, 徳島, 国内会議RNA結合タンパク質における疎水表面を用いた塩基認識機構の検証: NOVA-RNA複合体系での研究ポスター発表
- 第47回日本生物物理学会, 2009年10月, 英語, アスティ徳島, 国際会議Possibility of Mutation Prediction of Influenza Hemagglutinin by Combination of Hemadsorption Experiment and Quantum Chemical Calculation for Antibody Binding口頭発表（招待・特別）
- 第４７回日本生物物理学会年会, 2009年10月, 英語, 徳島, 国内会議Characterization of monomeric polyglutamine peptides by replica exchange molecular dynamics simulationポスター発表
- 日本物理学会2009年秋季大会, 2009年09月, 日本語, 熊本大学, 国内会議大規模シミュレーションによる生体反応の理解口頭発表（招待・特別）
- 第58回高分子討論会, 2009年09月, 日本語, 国内会議生体高分子における分子認識と情報伝達―計算機シミュレーションの立場から口頭発表（招待・特別）
- Institute of Atomic and Molecular Sciences, Academia Sinica, 2009年09月, 英語, National Taiwan University, 国際会議Understanding Protein Functions through First-Principles Molecular Simulations口頭発表（招待・特別）
- National Chiao Tung Tung University, 2009年09月, 英語, Hsinchu, 国際会議Ab Initio Biomolecular Simulations Based on the Fragment Molecular Orbital Method口頭発表（招待・特別）
- 日本科学教育学会年会, 2009年08月, 日本語, 日本科学教育学会, 同志社女子大学, 国内会議地域社会における市民科学活動支援システムの構築口頭発表（一般）
- 第318回「医学研究の基礎を語り合う集い」, 2009年07月, 日本語, 東京慈恵会医科大学, 国内会議大規模第一原理分子シミュレーションによるインフルエンザウイルスの理論解析口頭発表（招待・特別）
- CREST International Symposium on Theory and Simulations of Complex Molecular Systems, 2009年07月, 英語, Fukui Institute for Fundamental Chemistry, 国際会議Large-Scale Biomolecular Simulations Based on the Fragment Molecular Orbital Method口頭発表（招待・特別）
- 第12回理論化学討論会, 2009年05月, 日本語, 東京, 国内会議赤血球凝集反応実験と量子化学計算に基づく インフルエンザウイルス・ヘマグルチニンの変異予測ポスター発表
- 大阪大学サイバーメディアセンター・セミナー, 2009年05月, 日本語, 大阪大学サイバーメディアセンター, 国内会議生体分子系の大規模第一原理計算からインフルエンザウイルスの変異予測まで口頭発表（招待・特別）
- 第9回日本蛋白質科学会年会, 2009年05月, 日本語, 熊本, 国内会議レプリカ交換MDによるポリグルタミンタンパクの構造解析；Conformation ensemble of polyglutamine peptide by replica exchange molecular dynamics.ポスター発表
- 日本コンピュータ化学会春季年会2009年春季年会, 2009年05月, 日本語, 東京, 国内会議Poisson-Boltzmann方程式によるFMO法への溶媒効果の取り込みポスター発表
- International Conference on Computational & Experimental Engineering & Sciences 2009 (ICCES’09), 2009年04月, 英語, Phuket, 国際会議Fragment Molecular Orbital Method for Large-Scale Biomolecular Systems口頭発表（招待・特別）
- 日本物理学会第６４回年次大会, 2009年03月, 日本語, 東京, 国内会議核内受容体における揺らぎと構造変化の線形応答理論解析口頭発表（一般）
- 日本物理学会第64回年次大会, 2009年03月, 日本語, 東京, 国内会議フラグメント分子軌道法を用いた経路積分分子動力学法の開発口頭発表（一般）
- 第８回蛋白質科学会, 2009年02月, 日本語, 東京, 国内会議計算機シミュレーションによるRNA結合タンパク質NOVAの塩基配列特異性の研究ポスター発表
