Research activity information

• Atomistic simulation study reveals transduction of mechanical work generated by ATP hydrolysis onto myosin II functional loops

  Ikuo Kurisaki, Hideo Higuchi, Shigenori Tanaka, Madoka Suzuki

  Jan. 2026


• Understanding dielectric loss in water via distance-dependent dipole correlation functions

  Miki Nakano, Shigenori Tanaka

  2026, Physical Chemistry Chemical Physics

  Scientific journal


• Comprehensive Protein-Ligand Interaction Analysis: Fragment Molecular Orbital Calculation on the Complexes of Human Protease Renin and its Inhibitors

  Yoichiro Yagi, Takatomo Kimura, Chiduru Watanabe, Yoshio Okiyama, Shigenori Tanaka, Teruki Honma, Kaori Fukuzawa

  Chem-Bio Informatics Society, Dec. 2025, Chem-Bio Informatics Journal, 25, 107 - 129

  Scientific journal


• Parametric Resonance via Neuronal Microtubules: Filtering Optical Signals by Tryptophan Qubits

  Akihiro Nishiyama, Shigenori Tanaka, Jack Adam Tuszynski

  Sep. 2025, Quantum Reports

  Scientific journal


• Evolutionary and structural basis of SLAMF1 utilization in morbilliviruses-Implications for host range and cross-species transmission.

  Ayumu Hyodo, Fumio Seki, Kento Fukuda, Kaede Tashiro, Yuki Kitai, Yukiko Akahori, Hideko Watabe, Hiroshi Katoh, Rikuto Osaki, Daisuke Takaya, Norihito Kawashita, Hideo Fukuhara, Satoshi Ikegame, Tomoki Yoshikawa, Park Eunsil, Shigeru Morikawa, Ryoji Yamaguchi, Benhur Lee, Katsumi Maenaka, Tsuyoshi Shirai, Kaori Fukuzawa, Shigenori Tanaka, Makoto Takeda

  Morbilliviruses, including measles virus (MV), canine distemper virus (CDV), peste des petits ruminants virus, and cetacean morbillivirus pose a significant threat to humans and animals. While the host range of morbilliviruses is generally well-defined, cross-species transmission events with significant mortality have also been reported. Their entry into immune cells, the primary targets of morbilliviruses, relies on the signaling lymphocytic activation molecule (SLAM), also known as SLAMF1 or CD150. In this study, we hypothesize that the ability of morbilliviruses to utilize heterologous SLAM receptors stems from evolutionarily conserved structural determinants within the SLAM protein and that minimal genetic changes in the viral receptor-binding H protein can enable adaptation to novel hosts. To test this, we systematically assessed SLAM utilization and adaptation by diverse morbilliviruses. We found that most morbilliviruses efficiently utilize SLAM from multiple host species, including Myotis bat SLAM, but not human SLAM. Only MV could efficiently utilize human SLAM. Additionally, unlike other morbilliviruses, MV utilized Myotis bat SLAM inefficiently. As an example of morbillivirus adaptation to non-host animal SLAM, we conducted an MV adaptation experiment with Myotis bat SLAM. We demonstrated that MV readily adapted to utilize Myotis bat SLAM by acquiring a single N187Y mutation in its hemagglutinin protein. Notably, hypothetical ancestral SLAMs acted as universal receptors for all morbilliviruses. These results reinforced that morbillivirus receptor usage is primarily supported by evolutionarily conserved structural features of SLAM, highlighting a molecular basis that enables morbilliviruses to rapidly adapt to diverse animal SLAMs.

  Jun. 2025, PLoS pathogens, 21(6) (6), e1012990, English, International magazine

  Scientific journal


• A Structure-Based Approach for Predicting Odor Similarity of Molecules via Docking Simulations with Human Olfactory Receptors

  Hirotada Kaneshiro, Masakazu Sato, Airi Tanaka, Shuya Nakata, Yoshiko Aihara, Hirotaka Kitoh-Nishioka, Yoshiharu Mori, Shigenori Tanaka

  May 2025, ACS Omega

  Scientific journal

  Link to Kobe Univ. Repository (Kernel)


• Energy transfer and non-equipartition in nonlinearly coupled oscillators with Fermi resonance

  Shigenori Tanaka, Yoshio Okiyama

  Apr. 2025, Chemical Physics Letters

  Scientific journal

  Link to Kobe Univ. Repository (Kernel)


• Waveguide Quantum Electrodynamics: Tryptophans Entangled with Water as Data Qubits in a Microtubule

  Akihiro Nishiyama, Shigenori Tanaka, Jack Adam Tuszynski

  Mar. 2025, Dynamics

  Scientific journal

  Link to Kobe Univ. Repository (Kernel)


• Non-Equilibrium Quantum Brain Dynamics: Water Coupled with Phonons and Photons

  Akihiro Nishiyama, Shigenori Tanaka, Jack Tuszynski

  Nov. 2024, Entropy

  Scientific journal

  Link to Kobe Univ. Repository (Kernel)


• Vibrational frequency fluctuations of poly(N,N-diethylacrylamide) in the vicinity of coil-to-globule transition studied by two-dimensional infrared spectroscopy and molecular dynamics simulations

  Yuki Fujii, Hikaru Ioka, Chihiro Minamoto, Ikuo Kurisaki, Shigenori Tanaka, Kaoru Ohta, Keisuke Tominaga

  Aug. 2024, The Journal of Chemical Physics

  Scientific journal


• Stabilization Mechanism of Initiator Transfer RNA in the Small Ribosomal Subunit from Coarse-Grained Molecular Simulations

  Yoshiharu Mori, Shigenori Tanaka

  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 Graphic

  Cold Spring Harbor Laboratory, Jul. 2024


• Navigating Ultra-Large Virtual Chemical Spaces with Product-of-Experts Chemical Language Models

  Shuya Nakata, Yoshiharu Mori, Shigenori Tanaka

  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), Jul. 2024


• Quantum Brain Dynamics: Optical and Acoustic Super-Radiance via a Microtubule

  Akihiro Nishiyama, Shigenori Tanaka, Jack Tuszynski

  Jun. 2024, Foundations

  Scientific journal

  Link to Kobe Univ. Repository (Kernel)


• In Silico Search for Drug Candidates Targeting the PAX8–PPARγ Fusion Protein in Thyroid Cancer

  Kaori Sakaguchi, Yoshio Okiyama, Shigenori Tanaka

  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, May 2024, International Journal of Molecular Sciences, 25(10) (10), 5347 - 5347

  Scientific journal

  Link to Kobe Univ. Repository (Kernel)


• Holographic Brain Theory: Super-Radiance, Memory Capacity and Control Theory

  Akihiro Nishiyama, Shigenori Tanaka, Jack A. Tuszynski, Roumiana Tsenkova

  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, Feb. 2024, International Journal of Molecular Sciences, 25(4) (4), 2399 - 2399

  Scientific journal

  Link to Kobe Univ. Repository (Kernel)


• Manipulation of photosynthetic energy transfer by vibrational strong coupling

  Jun-Yu Dong, Yasutaka Kitahama, Takatoshi Fujita, Motoyasu Adachi, Yasuteru Shigeta, Akihito Ishizaki, Shigenori Tanaka, Ting-Hui Xiao, Keisuke Goda

  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, Jan. 2024, The Journal of Chemical Physics, 160(4) (4)

  Scientific journal


• Quantum Brain Dynamics and Virtual Reality

  Shigenori Tanaka

  2024, BioSystems

  Scientific journal


• Quantum Brain Dynamics: History and New Perspectives

  Akihiro NISHIYAMA, Shigenori TANAKA

  The Japan Association for Philosophy of Science, 2024, Journal of the Japan Association for Philosophy of Science, 51(1-2) (1-2), 57 - 73

  Scientific journal

  Link to Kobe Univ. Repository (Kernel)


• Deciphering the Potential of Multidimensional Carbon Materials for Surface-Enhanced Raman Spectroscopy through Density Functional Theory

  Shigenori Tanaka

  Nov. 2023, Journal of Physical Chemistry Letters

  Scientific journal


• Prediction of Binding Pose and Affinity of SARS-CoV-2 Main Protease and Repositioned Drugs by Combining Docking, Molecular Dynamics, and Fragment Molecular Orbital Calculations

  Yuma Handa, Koji Okuwaki, Yusuke Kawashima, Ryo Hatada, Yuji Mochizuki, Yuto Komeiji, Shigenori Tanaka, Takayuki Furuishi, Etsuo Yonemochi, Teruki Honma, Kaori Fukuzawa

  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), Jul. 2023


• Anesthetic Binding Induced Motion of GABA_A Receptors Revealed by Coarse-Grained Molecular Dynamics Simulations

  Shuya Nakata, Yoshiharu Mori, Shigenori Tanaka

  Corresponding, American Chemical Society (ACS), Jul. 2023, The Journal of Physical Chemistry B, 127(28) (28), 6306 - 6315

  [Refereed]

  Scientific journal


• End-to-end protein–ligand complex structure generation with diffusion-based generative models

  Shuya Nakata, Yoshiharu Mori, Shigenori Tanaka

  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.

  Corresponding, Springer Science and Business Media LLC, Jun. 2023, BMC Bioinformatics, 24(1) (1)

  [Refereed]

  Scientific journal

  Link to Kobe Univ. Repository (Kernel)


• Quantum Chemical Interaction Analysis between SARS-CoV-2 Main Protease and Ensitrelvir Compared with Its Initial Screening Hit

  Chiduru Watanabe, Shigenori Tanaka, Yoshio Okiyama, Hitomi Yuki, Tatsuya Ohyama, Kikuko Kamisaka, Daisuke Takaya, Kaori Fukuzawa, Teruki Honma

  American Chemical Society (ACS), Apr. 2023, The Journal of Physical Chemistry Letters, 3609 - 3620

  [Refereed]

  Scientific journal


• Renormalization in Quantum Brain Dynamics

  Akihiro Nishiyama, Shigenori Tanaka, Jack A. Tuszynski

  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, Feb. 2023, AppliedMath, 3(1) (1), 117 - 146

  [Refereed]

  Scientific journal


• Non-Equilibrium ϕ4 Theory in a Hierarchy: Towards Manipulating Holograms in Quantum Brain Dynamics

  Akihiro Nishiyama, Shigenori Tanaka, Jack A. Tuszynski

  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, Jan. 2023, Dynamics, 3(1) (1), 1 - 17

  [Refereed]

  Scientific journal


• Non-micelle-like Amyloid Aggregate Stabilizes Amyloid β (1-42) Growth Nuclei Formation

  Ikuo Kurisaki, Shigenori Tanaka

  Dec. 2022


• Thermal conductivity and conductance of protein in aqueous solution: Effects of geometrical shape

  Ikuo Kurisaki, Seiya Tanaka, Ichiro Mori, Toshihito Umegaki, Yoshiharu Mori, Shigenori Tanaka

  Corresponding, Wiley, Dec. 2022, Journal of Computational Chemistry, 44(7) (7), 857 - 868

  [Refereed]

  Scientific journal


• Thermal and Quantum Fluctuations of Harmonic Oscillator

  Corresponding, Pubtexto, Dec. 2022, JOURNAL OF PHYSICS AND CHEMISTRY RESEARCH, 4(3) (3), 1 - 2

  [Refereed]

  Scientific journal


• Dynamical free energy based model for quantum decision making

  Shigenori Tanaka, Toshihito Umegaki, Akihiro Nishiyama, Hirotaka Kitoh-Nishioka

  Elsevier BV, Nov. 2022, Physica A: Statistical Mechanics and its Applications, 605, 127979 - 127979

  [Refereed]

  Scientific journal


• Interspecies Comparison of Interaction Energies between Photosynthetic Protein RuBisCO and 2CABP Ligand

  Shigenori Tanaka

  Corresponding, Sep. 2022, International Journal of Molecular Sciences, 23(19) (19), 11347 - 11347

  [Refereed]

  Scientific journal


• Fragment molecular orbital calculations containing Mg2+ ions: PPlase domain of Cyclophilin G

  Masayasu Fujii, Chiduru Watanabe, Kaori Fukuzawa, Shigenori Tanaka

  Corresponding, Chem-Bio Informatics Society, Sep. 2022, Chem-Bio Informatics Journal, 22, 55 - 62

  [Refereed]

  Scientific journal


• Inhibition of Melittin Activity Using a Small Molecule with an Indole Ring

  Sayuki Kanemitsu, Kenta Morita, Yudai Tominaga, Kanon Nishimura, Tomoko Yashiro, Haruka Sakurai, Yumemi Yamamoto, Ikuo Kurisaki, Shigenori Tanaka, Masaki Matsui, Tooru Ooya, Atsuo Tamura, Tatsuo Maruyama

  American Chemical Society (ACS), Aug. 2022, The Journal of Physical Chemistry B, 126(31) (31), 5793 - 5802

  [Refereed]

  Scientific journal


• Protein–ligand binding affinity prediction of cyclin‐dependent kinase‐2 inhibitors by dynamically averaged fragment molecular orbital‐based interaction energy

  Kenichiro Takaba, Chiduru Watanabe, Atsushi Tokuhisa, Yoshinobu Akinaga, Biao Ma, Ryo Kanada, Mitsugu Araki, Yasushi Okuno, Yusuke Kawashima, Hirotomo Moriwaki, Norihito Kawashita, Teruki Honma, Kaori Fukuzawa, Shigenori Tanaka

  Corresponding, Wiley, Jul. 2022, Journal of Computational Chemistry, 43(20) (20), 1362 - 1371

  [Refereed]

  Scientific journal


• Quantum Brain Dynamics in 2+1 dimensions: Non-equilibrium analysis towards memory formations

  Akihiro Nishiyama, Shigenori Tanaka, Jack A. Tuszynski

  Jul. 2022, Physica A: Statistical Mechanics and its Applications, 598

  [Refereed]

  Scientific journal


• Remarked suppression of Aβ 42 protomer–protomer dissociation reaction elucidated by molecular dynamics simulation

  Ikuo Kurisaki, Shigenori Tanaka

  Corresponding, Wiley, Jul. 2022, Proteins: Structure, Function, and Bioinformatics

  [Refereed]

  Scientific journal


• Quantum Brain Dynamics and Holography

  Shigenori Tanaka

  Jun. 2022, Dynamics, 2(2) (2), 187 - 218

  [Refereed]

  Scientific journal


• Fragment molecular orbital calculations for biomolecules

  Shigenori Tanaka

  Feb. 2022, Current Opinion in Structural Biology, 72, 127 - 134

  [Refereed]

  Scientific journal


• Computational prediction of heteromeric protein complex disassembly order using hybrid Monte Carlo/molecular dynamics simulation

  Ikuo Kurisaki, Shigenori Tanaka

  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 without 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.

  Corresponding, Royal Society of Chemistry ({RSC}), Jan. 2022, Physical Chemistry Chemical Physics

  [Refereed]

  Scientific journal


• Atomistic Simulation Approach for Multimolecular Crowding Biosystem: Developments and Applications

  Ikuo KURISAKI, Shigenori TANAKA

  Biophysical Society of Japan, 2022, Seibutsu Butsuri, 62(4) (4), 215 - 218

  [Refereed]

  Scientific journal


• Collective residue interactions in trimer complexes of SARS-CoV-2 spike proteins analyzed by fragment molecular orbital method

  Koji Okuwaki, Kazuki Akisawa, Ryo Hatada, Yuji Mochizuki, Kaori Fukuzawa, Yuto Komeiji, Shigenori Tanaka

  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.

  Corresponding, {IOP} Publishing, Jan. 2022, Applied Physics Express, 15(1) (1), 017001 - 017001

  [Refereed]

  Scientific journal


• Improvement of the Force Field for β-d-Glucose with Machine Learning

  Makoto Ikejo, Hirofumi Watanabe, Kohei Shimamura, Shigenori Tanaka

  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.

  Corresponding, Nov. 2021, Molecules, 26(21) (21), English, International magazine

  [Refereed]

  Scientific journal


• Fragment molecular orbital based interaction analyses on complexes between SARS-CoV-2 RBD variants and ACE2

  Kazuki Akisawa, Ryo Hatada, Koji Okuwaki, Shun Kitahara, YusukeF Tachino, Yuji Mochizuki, Yuto Komeiji, Shigenori Tanaka

  Sep. 2021, JAPANESE JOURNAL OF APPLIED PHYSICS, 60(9) (9), 090901 - 090901, English

  [Refereed]

  Scientific journal


• Dynamic Cooperativity of Ligand–Residue Interactions Evaluated with the Fragment Molecular Orbital Method

  Shigenori Tanaka, Shusuke Tokutomi, Ryo Hatada, Koji Okuwaki, Kazuki Akisawa, Kaori Fukuzawa, Yuto Komeiji, Yoshio Okiyama, Yuji Mochizuki

  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 discovery

  Corresponding, American Chemical Society ({ACS}), Jun. 2021, The Journal of Physical Chemistry B, 125(24) (24), 6501 - 6512

  [Refereed]

  Scientific journal


• Density-Matrix Based Scheme of Basis Selection for Linear Combination of Fragment Molecular Orbitals

  Yoshio Okiyama, Yuji Mochizuki, Masanori Yamanaka, Shigenori Tanaka

  Corresponding, Physical Society of Japan, Jun. 2021, Journal of the Physical Society of Japan, 90(6) (6), 064301 - 064301

  [Refereed]

  Scientific journal


• In silico modeling of PAX8–PPARγ fusion protein in thyroid carcinoma: influence of structural perturbation by fusion on ligand-binding affinity

  Kaori Sakaguchi, Yoshio Okiyama, Shigenori Tanaka

  Corresponding, Springer Science and Business Media {LLC}, May 2021, Journal of Computer-Aided Molecular Design, 35(5) (5), 629 - 642

  [Refereed]

  Scientific journal


• Non-equilibrium Quantum Brain Dynamics II: Formulation in 3+1 dimensions

  Shigenori Tanaka

  Apr. 2021, Physica A: Statistical Mechanics and Its Applications, 567, 125706 - 125706

  [Refereed]

  Scientific journal


• 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

  半田 佑磨, 川嶋 裕介, 畑田 崚, 奥脇 弘次, 望月 祐志, 古明地 勇人, 田中 成典, 本間 光貴, 古石 誉之, 福澤 薫, 米持 悦生

  (公社)日本薬学会, Mar. 2021, 日本薬学会年会要旨集, 141年会, 27V04 - am12S, Japanese


• Reaction Pathway Sampling and Free-Energy Analyses for Multimeric Protein Complex Disassembly by Employing Hybrid Configuration Bias Monte Carlo/Molecular Dynamics Simulation

  Ikuo Kurisaki, Shigenori Tanaka

  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.

  Corresponding, American Chemical Society ({ACS}), Feb. 2021, ACS Omega, 6(7) (7), 4749 - 4758

  [Refereed]

  Scientific journal


• Remarked Suppression of Aβ42 Protomer-protomer Dissociation Reaction via Pentamer Dimerization

  Ikuo Kurisaki, Shigenori Tanaka

  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.

  Corresponding, Cold Spring Harbor Laboratory, Feb. 2021

  [Refereed]


• Statistical interaction analyses between SARS-CoV-2 main protease and inhibitor N3 by combining molecular dynamics simulation and fragment molecular orbital calculation

  Ryo Hatada, Koji Okuwaki, Kazuki Akisawa, Yuji Mochizuki, Yuma Handa, Kaori Fukuzawa, Yuto Komeiji, Yoshio Okiyama, Shigenori Tanaka

  {IOP} Publishing, Feb. 2021, Applied Physics Express, 14(2) (2), 027003 - 027003

  [Refereed]

  Scientific journal


• FMODB: The World's First Database of Quantum Mechanical Calculations for Biomacromolecules Based on the Fragment Molecular Orbital Method.

  Daisuke Takaya, Chiduru Watanabe, Shunpei Nagase, Kikuko Kamisaka, Yoshio Okiyama, Hirotomo Moriwaki, Hitomi Yuki, Tomohiro Sato, Noriyuki Kurita, Yoichiro Yagi, Tatsuya Takagi, Norihito Kawashita, Kenichiro Takaba, Tomonaga Ozawa, Midori Takimoto-Kamimura, Shigenori Tanaka, Kaori Fukuzawa, Teruki Honma

  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.

  Jan. 2021, Journal of chemical information and modeling, 61(2) (2), 777 - 794, English, International magazine

  [Refereed]

  Scientific journal


• Paper: Research on Identification of Road Features from Point Cloud Data Using Deep Learning

  Shigenori Tanaka

  2021, International Journal of Automation Technology

  Scientific journal


• Elucidating microscopic events driven by GTP hydrolysis reaction in the Ras–GAP system with semi-reactive molecular dynamics simulations: the alternative role of a phosphate binding loop for mechanical energy storage

  Ikuo Kurisaki, Shigenori Tanaka

  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.

  Corresponding, Royal Society of Chemistry (RSC), 2021, Physical Chemistry Chemical Physics, 23(46) (46), 26151 - 26164

  [Refereed]

  Scientific journal


• The ABINIT-MP Program

  Yuji Mochizuki, Tatsuya Nakano, Kota Sakakura, Yoshio Okiyama, Hiromasa Watanabe, Koichiro Kato, Yoshinobu Akinaga, Shinya Sato, Jun-inchi Yamamoto, Katsumi Yamashita, Tadashi Murase, Takeshi Ishikawa, Yuto Komeiji, Yuji Kato, Naoki Watanabe, Takashi Tsukamoto, Hirotoshi Mori, Koji Okuwaki, Shigenori Tanaka, Akifumi Kato, Chiduru Watanabe, Kaori Fukuzawa

  Springer Singapore, 2021, Recent Advances of the Fragment Molecular Orbital Method, 53 - 67

  In book


• Molecular recognition of SARS-CoV-2 spike glycoprotein: quantum chemical hot spot and epitope analyses

  Shigenori Tanaka

  2021, Chemical Science, 12(13) (13), 4722 - 4739

  [Refereed]

  Scientific journal


• Interaction analyses of SARS-CoV-2 spike protein based on fragment molecular orbital calculations

  Shigenori Tanaka

  2021, RSC Advances, 11(6) (6), 3272 - 3279

  [Refereed]

  Scientific journal


• Effective Static Approximation: A Fast and Reliable Tool for Warm-Dense Matter Theory

  Shigenori Tanaka

  Dec. 2020, Physical Review Letters, 125(23) (23)

  [Refereed]

  Scientific journal


• Identification of correlated inter-residue interactions in protein complex based on the fragment molecular orbital method

  Shigenori Tanaka, Chiduru Watanabe, Teruki Honma, Kaori Fukuzawa, Kazue Ohishi, Tadashi Maruyama

  Corresponding, Nov. 2020, Journal of Molecular Graphics and Modelling, 100, 107650 - 107650, English

  [Refereed]

  Scientific journal


• Comparative study on model parameter evaluations for the energy transfer dynamics in Fenna–Matthews–Olson complex

  Yosuke Suzuki, Hirofumi Watanabe, Yoshio Okiyama, Kuniyoshi Ebina, Shigenori Tanaka

  Corresponding, Elsevier BV, Nov. 2020, Chemical Physics, 539, 110903 - 110903

  [Refereed]

  Scientific journal


• Machine learning prediction of inter-fragment interaction energies between ligand and amino-acid residues on the fragment molecular orbital calculations for Janus kinase – inhibitor complex

  Shusuke Tokutomi, Kohei Shimamura, Kaori Fukuzawa, Shigenori Tanaka

  Corresponding, Oct. 2020, Chemical Physics Letters, 757, 137883 - 137883, English

  [Refereed]

  Scientific journal


• Temperature relaxation in binary hard-sphere mixture system: Molecular dynamics and kinetic theory study

  Shigenori Tanaka, Kohei Shimamura

  Corresponding, Jul. 2020, The Journal of Chemical Physics, 153(3) (3), 034114 - 034114, English

  [Refereed]

  Scientific journal


• Fragment Molecular Orbital Based Interaction Analyses on COVID-19 Main Protease - Inhibitor N3 Complex (PDB ID: 6LU7).

  Ryo Hatada, Koji Okuwaki, Yuji Mochizuki, Yuma Handa, Kaori Fukuzawa, Yuto Komeiji, Yoshio Okiyama, Shigenori Tanaka

  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), Jun. 2020, Journal of chemical information and modeling, 60(7) (7), 3593 - 3602, English, International magazine

  [Refereed]

  Scientific journal


• Nanoscale Quantum Thermal Conductance at Water Interface: Green's Function Approach Based on One-Dimensional Phonon Model

  Shigenori Tanaka

  Mar. 2020, Molecules, 25(5) (5), 1185 - 1185

  [Refereed]

  Scientific journal


• ERβ選択的リガンドの設計に向けたFMO創薬の取り組み

  福澤 薫, 関 祐哉, 上村 舞, 加藤 司, 安崎 聡, 田中 成典, 古石 誉之, 米持 悦生

  (公社)日本薬学会, Mar. 2020, 日本薬学会年会要旨集, 140年会, 27P - am095, Japanese


• New Modified Deoxythymine with Dibranched Tetraethylene Glycol Stabilizes G-Quadruplex Structures.

  Hisae Tateishi-Karimata, Tatsuya Ohyama, Takahiro Muraoka, Shigenori Tanaka, Kazushi Kinbara, Naoki Sugimoto

  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.

  Feb. 2020, Molecules (Basel, Switzerland), 25(3) (3), 705 - 715, English, International magazine

  [Refereed]

  Scientific journal


• Appearance of Thermal Time

  Shigenori Tanaka

  2020, ArXiv, 51(2) (2)

  [Refereed]

  Scientific journal


• Nonequilibrium quantum brain dynamics

  Akihiro Nishiyama, Shigenori Tanaka, Jack A. Tuszynski

  2020, QUANTUM BOUNDARIES OF LIFE, 82, 159 - 180, English

  In book


• Non-Equilibrium Quantum Electrodynamics in Open Systems as a Realizable Representation of Quantum Field Theory of the Brain

  Shigenori Tanaka

  2020, Entropy, 22(1) (1), 43 - 43

  [Refereed]

  Scientific journal


• Strongly coupled electron liquid: Ab initio path integral Monte Carlo simulations and dielectric theories

  Tobias Dornheim, Travis Sjostrom, Shigenori Tanaka, Jan Vorberger

  Jan. 2020, PHYSICAL REVIEW B, 101(4) (4), English

  [Refereed]

  Scientific journal


• ATP Converts A beta(42) Oligomer into Off-Pathway Species by Making Contact with Its Backbone Atoms Using Hydrophobic Adenosine

  Ikuo Kurisaki, Shigenori Tanaka

  Nov. 2019, JOURNAL OF PHYSICAL CHEMISTRY B, 123(46) (46), 9922 - 9933, English

  [Refereed]

  Scientific journal


• Non-Equilibrium Quantum Brain Dynamics: Super-Radiance and Equilibration in 21 Dimensions+

  Akihiro Nishiyama, Shigenori Tanaka, Jack A. Tuszynski

  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, Oct. 2019, Entropy, 21(11) (11), 1066 - 1066

  [Refereed]

  Scientific journal


• Guidelines for creating artificial neural network empirical interatomic potential from first-principles molecular dynamics data under specific conditions and its application to α-Ag2Se

  Kohei Shimamura, Shogo Fukushima, Akihide Koura, Fuyuki Shimojo, Masaaki Misawa, Rajiv K. Kalia, Aiichiro Nakano, Priya Vashishta, Takashi Matsubara, Shigenori Tanaka

  Sep. 2019, The Journal of Chemical Physics, 151(12) (12), 124303 - 124303, English

  [Refereed]

  Scientific journal


• 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

  関 祐哉, 加藤 司, 安崎 聡, 田中 成典, 古石 誉之, 福澤 薫, 米持 悦生

  (公社)日本薬学会, Mar. 2019, 日本薬学会年会要旨集, 139年会(2) (2), 96 - 96, Japanese

  [Refereed]


• Development of an automated fragment molecular orbital (FMO) calculation protocol toward construction of quantum mechanical calculation database for large biomolecules

  Chiduru Watanabe, Hirofumi Watanabe, Yoshio Okiyama, Daisuke Takaya, Kaori Fukuzawa, Shigenori Tanaka, Teruki Honma

  Chem-Bio Informatics Society, Mar. 2019, Chem-Bio Informatics Journal, 19(0) (0), 5 - 18, English

  [Refereed]

  Scientific journal


• Fragment Molecular Orbital Calculations with Implicit Solvent Based on the Poisson-Boltzmann Equation: II. Protein and Its Ligand-Binding System Studies

  Shigenori Tanaka

  Feb. 2019, The Journal of Physical Chemistry B, 123(5) (5), 957 - 973

  [Refereed]

  Scientific journal


• Ab initio molecular dynamics study of prebiotic production processes of organic compounds at meteorite impacts on ocean

  Kohei Shimamura, Fuyuki Shimojo, Aiichiro Nakano, Shigenori Tanaka

  Wiley, Jan. 2019, Journal of Computational Chemistry, 40(2) (2), 349 - 359

  [Refereed]

  Scientific journal


• Development of an automated fragment molecular orbital (FMO) calculation protocol toward construction of quantum mechanical calculation database for large biomolecules

  Watanabe Chiduru, Watanabe Hirofumi, Okiyama Yoshio, Takaya Daisuke, Fukuzawa Kaori, Tanaka Shigenori, Honma Teruki

  2019, Chem-Bio Informatics Journal, 19(0) (0), 5 - 18, English

  [Refereed]

  Scientific journal


• 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

  島村孝平、下條冬樹、田中成典

  Corresponding, 2019, 日本神経回路学会誌, 26(4) (4), 1 - 11, Japanese

  [Refereed]


• 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

  渡邉博文, 鈴木洋介, 八木 学, 石野麻由子, 土井陽子, 江口至洋, TANAKA SHIGENORI, TSURUTA HIROKI, 白井剛, MORI ICHIRO, USUI HIDEYUKI, YOKOKAWA MITSUO

  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．．

  Nov. 2018, 大学ICT推進協議会2018年度年次大会論文集, 1 - 4, Japanese

  Symposium


• Towards good correlation between fragment molecular orbital interaction energies and experimental IC50 for ligand binding: A case study of p38 MAP kinase

  Yinglei Sheng, Hirofumi Watanabe, Keiya Maruyama, Chiduru Watanabe, Yoshio Okiyama, Teruki Honma, Kaori Fukuzawa, Shigenori Tanaka

  Elsevier {BV}, Oct. 2018, Computational and Structural Biotechnology Journal, 16, 421 - 434, English

  [Refereed]

  Scientific journal


• Application of singular value decomposition to the inter-fragment interaction energy analysis for ligand screening

  Keiya Maruyama, Yinglei Sheng, Hirofumi Watanabe, Kaori Fukuzawa, Shigenori Tanaka

  Elsevier B.V., May 2018, Computational and Theoretical Chemistry, 1132, 23 - 34, English

  [Refereed]

  Scientific journal


• Pursuing origins of (poly)ethylene glycol-induced G-quadruplex structural modulations.

  Marko Trajkovski, Tamaki Endoh, Hisae Tateishi-Karimata, Tatsuya Ohyama, Shigenori Tanaka, Janez Plavec, Naoki Sugimoto

  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.

  May 2018, Nucleic acids research, 46(8) (8), 4301 - 4315, English, International magazine

  [Refereed]

  Scientific journal


• Computational analysis of the interaction energies between amino acid residues of the measles virus hemagglutinin and its receptors

  Fengqi Xu, Shigenori Tanaka, Hirofumi Watanabe, Yasuhiro Shimane, Misako Iwasawa, Kazue Ohishi, Tadashi Maruyama

  MDPI AG, May 2018, Viruses, 10(5) (5), 18, English

  [Refereed]

  Scientific journal


• Fragment Molecular Orbital Calculations with Implicit Solvent Based on the Poisson–Boltzmann Equation: Implementation and DNA Study

  Yoshio Okiyama, Tatsuya Nakano, Chiduru Watanabe, Kaori Fukuzawa, Yuji Mochizuki, Shigenori Tanaka

  American Chemical Society (ACS), Apr. 2018, The Journal of Physical Chemistry B, 122(16) (16), 4457 - 4471

  [Refereed]

  Scientific journal


• 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

  大山達也, 建石寿枝, 田中成典, 杉本直己

  2018, 日本核酸化学会誌, 2, 3 - 10


• Information geometrical characterization of the Onsager-Machlup process

  Shigenori Tanaka

  Dec. 2017, CHEMICAL PHYSICS LETTERS, 689, 152 - 155, English

  [Refereed]

  Scientific journal


• Structural transition of solvated H-Ras/GTP revealed by molecular dynamics simulation and local network entropy

  Shota Matsunaga, Yuta Hano, Yuta Saito, Kazuhiro J. Fujimoto, Takashi Kumasaka, Shigeyuki Matsumoto, Tohru Kataoka, Fumi Shima, Shigenori Tanaka

  Oct. 2017, JOURNAL OF MOLECULAR GRAPHICS & MODELLING, 77, 51 - 63, English

  [Refereed]

  Scientific journal


• Newly characterized interaction stabilizes DNA structure: oligoethylene glycols stabilize G-quadruplexes CH-pi interactions

  Hisae Tateishi-Karimata, Tatsuya Ohyama, Takahiro Muraoka, Peter Podbevsek, Adam M. Wawro, Shigenori Tanaka, Shu-ichi Nakano, Kazushi Kinbara, Janez Plavec, Naoki Sugimoto

  Jul. 2017, NUCLEIC ACIDS RESEARCH, 45(12) (12), 7021 - 7030, English

  [Refereed]

  Scientific journal


• Meteorite impacts on ancient oceans opened up multiple NH3 production pathways

  Kohei Shimamura, Fuyuki Shimojo, Aiichiro Nakano, Shigenori Tanaka

  May 2017, PHYSICAL CHEMISTRY CHEMICAL PHYSICS, 19(18) (18), 11655 - 11667, English

  [Refereed]

  Scientific journal


• Cosolvent-Based Molecular Dynamics for Ensemble Docking: Practical Method for Generating Druggable Protein Conformations

  Shota Uehara, Shigenori Tanaka

  Apr. 2017, JOURNAL OF CHEMICAL INFORMATION AND MODELING, 57(4) (4), 742 - 756, English

  [Refereed]

  Scientific journal


• Improved equation of state for finite-temperature spin-polarized electron liquids on the basis of Singwi-Tosi-Land-Sjlander approximation

  Shigenori Tanaka

  Mar. 2017, CONTRIBUTIONS TO PLASMA PHYSICS, 57(3) (3), 126 - 136, English

  [Refereed]

  Scientific journal


• Current Status of ABINIT-MP as a FMO Program and Related Works with Machine Learning

  Yuji MOCHIZUKI, Kota SAKAKURA, Yoshinobu AKINAGA, Kouichiro KATO, Hiromasa WATANABE, Yoshio OKIYAMA, Tatsuya NAKANO, Yuto KOMEIJI, Akira OKUSAWA, Kaori FUKUZAWA, Shigenori TANAKA

  Society of Computer Chemistry Japan, 2017, Journal of Computer Chemistry, Japan, 16(5) (5), 119 - 122

  [Refereed]

  Scientific journal


• 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」

  渡邉博文, 鈴木洋介, 近藤洋隆, 石野麻由子, 土井陽子, 江口至洋, TANAKA SHIGENORI, TSURUTA HIROKI, 白井剛, MORI ICHIRO, USUI HIDEYUKI, YOKOKAWA MITSUO

  2017, 大学ICT推進協議会2017年度年次大会論文集, TF1-2, 1 - 5, Japanese

  Symposium


• Theoretical Analysis of Activity Cliffs among Benzofuranone-Class Pim1 Inhibitors Using the Fragment Molecular Orbital Method with Molecular Mechanics Poisson–Boltzmann Surface Area (FMO+MM-PBSA) Approach

  Chiduru Watanabe, Hirofumi Watanabe, Kaori Fukuzawa, Lorien J. Parker, Yoshio Okiyama, Hitomi Yuki, Shigeyuki Yokoyama, Hirofumi Nakano, Shigenori Tanaka, Teruki Honma

  American Chemical Society ({ACS}), 2017, Journal of Chemical Information and Modeling, 57(12) (12), 2996 - 3010, English

  [Refereed]

  Scientific journal


• An Effective Microscopic Index Associated with Cell Survival and DNA Lesions for Estimating Radiation Risk

  K. Yoshinari, TANAKA SHIGENORI, K. Ebina

  2017, J. Environ. Health Sci., 3(1) (1), 1 - 5, English

  [Refereed]

  Scientific journal


• Meteorite Impact-Induced Rapid NH3 Production on Early Earth: Ab Initio Molecular Dynamics Simulation

  Kohei Shimamura, Fuyuki Shimojo, Aiichiro Nakano, Shigenori Tanaka

  Dec. 2016, SCIENTIFIC REPORTS, 6(38953) (38953), 10, English

  [Refereed]

  Scientific journal


• Correlational and thermodynamic properties of finite-temperature electron liquids in the hypernetted-chain approximation

  Shigenori Tanaka

  Dec. 2016, JOURNAL OF CHEMICAL PHYSICS, 145(21) (21), 11, English

  [Refereed]

  Scientific journal


• AutoDock-GIST: Incorporating Thermodynamics of Active-Site Water into Scoring Function for Accurate Protein-Ligand Docking

  Shota Uehara, Shigenori Tanaka

  Nov. 2016, MOLECULES, 21(11) (11), 21, English

  [Refereed]

  Scientific journal


• Local thermodynamics of the water molecules around single- and double-stranded DNA studied by grid inhomogeneous solvation theory

  Miki Nakano, Hisae Tateishi-Karimata, Shigenori Tanaka, Florence Tama, Osamu Miyashita, Shu-ichi Nakano, Naoki Sugimoto

  Sep. 2016, CHEMICAL PHYSICS LETTERS, 660, 250 - 255, English

  [Refereed]

  Scientific journal


• Four-electron model for singlet and triplet excitation energy transfers with inclusion of coherence memory, inelastic tunneling and nuclear quantum effects

  Yosuke Suzuki, Kuniyoshi Ebina, Shigenori Tanaka

  Aug. 2016, CHEMICAL PHYSICS, 474, 18 - 24, English

  [Refereed]

  Scientific journal


• Reduced minimum model for the photosynthetic induction processes in photosystem I

  Takeshi Matsuoka, Shigenori Tanaka, Kuniyoshi Ebina

  Jul. 2016, JOURNAL OF PHOTOCHEMISTRY AND PHOTOBIOLOGY B-BIOLOGY, 160, 364 - 375, English

  [Refereed]

  Scientific journal


• Diffusion Monte Carlo study on temporal evolution of entropy and free energy in nonequilibrium processes

  Shigenori Tanaka

  Mar. 2016, JOURNAL OF CHEMICAL PHYSICS, 144(9) (9), 14, English

  [Refereed]

  Scientific journal


• AutoDock-GIST: Incorporating thermodynamics of active-site water into scoring function for accurate protein-ligand docking

  Shigenori Tanaka

  2016, Abstracts of Papers of the American Chemical Society

  Scientific journal


• 19aBW-1 Ab Initio Molecular Dynamics Simulation of Mechanism of Shock-Wave-Induced Ammonia Generation

  Shimamura K., Shimojo F., Nakano Aiichiro, Tanaka S.

  The Physical Society of Japan (JPS), 2016, Meeting Abstracts of the Physical Society of Japan, 71, 3156 - 3156, Japanese


• Incorporation of thermodynamics of water into scoring functions for accurate protein-ligand docking

  Uehara Shota, Tanaka Shigenori

  Water plays a significant role in binding process between a protein and a ligand. However, water molecules are often underappreciated or even ignored in protein-ligand docking. Usually, 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 displacement of these waters from an active site to bulk, and this displacement process contributes to the free energy change of protein-ligand binding significantly. For instance, water molecules in a hydrophobic region of protein which cannot make appropriate hydrogen bonds are energetically unfavorable, and the displacement of such water molecules into bulk region earns a substantial contribution in binding free energy. The free energy of active-site water molecules can be calculated by grid inhomogeneous solvation theory (GIST), using molecular dynamics trajectory (MD) of a target protein and water. In this work, we combined GIST-based desolvation energy with the scoring function of AutoDock4 and discussed the accuracies of scoring and binding pose prediction.