- Supercomputing in Solid State Physics (SciSSP) 2009, 2009年02月, 英語, 柏, 国際会議Relationship between Structural Fluctuation and Positions of Helix 12 in Nuclear Receptors Studied by Molecular Dynamics Simulationポスター発表
- スーパーコンピューターワークショップ2009「次世代理論化学の新展開と超並列計算への挑戦」, 2009年01月, 日本語, 岡崎, 国内会議赤血球凝集反応実験と量子化学計算に基づくインフルエンザウイルス・ヘマグルチニンの変異予測ポスター発表
- スーパーコンピュータワークショップ2009, 2009年01月, 日本語, 愛知, 国内会議フラグメント分子軌道法を用いた経路積分分子動力学法の開発ポスター発表
- スーパーコンピューターワークショップ2009「次世代理論化学の新展開と超並列計算への挑戦」, 2009年01月, 日本語, 岡崎, 国内会議フラグメント分子軌道法を用いたポリペプチドのESP電荷の決定と古典MDへの応用ポスター発表
- バイオスーパーコンピューティングシンポジウム(BSCS)2008, 2008年12月, 日本語, 東京, 国内会議赤血球凝集反応実験と量子化学計算に基づくインフルエンザウイルス・ヘマグルチニンの変異予測ポスター発表
- バイオスーパーコンピューティングシンポジウム(BSCS)2008, 2008年12月, 日本語, 東京, 国内会議フラグメント分子軌道法を用いたポリペプチドのESP電荷の決定とMD応用ポスター発表
- バイオスーパーコンピューティングシンポジウム(BSCS)2008, 2008年12月, 日本語, 東京, 国内会議Structure Based Drug Designにおける計算手法の評価 (1)フラグメント分子軌道法によるタンパク質・リガンド結合エネルギーポスター発表
- 第22回分子シミュレーション討論会, 2008年11月, 日本語, 岡山, 国内会議レプリカ交換MDによるポリグルタミンタンパクの構造解析ポスター発表
- JST-CREST 第4回「シミュレーション技術の革新と実用化基盤の構築」領域シンポジウム, 2008年11月, 日本語, 東京, 国内会議フラグメント分子軌道法に基づく古典力学的分子シミュレーションポスター発表
- 第11回スーパーコンピューティング・セミナー, 2008年11月, 日本語, スーパーコンピューティング技術産業応用協議会, 東京, 国内会議FMO法による生体高分子の第一原理計算口頭発表（招待・特別）
- 第2回分子科学討論会, 2008年10月, 日本語, 福岡, 国内会議第一原理経路積分法を用いたポリペプチドにおける同位体効果の解析ポスター発表
- 大学連携「ひょうご講座」, 2008年10月, 日本語, 神戸, 国内会議「奪われし未来」と環境ホルモン口頭発表（招待・特別）
- CBI学会2008 年大会, 2008年10月, 英語, 東京, 国際会議Relationship between Structural Fluctuation and Positions of Helix 12 in the Nuclear Receptors Studied by Molecular Dynamics Simulationポスター発表
- CBI学会2008 年大会, 2008年10月, 英語, 東京, 国際会議Determination of ESP charges on polypeptides using the fragment molecular orbital method and the applications for molecular simulationsポスター発表
- 第2回分子科学討論会, 2008年09月, 日本語, 福岡, 国内会議実用を目指した生体高分子の第一原理計算口頭発表（招待・特別）
- 第2回分子科学討論会, 2008年09月, 日本語, 福岡, 国内会議フラグメント分子軌道法計算を応用したインフルエンザヘマグルチニンの変異基盤解析ポスター発表
- 第二回分子科学討論会2008福岡, 2008年09月, 日本語, 福岡, 国内会議ハロ酸脱ハロゲン化酵素（L-DEX YL）によるL-2-chloro propionic acid 脱ハロゲン化反応機構の理論的解析ポスター発表
- WATOC 2008, 2008年09月, 英語, オーストラリア, 国際会議Theoretical Study on Isotope Effects in Polypeptides Based on Path Integral Molecular Dynamics and Fragment Molecular Orbital Methodポスター発表