  Division of Chemical Information and Computer Sciences The Chemical Society of Japan, 2016, Proceedings of the Symposium on Chemoinformatics, 2016, Y2, Japanese


• タンパク質－リガンドドッキングの現状と課題

  上原彰太, TANAKA SHIGENORI

  公益社団法人 日本化学会・情報化学部会, 2016, CICSJ Bull., 34(No. 1) (No. 1), 10 - 16, Japanese

  [Refereed]

  Symposium


• Recent Progress in Quantum Monte Carlo

  TANAKA SHIGENORI, P.-N. Roy, L. Mitas

  2016, ACS Symposium Series 1234, 173, English

  [Invited]

  International conference proceedings


• Thermodynamic properties of water molecules in the presence of cosolute depend on DNA structure: a study using grid inhomogeneous solvation theory

  Miki Nakano, Hisae Tateishi-Karimata, Shigenori Tanaka, Florence Tama, Osamu Miyashita, Shu-ichi Nakano, Naoki Sugimoto

  Dec. 2015, NUCLEIC ACIDS RESEARCH, 43(21) (21), 10114 - 10125, English

  [Refereed]

  Scientific journal


• 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

  YOSHINARI KOHEI, TANAKA SHIGENORI, EBINA KUNIYOSHI

  日本放射線影響学会, Oct. 2015, 第1回放射線ワークショップ 講演論文集, 2015, 84, Japanese

  Symposium


• Systems approach to excitation-energy and electron transfer reaction networks in photosystem II complex: model studies for chlorophyll a fluorescence induction kinetics

  Takeshi Matsuoka, Shigenori Tanaka, Kuniyoshi Ebina

  Sep. 2015, JOURNAL OF THEORETICAL BIOLOGY, 380, 220 - 237, English

  [Refereed]

  Scientific journal


• Novel type of virtual ligand screening on the basis of quantum-chemical calculations for protein-ligand complexes and extended clustering techniques

  Ryo Kurauchi, Chiduru Watanabe, Kaori Fukuzawa, Shigenori Tanaka

  Jun. 2015, COMPUTATIONAL AND THEORETICAL CHEMISTRY, 1061, 12 - 22, English

  [Refereed]

  Scientific journal


• Effects of Bridge Functions on Radial Distribution Functions of Liquid Water

  Shigenori Tanaka, Miki Nakano

  Jun. 2015, INTERDISCIPLINARY SCIENCES-COMPUTATIONAL LIFE SCIENCES, 7(2) (2), 152 - 156, English

  [Refereed]

  Scientific journal


• Theoretical prediction and experimental verification on enantioselectivity of haloacid dehalogenase L-DEX YL with chloropropionate

  Hirotaka Kondo, Kazuhiro J. Fujimoto, Shigenori Tanaka, Hiroyuki Deki, Takashi Nakamura

  Mar. 2015, CHEMICAL PHYSICS LETTERS, 623, 101 - 107, English

  [Refereed]

  Scientific journal


• Explicit solvation modulates intra- and inter-molecular interactions within DNA: Electronic aspects revealed by the ab initio fragment molecular orbital (FMO) method

  Kaori Fukuzawa, Ikuo Kurisaki, Chiduru Watanabe, Yoshio Okiyama, Yuji Mochizuki, Shigenori Tanaka, Yuto Komeiji

  Elsevier {BV}, Feb. 2015, Computational and Theoretical Chemistry, 1054, 29 - 37, English

  [Refereed]

  Scientific journal


• Germ-line mutation of KCNQ2, p.R213W, in a Japanese family with benign familial neonatal convulsion (vol 50, pg 167, 2008)

  Shigenori Tanaka

  2015, Pediatrics International

  Scientific journal


• Protein-ligand docking using fitness learning-based artificial bee colony with proximity stimuli

  Shota Uehara, Kazuhiro J. Fujimoto, Shigenori Tanaka

  2015, PHYSICAL CHEMISTRY CHEMICAL PHYSICS, 17(25) (25), 16412 - 16417, English

  [Refereed]

  Scientific journal


• i-Motifs are more stable than G-quadruplexes in a hydrated ionic liquid

  Hisae Tateishi-Karimata, Miki Nakano, Smritimoy Pramanik, Shigenori Tanaka, Naoki Sugimoto

  2015, CHEMICAL COMMUNICATIONS, 51(32) (32), 6909 - 6912, English

  [Refereed]

  Scientific journal


• Choline Ions Stabilize A-T Base Pairs by Fitting into Minor Groove

  M. Nakano, H. Tateishi-Karimata, TANAKA SHIGENORI, N. Sugimoto

  2015, JPS Conf. Proc., 5, 011008, English

  [Refereed]

  International conference proceedings


• A significant role of Arg41 residue in the enzymatic reaction of haloacid dehalogenase L-DEX YL studied by QM/MM method

  hirotaka Kondo, Takashi Nakamura, Shigenori Tanaka

  Dec. 2014, JOURNAL OF MOLECULAR CATALYSIS B-ENZYMATIC, 110, 23 - 31, English

  [Refereed]

  Scientific journal


• Interaction energy analysis on specific binding of influenza virus hemagglutinin to avian and human sialosaccharide receptors: Importance of mutation-induced structural change

  Satoshi Anzaki, Chiduru Watanabe, Kaori Fukuzawa, Yuji Mochizuki, Shigenori Tanaka

  Sep. 2014, JOURNAL OF MOLECULAR GRAPHICS & MODELLING, 53, 48 - 58, English

  [Refereed]

  Scientific journal


• Affinity of Molecular Ions for DNA Structures Is Determined by Solvent-Accessible Surface Area

  Miki Nakano, Hisae Tateishi-Karimata, Shigenori Tanaka, Naoki Sugimoto

  Aug. 2014, JOURNAL OF PHYSICAL CHEMISTRY B, 118(32) (32), 9583 - 9594, English

  [Refereed]

  Scientific journal


• Charge Clamps of Lysines and Hydrogen Bonds Play Key Roles in the Mechanism to Fix Helix 12 in the Agonist and Antagonist Positions of Estrogen Receptor alpha: Intramolecular Interactions Studied by the Ab Initio Fragment Molecular Orbital Method

  Chiduru Watanabe, Kaori Fukuzawa, Shigenori Tanaka, Sachiko Aida-Hyugaji

  May 2014, JOURNAL OF PHYSICAL CHEMISTRY B, 118(19) (19), 4993 - 5008, English

  [Refereed]

  Scientific journal


• Accuracy of the fragment molecular orbital (FMO) calculations for DNA: Total energy, molecular orbital, and inter-fragment interaction energy

  Kaori Fukuzawa, Chiduru Watanabe, Ikuo Kurisaki, Naoki Taguchi, Yuji Mochizuki, Tatsuya Nakano, Shigenori Tanaka, Yuto Komeiji

  Apr. 2014, COMPUTATIONAL AND THEORETICAL CHEMISTRY, 1034, 7 - 16, English

  [Refereed]

  Scientific journal


• Classical density functional calculation of radial distribution functions of liquid water

  Shigenori Tanaka, Miki Nakano

  Feb. 2014, CHEMICAL PHYSICS, 430, 18 - 22, English

  [Refereed]

  Scientific journal


• 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

  上原 彰太, 藤本 和宏, TANAKA SHIGENORI

  2014, J. Comput. Chem. Jpn., 13, 163 - 164, Japanese

  [Refereed]

  Scientific journal


• 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

  甘利 真司, 望月 祐志, 加藤 昭史, 福澤 薫, 渡邉 千鶴, 沖山 佳生, TANAKA SHIGENORI, 中野 達也

  2014, CBI学会誌, 2(No.4) (No.4), 17 - 25, Japanese

  [Refereed]

  Scientific journal


• Hierarchical Coarse-Graining Model for Photosystem II Including Electron and Excitation-Energy Transfer Processes

  T. Matsuoka, TANAKA SHIGENORI, K. Ebina

  2014, BioSystems, 117(1) (1), 15 - 29, English

  [Refereed]

  Scientific journal


• Choline Ion Interactions with DNA Atoms Explain Unique Stabilization of A-T Base Pairs in DNA Duplexes: A Microscopic View

  Miki Nakano, Hisae Tateishi-Karimata, Shigenori Tanaka, Naoki Sugimoto

  Jan. 2014, JOURNAL OF PHYSICAL CHEMISTRY B, 118(2) (2), 379 - 389, English

  [Refereed]

  Scientific journal


• Variational Quantum Monte Carlo with Inclusion of Orbital Correlations

  Shigenori Tanaka

  Jul. 2013, JOURNAL OF THE PHYSICAL SOCIETY OF JAPAN, 82(7) (7), 075001, English

  [Refereed]


• Triplet correlations and bridge functions in classical density functional theory for liquid water

  Shigenori Tanaka, Miki Nakano

  May 2013, CHEMICAL PHYSICS LETTERS, 572, 38 - 43, English

  [Refereed]

  Scientific journal


• Three- and four-body corrected fragment molecular orbital calculations with a novel subdividing fragmentation method applicable to structure-based drug design

  Chiduru Watanabe, Kaori Fukuzawa, Yoshio Okiyama, Takayuki Tsukamoto, Akifumi Kato, Shigenori Tanaka, Yuji Mochizuki, Tatsuya Nakano

  Elsevier {BV}, Apr. 2013, Journal of Molecular Graphics and Modelling, 41, 31 - 42, English

  [Refereed]

  Scientific journal


• Study of the aggregation mechanism of polyglutamine peptides using replica exchange molecular dynamics simulations

  Miki Nakano, Kuniyoshi Ebina, Shigenori Tanaka

  Apr. 2013, JOURNAL OF MOLECULAR MODELING, 19(4) (4), 1627 - 1639, English

  [Refereed]

  Scientific journal


• Modeling of peptide–silica interaction based on four-body corrected fragment molecular orbital (FMO4) calculations

  Yoshio Okiyama, Takayuki Tsukamoto, Chiduru Watanabe, Kaori Fukuzawa, Shigenori Tanaka, Yuji Mochizuki

  Elsevier {BV}, Apr. 2013, Chemical Physics Letters, 566, 25 - 31, English

  [Refereed]

  Scientific journal


• Research on Estimation of Relative Position and Construction of Three-dimensional Space Using Range Image Sensor

  Shigenori Tanaka

  2013, Proceedings of the Conference on Technologies and Applications of Artificial Intelligence (TAAI)

  Scientific journal


• 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

  中野 達也, 田中 成典, 沖山 佳生, 瀬川 勝智

  公益社団法人 日本化学会・情報化学部会, 2013, 日本化学会情報化学部会誌, 31(3) (3), 54 - 54, Japanese


• 3P253 Hierarchical coarse-graining kinetic model for excitation energy and electron transfer processes in photosystem II(18B. Photobiology: Photosynthesis,Poster)

  Matsuoka Takeshi, Tanaka Shigenori, Ebina Kuniyoshi

  The Biophysical Society of Japan General Incorporated Association, 2013, Seibutsu Butsuri, 53(1) (1), S253, English


• Statistical correction to effective interactions in the fragment molecular orbital method

  Shigenori Tanaka, Chiduru Watanabe, Yoshio Okiyama

  Elsevier {BV}, Jan. 2013, Chemical Physics Letters, 556, 272 - 277, English

  [Refereed]

  Scientific journal


• Ab initio path integral Monte Carlo simulations for water trimer with electron correlation effects

  Takatoshi Fujita, Shigenori Tanaka, Takayuki Fujiwara, Masa-Aki Kusa, Yuji Mochizuki, Motoyuki Shiga

  Oct. 2012, COMPUTATIONAL AND THEORETICAL CHEMISTRY, 997, 7 - 13, English

  [Refereed]

  Scientific journal


• Excitation energy transfer modulated by oscillating electronic coupling of a dimeric system embedded in a molecular environment

  Yosuke Suzuki, Shigenori Tanaka

  Aug. 2012, PHYSICAL REVIEW E, 86(2) (2), 021914, English

  [Refereed]

  Scientific journal


• Renormalization-Group Inspired Approach to Vibrational Energy Transfer in Protein

  Shigenori Tanaka

  Mar. 2012, JOURNAL OF THE PHYSICAL SOCIETY OF JAPAN, 81(3) (3), 033801, English

  [Refereed]

  Scientific journal


• Method to Construct Conceptual Graph with Technical Term Dictionary for Schema Matching

  Shigenori Tanaka

  2012, Proceedings of the Joint World Congress of International Fuzzy Systems Association and International Conference on Soft Computing and Intelligent Systems (IFSA-SCIS)

  Scientific journal


• Research for Measuring Velocity and Direction of Current from Dynamic Image

  Shigenori Tanaka

  2012, Proceedings of the Joint World Congress of International Fuzzy Systems Association and International Conference on Soft Computing and Intelligent Systems (IFSA-SCIS)

  Scientific journal


• Research of Technology for Recognizing Photography Management Items from Image Data of Construction Fields

  Shigenori Tanaka

  2012, Proceedings of the Joint World Congress of International Fuzzy Systems Association and International Conference on Soft Computing and Intelligent Systems (IFSA-SCIS)

  Scientific journal


• Measurement of People Using Range Image Sensor

  Shigenori Tanaka

  2012, Proceedings of the Joint World Congress of International Fuzzy Systems Association and International Conference on Soft Computing and Intelligent Systems (IFSA-SCIS)

  Scientific journal


• New fragmentation of fragment molecular orbital method applicable to fragment based drug design

  Watanabe Chiduru, Fukuzawa Kaori, Okiyama Yoshio, Tsukamoto Takayuki, Kato Akifumi, Tanaka Shigenori, Nakano Tatsuya, Mochizuki Yuji

  2012

  [Refereed]


• Multiparticle Distribution of Fermi Gas System in Any Dimension

  Shigenori Tanaka

  2012, ADVANCES IN THE THEORY OF QUANTUM SYSTEMS IN CHEMISTRY AND PHYSICS, 22, 249 - 266, English

  [Refereed]

  International conference proceedings


• Development of the four-body corrected fragment molecular orbital (FMO4) method

  Tatsuya Nakano, Yuji Mochizuki, Katsumi Yamashita, Chiduru Watanabe, Kaori Fukuzawa, Katsunori Segawa, Yoshio Okiyama, Takayuki Tsukamoto, Shigenori Tanaka

  Elsevier {BV}, Jan. 2012, Chemical Physics Letters, 523, 128 - 133, English

  [Refereed]

  Scientific journal


• Efficient Calculation of Fragment Molecular Orbital Method with Continuous Multipole Method

  Tatsuya Nakano, Katsumi Yamashita, Katsunori Segawa, Yoshio Okiyama, Chiduru Watanabe, Kaori Fukuzawa, Shigenori Tanaka, Yuji Mochidzuki

  Division of Chemical Information and Computer Sciences, 2012, Journal of Computer Aided Chemistry, 13(0) (0), 44 - 50, Japanese

  [Refereed]

  Scientific journal


• Ab Initio Path Integral Molecular Dynamics and Monte Carlo Simulations for Water Trimer and Oligopeptide

  Takatoshi Fujita, Masa-Aki Kusa, Takayuki Fujiwara, Yuji Mochizuki, Shigenori Tanaka

  2012, ADVANCES IN QUANTUM MONTE CARLO, 1094, 187 - +, English

  [Refereed]

  International conference proceedings


• Antigen-antibody interactions of influenza virus hemagglutinin revealed by the fragment molecular orbital calculation

  Akio Yoshioka, Kazutomo Takematsu, Ikuo Kurisaki, Kaori Fukuzawa, Yuji Mochizuki, Tatsuya Nakano, Eri Nobusawa, Katsuhisa Nakajima, Shigenori Tanaka

  Dec. 2011, THEORETICAL CHEMISTRY ACCOUNTS, 130(4-6) (4-6), 1197 - 1202, English

  [Refereed]

  Scientific journal


• Higher-order correlated calculations based on fragment molecular orbital scheme

  Yuji Mochizuki, Katsumi Yamashita, Tatsuya Nakano, Yoshio Okiyama, Kaori Fukuzawa, Naoki Taguchi, Shigenori Tanaka

  Oct. 2011, THEORETICAL CHEMISTRY ACCOUNTS, 130(2-3) (2-3), 515 - 530, English

  [Refereed]

  Scientific journal


• Prediction of probable mutations in influenza virus hemagglutinin protein based on large-scale ab initio fragment molecular orbital calculations

  Akio Yoshioka, Kaori Fukuzawa, Yuji Mochizuki, Katsumi Yamashita, Tatsuya Nakano, Yoshio Okiyama, Eri Nobusawa, Katsuhisa Nakajima, Shigenori Tanaka

  Elsevier {BV}, Sep. 2011, Journal of Molecular Graphics and Modelling, 30, 110 - 119, English

  [Refereed]

  Scientific journal


• Counterpoise-corrected interaction energy analysis based on the fragment molecular orbital scheme

  Yoshio Okiyama, Kaori Fukuzawa, Haruka Yamada, Yuji Mochizuki, Tatsuya Nakano, Shigenori Tanaka

  Elsevier {BV}, Jun. 2011, Chemical Physics Letters, 509(1-3) (1-3), 67 - 71, English

  [Refereed]

  Scientific journal


• Sialic Acid Recognition of the Pandemic Influenza 2009 H1N1 Virus: Binding Mechanism Between Human Receptor and Influenza Hemagglutinin

  Kaori Fukuzawa, Katsumi Omagari, Katsuhisa Nakajima, Eri Nobusawa, Shigenori Tanaka

  May 2011, PROTEIN AND PEPTIDE LETTERS, 18(5) (5), 530 - 539, English

  [Refereed]

  Scientific journal


• Modulation of excitation energy transfer by conformational oscillations in biomolecular systems

  Shigenori Tanaka

  May 2011, CHEMICAL PHYSICS LETTERS, 508(1-3) (1-3), 139 - 143, English

  [Refereed]

  Scientific journal


• Fragment molecular orbital calculations under periodic boundary condition

  Takatoshi Fujita, Tatsuya Nakano, Shigenori Tanaka

  Apr. 2011, CHEMICAL PHYSICS LETTERS, 506(1-3) (1-3), 112 - 116, English

  [Refereed]

  Scientific journal


• Multiparticle Distributions of Ideal Fermi Gas: Analogy to Random Matrices and the Riemann Zeros

  Shigenori Tanaka

  Mar. 2011, JOURNAL OF THE PHYSICAL SOCIETY OF JAPAN, 80(3) (3), English

  [Refereed]

  Scientific journal


• Resonant neutral particle emission in collisions of electrons with protonated peptides with disulfide bonds at high energies

  Tetsumi Tanabe, Koji Noda, Satoshi Miyagi, Noriyuki Kurita, Shigenori Tanaka, Julia Setzler, Wolfgang Wenzel, Evgeni B. Starikov, Gianaurelio Cuniberti

  Feb. 2011, CHEMICAL PHYSICS LETTERS, 504(1-3) (1-3), 83 - 87, English

  [Refereed]

  Scientific journal


• Spontaneous Adjustment Mechanism in an RNA-Binding Protein: Cooperation Between Energetic Stabilization and Target Search Enhancement

  Ikuo Kurisaki, Hirofumi Watanabe, Shigenori Tanaka

  Dec. 2010, PROTEIN AND PEPTIDE LETTERS, 17(12) (12), 1547 - 1552, English

  [Refereed]

  Scientific journal


• Fragment molecular orbital (FMO) study on stabilization mechanism of neuro-oncological ventral antigen (NOVA)-RNA complex system

  Ikuo Kurisaki, Kaori Fukuzawa, Tatsuya Nakano, Yuji Mochizuki, Hirofumi Watanabe, Shigenori Tanaka

  Dec. 2010, JOURNAL OF MOLECULAR STRUCTURE-THEOCHEM, 962(1-3) (1-3), 45 - 55, English

  [Refereed]

  Scientific journal


• Incorporation of solvation effects into the fragment molecular orbital calculations with the Poisson–Boltzmann equation

  Hirofumi Watanabe, Yoshio Okiyama, Tatsuya Nakano, Shigenori Tanaka

  Elsevier {BV}, Nov. 2010, Chemical Physics Letters, 500(1-3) (1-3), 116 - 119, English

  [Refereed]

  Scientific journal


• An interpretation of positional displacement of the helix12 in nuclear receptors: Preexistent swing-up motion triggered by ligand binding

  Chiduru Watanabe, Hirofumi Watanabe, Shigenori Tanaka

  Sep. 2010, BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS, 1804(9) (9), 1832 - 1840, English

  [Refereed]

  Scientific journal


• Support to Science Activities by Citizens for Sustainable Society in Hyogo Prefecture

  Masayuki Itoh, Yoshiaki Takeda, Kuniyoshi Ebina, SHigenori Tanaka, Ikumi Dohzono, Emiko Maekawa

  Sep. 2010, 日本科学教育学会年会論文集, 34, 271-274, Japanese

  Scientific journal


• Large-scale FMO-MP3 calculations on the surface proteins of influenza virus, hemagglutinin (HA) and neuraminidase (NA)

  Yuji Mochizuki, Katsumi Yamashita, Kaori Fukuzawa, Kazutomo Takematsu, Hirofumi Watanabe, Naoki Taguchi, Yoshio Okiyama, Misako Tsuboi, Tatsuya Nakano, Shigenori Tanaka

  Elsevier {BV}, Jun. 2010, Chemical Physics Letters, 493(4-6) (4-6), 346 - 352, English

  [Refereed]

  Scientific journal


• Comparative Characterization of Short Monomeric Polyglutamine Peptides by Replica Exchange Molecular Dynamics Simulation

  Miki Nakano, Hirofumi Watanabe, Stuart M. Rothstein, Shigenori Tanaka

  May 2010, JOURNAL OF PHYSICAL CHEMISTRY B, 114(20) (20), 7056 - 7061, English

  [Refereed]

  Scientific journal


• Acceleration of fragment molecular orbital calculations with Cholesky decomposition approach

  Yoshio Okiyama, Tatsuya Nakano, Katsumi Yamashita, Yuji Mochizuki, Naoki Taguchi, Shigenori Tanaka

  Elsevier {BV}, Apr. 2010, Chemical Physics Letters, 490(1-3) (1-3), 84 - 89, English

  [Refereed]

  Scientific journal


• Molecular mechanics and all-electron fragment molecular orbital calculations on mutated polyglutamine peptides

  Bryan M. B. Van Schouwen, Miki Nakano, Hirofumi Watanabe, Shigenori Tanaka, Heather L. Gordon, Stuart M. Rothstein

  Mar. 2010, JOURNAL OF MOLECULAR STRUCTURE-THEOCHEM, 944(1-3) (1-3), 12 - 20, English

  [Refereed]

  Scientific journal


• Analysis of electron-transfer rate constant in condensed media with inclusion of inelastic tunneling and nuclear quantum effects

  Shigenori Tanaka, E. B. Starikov

  Feb. 2010, PHYSICAL REVIEW E, 81(2) (2), English

  [Refereed]

  Scientific journal


• 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

  Ikuo Kurisaki, Kaori Fukuzawa, Tatsuya Nakano, Yuji Mochizuki, Hirofumi Watanabe, Shigenori Tanaka

  Jan. 2010, BIOPHYSICAL JOURNAL, 98(3) (3), 74A - 74A, English

  [Refereed]


• Comparison of binding affinity evaluations for FKBP ligands with state-of-the-art computational methods: FMO, QM/MM, MM-PB/SA and MP-CAFEE approaches

  Hirofumi Watanabe, Shigenori Tanaka, Noriaki Okimoto, Aki Hasegawa, Makoto Taiji, Yoshiaki Tanida, Takashi Mitsui, Mariko Katsuyama, Hideaki Fujitani

  Chem-Bio Informatics Society, 2010, Chem-Bio Informatics Journal, 10(1) (1), 32 - 45, English

  [Refereed]

  Scientific journal


• Roles of K151 and D180 in L-2-Haloacid Dehalogenase from Pseudomonas sp YL: Analysis by Molecular Dynamics and Ab Initio Fragment Molecular Orbital Calculations

  Takashi Nakamura, Azusa Yamaguchi, Hirotaka Kondo, Hirofumi Watanabe, Tatsuo Kurihara, Nobuyoshi Esaki, Shuichi Hirono, Shigenori Tanaka

  Dec. 2009, JOURNAL OF COMPUTATIONAL CHEMISTRY, 30(16) (16), 2625 - 2634, English

  [Refereed]

  Scientific journal


• Ab initio Path Integral Molecular Dynamics Based on Fragment Molecular Orbital Method

  Takatoshi Fujita, Hirofumi Watanabe, Shigenori Tanaka

  Oct. 2009, JOURNAL OF THE PHYSICAL SOCIETY OF JAPAN, 78(10) (10), English

  [Refereed]

  Scientific journal


• Accuracy of fragmentation in ab initio calculations of hydrated sodium cation

  Takatoshi Fujita, Kaori Fukuzawa, Yuji Mochizuki, Tatsuya Nakano, Shigenori Tanaka

  Aug. 2009, CHEMICAL PHYSICS LETTERS, 478(4-6) (4-6), 295 - 300, English

  [Refereed]

  Scientific journal


• Creation of a system to support civil science activities in regional community

  Masayuki Itoh, Kuniyoshi Ebina, Yoshiaki Takeda, Shigenori Tanaka

  Aug. 2009, 日本科学教育学会年会論文集, 33, 395-396, Japanese

  Scientific journal


• Conformation Dependence of DNA Exciton Parentage

  E. B. Starikov, G. Cuniberti, Shigenori Tanaka

  Jul. 2009, JOURNAL OF PHYSICAL CHEMISTRY B, 113(30) (30), 10428 - 10435, English

  [Refereed]

  Scientific journal


• Possibility of Mutation Prediction of Influenza Hemagglutinin by Combination of Hemadsorption Experiment and Quantum Chemical Calculation for Antibody Binding

  Kazutomo Takematsu, Kaori Fukuzawa, Katsumi Omagari, Setsuko Nakajima, Katsuhisa Nakajima, Yuji Mochizuki, Tatsuya Nakano, Hirofumi Watanabe, Shigenori Tanaka

  Apr. 2009, JOURNAL OF PHYSICAL CHEMISTRY B, 113(15) (15), 4991 - 4994, English

  [Refereed]

  Scientific journal


• Ab initio quantum-chemical study on emission spectra of bioluminescent luciferases by fragment molecular orbital method

  Ayumu Tagami, Nobuhiro Ishibashi, Dai-ichiro Kato, Naoki Taguchi, Yuji Mochizuki, Hirofumi Watanabe, Mika Ito, Shigenori Tanaka

  Apr. 2009, CHEMICAL PHYSICS LETTERS, 472(1-3) (1-3), 118 - 123, English

  [Refereed]

  Scientific journal


• Simulation Study of RNA-Binding Protein, Pumilio

  Shigenori Tanaka

  2009, Journal of Computer Chemistry, Japan

  Scientific journal


• Production of Capacitively Coupled Atmospheric Plasma Jet With Multiring Electrodes for the Medical Plasma Tool

  Shigenori Tanaka

  2009, IEEE Transactions on Plasma Science

  Scientific journal


• 1P-055 Characterization of monomeric polyglutamine peptides by replica exchange molecular dynamics simulation(Protein:Property, The 47th Annual Meeting of the Biophysical Society of Japan)

  Nakano Miki, Watanabe Hirofumi, Tanaka Shigenori

  The Biophysical Society of Japan General Incorporated Association, 2009, Seibutsu Butsuri, 49, S71 - S72, English


• 3P-063 Possibility of Mutation Prediction of Influenza Hemagglutinin by Combination of Hemadsorption Experiment and Quantum Chemical Calculation for Antibody Binding(Protein:Function,2SP6 Towards Supercomputiong for Electronic Structures of Biological Macromolecules,Symposia,The 47th Annual Meeting of the Biophysical Society of Japan)

  Takematsu Kazutomo, Fukuzawa Kaori, Omagari Katsumi, Nakajima Katsuhisa, Nakajima Setsuko, Mochizuki Yuji, Nakano Tatsuya, Watanabe Hirofumi, Tanaka Shigenori

  The Biophysical Society of Japan General Incorporated Association, 2009, Seibutsu Butsuri, 49, S161, English


• Developments of FMO methodology and graphical user interface in ABINIT-MP

  Nakano Tatsuya, Mochizuki Yuji, Kato Akifumi, Fukuzawa Kaori, Ishikawa Takeshi, Amari Shinji, Kurisaki Ikuo, Tanaka Shigenori

  CRC Press: Boca Raton, FL, 2009, The Fragment Molecular Orbital Method: Practical Applications to Large Molecular Systems, 37 - 62

  [Refereed]

  In book


• Analysis of Mutation Mechanisms of Influenza Virus Based on the Fragment Molecular Orbital Method

  Tanaka Shigenori, Mochizuki Yuji, Fukuzawa Kaori, Yamashita Katsumi, Nakano Tatsuya

  2009, Annual Report of the Earth Simulator Center April, 2010

  [Refereed]


• 7 Application of the FMO Method to Specific Molecular Recognition of Biomacromolecules

  Fukuzawa Kaori, Mochizuki Yuji, Nakano Tatsuya, Tanaka Shigenori

  CRC Press, 2009, The Fragment Molecular Orbital Method: Practical Applications to Large Molecular Systems, 133 - 169

  [Refereed]

  In book


• 4 Excited States of Photoactive Proteins by Configuration Interaction Studies

  Mochizuki Yuji, Nakano Tatsuya, Taguchi Naoki, Tanaka Shigenori

  CRC Press, 2009, The Fragment Molecular Orbital Method: Practical Applications to Large Molecular Systems, 63 - 89

  [Refereed]

  In book


• 3P-063 Possibility of Mutation Prediction of Influenza Hemagglutinin by Combination of Hemadsorption Experiment and Quantum Chemical Calculation for Antibody Binding (Protein: Function, 2SP6 Towards Supercomputiong for Electronic Structures of Biological

  Takematsu Kazutomo, Fukuzawa Kaori, Omagari Katsumi, Nakajima Katsuhisa, Nakajima Setsuko, Mochizuki Yuji, Nakano Tatsuya, Watanabe Hirofumi, Tanaka Shigenori

  The Biophysical Society of Japan General Incorporated Association, 2009, Seibutsu Butsuri, 49(supplement) (supplement), S161

  [Refereed]


• 2SP6-07 Possibility of Mutation Prediction of Influenza Hemagglutinin by Combination of Hemadsorption Experiment and Quantum Chemical Calculation for Antibody Binding (2SP6 Towards Supercomputing for Electronic Structures of Biological Macromolecules, The

  Takematsu Kazutomo, Fukuzawa Kaori, Omagari Katsumi, Nakajima Katsuhisa, Nakajima Setsuko, Mochizuki Yuji, Nakano Tatsuya, Watanabe Hirofumi, Tanaka Shigenori

  The Biophysical Society of Japan General Incorporated Association, 2009, Seibutsu Butsuri, 49(supplement) (supplement), S15

  [Refereed]


• 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

  栗崎 以久男, 渡邉 博文, 田中 成典

  2009, J. Comput. Chem. Jpn., 8 (2009) pp. 41-50, Japanese

  [Refereed]

  Scientific journal


• Molecular geometry-dependent atomic charge calculation with modified charge equilibration method

  Kozo Aoki, Shigenori Tanaka, Tatsuya Nakano

  Chem-Bio Informatics Society, 2009, Chem-Bio Informatics Journal, 9(1) (1), 30 - 40, English

  [Refereed]

  Scientific journal


• Fragment Molecular Orbital Calculations on Red Fluorescent Proteins (DsRed and mFruits)

  Naoki Taguchi, Yuji Mochizuki, Tatsuya Nakano, Shinji Amari, Kaori Fukuzawa, Takeshi Ishikawa, Minoru Sakurai, Shigenori Tanaka

  Jan. 2009, JOURNAL OF PHYSICAL CHEMISTRY B, 113(4) (4), 1153 - 1161, English

  [Refereed]

  Scientific journal


• Fragment Molecular Orbital (FMO) and FMO-MO Calculations of DNA: Accuracy Validation of Energy and Interfragment Interaction Energy

  T. Watanabe, Y. Inadomi, H. Umeda, K. Fukuzawa, S. Tanaka, T. Nakano, U. Nagashima

  Jan. 2009, J. Comput. Theor. Nanosci., 6 (2009) pp. 1328-1337.(6) (6), 1328 - 1337, English

  [Refereed]

  Scientific journal


• Application of the fragment molecular orbital method for determination of atomic charges on polypeptides. II. Towards an improvement of force fields used for classical molecular dynamics simulations

  Yoshio Okiyama, Hirofumi Watanabe, Kaori Fukuzawa, Tatsuya Nakano, Yuji Mochizuki, Takeshi Ishikawa, Kuniyoshi Ebina, Shigenori Tanaka

  Elsevier {BV}, Jan. 2009, Chemical Physics Letters, 467(4-6) (4-6), 417 - 423, English

  [Refereed]

  Scientific journal


• An application of fragment interaction analysis based on local MP2

  Takeshi Ishikawa, Yuji Mochizuki, Shinji Amari, Tatsuya Nakano, Shigenori Tanaka, Kiyoshi Tanaka

  Sep. 2008, CHEMICAL PHYSICS LETTERS, 463(1-3) (1-3), 189 - 194, English

  [Refereed]

  Scientific journal


• Ab initio fragment molecular orbital study of molecular interactions in liganded retinoid X receptor: Specification of residues associated with ligand inducible information transmission

  Mika Ito, Kaori Fukuzawa, Takeshi Ishikawa, Yuji Mochizuki, Tatsuya Nakano, Shigenori Tanaka

  Sep. 2008, JOURNAL OF PHYSICAL CHEMISTRY B, 112(38) (38), 12081 - 12094, English

  [Refereed]

  Scientific journal


• COMP 246-Simulation study of RNA-binding protein by fragment molecular orbital (FMO) method

  Ikuo Kurisaki, Kaori Fukuzawa, Tatsuya Nakano, Yuji Mochizuki, Stuart M. Rothstein, Hirofumi Watanabe, Shigenori Tanaka

  Aug. 2008, ABSTRACTS OF PAPERS OF THE AMERICAN CHEMICAL SOCIETY, 236, English

  [Refereed]


• Theoretical analysis of binding specificity of influenza viral hemagglutinin to avian and human receptors based on the fragment molecular orbital method

  Tatsunori Iwata, Kaori Fukuzawa, Katsuhisa Nakajima, Sachiko Aida-Hyugaji, Yuji Mochizuki, Hirofumi Watanabe, Shigenori Tanaka

  Jun. 2008, COMPUTATIONAL BIOLOGY AND CHEMISTRY, 32(3) (3), 198 - 211, English

  [Refereed]

  Scientific journal


• Large scale FMO-MP2 calculations on a massively parallel-vector computer

  Yuji Mochizuki, Katsumi Yamashita, Tadashi Murase, Tatsuya Nakano, Kaori Fukuzawa, Kazutomo Takematsu, Hirofumi Watanabe, Shigenori Tanaka

  May 2008, CHEMICAL PHYSICS LETTERS, 457(4-6) (4-6), 396 - 403, English

  [Refereed]

  Scientific journal


• Germ-line mutation of KCNQ2, p.R213W, in a Japanese family with benign familial neonatal convulsion

  Ahmad H. Sadewa, Teguh H. Sasongko, Gunadi, Myeong J. Lee, Kazunari Daikoku, Akiyo Yamamoto, Takemi Yamasaki, Shigenori Tanaka, Masafumi Matsuo, Hisahide Nishio

  Apr. 2008, PEDIATRICS INTERNATIONAL, 50(2) (2), 167 - 171, English

  [Refereed]

  Scientific journal


• Derivation of extremely slow dynamics of protein motion based on entropy invariance

  Shigenori Tanaka

  Feb. 2008, PHYSICS LETTERS A, 372(8) (8), 1280 - 1282, English

  [Refereed]

  Scientific journal


• Theoretical Study on Emission Spectra of Bioluminescent Luciferases by Fragment Molecular Orbital Method

  Shigenori Tanaka

  2008, Journal of Computer Aided Chemistry

  Scientific journal


• 2P-106 Simulation study on sequence recognition mechanism of RNA-binding protein(The 46th Annual Meeting of the Biophysical Society of Japan)

  Kurisaki Ikuo, Mastumoto Astushi, Yura Kei, Tanaka Shigenori

  The Biophysical Society of Japan General Incorporated Association, 2008, Seibutsu Butsuri, 48, S91, English


• 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

  田上 歩, 石橋 延裕, 加藤 太一郎, 田口 尚貴, 望月 祐志, 渡邉 博文, 伊藤 三香, 田中 成典

  2008, J. Comput. Aided Chem., 9 (2008) pp. 47-54., Japanese

  [Refereed]

  Scientific journal


• Mutation Effects on Structural Stability of Polyglutamine Peptides by Molecular Dynamics Simulation

  M. Nakano, H. Watanabe, E.B. Starikov, S.M. Rothstein, S. Tanaka

  2008, Interdiscip. Sci. Comput. Life Sci., 1 (2009) pp. 21-29(1) (1), 21 - 29, English

  [Refereed]

  Scientific journal


• Water-Mediated Interactions in the CRP-cAMP-DNA Complex: Does Water Mediate Sequence-Specific Binding at the DNA Primary-Kink Site ?

  B. VanSchouwen, H. L. Gordon, S. M. Rothstein, Y. Komeiji, K. Fukuzawa, S. Tanaka

  Jan. 2008, Comput. Biol. Chem., 32 (2008) pp. 149-158(3) (3), 149 - 158, English

  [Refereed]

  Scientific journal


• Fragment interaction analysis based on local MP2

  Takeshi Ishikawa, Yuji Mochizuki, Shinji Amari, Tatsuya Nakano, Hiroaki Tokiwa, Shigenori Tanaka, Kiyoshi Tanaka

  Dec. 2007, THEORETICAL CHEMISTRY ACCOUNTS, 118(5-6) (5-6), 937 - 945, English

  [Refereed]

  Scientific journal


• Intra- and intermolecular interactions between Cyclic-AMP receptor protein and DNA: Ab initio fragment molecular orbital study (vol 27, pg 948, 2006)

  Kaori Fukuzawa, Yuto Komeiji, Yujj Mochizuki, Akifumi Kato, Tatsuya Nakano, Shigenori Tanaka

  Oct. 2007, JOURNAL OF COMPUTATIONAL CHEMISTRY, 28(13) (13), 2237 - 2239, English

  [Refereed]


• Visualization analysis of inter-fragment interaction energies of CRP-cAMP-DNA complex based on the fragment molecular orbital method

  Ikuo Kurisaki, Kaori Fukuzawa, Yuto Komeiji, Yuji Mochizuki, Tatsuya Nakano, Janine Imada, Arleta Chmielewski, Stuart M. Rothstein, Hirofumi Watanabe, Shigenori Tanaka

  Oct. 2007, BIOPHYSICAL CHEMISTRY, 130(1-2) (1-2), 1 - 9, English

  [Refereed]

  Scientific journal


• DNA and estrogen receptor interaction revealed by fragment molecular orbital calculations

  Toshio Watanabe, Yuichi Inadomi, Kaori Fukuzawa, Tatsuya Nakano, Shigenori Tanaka, Lennart Nilsson, Umpei Nagashima

  Aug. 2007, JOURNAL OF PHYSICAL CHEMISTRY B, 111(32) (32), 9621 - 9627, English

  [Refereed]

  Scientific journal


• Fragmentation method combined with quantum Monte Carlo calculations

  Ryo Maezono, Hirofumi Watanabe, Shigenori Tanaka, M. D. Towler, R. J. Needs

  Jun. 2007, JOURNAL OF THE PHYSICAL SOCIETY OF JAPAN, 76(6) (6), English

  [Refereed]

  Scientific journal


• Determination of the tertiary structure of exon 1 Huntingtin

  T. Zuchner, A. R. Kazemi, J. Weigelt, J. Starikow, S. Tanaka, S. Rothstein, P. Brundin

  Jun. 2007, JOURNAL OF NEUROCHEMISTRY, 101, 65 - 66, English

  [Refereed]

  International conference proceedings


• Ab initio fragment molecular orbital study of molecular interactions between liganded retinoid x receptor and its coactivator: Roles of helix 12 in the coactivator binding mechanism

  Mika Ito, Kaori Fukuzawa, Yuji Mochizuki, Tatsuya Nakano, Shigenori Tanaka

  Apr. 2007, JOURNAL OF PHYSICAL CHEMISTRY B, 111(13) (13), 3525 - 3533, English

  [Refereed]

  Scientific journal


• Application of Fragment Molecular Orbital (FMO) Method to Nano-Bio Field

  Shigenori Tanaka

  2007, Journal of Computer Chemistry, Japan

  Scientific journal


• Applications of the Fragment Molecular Orbital Method for Bio-Macromolecules

  Shigenori Tanaka

  2007, Journal of Computer Chemistry, Japan

  Scientific journal


• Erratum: Intra- and intermodular interactions between cyclic-AMP receptor protein and DNA: Ab initio fragment molecular orbital study (Journal of Computational Chemistry (2006) 27 (948))

  Fukuzawa, K., Komeiji, Y., Mochizuki, Y., Kato, A., Nakano, T., Tanaka, S.