- The International Conference on Theory and Applications of Computational Chemistry 2008, 2008年09月, 英語, China, 国際会議Applications of the Fragment Molecular Orbital Method to Biomolecular Systems口頭発表（招待・特別）
- 生物物理若手の会・関西３支部合同セミナー, 2008年08月, 日本語, 神戸, 国内会議生体分子の第一原理ボトムアップ・シミュレーション―実用を目指して―口頭発表（招待・特別）
- 岐阜大学人獣感染防御研究センターセミナー, 2008年08月, 日本語, 岐阜, 国内会議フラグメント分子軌道法によるインフルエンザ・ヘマグルチニンの相互作用解析口頭発表（招待・特別）
- 236th ACS National Meeting, 2008年08月, 英語, アメリカ, 国際会議Simulation study of the RNA binding protein, NOVA-2, by Fragment molecular orbital (FMO) methodポスター発表
- 6th Congress of the International Society for Theoretical Chemical Physics, 2008年07月, 英語, Canada, 国際会議Quantum Monte Carlo Combined with Fragment Molecular Orbital Method口頭発表（招待・特別）
- 第8回蛋白質科学会年会, 2008年06月, 日本語, 東京, 国内会議分子動力学シミュレーションによるポリグルタミンの構造安定性の置換解析ポスター発表
- 第８回日本蛋白質科学会年会, 2008年06月, 日本語, 東京, 国内会議フラグメント分子軌道法（FMO 法）によるインフルエンザウイルスヘマグルチニンと抗体間の抗原変異予測へ向けた相互作用解析ポスター発表
- 第11回理論化学討論会, 2008年05月, 日本語, 横浜, 国内会議変異のあるエストロゲン受容体とリガンドの結合エネルギーの第一原理的解析ポスター発表
- 第11回理論化学討論会, 2008年05月, 日本語, 横浜, 国内会議分子動力学シミュレーションによるポリグルタミンの構造安定性の置換解析ポスター発表
- 第11回理論化学討論会, 2008年05月, 日本語, 横浜, 国内会議第一原理経路積分法を用いたポリペプチドにおける同位体効果の解析ポスター発表
- 第11回理論化学討論会, 2008年05月, 日本語, 横浜, 国内会議フラグメント分子軌道法を用いたポリペプチド・タンパク質のESP電荷の決定とMD応用ポスター発表
- フラグメント分子軌道法によるインフルエンザヘマグルチニンの変異予測可能性, 2008年05月, 日本語, 横浜, 国内会議フラグメント分子軌道法によるインフルエンザヘマグルチニンの変異予測可能性ポスター発表
- University of Aarhus, 2008年05月, 英語, Denmark, 国際会議Developments and Applications of Fragment Molecular Orbital Method口頭発表（招待・特別）
- 文部科学省大学院教育改革支援プログラム「大学連合による計算科学の最先端人材育成」第1回若手シミュレーションスクール SS2007, 2008年03月, 日本語, 神戸, 国内会議生体分子系の第一原理ボトムアップ的シミュレーション口頭発表（招待・特別）
- 第３回「電子状態計算における電子相関の諸問題」研究会, 2007年12月, 日本語, 北陸先端科学技術大学院大学, 石川県能美市, 国内会議「生体分子第一原理計算における電子相関の役割」口頭発表（招待・特別）
- 神戸大学理学部・物性セミナー, 2007年12月, 日本語, 神戸大学理学部, 国内会議「フラグメント分子軌道法による生体高分子系の第一原理計算」口頭発表（招待・特別）
- 第45回生物物理学会, 2007年12月, 日本語, パシフィコ横浜, 国内会議Theoretical study on the physicochemical properties of Pumilio RNA-binding domain by Fragment Molecular Orbital (FMO) methodポスター発表
- 独立行政法人科学技術振興機構（JST）「シミュレーション技術の革新と実用化基盤の構築」CREST・さきがけシンポジウム, 2007年11月, 日本語, 独立行政法人科学技術振興機構（JST）, 慶応義塾大学（三田）, 国内会議フラグメント分子軌道法による生体分子計算システムの開発口頭発表（招待・特別）
- 徳島大学薬学部・薬品物理化学特論集中講義, 2007年10月, 日本語, 徳島大学薬学部, 徳島大学薬学部, 国内会議「フラグメント分子軌道法による生体高分子の電子状態計算手法の開発」口頭発表（招待・特別）
- CBI学会2007年大会, 2007年10月, 英語, 広島大学, 国際会議Molecular dynamics simulation study on the structural stabilities of polyglutamine peptidesポスター発表
- CBI学会2007年大会, 2007年10月, 英語, 広島大学, 国際会議Computational Evalution of Binding Energy of Mutated Estrogen Receptors with the Fragment Molecular Orbital Methodポスター発表
- 第１回分子科学討論会, 2007年09月, 日本語, 東北大学, 国内会議分子動力学シミュレーションによるポリグルタミンの構造安定性の解析ポスター発表
- 神戸大学自然科学先端融合研究環・材料物理コロキウム, 2007年09月, 日本語, 神戸大学自然科学先端融合研究環, 神戸大学自然科学先端融合研究環, 国内会議「フラグメント分子軌道法による大規模系電子状態の高速計算」口頭発表（招待・特別）
- 第１回分子科学討論会, 2007年09月, 日本語, 東北大学, 国内会議レチノイドXレセプターのへリックス12の変位機構に関する理論的研究ポスター発表
- 第１回分子科学討論会, 2007年09月, 日本語, 東北大学, 国内会議フラグメント分子軌道法を用いたポリペプチドのESP電荷の決定ポスター発表
- 第１回分子科学討論会, 2007年09月, 日本語, 東北大学, 国内会議フラグメント分子軌道法によるアミノ酸変異のあるエストロゲン受容体のリガンド結合エネルギーの解析ポスター発表
- 第１回分子科学討論会, 2007年09月, 日本語, 東北大学, 国内会議インフルエンザウイルス感染の分子メカニズムを第一原理計算で探るポスター発表
- 第１回分子科学討論会, 2007年09月, 日本語, 東北大学, 国内会議RNA結合タンパク質NOVA2の塩基配列特異的結合機構の理論研究ポスター発表
- Asia Pacific Physics Conference 10, 2007年08月, 英語, Pohang, Korea, 国際会議Effects of non-thermal radiative electromagnetic field on dispersion forcesポスター発表
- ISSP International Workshop and Symposium on Foundations and Applications of the Density Functional Theor, 2007年08月, 英語, Institute for Solid State Physics, University of Tokyo, 国際会議Biomolecular Calculations Based on Electron-Correlated Fragment Molecular Orbital Methods口頭発表（招待・特別）
- The 22nd International Course & Conference on the Interfaces among Mathematics, 2007年06月, 英語, Chemistry & Computer Sciences, クロアチア・ドブロブニク, 国際会議AB INITIO FRAGMENT MOLECULAR ORBITAL STUDY OF MOLECULAR INTERACTIONS BETWEEN LIGANDED RETINOID X RECEPTOR AND ITS COACTIVATORポスター発表
- 第１０回理論化学討論会, 2007年05月, 日本語, 名古屋大学, 国内会議レチノイドXレセプターとコアクチベーターの相 互作用に関する理論的研究ポスター発表
- 理研研究会「分子系の構造と電子状態－『生物物質科学』を目指して」, 2007年04月, 日本語, 理化学研究所, 理化学研究所、和光市, 国内会議「DNAの電子状態」口頭発表（招待・特別）
- 日本物理学会春季大会, 2007年03月, 日本語, 鹿児島大学, 国内会議分子間力は振動電場の下で増大するか口頭発表（一般）
- 日本物理学会 2007年春季大会, 2007年03月, 日本語, 鹿児島大学, 国内会議光合成における物質の移動と状態変化－BOXモデルを用いた解析III－口頭発表（一般）
- Symposium in Honor of Professor William A. Lester Jr’s 70th Birthday, 2007年03月, 英語, Berkeley, CA, USA, 国際会議Quantum Monte Carlo Calculations of Biomolecules Based on Fragment Molecular Orbital Method[招待有り]口頭発表（招待・特別）
- University of California, 2007年03月, 英語, San Diego, CA, USA, 国際会議Applications of the Fragment Molecular Orbital Method to Biomolecular Systems[招待有り]口頭発表（招待・特別）