  2007, Journal of Computational Chemistry, 28(13) (13), 2237 - 2239

  [Refereed]

  Scientific journal


• 2P058 Theoretical study on the sequence specific recognition mechanism of Pumilio RNA-binding domain by Fragment Molecular Orbital (FMO) method (Proteins-structure and structure-function relationship, Poster Presentations)

  Kurisaki Ikuo, Fukuzawa Kaori, Nakano Tatsuya, Mochizuki Yuji, Watanabe Hirofumi, Tanaka Shigenori

  The Biophysical Society of Japan General Incorporated Association, 2007, Seibutsu Butsuri, 47(supplement) (supplement), S127, English

  [Refereed]


• 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

  中野 達也, 望月 祐志, 甘利 真司, 小林 将人, 福澤 薫, 田中 成典

  2007, J. Comput. Chem. Jpn., 6, No. 3 (2007) pp. 173-184., English

  Scientific journal


• 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

  S. Tanaka

  2007, 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., Japanese

  International conference proceedings


• フラグメント分子軌道法による生体高分子の応用計算

  福澤 薫, 中野 達也, 加藤 昭史, 望月 祐志, 田中 成典

  2007, J. Comput. Chem. Jpn. 6,, 6, No. 3 (2007) pp. 185-198., English

  [Refereed]

  Scientific journal


• エストロゲン受容体のアミノ酸変異によるエストラジオール結合エネルギーの変化

  前田 紘輔, Alexander Schug, 渡邉 博文, 福澤 薫, 望月 祐志, 中野 達也, 田中 成典

  We have studied the molecular mechanism for the binding between estrogen receptor and estradiol using ab initio methods. To examine the validity of in silico analysis of mutation effects, we made point mutations of receptor employed in experiments, and compared the calculated results for the binding energies with experimental data. We performed the calculations at the HF/STO-3G and MP2/STO-3G levels by using the Fragment Molecular Orbital (FMO) method. The calculated results for three of six mutants qualitatively agreed with experimental data. However, the other three examples failed to reproduce the experimental data. We discussed the reasons for these discrepancies.

  Society of Computer Chemistry, Japan, 2007, J. Comput. Chem. Jpn., 6 (2007) pp. 33-46(1) (1), 33 - 46, Japanese

  [Refereed]

  Scientific journal


• On Mechanism of Enhanced Fluorescence in Green Fluorescent Protein

  E.B. Starikov, I. Panas, Y. Mochizuki, S. Tanaka, Y. Luo, H. Agren

  2007, Biophys. Rev. Lett., 2, Nos. 3&4 (2007) pp. 221-227(3-4) (3-4), 221 - 227, English

  [Refereed]

  Scientific journal


• Molecular Dynamics Simulation Study on the Structural Stabilities of Polyglutamine Peptides

  H. Ogawa, M. Nakano, H. Watanabe, E.B. Starikov, S.M. Rothstein, S. Tanaka

  2007, Comput. Biol. Chem., 32 (2008) pp. 102-110(2) (2), 102 - 110, English

  [Refereed]

  Scientific journal


• Fragment molecular orbital calculations on red fluorescent protein (DsRed)

  Yuji Mochizuki, Tatsuya Nakano, Shinji Amari, Takeshi Ishikawa, Kiyoshi Tanaka, Minoru Sakurai, Shigenori Tanaka

  Jan. 2007, CHEMICAL PHYSICS LETTERS, 433(4-6) (4-6), 360 - 367, English

  [Refereed]

  Scientific journal


• Comparison of epitope structures of H3HAs through protein modeling of influenza a virus hemagglutinin: Mechanism for selection of antigenic variants in the presence of a monoclonal antibody

  Setsuko Nakajima, Katsuhisa Nakajima, Eri Nobusawa, Jin Zhao, Shigenori Tanaka, Kaori Fukuzawa

  2007, MICROBIOLOGY AND IMMUNOLOGY, 51(12) (12), 1179 - 1187, English

  [Refereed]

  Scientific journal


• Application of the fragment molecular orbital method for determination of atomic charges on polypeptides

  Yoshio Okiyama, Hirofumi Watanabe, Kaori Fukuzawa, Tatsuya Nakano, Yuji Mochizuki, Takeshi Ishikawa, Shigenori Tanaka, Kuniyoshi Ebina

  Elsevier {BV}, 2007, Chemical Physics Letters, 449(4-6) (4-6), 329 - 335, English

  [Refereed]

  Scientific journal


• Ab Initio Study of Molecular Interactions in Higher Plant and Galdieria Partita Rubiscos with the Fragment Molecular Orbital Method

  H. Watanabe, T. Enomoto, S. Tanaka

  2007, Biochem. Biophys. Res. Commun., 361 (2007) pp. 367-372(2) (2), 367 - 372, English

  [Refereed]

  Scientific journal


• Ab Initio Fragment Molecular Orbital Study of Molecular Interactions between Liganded Retinoid X Receptor and Its Coactivator. Part II: Influence of Mutations in Transcriptional Activation Function 2 Activating Domain Core on the Molecular Interactions

  M. Ito, K. Fukuzawa, Y. Mochizuki, T. Nakano, S. Tanaka

  2007, J. Phys. Chem. A, 112 (2008) pp. 1986-1998(10) (10), 1986 - 1998, English

  [Refereed]

  Scientific journal


• Ab Initio Biomolecular Calculations Using Quantum Monte Carlo Combined with the Fragment Molecular Orbital Method

  R. Maezono, H. Watanabe, S. Tanaka

  2007, “Advances in Quantum Monte Carlo”, pp. 141-146., 141 - 146, English

  Scientific journal


• Differences in characteristics of dye-sensitized solar cells containing acetonitrile and ionic liquid-based electrolytes studied using a novel model

  Toshihiro Oda, Shigenori Tanaka, Shuzi Hayase

  Oct. 2006, SOLAR ENERGY MATERIALS AND SOLAR CELLS, 90(16) (16), 2696 - 2709, English

  [Refereed]

  Scientific journal


• Application of fragment molecular orbital scheme to silicon-containing systems

  Takeshi Ishikawa, Yuji Mochizuki, Kenji Imamura, Tatsuya Nakano, Hirotoshi Mori, Hiroaki Tokiwa, Kiyoshi Tanaka, Eisaku Miyoshi, Shigenori Tanaka

  Oct. 2006, CHEMICAL PHYSICS LETTERS, 430(4-6) (4-6), 361 - 366, English

  [Refereed]

  Scientific journal


• Fragment molecular orbital calculations on large scale systems containing heavy metal atom

  Takeshi Ishikawa, Yuji Mochizuki, Tatsuya Nakano, Shinji Amari, Hirotoshi Mori, Hiroaki Honda, Takatoshi Fujita, Hiroaki Tokiwa, Shigenori Tanaka, Yuto Komeiji, Kaori Fukuzawa, Kiyoshi Tanaka, Eisaku Miyoshi

  Aug. 2006, CHEMICAL PHYSICS LETTERS, 427(1-3) (1-3), 159 - 165, English

  [Refereed]

  Scientific journal


• Effects of molecular motion on charge transfer/transport through DNA duplexes with and without base pair mismatch

  E. B. Starikov, T. Fujita, H. Watanabe, Y. Sengoku, S. Tanaka, W. Wenzel

  Aug. 2006, MOLECULAR SIMULATION, 32(9) (9), 759 - 764, English

  [Refereed]

  Scientific journal


• Development of an Empowerment System for Citizens in Science and Technology II : Starting Science Cafe Kobe

  ITOH Masayuki, TANAKA Shigenori, EBINA Kuniyoshi, NAGASAKA Kosaku, OHMIDO Nobuko, OGASAWARA Fumie, SAKURAI Kaori, HAMAOKA Rie

  「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。

  Japan Society of Science Education, Aug. 2006, 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, Japanese

  Scientific journal


• Intra- and intermolecular interactions between cyclic-AMP receptor protein and DNA: Ab initio fragment molecular orbital study

  K Fukuzawa, Y Komeiji, Y Mochizuki, A Kato, T Nakano, S Tanaka

  Jun. 2006, JOURNAL OF COMPUTATIONAL CHEMISTRY, 27(8) (8), 948 - 960, English

  [Refereed]

  Scientific journal


• Analysis of dominant factors for increasing the efficiencies of dye-sensitized solar cells: Comparison between acetonitrile and ionic liquid based electrolytes

  T Oda, S Tanaka, S Hayase

  Apr. 2006, JAPANESE JOURNAL OF APPLIED PHYSICS PART 1-REGULAR PAPERS BRIEF COMMUNICATIONS & REVIEW PAPERS, 45(4A) (4A), 2780 - 2787, English

  [Refereed]

  Scientific journal


• Dynamic polarizability calculation with fragment molecular orbital scheme

  Y Mochizuki, T Ishikawa, K Tanaka, H Tokiwa, T Nakano, S Tanaka

  Feb. 2006, CHEMICAL PHYSICS LETTERS, 418(4-6) (4-6), 418 - 422, English

  [Refereed]

  Scientific journal


• Quasi-solid dye-sensitized solar cells containing nanoparticles modified with ionic liquid-type molecules

  T Kato, T Kado, S Tanaka, A Okazaki, S Hayase

  2006, JOURNAL OF THE ELECTROCHEMICAL SOCIETY, 153(3) (3), A626 - A630, English

  [Refereed]

  Scientific journal


• Quasi-solid dye sensitized solar cells with ionic liquid type gel electrolytes

  T. Kato, A. Okazaki, Y. Ogomi, T. Kado, S. Tanaka, T. Beppu, S. Hayase

  2006, ECS Transactions, 1(32) (32), 23 - 30

  International conference proceedings


• Drug discovery using grid technology

  Hitoshi Goto, Sigeaki Obata, Toshiyuki Kamakura, Naofumi Nakayama, Mitsuhisa Sato, Yoshihiro Nakajima, Umpei Nagashima, Toshio Watanabe, Yuichi Inadomi, Masakatsu Ito, Takeshi Nishikawa, Tatsuya Nakano, Lennart Nilsson, Shigenori Tanaka, Kaori Fukuzawa, Yuichiro Inagaki, Michiaki Hamada, Hiroshi Chuman

  2006, Modern Methods for Theoretical Physical Chemistry of Biopolymers, 227 - 248

  In book


• 1P056 Theoretical study on the physicochemical properties of Pumilio RNA-binding domain by quantum chemical calculations(1. Protein structure and dynamics (I),Poster Session,Abstract,Meeting Program of EABS & BSJ 2006)

  Kurisaki Ikuo, Fukuzawa Kaori, Nakano Tatsuya, Watanabe Hirofumi, Tanaka Shigenori

  The Biophysical Society of Japan General Incorporated Association, 2006, Seibutsu Butsuri, 46(2) (2), S160, English


• Ballistic conductance for all-atom models of native and chemically modified DNA. A review of a Kubo-formula-based approach

  Ewgeni B. Starikov, Shigenori Tanaka, Noriyuki Kurita, Yasuo Sengoku, Takayuki Natsume, Aina Quintilla, Wolfgang Wenzel

  Elsevier, 2006, Modern Methods for Theoretical Physical Chemistry of Biopolymers, 535 - 546, English

  [Refereed]

  In book


• Developments and applications of ABINIT-MP software based on the fragment molecular orbital method

  Tatsuya Nakano, Yuji Mochizuki, Kaori Fukuzawa, Shinji Amari, Shigenori Tanaka

  Elsevier, 2006, Modern Methods for Theoretical Physical Chemistry of Biopolymers, 39 - 52, English

  [Refereed]

  In book


• Molecular Interactions between Estrogen Receptor and Its Ligand Studied by the ab Initio Fragment Molecular Orbital Method

  K. Fukuzawa, Y. Mochizuki, S. Tanaka, K. Kitaura, T. Nakano

  2006, J. Phys. Chem. B, 110 (2006) 16102-16110(47) (47), 24276 - 16110, English

  [Refereed]

  Scientific journal


• Fragment molecular orbital calculations on red fluorescent protein (DsRed)

  Y. Mochizuki, T. Nakano, S. Amari, T. Ishikawa, K. Tanaka, M. Sakurai, S. Tanaka

  2006, Chem. Phys. Lett., 433 (2007) 360, English

  [Refereed]

  Scientific journal


• Investigation of a Kubo-formula-based approach to estimate DNA conductance in an atomistic model

  EB Starikov, S Tanaka, N Kurita, Y Sengoku, T Natsume, W Wenzel

  Dec. 2005, EUROPEAN PHYSICAL JOURNAL E, 18(4) (4), 437 - 445, English

  [Refereed]

  Scientific journal


• Developement of an Empowerment System for Citizens in Science and Technology

  ITOH, Masayuki, OGAWA, Masataka, TAKEDA, Yoshiaki, USHIMARU, Atsushi, TAINOSHO, Yoshiaki, EBINA, Kuniyoshi, OHMIDO, Nobuko, SHIRASUGI, Naoko, NAGASAKA, Kosaku, TANAKA, Shigenori, SANUKIDA, Satoshi, NOBUKAWA, Takako

  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。

  Japan Society of Science Education, Sep. 2005, 科教研報, 20・2, 47-51(2) (2), 47 - 51, Japanese

  Scientific journal


• 1A configuration analysis for fragment interaction

  Y Mochizuki, K Fukuzawa, A Kato, S Tanaka, K Kitaura, T Nakano

  Jul. 2005, CHEMICAL PHYSICS LETTERS, 410(4-6) (4-6), 247 - 253, English

  [Refereed]

  Scientific journal


• Charge transfer through double-strand DNA and its base-mismatched ones: Theoretical analysis based on semiempirical molecular orbital calculations

  T Natsume, K Dedachi, S Tanaka, T Higuchi, N Kurita

  Jun. 2005, CHEMICAL PHYSICS LETTERS, 408(4-6) (4-6), 381 - 388, English

  [Refereed]

  Scientific journal


• Density functional calculations on the interaction between catabolite activator protein and cyclic AMP using the fragment molecular orbital method

  SI Sugiki, M Matsuoka, R Usuki, Y Sengoku, N Kurita, H Sekino, S Tanaka

  Mar. 2005, JOURNAL OF THEORETICAL & COMPUTATIONAL CHEMISTRY, 4(1) (1), 183 - 195, English

  [Refereed]

  Scientific journal


• Functionally relevant protein motions: Extracting basin-specific collective coordinates from molecular dynamics trajectories

  PW Pan, RJ Dickson, HL Gordon, SM Rothstein, S Tanaka

  Jan. 2005, JOURNAL OF CHEMICAL PHYSICS, 122(3) (3), English

  [Refereed]

  Scientific journal


• Fragment Molecular Orbital Study on Molecular Interaction between Estrogen Receptor and Their Ligands

  FUKUZAWA, MOCHIZUKI, TANAKA, AMARI, KITAURA, AND, Nakano

  2005, Proceedings of 7th Congress of the World Association of Theoretically Oriented Chemists (WATOC) (Cape Town, South Africa), ES-P23,

  International conference proceedings


• Consistent charge equilibration (CQEq) method: application to amino acids and crambin protein

  T Ogawa, N Kurita, H Sekino, O Kitao, S Tanaka

  Oct. 2004, CHEMICAL PHYSICS LETTERS, 397(4-6) (4-6), 382 - 387, English

  [Refereed]

  Scientific journal


• Solvent effects on the suppression of oxidative decomposition of guanines by phenyl group attachment in deoxyribonucleic acid (DNA)

  S Yokojima, W Yanoi, N Yoshiki, N Kurita, S Tanaka, K Nakatani, A Okada

  Jun. 2004, JOURNAL OF PHYSICAL CHEMISTRY B, 108(22) (22), 7500 - 7505, English

  [Refereed]

  Scientific journal


• Drug discovery using grid technologies and DrugML.

  M Hamada, Y Inagaki, H Goto, S Tanaka, H Chuman

  Mar. 2004, ABSTRACTS OF PAPERS OF THE AMERICAN CHEMICAL SOCIETY, 227, U685 - U685, English

  International conference proceedings


• １重鎖及び２重鎖DNAの電流電圧特性の理論的解析

  DEDACHI, NATUME, TANAKA, HIGUCHI, KURITA

  2004, J. Comput. Aided Chem., 5, 52p-61p

  [Refereed]

  Scientific journal


• 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

  SENGOKU, MATUOKA, SUGIKI, TANAKA, KURITA, SEKINO

  2004, J. Comput. Aided Chem., 5, 1p-8p

  [Refereed]

  Scientific journal


• 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

  USUKI, SENGOKU, MATUOKA, TANAKA, KURITA

  2004, J. Comput. Aided Chem., 5, 19p-25p

  [Refereed]

  Scientific journal


• DNA and estrogen receptor interaction revealed by the fragment molecular orbital method - Implementation of SCF convergence

  T Watanabe, Y Inadomi, S Tanaka, U Nagashima'

  2004, NSTI NANOTECH 2004, VOL 1, TECHNICAL PROCEEDINGS, Vol. 1, 176p-179p, 176 - 179, English

  International conference proceedings


• Ab Initio Approach to Nanoscale Dynamics of DNA

  TANAKA

  2004, Proceedings of 3rd International Conference “Computational Modeling and Simulation of Materials” (Acireale, Sicily, Italy), ,

  International conference proceedings


• Ab Initio Approach to Nanoscale Dynamics of DNA

  TANAKA

  2004, Abstr. Joint Meeting of “International Conference on Molecular Simulation (ICMS)” and “Computational Science Workshop 2004 (CSW2004)” (Tsukuba, Japan), , 12p-13p

  International conference proceedings


• First-Principles Calculations for DNA and Related Systems

  TANAKA Shigenori, FUKUZAWA Kaori, NAKANO Tatsuya, KURITA Noriyuki

  日本表面科学会, Nov. 2003, Journal of the Surface Science Society of Japan, 24, 664-670(11) (11), 664 - 670, Japanese


• Quantum Monte Carlo descriptions of molecular interactions relevant to biopolymers.

  S Tanaka

  Sep. 2003, ABSTRACTS OF PAPERS OF THE AMERICAN CHEMICAL SOCIETY, 226, U302 - U302, English

  International conference proceedings


• Charge transfer in duplex DNA containing mismatch

  A Okada, S Yokojima, N Kurita, Y Sengoku, S Tanaka

  Jul. 2003, JOURNAL OF MOLECULAR STRUCTURE-THEOCHEM, 630(1-3) (1-3), 283 - 290, English

  [Refereed]

  Scientific journal


• Hydrogen bonding of DNA base pairs by consistent charge equilibration method combined with universal force field

  T Ogawa, N Kurita, H Sekino, O Kitao, S Tanaka

  Jun. 2003, CHEMICAL PHYSICS LETTERS, 374(3-4) (3-4), 271 - 278, English

  [Refereed]

  Scientific journal


• .