- 第二回「電子状態計算における電子相関の諸問題 」研究会, 2007年02月, 英語, 北海道大学(ファカルティハウスエンレイソウ), 国際会議A New Approach for the Electron Correlation in Biological Molecules: Combination of Quantum Monte Carlo Method and Fragment Molecular Orbital Method口頭発表（一般）
- 「シミュレーション技術の革新と実用化基盤の構築」, 2007年01月, 日本語, 東京, 国内会議核酸-タンパク質複合体のFMO計算と相互作用解析の可視化ポスター発表
- 独立行政法人科学技術振興機構（JST）「シミュレーション技術の革新と実用化基盤の構築」第2回シンポジウム, 2007年01月, 日本語, 東京, 国内会議フラグメント分子軌道法による生体分子計算システムの開発口頭発表（招待・特別）
- Theory and simulation of biomolecular nano-machines, 2006年12月, 英語, Hyogo, Japan, 国際会議Theoretical study on the physicochemical properties of Pumilio RNA-binding domain by quantum chemical calculationsポスター発表
- 第7回先端医療セミナー, 2006年11月, 日本語, 先端医療振興財団・臨床研究情報センター、神戸, 国内会議生体高分子の第一原理シミュレーションの最近の展開口頭発表（招待・特別）
- 第34回構造活性相関シンポジウム, 2006年11月, 日本語, 神戸, 国内会議生体高分子ドッキング解析システムMIZUHO/BioStationの開発その他
- Fifth East Asian Biophysics Symposium & Forty-Fourth Annual Meeting of the Biophysical Society of Japan, 2006年11月, 英語, Okinawa, Japan, 国際会議Theoretical study on the physicochemical properties of Pumilio RNA-binding domain by quantum chemical calculationsポスター発表
- 京都大学基礎物理学研究所研究会「環境物理学－先端領域の創出へ向けて－」, 2006年10月, 日本語, 京都大学基礎物理学研究所、京都, 国内会議生体電子物性と環境応答口頭発表（招待・特別）
- 大学連携「ひょうご講座」、環境科学の金字塔と今後への展開, 2006年10月, 日本語, 兵庫県立神戸学習プラザ、神戸, 国内会議「奪われし未来」をめぐって口頭発表（招待・特別）
- 分子構造総合討論会, 2006年09月, 日本語, 静岡, 国内会議二酸化炭素固定酵素Rubisco改良に向けた分子シミュレーションポスター発表
- 分子構造総合討論会, 2006年09月, 日本語, 静岡, 国内会議疎水性相互作用へのイオンによる影響の検討ポスター発表
- 日本物理学会秋季大会, 2006年09月, 日本語, 千葉大学, 国内会議振動電場下の分子間力の調和振動子モデルによる解析II口頭発表（一般）
- 日本物理学会秋季大会, 2006年09月, 日本語, 千葉大学, 国内会議光合成における物質の移動と状態変化−BOXモデルを用いた解析II−口頭発表（一般）
- 分子構造総合討論会, 2006年09月, 日本語, 静岡, 国内会議レチノイドＸレセプターのヘリックス１２に関する理論的研究ポスター発表
- XIIth International Congress of Quantum Chemistry, 2006年09月, 英語, 京都, 国際会議Molecular Interactions Between Estrogen Receptor and its Ligand studied by the ab initio fragment molecular orbital methodポスター発表
- 分子構造総合討論会, 2006年09月, 日本語, 静岡, 国内会議FMO法へのMCPの導入と生体分子系への適用ポスター発表
- 2006 Annual meeting of CBI society, 2006年07月, 英語, 東京, 国際会議Intra- and intermolecular interactions between cyclic-AMP receptor protein and DNA: Ab initio fragment molecular orbital studyポスター発表
- 東京工業大学, 2006年06月, 日本語, 東京, 国内会議疎水性相互作用へのイオンによる影響の検討口頭発表（一般）
- Charge Migration in DNA, University of Manitoba, 2006年06月, 英語, Winnipeg, Canada, 国際会議Ab initio Studies on electronic structure of DNAポスター発表
- XIIth International Congress of Quantum Chemistry, 2006年05月, 英語, 京都, 国際会議Intra- and intermolecular interactions between cyclic-amp receptor protein and DNA: Ab initio fragment molecular orbital studyポスター発表
- The XIIth International Congress of Quantum Chemistry, 2006年05月, 英語, 京都, 国際会議Computational Study for Improvement of Carbon Fixation Enzyme, Rubisco, with Fragment Molecular Orbital Methodポスター発表
- The XIIth International Congress of Quantum Chemistry, 2006年05月, 英語, 京都, 国際会議A Combinatorial Approach of Quantum Monte Carlo Method and Fragment Molecular Orbital Methodシンポジウム・ワークショップパネル（公募）
- 日本コンピューター化学会2005春季年会・特別講演, 2005年05月, 日本コンピューター化学会, 東京工業大学（東京）,, 国内会議「フラグメント分子軌道法に基づく生体分子計算システムの開発」口頭発表（一般）
- QEq2005; The state of the arts of QEq (Charge Equilibration), 2005年05月, 奈良県新公会堂（奈良市）,, 国内会議“Application of MQEq (Modified Charge Equilibration) to the Biological System”口頭発表（一般）
- 日本コンピューター化学会2005春季年会, 2005年, 日本語, 東京工業大学、東京, 国内会議「フラグメント分子軌道法に基づく生体分子計算システムの開発」口頭発表（招待・特別）
- 第250回CBI学会研究講演会, 2005年, 日本語, 日本化学会化学会館、東京, 国内会議「FMO法による核内受容体へのアプローチ」口頭発表（招待・特別）
- 「生命量子科学」研究会, 2005年, 日本語, 総合研究大学院大学葉山高等教育センター、神奈川県葉山町, 国内会議「DNAのナノ領域ダイナミクスの第一原理的解析」口頭発表（招待・特別）
- 「情報」の視点からの環境科学へのアプローチ, 2005年, 日本語, 大学連携「ひょうご講座」, 兵庫県立神戸学習プラザ、神戸, 国内会議バイオインフォマティクスと環境科学口頭発表（招待・特別）
- Symposium “Advances in Quantum Monte Carlo” in the 2005, 2005年, 英語, International Chemical Congress of Pacific Basin Societie, Honolulu, Hawaii, USA, 国際会議Biomolecular Calculations Using Ab Initio Quantum Monte Carlo Technique Combined with Fragment Molecular Orbital Method口頭発表（招待・特別）
- QEq2005; The state of the arts of QEq (Charge Equilibration, 2005年, 英語, 奈良県新公会堂、奈良市, 国際会議Application of MQEq (Modified Charge Equilibration) to the Biological System口頭発表（招待・特別）
- 独立行政法人科学技術振興機構（JST）平成16年度「シミュレーション技術の革新と実用化基盤の構築」研究報告会, 2004年12月, 独立行政法人科学技術振興機構（JST）, JST東京本部（東京）,, 国内会議「フラグメント分子軌道法による生体分子計算システムの開発」口頭発表（一般）
- 独立行政法人科学技術振興機構（JST）計算科学技術活用型特定研究開発推進事業・平成13年度採択課題終了シンポジウム, 2004年10月, 独立行政法人科学技術振興機構（JST）, TEPIAホール（東京）,, 国内会議「DNAのナノ領域ダイナミクスの第一原理的解析」口頭発表（一般）
- The Ninth Asia Pacific Physics Conference (9th APPC), 2004年10月, 英語, Association of Asia Pacific Physics Societies, Hanoi, ヴェトナム, 国際会議CD spectra of glycine and polyglycine[招待有り]口頭発表（招待・特別）