  TANAKA Shigenori

  .

  Division of Chemical Information and Computer Sciences The Chemical Society of Japan, 2003, CICSJ Bulletin, 21(5) (5), 95 - 95, Japanese


• Theoretical modeling for electron transfer and transport in DNA

  S Tanaka

  2003, 7TH WORLD MULTICONFERENCE ON SYSTEMICS, CYBERNETICS AND INFORMATICS, VOL VIII, PROCEEDINGS, Vol. VIII, 318p, 318 - 318, English

  International conference proceedings


• Electrochemical DNA Chip: Simulations and Applications

  TANAKA

  2003, Abstr. International Symposium on Fusion of Nano and Bio Technologies (FNB 2003) (Tsukuba International Congress Center, Tsukuba), , 14p

  International conference proceedings


• Consistent Charge Equilibration Method Combined with Universal Force Field: Application to Amino Acid Molecules

  OGAWA, KITAO, KURITA, SEKINO, TANAKA

  In the previous paper (O. Kitao and T. Ogawa, Mol. Phys., 101, 3-17 (2003).), we have proposed the consistent charge equilibration (CQEq) method. The CQEq energy term was combined with the universal force field (UFF) to develop the CQEq with UFF (CUFF). In this article, to confirm the accuracy of the CUFF, geometry optimizations by the CUFF were performed for a series of amino acid molecules. The CUFF can well reproduce the HF/6-31G ^** geometries aside from some flexible dihedral angles. The partial charges obtained by the CQEq deviate somewhat from those by the restrained electrostatic potential fit; this result suggested us a way to improve the CQEq and the CUFF.

  Chem-Bio Informatics Society, 2003, Chem-Bio Informatics J., 3, No. 2, 78p-85p, 78 - 85, English

  [Refereed]

  Scientific journal


• Ab Initio Approach to Nanoscale Dynamics of DNA,Abstr

  TANAKA

  2003, International Workshop on Radiation Risk and its Origin at Molecular and Cellular Level (Japan Atomic Energy Research Institute, Tokai, Ibaraki), , 13p

  International conference proceedings


• Nuclear quantum effects on electron transfer reactions in DNA hairpins

  Shigenori Tanaka, Yasuo Sengoku

  2003, Physical Review E - Statistical Physics, Plasmas, Fluids, and Related Interdisciplinary Topics, 68(3) (3), 5 - 319055, English

  [Refereed]

  Scientific journal


• Possibility of nonequilibrium isomerization of azobenzene triggered by vibrational excitations

  S Tanaka, S Itoh, N Kurita

  Aug. 2002, CHEMICAL PHYSICS LETTERS, 362(5-6) (5-6), 467 - 475, English

  [Refereed]

  Scientific journal


• Vibrational energy transfer in azodendrimer and azobenzene

  Shigenori Tanaka, Satoshi Itoh, Noriyuki Kurita

  Oct. 2001, Chemical Physics, 272(2-3) (2-3), 171 - 184

  [Refereed]

  Scientific journal


• Performance simulation for dye-sensitized solar cells: Toward high efficiency and solid state

  S. Tanaka

  Jan. 2001, Japanese Journal of Applied Physics, Part 1: Regular Papers and Short Notes and Review Papers, 40(1) (1), 97 - 107

  Scientific journal


• Ab initio molecular orbital and density functional studies on the stable structures and vibrational properties of trans- and cis-azobenzenes

  Noriyuki Kurita, Shigenori Tanaka, Satoshi Itoht

  Aug. 2000, Journal of Physical Chemistry A, 104(34) (34), 8114 - 8120

  Scientific journal


• Structural and vibrational analysis of azodendrimers by molecular orbital methods

  S Tanaka, S Itoh, N Kurita

  Jun. 2000, CHEMICAL PHYSICS LETTERS, 323(5-6) (5-6), 407 - 415, English

  [Refereed]

  Scientific journal


• Theory of nonadiabatic electron transfer at electrode/liquid interfaces: Role of quantum effects

  Shigenori Tanaka, Chao Ping Hsu

  Dec. 1999, Journal of Chemical Physics, 111(24) (24), 11117 - 11137

  Scientific journal


• アゾデンドリマーの構造シミュレーションと振動解析

  TANAKA SHIGENORI, ITO SATOSHI, KURITA NORIYUKI

  Dec. 1999, 分子シミュレーション討論会講演要旨集, 13th, 21 - 22, Japanese


• Electron transfer model for the electric field effect on quantum yield of charge separation in bacterial photosynthetic reaction centers

  Shigenori Tanaka, R. A. Marcus

  Jun. 1997, Journal of Physical Chemistry B, 101(25) (25), 5031 - 5045

  Scientific journal


• Strained lattice organic thin film growth by molecular beam epitaxy

  Toshio Nakayama, Shigenori Tanaka, Shin Ya Aoki

  1996, Molecular Crystals and Liquid Crystals Science and Technology Section A: Molecular Crystals and Liquid Crystals, 276-277, 267 - 271

  Scientific journal


• Charge distribution in Y1-xPrxBa2Cu3O7: A valency model for the depression of Tc

  Shigenori Tanaka, Yuichi Motoi

  1995, Physical Review B, 52(1) (1), 85 - 88

  Scientific journal


• Variational Quantum Monte Carlo Approach to the Electronic Structure of NiO

  Shigenori Tanaka

  1995, Journal of the Physical Society of Japan, 64(11) (11), 4270 - 4277

  Scientific journal


• Effects of electrostatic field on the phase properties of mixed-stack organic charge-transfer compounds

  Shigenori Tanaka, Shinya Aoki, Toshio Nakayama, Syun Egusa

  1995, Physical Review B, 52(3) (3), 1549 - 1565

  Scientific journal


• Carrier doping model for La2 - xSrxNiO4

  Shigenori Tanaka, Yuichi Motoi

  Dec. 1994, Physica C: Superconductivity and its applications, 234(3-4) (3-4), 355 - 360

  Scientific journal


• Bond ionicities of high-Tc oxides

  Shigenori Tanaka

  Feb. 1994, Physica C: Superconductivity and its applications, 220(3-4) (3-4), 341 - 346

  Scientific journal


• Relationship between madelung potentials and bond valence sums in copper-oxide superconductors

  Shigenori Tanaka

  Feb. 1994, Japanese Journal of Applied Physics, 33(2 R) (2 R), 1004 - 1011

  Scientific journal


• Structural optimization in variational quantum Monte Carlo

  Shigenori Tanaka

  1994, The Journal of Chemical Physics, 100(10) (10), 7416 - 7420

  Scientific journal


• 51V NMR study of the electronic correlation in layered perovskite compounds Srn+1VnO3n+1

  Masayuki Itoh, Noburu Fukushima, Shigenori Tanaka, Ken Ando

  May 1993, Physica B: Physics of Condensed Matter, 186-188(C) (C), 1062 - 1064, English

  [Refereed]

  Scientific journal


• New layered vanadium oxide with negative magnetization, sr4v308-5

  Noburu Fukushim, Shiro Takeno, Shigenori Tanaka, Ken Ando

  Feb. 1993, Japanese Journal of Applied Physics, 32(2 A) (2 A), 190 - 192

  Scientific journal


• Cohesive Energy of NiO:A Quantum Monte Carlo Approach

  Shigenori Tanaka

  1993, Journal of the Physical Society of Japan, 62(6) (6), 2112 - 2119

  Scientific journal


• Phenomenological two-carrier model for oxide superconductors

  Shigenori Tanaka

  Mar. 1992, Physica C: Superconductivity and its applications, 192(3-4) (3-4), 315 - 327

  Scientific journal


• Electronic Structure of Vanadium Oxide Clusters in Layered Perovskite Compounds Srn+1VnO3n+1 (n = l, 2, 3)

  Shigenori Tanaka, Noburu Fukushima, Reiko Yoshimura, Tsukasa Tada

  Mar. 1992, Journal of the Physical Society of Japan, 61(7) (7), 2399 - 2411

  Scientific journal


• Comparative study of electronic states of VO6 and CuO6 clusters

  Shigenori Tanaka, Noburu Fukushima, Reiko Yoshimura, Tsukasa Tada

  Dec. 1991, Physica C: Superconductivity and its applications, 185-189(PART 1) (PART 1), 709 - 710

  Scientific journal


• Metal-insulator transition in Sr3V2O7

  Noburu Fukushima, Shigenori Tanaka, Hiromi Niu, Ken Ando

  Dec. 1991, Physica C: Superconductivity and its applications, 185-189(PART 1) (PART 1), 715 - 716

  Scientific journal


• Metal insulator transition in layered perovskite sr3v207

  Noburu Fukushima, Shigenori Tanaka, Hiromi Niu, Ken Ando

  Dec. 1990, Japanese Journal of Applied Physics, 29(12) (12), 2190 - 2192

  Scientific journal


• Bond-valence-sum study on possible candidates for high-tcoxide superconductors

  Shigenori Tanaka, Noburu Fukushima, Hiromi Niu, Ken Ando

  Nov. 1990, Japanese Journal of Applied Physics, 29(11) (11), 1987 - 1990

  Scientific journal


• Fermi-liquid approach to the anomalous optical properties in the normal state of oxide superconductors

  Shigenori Tanaka

  Aug. 1990, Physica C: Superconductivity and its applications, 169(3-4) (3-4), 271 - 274

  Scientific journal


• Equation of state and conductivities of dense hydrogen plasmas near the metal-insulator transition

  Shigenori Tanaka, Xin Zhong Yan, Setsuo Ichimaru

  1990, Physical Review A, 41(10) (10), 5616 - 5625

  Scientific journal


• Statistical-Mechanical Theory of Cold Nuclear Fusion in Metal Hydrides

  Setsuo Ichimaru, Aiichiro Nakano, Shuji Ogata, Shigenori Tanaka, Hiroshi Iyetomi, Toshiki Tajima

  1990, Journal of the Physical Society of Japan, 59(4) (4), 1333 - 1340

  Scientific journal


• Spin-dependent correlations and thermodynamic functions for electron liquids at arbitrary degeneracy and spin polarization

  Shigenori Tanaka, Setsuo Ichimaru

  1989, Physical Review B, 39(2) (2), 1036 - 1051

  Scientific journal


• Dynamic theory of correlations in strongly coupled, classical one-component plasmas: Glass transition in the generalized viscoelastic formalism

  Shigenori Tanaka, Setsuo Ichimaru

  1987, Physical Review A, 35(11) (11), 4743 - 4754

  Scientific journal


• Spin-dependent electron interactions in metals across the compressibility and spin-susceptibility anomalies

  Setsuo Ichimaru, Shigenori Tanaka

  1987, Physical Review B, 36(11) (11), 6182 - 6185

  Scientific journal


• Thermodynamics and Correlational Properties of Finite-Temperature Electron Liquids in the Singwi-Tosi-Land-Sjölander Approximation

  Shigenori Tanaka, Setsuo Ichimaru

  Jul. 1986, Journal of the Physical Society of Japan, 55(7) (7), 2278 - 2289

  Scientific journal


• Generalized viscoelastic theory of the glass transition for strongly coupled, classical, one-component plasmas

  Setsuo Ichimaru, Shigenori Tanaka

  1986, Physical Review Letters, 56(26) (26), 2815 - 2818

  Scientific journal


• Theory of interparticle correlations in dense, high-temperature plasmas. VIII. Shear viscosity

  Shigenori Tanaka, Setsuo Ichimaru

  1986, Physical Review A, 34(5) (5), 4163 - 4170

  Scientific journal


• Theory of interparticle correlations in dense, high-temperature plasmas. III. Thermodynamic functions

  Shigenori Tanaka, Shinichi Mitake, Xin Zhong Yan, Setsuo Ichimaru

  1985, Physical Review A, 32(3) (3), 1779 - 1784

  Scientific journal


• Theory of interparticle correlations in dense, high-temperature plasmas. IV. Stopping power

  Xin Zhong Yan, Shigenori Tanaka, Shinichi Mitake, Setsuo Ichimaru

  1985, Physical Review A, 32(3) (3), 1785 - 1789

  Scientific journal


• Theory of interparticle correlations in dense, high-temperature plasmas. V. Electric and thermal conductivities

  Setsuo Ichimaru, Shigenori Tanaka

  1985, Physical Review A, 32(3) (3), 1790 - 1798

  Scientific journal


• Parametrized equation of state for dense hydrogenic plasmas

  Shigenori Tanaka, Setsuo Ichimaru

  1985, Physical Review A, 32(6) (6), 3756 - 3757

  Scientific journal


• Parametrized equation of state for electron liquids in the Singwi-Tosi-Land-Sjölander approximation

  Shigenori Tanaka, Shinichi Mitake, Setsuo Ichimaru

  1985, Physical Review A, 32(3) (3), 1896 - 1899

  Scientific journal


• Theory of interparticle correlations in dense, high-temperature plasmas. I. General formalism

  Setsuo Ichimaru, Shinichi Mitake, Shigenori Tanaka, Xin Zhong Yan

  1985, Physical Review A, 32(3) (3), 1768 - 1774

  Scientific journal


• Stopping Power of Degenerate Electron Liquid at Metallic Densities

  Shigenori Tanaka, Setsuo Ichimaru

  1985, Journal of the Physical Society of Japan, 54(7) (7), 2537 - 2542

  Scientific journal


• Theory of interparticle correlations in dense, high-temperature plasmas. II. Correlation functions

  Shinichi Mitake, Shigenori Tanaka, Xin Zhong Yan, Setsuo Ichimaru

  1985, Physical Review A, 32(3) (3), 1775 - 1778

  Scientific journal


• Ion-Density Correlations and Enhancement of Thermonuclear Reaction Rate in Dense, Inertially Confined Fusion Plasmas

  Shigenori Tanaka, Setsuo Ichtmaru

  1984, Journal of the Physical Society of Japan, 53(6) (6), 2039 - 2048

  Scientific journal


• Screening potential and enhancement of the thermonuclear reaction rate in dense plasmas

  Setsuo Ichimaru, Shigenori Tanaka, Hiroshi Iyetomi

  1984, Physical Review A, 29(4) (4), 2033 - 2035

  Scientific journal


• Erratum: Screening potential and enhancement of the thermonuclear reaction rate in dense plasmas (Physical Review A (1984) 30, 3 (1548))

  Setsuo Ichimaru, Shigenori Tanaka, Hiroshi Iyetomi

  1984, Physical Review A, 30(3) (3), 1548

  Scientific journal

• Molecular simulation analysis on the adaptation of measles virus to bat SLAM by N187Y substitution in the H protein

  福田健人, 田中成典, 高谷大輔, 福澤薫, 兵藤歩, 竹田誠

  2024, 日本ウイルス学会学術集会プログラム・予稿集(Web), 71st


• HPC技術の量子関連技術への展開~疑似量子アニーリングからGPUによる量子回路シミュレーション~フラグメント分子軌道計算による開殻・多参照の量子系の扱い

  望月祐志, 中野達也, 坂倉耕太, 杉崎研司, 田中成典

  2024, 計算工学, 29(3) (3)


• Interaction analysis of IL-10 receptor complex using MD and FMO calculations

  MIYAGISHI Toma, KAMIMURA Kenta, HANDA Yuma, HANDA Yuma, TAKIMOTO-KAMIMURA Midori, TAKIMOTO-KAMIMURA Midori, ENDO Mayumi, OKUWAKI Koji, MORI Yoshiharu, TANAKA Shigenori, TIAN Yu-Shi, TAKAYA Daisuke, FUKUZAWA Kaori

  2023, CBI学会大会(CD-ROM), 2023


• Benchmarking of Quasi-Classical Mapping Approach to Quantum Dissipative System

  鬼頭宏任, 梅垣俊仁, 西山陽大, 田中成典

  2023, 日本物理学会講演概要集(CD-ROM), 78(1) (1)


• Nucleic Acids Chemistry beyond the Watson-Crick Double Helix (77): The effect of high-pressure on non-canonical structures of DNA

  大山達也, 高橋俊太郎, 建石寿枝, 田中成典, 杉本直己, 杉本直己

  2022, 日本化学会春季年会講演予稿集(Web), 102nd


• Method for regulation of the interaction between C9orf72-derived repeat RNA and peptides based on quantitative analysis of nucleic acid structure

  建石寿枝, 松本咲, 大山達也, YE Teng, 田中成典, 杉本直己, 杉本直己

  2022, 日本核酸医薬学会年会講演要旨集(CD-ROM), 7th


• Application of the symmetrical quasi-classical method to electronically non-adiabatic processes

  鬼頭宏任, 梅垣俊仁, 西山陽大, 田中成典

  2022, 日本物理学会講演概要集(CD-ROM), 77(1) (1)


• 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

  渡邉千鶴, 渡邉千鶴, 神坂紀久子, 今井恭平, 滝本大地, 斎藤涼祐, 栗田典之, 岡山友樹, 宮嶋起徳, 吉本耀, 原田一真, 川下理日人, 藤井真靖, 森義治, 田中成典, 本間光貴, 福澤薫

  2022, 日本蛋白質科学会年会プログラム・要旨集, 22nd (Web)


• 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

  渡邉千鶴, 田中成典, 沖山佳生, 大山達也, 神坂紀久子, 幸瞳, 高谷大輔, 福澤薫, 本間光貴

  2022, 構造活性相関シンポジウム講演要旨集, 50th (CD-ROM)


• Accumulation mechanism for RNA G-quadruplex of GGGGCC repeated sequence with dipeptide repeats associated with neurodegenerative diseases

  大山達也, 建石寿枝, 田中成典, 杉本直己, 杉本直己

  2021, 日本核酸医薬学会年会講演要旨集(CD-ROM), 6th


• 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

  堺大輔, 半田佑磨, 平井優樹, 奥脇弘次, 古石誉之, 米持悦生, 沖山佳生, 田中成典, 福澤薫, 福澤薫

  2021, 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

  半田佑磨, 川嶋裕介, 畑田崚, 奥脇弘次, 望月祐志, 古石誉之, 米持悦生, 本間光貴, 古明地勇人, 田中成典, 福澤薫, 福澤薫

  2021, 構造活性相関シンポジウム講演要旨集, 49th (CD-ROM)


• Recent Advances of the Fragment Molecular Orbital Method

  ed. by Yuji Mochizuki, Shigenori Tanaka, Kaori Fukuzawa

  Springer Singapore, 2021


• 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

  川嶋裕介, 田雨時, 半田佑磨, 奥脇弘次, 渡邉千鶴, 渡邉千鶴, 川下理日人, 古石誉之, 米持悦生, 本間光貴, 田中成典, 望月祐志, 高木達也, 福澤薫

  2021, 日本薬学会関東支部大会講演要旨集, 65th (CD-ROM)


• FMO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

  半田佑磨, 奥脇弘次, 畑田崚, 望月祐志, 望月祐志, 古明地勇人, 田中成典, 古石誉之, 米持悦生, 川嶋裕介, 本間光貴, 福澤薫, 福澤薫

  2021, 日本コンピュータ化学会年会講演予稿集, 2021


• Nucleic Acids Chemistry beyond the Watson-Crick Double Helix (69): Analysis of interactions between RNA G-quadruplexes and dipeptide repeats related to neurodegenerative diseases

  大山達也, 建石寿枝, 田中成典, 杉本直己, 杉本直己

  2021, 日本化学会春季年会講演予稿集(Web), 101st


• 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

  川嶋裕介, 半田佑磨, 奥脇弘次, 望月祐志, 古明地勇人, 田中成典, 渡邉千鶴, 本間光貴, 福澤薫

  2020, 構造活性相関シンポジウム講演要旨集, 48th (CD-ROM)


• Nucleic Acids Chemistry beyond the Watson-Crick Double Helix (63): Accumulation mechanism of GGGGCC repeated RNA G-quadruplex with dipeptide repeats using molecular simulations

  大山達也, 建石寿枝, 田中成典, 杉本直己, 杉本直己

  2020, 日本化学会春季年会講演予稿集(CD-ROM), 100th


• Prediction of Binding of Existing Drugs to SARS-CoV-2 Main Protease Using Molecular Dynamics and Fragment Molecular Orbital Calculations

  HANDA Yuma, KAWASHIMA Yusuke, HATADA Ryo, OKUWAKI Koji, AKISAWA Kazuki, MOCHIZUKI Yuji, KOMEIJI Yuto, TANAKA Shigenori, FURUISHI Takayuki, FUKUZAWA Kaori, YONEMOCHI Etsuo

  2020, CBI学会大会, 2020 (CD-ROM)


• 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

  半田佑磨, 川嶋裕介, 畑田崚, 奥脇弘次, 秋澤和輝, 望月祐志, 古明地勇人, 田中成典, 古石誉之, 福澤薫, 福澤薫, 米持悦生

  2020, 日本薬学会関東支部大会講演要旨集, 64th


• Taking Water into Account with the Fragment Molecular Orbital Method.