- CBI学会人材育成シンポジウム, 2004年08月, 日本化学会, 日本化学会化学会館（東京）,, 国内会議「新しい時代に皆で考えたいこと」口頭発表（一般）
- 分子科学研究所研究会「分子機能の物理化学－理論・計算化学と分光学による新展開－」, 2004年07月, 分子科学研究所研究会, 自然科学研究機構岡崎コンファレンスセンター（岡崎）,, 国内会議「核酸および蛋白質の分子計算からマクロな機能発現へ向けて」口頭発表（一般）
- 第102回自然環境論セミナー, 2004年05月, 神戸大学発達科学部（神戸）,, 国内会議「コンピュータによる疾病や化学物質影響の分子モデリング」口頭発表（一般）
- 2003年10月, 産業技術総合研究所生命情報科学研究センター（東京）,, 国内会議「Ab Initio Approach to Nanoscale Dynamics of DNA」口頭発表（一般）
- 226th American Chemical Society National Meeting, 2003年09月, ***（New York City, USA),, 国内会議“Quantum Monte Carlo Descriptions of Molecular Interactions Relevant to Biopolymers”口頭発表（一般）
- 2003年09月, Brock University（St. Catharines, Canada),, 国内会議“Ab Initio Approach to Nanoscale Dynamics of DNA”口頭発表（一般）
- The 7th World Multi-Conference on Systemics, Cybernetics and Informatics (SCI 2003), 2003年07月, ***(Orlando, Florida, USA),, 国内会議“Theoretical Modeling for Electron Transfer and Transport in DNA”口頭発表（一般）
- 企業研究会第16期CAMMフォーラム５月例会, 2003年05月, 企業研究会, 虎ノ門パストラル（東京）,, 国内会議「DNA・蛋白質の電子構造とダイナミクス」口頭発表（一般）
- 「有機太陽電池の高効率・プラスチック化への課題と対策」技術セミナー, 2003年04月, 技術情報協会, 五反田ゆうぽうと（東京）,, 国内会議「湿・乾式セル・モジュールにおける効率シミュレーション技術とポイント」口頭発表（一般）
- 第229回CBI学会研究講演会, 2003年03月, CBI学会, 日本化学会化学会館（東京）,, 国内会議「核内受容体を介する疾患モデルと創薬への応用：計算化学からのアプローチ」口頭発表（一般）
- 2003年03月, 山口大学（宇部市）,, 国内会議「Ab Initio Approach to Nanoscale Dynamics of DNA」口頭発表（一般）
- 「太陽電池の開発と高効率化および応用」技術セミナー, 2003年01月, 日本テクノセンター, 九段ポンピアンビル（東京）,, 国内会議「色素増感型太陽電池の開発・設計と実用化への課題」口頭発表（一般）
- 日本学術振興会, 科学研究費助成事業, 基盤研究(C), 神戸大学, 2021年04月01日 - 2024年03月31日生体分子系におけるミクロな熱緩和現象の理論・シミュレーション解析今年度はまず、水中に置かれたタンパク質内部の熱伝導度κならびに周囲の水との界面における熱伝達率Gを非平衡全原子分子動力学（MD）シミュレーションを用いて理論的に評価する研究を行った。タンパク質としてはミオグロビンと緑色蛍光タンパク質GFPを対象とし、球対称あるいは円筒対称性を仮定して立てた熱拡散方程式にMDにより得られるタンパク質の温度の時間変化をマッピングすることでκとGを求めることができた。得られた結果は実験値ならびに球対称を仮定した先行理論研究の値と概ね整合的であった。ミオグロビンの形状はおおよそ球対称だが、GFPはどちらかというと円筒対称の形状をしており、後者に対しては円筒対称性を仮定した異方的モデリングのほうがより現実的な理論評価値を与えると考えられる。さらに、周囲が純水ではなくKClなどの電解質溶液を用いた計算も行ったが、κやGに大きな変化は認められなかった。2021年度はまた、非平衡解離過程にあるタンパク質複合体における化学反応（発熱反応）に伴う温度・熱緩和のシミュレーション解析も行った。対象とした系はRas-GAP-GTP系で、GTPの加水分解により発生する自由エネルギーを用いてRas-GAPタンパク質複合体における解離が進行すると考えられている。このメカニズムを説明する従来の有力な仮説の一つ（J. Ross, 2006）として、GTPがGDPとPiに分裂した際に生まれる斥力的な静電相互作用エネルギーが方向性を持った運動エネルギーに変換されることが重要であるという説があったが、その是非を非平衡MDで系の局所的な温度や原子の速度ベクトルの方向相関の時間変化を詳しく調べることで検証した。その結果、タンパク質の構造変化に利用できる方向性を持った（質の高い）運動エネルギーやそれに付随した温度の緩和は極めて速く（1ピコ秒以内）、上記仮説は妥当ではないことがわかった。
- 科学研究費補助金／新学術領域研究, 2017年04月 - 2022年03月, 研究代表者競争的資金
- 学術研究助成基金助成金／基盤研究(C), 2018年04月 - 2021年03月, 研究代表者競争的資金
- 日本学術振興会, 科学研究費助成事業, 基盤研究(C), 長浜バイオ大学, 2016年07月19日 - 2019年03月31日酵素の機能改良のための遷移状態解析法の開発実験研究者が計算化学を利用して簡単に精度よく酵素機能改良のためのデザインができる方法論を確立したいと考え、酵素反応に要するエネルギー（活性化エネルギー）を見積もるために必要な遷移状態構造の探索や、活性化エネルギーを量子化学計算により算出し、実験結果と比較した。その結果、計算結果と実験結果と対応させるためにはまず、反応座標が複雑な経路でも精度の高い計算方法で反応の遷移状態構造を決定する必要があることがわかった。
- 日本学術振興会, 科学研究費助成事業, 基盤研究(C), 2015年04月01日 - 2018年03月31日量子化学計算に基づく生体高分子の超分解能構造解析技術の開発と創薬への応用本研究では、X線結晶構造解析と量子化学計算を融合した、タンパク質－リガンド複合体の新しい精密構造決定手法を開発している。フラグメント分子軌道法に基づいて、エネルギー計算、構造最適化、相互作用解析、および電子密度解析を駆使し、実験による構造解析の分解能を実質的に上げることを試みた。結果として、Pim1キナーゼ阻害剤の高精度活性予測や抗インフルエンザ薬の水和、またエストロゲン受容体の低分解能結晶構造からの高分解能構造の予測、特徴量の抽出、などにおいて、量子化学計算が極めて有用であることを示した。
- 科学研究費補助金／基盤研究(B), 2014年04月 - 2017年03月競争的資金
- 学術研究助成基金助成金／基盤研究(C), 2014年04月 - 2017年03月, 研究代表者競争的資金
- 学術研究助成基金助成金／基盤研究(C), 2011年, 研究代表者競争的資金
- 2010年, 研究代表者厚生科研「新型インフルエンザＨ１Ｎ１のウイルスの病原性等の解析に関する研究」競争的資金
- 2007年, 研究代表者戦略的：フラグメント分子軌道法による生体分子計算システムの開発競争的資金
- 2006年, 研究代表者フラグメント分子軌道法による生体分子計算システムの開発競争的資金
- 日本学術振興会, 科学研究費助成事業, 基盤研究(B), 豊橋技術科学大学, 2003年 - 2005年量子化学計算による電流検出型DNAチップの特性解析(1)DNA等の鎖状高分子の電流電圧(I-V)特性を解析する手法の開発 DNAの各塩基サイトのエネルギーレベルとサイト間の電荷の移動積分を与えると、電極に挟まれたDNAのI-V特性を求めるプログラムを開発した。ここで、移動積分は、Generalized Mulliken-Hush理論を基に構築した式を用い、DNAの電子状態計算により得たフロンティア分子軌道のエネルギーレベルを基に見積もった。電子状態計算は、DNA周囲のカウンターイオン、溶媒水による電場の影響を考慮して行った。 (2)ミスマッチのあるDNA2重鎖の電流電圧特性の解析 実験で電気伝導特性が得られているミスマッチのあるDNA鎖について、I-V特性を解析し、実験結果と定性的に一致する結果を得た。つまり、G-CからG-Aへのミスマッチにより、I-V特性は殆ど変化しないが、A-TからA-Cへのミスマッチでは、電流値が大きく減少する現象を、シミュレーションにより再現した。この原因は、塩基対周辺の構造変化とそれに伴うフロンティア分子軌道のエネルギーレベルと空間分布の変化にあることを、シミュレーション結果を基に明らかにした。 (3)1重鎖及び2重鎖DNAの電流電圧特性の解析 1重鎖及び2重鎖DNAの構造と電子状態の違いを、DNA周囲に存在するカウンターイオンと水分子の影響を考慮した分子動力学及び分子軌道計算により明らかにした。さらに、DNA中のホール及び電子の移動積分を見積り、1重鎖と2重鎖DNAのI-V特性の違いを明らかにし、実験と定性的に一致する結果を得た。その結果を基に、1重鎖DNAでは、構造が大きく変化し、塩基間のスタッキング構造が崩れ、その結果、電荷移動の起り易さが大幅に減少することを明らかにした。 (4)PNA(ペプチド核酸)とDNAの2重鎖の電子状態の解析 実験でDNA1重鎖とより強く2重鎖構造を形成することが観測されているPNAに対して、密度汎関数法に基づく分子軌道計算を行い、PNA-DNAの結合がDNA-DNAの結合より強くなること、及びその原因を、初めて明らかにした。今後、PNA-DNAの電流電圧特性を解析し、DNAチップに代わる新規バイオチップとして、PNAが適しているかどうかを明らかにする予定である。
- 2005年, 研究代表者フラグメント分子軌道法による生体系の応用計算競争的資金