  Yoshio Okiyama, Kaori Fukuzawa, Yuto Komeiji, Shigenori Tanaka

  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, Methods in molecular biology (Clifton, N.J.), 2114, 105 - 122, English, International magazine


• 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

  大山達也, 建石寿枝, 田中成典, 杉本直己, 杉本直己

  2019, 日本化学会春季年会講演予稿集(CD-ROM), 99th


• 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

  関祐哉, 加藤司, 安崎聡, 田中成典, 古石誉之, 福澤薫, 米持悦生

  2019, 日本コンピュータ化学会年会講演予稿集, 2019


• FMO計算を用いたJAK阻害剤のサブタイプ選択性の評価

  半田佑磨, 町田大樹, 田中成典, 古石誉之, 福澤薫, 米持悦生

  2019, 日本コンピュータ化学会年会講演予稿集, 2019


• 「量子生物学」とは何か？

  田中成典

  2019, 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, Japanese


• 計算生命科学の基礎

  鈴木洋介、渡邉博文、石野麻由子、土井陽子、倉仁美、江口至洋、田中成典、鶴田宏樹、白井剛、森一郎、伊藤眞里、臼井英之、横川三津夫

  2019, 大学ICT推進協議会2019年度年次大会論文集, Japanese


• 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

  大山達也, 建石寿枝, 田中成典, 杉本直己

  Mar. 2018, 日本化学会春季年会講演予稿集(CD-ROM), 98th, ROMBUNNO.4D5‐32, Japanese


• 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

  関祐哉, 加藤司, 安崎聡, 田中成典, 古石誉之, 福澤薫, 米持悦生

  2018, 日本薬学会関東支部大会講演要旨集, 62nd


• 共溶質存在下におけるDNA水和水の熱力学的性質の解析

  中野美紀, 建石寿枝, 田中成典, FLORENCE Tama, FLORENCE Tama, 宮下治, 杉本直己

  29 Nov. 2017, 分子シミュレーション討論会講演要旨集, 31st, 64‐65, Japanese


• 量子生命科学の展望

  TANAKA SHIGENORI

  Sep. 2017, 実験医学, Vol. 35(No. 14(9月号)) (No. 14(9月号)), 2423 - 2427, Japanese

  [Invited]

  Introduction commerce magazine


• 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

  建石寿枝, 大山達也, 村岡貴博, PODBEVSEK Peter, WAWRO Adam M, 田中成典, 金原数, PLAVEC Janez, 杉本直己, 杉本直己

  01 Jul. 2017, 日本核酸医薬学会年会講演要旨集, 3rd, 67, Japanese


• 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

  大山達也, 建石寿枝, 高橋俊太郎, 佐藤しのぶ, 田中成典, 竹中繁織, 杉本直己, 杉本直己

  03 Mar. 2017, 日本化学会春季年会講演予稿集(CD-ROM), 97th, ROMBUNNO.2C4‐47, Japanese


• FMO創薬を加速する大規模データ解析

  TANAKA SHIGENORI, 福澤薫, 本間光貴

  2017, CICSJ Bull., 35(No. 3) (No. 3), 205 - 209, Japanese

  Introduction scientific journal


• FMO プログラムABINIT-MP の開発状況と機械学習との連携

  望月祐志, 坂倉耕太, 秋永宜伸, 加藤幸一郎, 渡邊啓正, 沖山佳生, 中野達也, 古明地勇人, 奥沢明, 福澤薫, TANAKA SHIGENORI

  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.

  Society of Computer Chemistry, Japan, 2017, J. Comput. Chem. Jpn., 16(No. 5) (No. 5), 119 - 122, Japanese

  [Refereed]

  Introduction scientific journal


• 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

  建石寿枝, 大山達也, 村岡貴博, PODBEVSEK Peter, 田中成典, 金原数, PLAVEC Janez, 杉本直己, 杉本直己

  01 Nov. 2016, 日本核酸医薬学会年会講演要旨集, 2nd, 93, Japanese


• 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

  大山達也, 建石寿枝, 田中成典, 村岡貴博, 金原数, 杉本直己, 杉本直己

  2016, 分子科学討論会講演プログラム&要旨(Web), 10th


• Preface

  Shigenori Tanaka, Pierre-Nicholas Roy, Lubos Mitas

  American Chemical Society, 2016, ACS Symposium Series, 1234, ix, English

  Others


• Analysis of Biological Interaction by Fragment Molecular Orbital (FMO) Method – Analyses of the Interactions between Measles Virus Hemagglutinin and Their Receptors –

  T. Maruyama, Y. Shimane, M. Iwasawa, Y. Hatada, T. Yoshida, Y. Takaki, K. Ohishi, TANAKA SHIGENORI, H. Watanabe

  Center for Earth Information Science and Technology, Japan Agency for Marine-Earth Science and Technology, 2016, Annual Report of the Earth Simulator Center, April 2015 – March 2016, 251 - 257, English

  [Invited]

  Report research institution


• フラグメント分子軌道法のインシリコ創薬への応用

  福澤薫, 渡邉千鶴, 沖山佳生, 渡邉博文, 本間光貴, 望月祐志, 田中成典

  11 Mar. 2015, 日本化学会講演予稿集, 95th(2) (2), 232, Japanese


• Analysis of Global Ecosystem Ecology by Fragment Molecular Orbital (FMO) Method: Analyses of the Interactions between Virus Hamagglutinins and Their Receptors

  T. Maruyama, Y. Shimane, K. Ohishi, M. Iwasawa, Y. Hatada, Y. Takaki, T. Yoshida, TANAKA SHIGENORI, S. Anzaki, Y. Komeiji, Y. Mochizuki, K. Fukuzawa

  Center for Earth Information Science and Technology, Japan Agency for Marine-Earth Science and Technology, 2015, Annual Report of the Earth Simulator Center, April 2014 – March 2015, 131 - 135, English

  [Invited]

  Report research institution


• 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

  望月祐志, 福澤薫, 沖山佳生, 渡邉千鶴, 本間光貴, 田中成典

  26 May 2014, 日本蛋白質科学会年会プログラム・要旨集, 14th, 63, Japanese


• ABINIT‐MPによる京でのフラグメント分子軌道計算

  沖山佳生, 渡邉千鶴, 望月祐志, 坂倉耕太, 山本純一, 野口孝明, 小久保達信, 新宮哲, 古明地勇人, 福澤薫, 中野達也, 田中成典

  12 Mar. 2014, 日本化学会講演予稿集, 94th(2) (2), 300, Japanese


• FMO電子状態計算によるX線結晶構造の精密化の検討

  福澤薫, 渡邉千鶴, 塚本貴志, 加藤昭史, 沖山佳生, 田中成典, 望月祐志

  12 Mar. 2014, 日本化学会講演予稿集, 94th(2) (2), 300, Japanese


• Theorectical calculations on proteins with fragment molecular orbital method

  MOCHIZUKI Yuji, FUKUZAWA Kaori, OKIYAMA Yoshio, WATANABE Chiduru, HONMA Teruki, TANAKA Shigenori

  2014, CBI学会大会, 2014, 1, English


• Electron-correlated fragment-molecular-orbital calculations for biomolecular and nano systems

  Shigenori Tanaka, Yuji Mochizuki, Yuto Komeiji, Yoshio Okiyama, Kaori Fukuzawa

  Royal Society of Chemistry ({RSC}), 2014, Phys. Chem. Chem. Phys., 16(22) (22), 10310 - 10344, English

  [Invited]

  Introduction scientific journal


• Analysis of Global Ecosystem Ecology by Fragment Molecular Orbital (FMO) Method: Analyses of the Interactions between Virus Hamagglutinins and Their Receptors

  T. Maruyama, Y. Shimane, K. Ohishi, M. Iwasawa, Y. Hatada, K. Usui, Y. Takaki, T. Yoshida, TANAKA SHIGENORI, S. Anzaki, Y. Komeiji, C. Watanabe, Y. Okiyama, Y. Mochizuki, K. Fukuzawa

  Earth Simulator Center, Japan Agency for Marine-Earth Science and Technology, 2014, Annual Report of the Earth Simulator Center, April 2013 – March 2014, 155 - 160, English

  [Invited]

  Report research institution


• 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

  望月祐志, 沖山佳生, 渡邉千鶴, 塚本貴志, 福澤薫, 田中成典

  31 Aug. 2013, 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, Japanese


• 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

  渡邉千鶴, 福澤薫, 沖山佳生, 加藤昭史, 塚本貴志, 田中成典, 望月祐志

  2013, 日本分子生物学会年会プログラム・要旨集(Web), 36th, 3P-0116 (WEB ONLY), Japanese


• 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

  TANAKA SHIGENORI

  日本磁気学会, 2013, 日本磁気学会第190回研究会「生体物質の物理」資料, 31 - 36, Japanese

  Introduction other


• 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

  中野 達也, TANAKA SHIGENORI, 沖山 佳生, 瀬川 勝智

  2013, CICSJ Bull., 31(3) (3), 56 - 63, Japanese

  Introduction scientific journal


• 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

  TANAKA SHIGENORI, 福澤 薫, 望月 祐志, 中野 達也

  2013, CBI学会誌, 1(1) (1), 25 - 31, Japanese

  Introduction scientific journal


• 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

  TANAKA SHIGENORI, 渡邉 千鶴, 福澤 薫, 沖山 佳生, 望月 祐志, 塚本 貴志, 加藤 昭史, 中野 達也

  2013, CBI学会誌, 1(1) (1), 32 - 41, Japanese

  Introduction scientific journal


• Large-Scale Electronic Structure Calculations of Biomolecular and Related Systems by the Fragment Molecular Orbital Method

  TANAKA SHIGENORI

  The Earth Simulator Center, Japan Agency for Marine-Earth Science and Technology, 2013, Annual Report of the Earth Simulator Center, 173 - 178, English

  Introduction research institution


• F402 Current Status and Future of Fragment Molecular Orbital Calculations

  Tanaka Shigenori

  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。

  The Japan Society of Mechanical Engineers, 06 Oct. 2012, The Computational Mechanics Conference, 2012(25) (25), "F - 61"-"F-62", Japanese


• 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

  渡邉千鶴, 福澤薫, 沖山佳生, 望月祐志, 塚本貴志, 加藤昭史, 山下勝美, 守田伸明, 田中成典, 中野達也

  09 Mar. 2012, 日本化学会講演予稿集, 92nd(2) (2), 276, Japanese


• 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

  福澤薫, 望月祐志, 及川茉貴穂, 三部浩輝, 渡邉千鶴, 田中成典, 中野達也

  09 Mar. 2012, 日本化学会講演予稿集, 92nd(2) (2), 275, Japanese


• 24pAA-10 Aggregation mechanism of polyglutamine peptides studied by replica exchange molecular dynamics simulations

  Nakano M., Ebina K., Tanaka S.

  The Physical Society of Japan (JPS), 05 Mar. 2012, Meeting abstracts of the Physical Society of Japan, 67(1) (1), 392 - 392, Japanese


• Preface

  Shigenori Tanaka, Stuart M. Rothstein, William A. Lester

  2012, ACS Symposium Series, 1094

  Others


• ABINIT‐MP(X)によるFMO計算の最近の展開

  望月祐志, 望月祐志, 福澤薫, 福澤薫, 沖山佳生, 古明地勇人, 渡邉千鶴, 塚本貴志, 中野達也, 中野達也, 森寛敏, 松田彩, 田中成典

  2012, 分子科学討論会講演プログラム&要旨(Web), 6th, ROMBUNNO.2E16 (WEB ONLY), Japanese


• ABINIT‐MP/BioStationによるFMO応用計算事例

  福澤薫, 福澤薫, 渡邉千鶴, 沖山佳生, 塚本貴志, 中野達也, 中野達也, 田中成典, 望月祐志, 望月祐志

  2012, 分子科学討論会講演プログラム&要旨(Web), 6th, ROMBUNNO.2E17 (WEB ONLY), Japanese


• ABINIT‐MP(X)による京でのFMO計算

  沖山佳生, 望月祐志, 望月祐志, 福澤薫, 福澤薫, 古明地勇人, 森寛敏, 渡邉千鶴, 田中成典

  2012, 分子科学討論会講演プログラム&要旨(Web), 6th, ROMBUNNO.4P105 (WEB ONLY), Japanese


• Large-Scale Electronic-State Calculations of Protein-Ligand Systems for Drug Design with Fragment Molecular Orbital Method

  TANAKA SHIGENORI, Y. Mochizuki, K. Yamashita, Y. Okiyama, K. Fukuzawa, T. Nakano

  Earth Simulator Center, Japan Agency for Marine-Earth Science and Technology, 2012, Annual Report of the Earth Simulator Center, April 2011 – March 2012, 185 - 190, English

  Technical report


• Fragment molecular orbital study for interaction between influenza virus neuraminidase and antiviral drug

  FUKUZAWA Kaori, MOCHIZUKI Yuji, MIBE Hiroki, WATANABE Chiduru, TANAKA Shigenori, NAKANO Tatsuya

  08 Nov. 2011, 情報計算化学生物学会大会予稿集, 2011 (CD-ROM), ROMBUNNO.CBI-P1-13, English


• Fragment‐based drug design(FBDD)を指向した新規分割法に基づくFMO計算

  渡邉千鶴, 福澤薫, 福澤薫, 沖山佳生, 望月祐志, 望月祐志, 塚本貴志, 塚本貴志, 山下勝美, 守田伸明, 田中成典, 中野達也, 中野達也

  2011, 分子科学討論会講演プログラム&要旨(Web), 5th, ROMBUNNO.3P099 (WEB ONLY), Japanese


• Development of ABINIT-MP(X) program for processing fragment molecular orbital calculations

  Yoshio Okiyama, Tatsuya Nakano, Yuji Mochizuki, Katsumi Yamashita, Kaori Fukuzawa, Takayuki Tsukamoto, Chiduru Watanabe, Shigenori Tanaka

  2011, Proceedings of JSST 2011, International Conference on Modeling and Simulation Technology, 101 - 104

  [Invited]

  Introduction international proceedings


• 量子モンテカルロ法による分子系のシミュレーション

  TANAKA SHIGENORI

  2011, 信学技報 IEICE Technical Report 111, 255, 47 - 48, Japanese

  Introduction scientific journal


• Large-Scale Electronic-State Calculations of Influenza Viral Proteins with Fragment Molecular Orbital Method and Applications to Mutation Prediction

  TANAKA SHIGENORI, A. Yoshioka, Y. Mochizuki, K. Fukuzawa, K. Yamashita, T. Nakano

  2011, Annual Report of the Earth Simulator Center, April 2010 – March 2011, 187 - 191, English

  Technical report


• Molecular Interaction of Estrogen Receptor .ALPHA. in Fluctuating State Studied by Ab initio Fragment Molecular Orbital Method

  WATANABE Chiduru, FUKUZAWA Kaori, TANAKA Shigenori, AIDA‐HYUGAJI Sachiko

  15 Sep. 2010, 情報計算化学生物学会大会予稿集, 2010, 89, English


• Comparative Characterization of Short Monomeric Polyglutamine Peptides by Replica Exchange Molecular Dynamics Simulation (vol 114, pg 7056, 2010)

  Miki Nakano, Hirofumi Watanabe, Stuart M. Rothstein, Shigenori Tanaka

  Aug. 2010, JOURNAL OF PHYSICAL CHEMISTRY B, 114(31) (31), 10234 - 10234, English


• Fragment Molecular Orbital Method: Application to Protein-Ligand Binding

  Watanabe, Hirofumi, Tanaka, Shigenori

  Jun. 2010, Interdisciplinary Bio Central, 2(2) (2), 6.1 - 6.5, English

  [Refereed]

  Introduction scientific journal


• 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

  渡邉千鶴, 合田(日向寺, 祥子, 渡邉博文, 田中成典

  The Physical Society of Japan (JPS), 01 Mar. 2010, 日本物理学会講演概要集, 65(1) (1), 382 - 382, Japanese


• 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)

  田中 成典

  一般社団法人日本物理学会, 18 Aug. 2009, 日本物理学会講演概要集, 64(2) (2), 589 - 589, Japanese


• 28aVC-5 Development of Path Integral Molecular Dynamics Method Based on Fragment Molecular Orbital Method

  Fujita T., Watanabe H., Tanaka S.

  The Physical Society of Japan (JPS), 03 Mar. 2009, Meeting abstracts of the Physical Society of Japan, 64(1) (1), 366 - 366, Japanese


• 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

  渡邉千鶴, 渡邉博文, 田中成典

  一般社団法人日本物理学会, 03 Mar. 2009, 日本物理学会講演概要集, 64(1) (1), 373 - 373, Japanese


• Theoretical study of the series of polysilanes by fragment molecular orbital method

  田口尚貴, 望月祐志, 石川岳志, 中野達也, 森寛敏, 三好永作, 田中成典

  2009, 日本化学会講演予稿集, 89th(1) (1)


• Relationship between Structural Fluctuation and Positions of Helix 12 in the Nuclear Receptors Studied by Molecular Dynamics Simulation

  WATANABE Chiduru, WATANABE Hirofumi, TANAKA Shigenori

  22 Oct. 2008, 情報計算化学生物学会大会予稿集, 2008, 77, English


• 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

  田口尚貴, 望月祐志, 望月祐志, 石川岳志, 中野達也, 中野達也, 森寛敏, 森寛敏, 三好永作, 三好永作, 田中成典, 田中成典

  2008, 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DsRed類縁種の励起状態に関する理論的研究

  田口尚貴, 望月祐志, 中野達也, 甘利真司, 石川岳志, 福澤薫, 櫻井実, 田中成典

  2008, 日本化学会講演予稿集, 88th(1) (1)


• 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

  渡邉 博文, 田中 成典, 佐々 和洋, 林 治尚

  エヌ・ティー・エス, 2008, 未来材料, Vol. 8, No. 9(2008)pp. 40-45(9) (9), 40 - 45, Japanese

  [Refereed]

  Introduction scientific journal


• 19pRH-13 Transfer and state change of materials in photosynthesis

  Kikuchi Daisuke, Ebina Kuniyoshi, Tanaka Shigenori, Watanabe Hirofumi

  The Physical Society of Japan (JPS), 28 Feb. 2007, Meeting abstracts of the Physical Society of Japan, 62(1) (1), 380 - 380, Japanese


• 21pTC-5 Do an oscillating electric field enhance intermolecular forces?

  Suzuki Yosuke, Ebina Kuniyoshi, Tanaka Shigenori, Morii Toshiyuki

  The Physical Society of Japan (JPS), 28 Feb. 2007, Meeting abstracts of the Physical Society of Japan, 62(1) (1), 376 - 376, Japanese


• Charge transfer through single- and double-strand DNAs: Simulations based on molecular dynamics and molecular orbital methods

  Ken-ichi Dedachi, Takayuki Natsume, Taisuke Nakatsu, Shigenori Tanaka, Yasuyuki Ishikawa, Noriyuki Kurita

  Feb. 2007, CHEMICAL PHYSICS LETTERS, 436(1-3) (1-3), 244 - 251, English

  [Refereed]


• 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

  沖山佳生, 渡邉博文, 渡邉博文, 福澤薫, 中野達也, 中野達也, 望月祐志, 望月祐志, 石川岳志, 石川岳志, 田中成典, 田中成典, 蛯名邦禎

  2007, 分子科学討論会講演要旨集(CD-ROM), 1st


• FMO-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

  望月祐志, 望月祐志, 望月祐志, 古明地勇人, 古明地勇人, 石川岳志, 石川岳志, 中野達也, 中野達也, 中野達也, 山高博, 山下勝美, 栗崎以久男, 田中成典, 田中成典

  2007, 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

  田中皓, 田中皓, 望月祐志, 望月祐志, 望月祐志, 石川岳志, 石川岳志, 山下勝美, 村瀬匡, 田口尚貴, 田中成典, 田中成典

  2007, 分子科学討論会講演要旨集(CD-ROM), 1st


• FMO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

  石川岳志, 石川岳志, 望月祐志, 望月祐志, 甘利真司, 中野達也, 中野達也, 常盤広明, 田中成典, 田中成典, 田中皓, 田中皓, 田中皓

  2007, 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

  望月祐志, 望月祐志, 望月祐志, 中野達也, 中野達也, 田中皓, 田中皓, 石川岳志, 石川岳志, 三好永作, 三好永作, 古明地勇人, 古明地勇人, 山下勝美, 村瀬匡, 甘利真司, 福澤薫, 福澤薫, 櫻井実, 田中成典, 田中成典

  2007, 分子科学討論会講演要旨集(CD-ROM), 1st


• Effects of salt addition on strength and dynamics of hydrophobic interactions

  Takatoshi Fujita, Hirofumi Watanabe, Shigenori Tanaka

  Jan. 2007, CHEMICAL PHYSICS LETTERS, 434(1-3) (1-3), 42 - 48, English

  [Refereed]


• 25pWA-11 The analysis of intermolecular force in the oscillatory Electric field by harmonic oscillator model

  Suzuki Yosuke, Ebina Kuniyoshi, Tanaka Shigenori, Morii Toshiyuki

  The Physical Society of Japan (JPS), 18 Aug. 2006, Meeting abstracts of the Physical Society of Japan, 61(2) (2), 306 - 306, Japanese


• 25aWA-2 Transfer and state change of materials in photosynthesis

  Kikuchi Daisuke, Ebina Kuniyoshi, Tanaka Shigenori, Watanabe Hirofumi

  The Physical Society of Japan (JPS), 18 Aug. 2006, Meeting abstracts of the Physical Society of Japan, 61(2) (2), 304 - 304, Japanese


• 30pZA-3 The analysis of intermolecular force in the oscillatory Electric field by harmonic oscillator model

  Suzuki Yosuke, Ebina Kuniyoshi, Tanaka Shigenori, Morii Toshiyuki

  The Physical Society of Japan (JPS), 04 Mar. 2006, Meeting abstracts of the Physical Society of Japan, 61(1) (1), 409 - 409, Japanese


• 30pZA-7 Transfer and state change of materials in photosynthesis

  Kikuchi Daisuke, Ebina Kuniyoshi, Tanaka Shigenori, Watanabe Hirofumi

  The Physical Society of Japan (JPS), 04 Mar. 2006, Meeting abstracts of the Physical Society of Japan, 61(1) (1), 410 - 410, Japanese


• FMO法へのMCPの導入と生体分子系への適用

  石川岳志, 石川岳志, 望月祐志, 望月祐志, 中野達也, 中野達也, 甘利真司, 森寛敏, 本田宏明, 藤田貴敏, 常盤広明, 常盤広明, 田中成典, 田中成典, 古明地勇人, 福澤薫, 福澤薫, 田中皓, 田中皓, 田中皓, 三好永作, 三好永作

  2006, 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

  伊藤三香, 伊藤三香, 福澤薫, 望月祐志, 望月祐志, 石川岳志, 石川岳志, 中野達也, 中野達也, 田中成典, 田中成典

  2006, 分子構造総合討論会講演要旨集(CD-ROM), 2006


• S1d1-7 DNA and Estrogen Receptor Interaction Revealed by the Fragment Molecular Orbital Method(S1-d1: "Structure and Function of Weak Interactions in Protein Molecules",Symposia,Abstract,Meeting Program of EABS & BSJ 2006)

  Watanabe Toshio, Inadomi Yuichi, Fukuzawa Kaori, Tanaka Shigenori, Nakano Tatsuya, Nilsson Lennart, Nagashima Umpei

  The Biophysical Society of Japan General Incorporated Association, 2006, Seibutsu Butsuri, 46(2) (2), S108, English


• 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)

  小川 哲司, 田中 成典, 中野 達也

  シーエムシー出版, Nov. 2005, 機能材料, 25(11) (11), 6 - 12, Japanese


• 25aWK-3 Is the argument for enhancement of dispersion forces between dielectric bodies in a microwave radiation field correct?

  Suzuki Y., Ebina K., Morii T., Tanaka S.

  The Physical Society of Japan (JPS), 04 Mar. 2005, Meeting abstracts of the Physical Society of Japan, 60(1) (1), 385 - 385, Japanese


• DNA and estrogen receptor interaction revealed by the fragment molecular orbital calculation.

  T Watanabe, Inadomi, V, S Tanaka, K Fukuzawa, T Nakano, L Nilsson, U Nagashima

  Mar. 2005, ABSTRACTS OF PAPERS OF THE AMERICAN CHEMICAL SOCIETY, 229, U779 - U779, English

  Summary international conference


• 13pTH-7 Circular dichroism of glycine and polyglycines

  OKIYAMA Yoshio

  The Physical Society of Japan (JPS), 25 Aug. 2004, Meeting abstracts of the Physical Society of Japan, 59(2) (2), 302 - 302, Japanese


• 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

  渡辺寿雄, 稲富雄一, 福沢薫, 田中成典, 中野達也, Nilsson L, 長嶋雲兵

  20 May 2004, 日本コンピュータ化学会年会講演予稿集, 2004, 86, Japanese


• Energetics of DNA bases

  Yokojima Satoshi, Okada Akira, Yanoi Wataru, Yoshiki Norifumi, Kurita Noriyuki, Tanaka Shigenori, Nakatani Kazuhiko

  The Physical Society of Japan (JPS), 06 Mar. 2003, Meeting abstracts of the Physical Society of Japan, 58(1) (1), 358 - 358, Japanese


• Solvent Effects in Electron Transfer Reactions in DNA

  Tanaka Shigenori, Sengoku Yasuo, Kurita Noriyuki, Yokojima Satoshi, Okada Akira

  The Physical Society of Japan (JPS), 06 Mar. 2003, Meeting abstracts of the Physical Society of Japan, 58(1) (1), 357 - 357, Japanese


• 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

  田中 成典, 仙石 康雄

  03 Jul. 2002, 日本コンピュータ化学会年会講演予稿集, 2002(1) (1), 2O02, Japanese


• 30p-PSA-2 Electronic States of NiO

  Tanaka S.

  The Physical Society of Japan (JPS), 16 Mar. 1993, Abstracts of the meeting of the Physical Society of Japan. Annual meeting, 48(3) (3), 289 - 289, Japanese


• 28p-PS-78 Two-Carrier Model for Oxide Superconductors

  Tanaka S.

  The Physical Society of Japan (JPS), 12 Mar. 1992, 年会講演予稿集, 47(3) (3), 307 - 307, Japanese


• Relationship between Bond Valence Sums and Pressure Effects on Tc of Oxide Superconductors

  Shigenori Tanaka, Noburu Fukushima, Hiromi Niu, Ken Ando

  1991, Journal of the Physical Society of Japan, 60(7) (7), 2481 - 2482

  Report scientific journal


• Statistical physics of dense plasmas: Thermodynamics, transport coefficients and dynamic correlations

  Setsuo Ichimaru, Hiroshi Iyetomi, Shigenori Tanaka

  May 1987, Physics Reports, 149(2-3) (2-3), 91 - 205

  Book review

• 量子と生命

  田中成典

  現代思想（青土社）, Feb. 2020


• 生体分子夾雑系の理論計算化学：分子論から生命論へ

  田中成典

  現代化学 No. 579, 東京化学同人, 2019


• Taking Water into Account with the Fragment Molecular Orbital Method

  Y. Okiyama, K. Fukuzawa, Y. Komeiji, and S. Tanaka

  Quantum Mechanics in Drug Discovery, Humana Press, 2019


• 計算分子生物学 : 物質科学からのアプローチ

  田中, 成典

  内田老鶴圃, Dec. 2018, Japanese, ISBN: 9784753623136


• 大学への数学

  TANAKA SHIGENORI

  Others, 東京出版, May 2018, Japanese

  General book


• 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

  TANAKA SHIGENORI

  Joint work, 技術情報協会, 2018, Japanese

  Scholarly book


• 量子生命科学の展望

  田中成典

  実験医学, Sep. 2017


• Recent progress in quantum Monte Carlo

  Tanaka, Shigenori, Roy, Pierre-Nicholas, Mitas, Lubos, American Chemical Society. Division of Physical Chemistry

  American Chemical Society,Distributed in print by Oxford University Press, 2016, English, ISBN: 9780841231795


• Advances in Quantum Monte Carlo

  TANAKA SHIGENORI, S.M. Rothstein, W.A. Lester

  Joint work, ACS Symposium Series 1094, American Chemical Society, 2012, English

  Scholarly book


• 量子生物学の展開

  田中 成典

  Single work, パリティ, 2011, Japanese

  Scholarly book


• Amberによる生体高分子シミュレーション入門

  田中 成典

  Joint editor, サイエンスハウス, 2011, Japanese

  Scholarly book


• Excited States of Photoactive Proteins by Configuration Interaction Studies, in "The Fragment Molecular Orbital Method: Practical Applications to Large Molecular Systems ",

  Y. Mochizuki, T. Nakano, N. Taguchi, S. Tanaka

  Joint work, CRC Press, Boca Raton, U.S.A., 2009, English

  Scholarly book


• Excited States of Photoactive Proteins by Configuration Interaction Studies, in "The Fragment Molecular Orbital Method: Practical Applications to Large Molecular Systems "

  Y. Mochizuki, T. Nakano, N. Taguchi, S. Tanaka

  Joint work, CRC Press, 2009, English

  Scholarly book


• Developments of FMO Methodology and Graphical User Interface in ABINIT-MP, in "The Fragment Molecular Orbital Method: Practical Applications to Large Molecular Systems "

  T. Nakano, Y. Mochizuki, A. Kato, K. Fukuzawa, T. Ishikawa, S. Amari, I. Kurisaki, S. Tanaka

  Joint work, CRC Press, 2009, English

  Scholarly book


• Developments of FMO Methodology and Graphical User Interface in ABINIT-MP, in "The Fragment Molecular Orbital Method: Practical Applications to Large Molecular Systems "

  T. Nakano, Y. Mochizuki, A. Kato, K. Fukuzawa, T. Ishikawa, S. Amari, I. Kurisaki, S. Tanaka

  Joint work, CRC Press, Boca Raton, U.S.A., 2009, English

  Scholarly book


• Application of FMO Method to Specific Molecular Recognition of Bio-Macromolecules, in "The Fragment Molecular Orbital Method: Practical Applications to Large Molecular Systems"

  K. Fukuzawa, Y. Mochizuki, T. Nakano, S. Tanaka

  Joint work, CRC Press, Boca Raton, U.S.A., 2009, English

  Scholarly book


• 学問を学ぶということ―物理学者としての経験から―

  S. Tanaka

  Single work, 「発達科学への招待」（かもがわ出版、2008）, 2008, Japanese

  Scholarly book


• FMO法の今後の展開

  S. Tanaka

  Single work, 「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, Japanese

  Scholarly book


• 対話＜知＞のクロスロード―「大数」読者だったわたし

  S. Tanaka

  Single work, 大学への数学, 2007, Japanese

  General book


• 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

  S. Tanaka

  Single work, 大学への数学, 2007, Japanese

  General book


• 「生体電子物性と環境応答」

  田中 成典

  Joint work, 物性研究, 2007, Japanese

  Scholarly book


• Modern Methods for Theoretical Physical Chemistry of Biopolymers

  E.B. Starikov, J.P. Lewis, S. Tanaka

  Joint work, Elsevier B.V., Amsterdam, The Netherlands, 2006, English

  Scholarly book


• Drug Discovery Using Grid Technology

  Hitoshi Goto, Sigeaki Obata, Toshiyuki Kamakura, Naofumi Nakayama, Mitsuhisa Sato, Yoshihiro Nakajima, Umpei Nagashima, Toshio Watanabe, Yuichi Inadomi, Masakatsu Ito, Takeshi Nishikawa, Tatsuya Nakano, Lennart Nilsson, Shigenori Tanaka, Kaori Fukuzawa, Yuichiro Inagaki, Michiaki Hamada, Hiroshi Chuman

  Joint work, Modern Methods for Theoretical Physical Chemistry for Biopolymers, 2006, English

  Scholarly book


• Developments and Applications of ABINIT-MP Software Based on the Fragment Molecular Orbital Method

  T. Nakano, K. Fukuzawa, Y. Mochizuki, S. Amari, S. Tanaka

  Joint work, Modern Methods for Theoretical Physical Chemistry of Biopolymers, 2006, English

  Scholarly book


• Ballistic Conductance for All-Atom Models of Native and Chemically Modified DNA: A Review of Kubo-Formula-Based Approach

  E.B. Starikov, S. Tanaka, N. Kurita, Y. Sengoku, T. Natsume, A. Quintilla, W. Wenzel

  Joint work, Modern Methods for Theoretical Physical Chemistry of Biopolymers, 2006, English

  Scholarly book


• Ab Initio Biomolecular Calculations Using Quantum Monte Carlo Combined with the Fragment Molecular Orbital Method

  R. Maezono, H. Watanabe, S. Tanaka

  Joint work, Advances in Quantum Monte Carlo, 2006, English

  Scholarly book


• 修正電荷平衡（MQEｑ）法の生体高分子系への応用

  S. Tanaka

  Joint work, 機能材料, 2005, Japanese

  Scholarly book


• 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

  S. Tanaka

  Single work, 「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, Japanese

  Scholarly book


• 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－

  TANAKA

  「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

  Scholarly book


• 色素増感太陽電池の合理的設計と実用化への課題

  TANAKA

  「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

  Scholarly book


• DNA鎖の第一原理計算の現状と将来

  TANAKA, FUKUZAWA, NAKANO, KURITA

  表面科学, 2003

  Scholarly book


• 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

  TANAKA

  CICSJ Bull., 2003

  Scholarly book

• Quantum Brain Dynamics from a Viewpoint of Field Theory

  S. Tanaka, A. Nishiyama

  The 2nd Workshop on Quantum Cognition, Dec. 2019, English

  [Invited]

  Invited oral presentation


• Perspectives of Computational Drug Discovery: AMED-BINDS Activities in Japan

  S. Tanaka

  AHeDD2019/IPAB2019 Joint Symposium, Nov. 2019, English

  [Invited]

  Keynote oral presentation


• 大規模分子系の第一原理計算と量子生命科学

  田中成典

  遠隔講義「計算生命科学の基礎VI」, Nov. 2019, Japanese

  [Invited]

  Public discourse


• 多体問題と生命

  田中成典

  研究会「計算生命科学：多体問題から生命システムへ」, Aug. 2019, Japanese

  [Invited]

  Public discourse


• 生命と量子

  田中成典

  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, Aug. 2019, Japanese

  [Invited]

  Invited oral presentation


• Resonant Energy Transfer in Biological Systems

  TANAKA SHIGENORI

  Himakajima Workshop 2019 Spring on “Multiscale Simulation and Data Science of Complex Molecular Systems, Mar. 2019, English, Aichi, International conference

  [Invited]

  Nominated symposium


• FMOデータベースの情報科学的な活用

  TANAKA SHIGENORI

  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」, Mar. 2019, Japanese, 千葉, Domestic conference

  [Invited]

  Nominated symposium


• ライフサイエンスと量子コンピューティング

  TANAKA SHIGENORI

  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」, Oct. 2018, Japanese, 大阪, Domestic conference

  Public discourse


• BINDSインシリコユニットの紹介

  TANAKA SHIGENORI

  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」, Oct. 2018, Japanese, 東京, Domestic conference

  [Invited]

  Nominated symposium


• Ab initio Molecular Dynamics Simulation of Continuous Production of Organic Molecules in Alkaline Hydrothermal Vents

  村木 志匡, MORI ICHIRO, Shimamura Kohei, TANAKA SHIGENORI

  Chem-Bio Informatics Society(CBI) Annual Meeting 2018, Oct. 2018, English, 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, Domestic conference

  Poster presentation


• インシリコ創薬の展望

  TANAKA SHIGENORI

  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)」, Sep. 2018, Japanese, 岡山, Domestic conference

  [Invited]

  Nominated symposium


• リガンド分子ドッキング－様々な階層での理解－

  TANAKA SHIGENORI

  科研費新学術領域「分子夾雑の生命化学」第2回領域会議, May 2018, Japanese, 福岡, Domestic conference

  [Invited]

  Nominated symposium


• Nonequilibrium Relaxation Processes in Biomolecular Systems

  TANAKA SHIGENORI

  USC-Kobe Bilateral Workshop on Computational Science, Mar. 2018, English, USA, International conference

  [Invited]

  Nominated symposium


• 生体分子系における非平衡緩和の記述

  TANAKA SHIGENORI

  第73回尾張コンプレックスセミナー, Dec. 2017, Japanese, 名古屋, Domestic conference

  Public discourse


• 量子生命科学の展望

  TANAKA SHIGENORI

  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」, Oct. 2017, Japanese, 東京, Domestic conference

  [Invited]

  Nominated symposium


• Charge and Energy Transfer Dynamics in Biological Systems

  TANAKA SHIGENORI

  1st QST International Symposium “Quantum Life Science”, Jul. 2017, English, Chiba, Japan, International conference

  [Invited]

  Nominated symposium


• 量子生命科学の展望

  TANAKA SHIGENORI

  第1回量子生命科学研究会, Apr. 2017, Japanese, 東京, Domestic conference

  [Invited]

  Invited oral presentation


• バイオシミュレーションにおける分子夾雑効果

  TANAKA SHIGENORI

  日本化学会第97春季年会・特別企画「分子夾雑の生命化学」, Mar. 2017, Japanese, 横浜, Domestic conference

  [Invited]

  Invited oral presentation


• 水和生体分子系の熱力学

  TANAKA SHIGENORI

  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」, Feb. 2017, Japanese, Domestic conference

  Public discourse


• 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

  TANAKA SHIGENORI

  FIBER未来大学・第2回研究成果報告会, Jan. 2017, Japanese, 神戸, Domestic conference

  Public discourse


• Entropic and Enthalpic Contributions to Thermodynamics of Biomolecular Systems

  TANAKA SHIGENORI

  Workshop on Multiscale Understanding of Nonequilibrium Processes, Jan. 2017, English, International conference

  Public discourse


• 電子状態計算を基盤とした量子生物学

  TANAKA SHIGENORI

  生物学・光源・物性研究者による量子生物学合宿勉強会, Jul. 2016, Japanese, Domestic conference

  Public discourse


• Theoretical Study on Dynamics and Functions of Solvated Biomolecules

  TANAKA SHIGENORI

  FIBER Future College: FIBER国際核酸サミット2016, Jul. 2016, English, International conference

  Public discourse


• Possible Applications of Large-Scale Molecular Simulations toward the Understanding of Real World

  TANAKA SHIGENORI

  University of Southern California / Kobe University Joint Research Kick-off Symposium, Mar. 2016, English, Kobe, International conference

  [Invited]

  Nominated symposium


• Multiscale Modeling of Photosynthetic Reactions

  TANAKA SHIGENORI

  Leipzig University, Feb. 2016, English, Leipzig, Germany, International conference

  Public discourse


• Diffusion Monte Carlo Study on Temporal Evolution of Thermodynamic Functions in Nonequilibrium Biomolecular Systems

  TANAKA SHIGENORI

  Karlsruhe Institute of Technology, Feb. 2016, English, Karlsruhe, Germany, International conference

  Public discourse


• 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

  TANAKA SHIGENORI

  High Performance Computing Chemistry 2015ワークショップ, Jan. 2016, Japanese, 神戸, Domestic conference

  [Invited]

  Nominated symposium


• Fragment Molecular Orbital Approach to Computational Drug Design

  TANAKA SHIGENORI

  University of Bonn, Jan. 2016, English, Bonn, Germany, International conference

  Public discourse


• 生体分子系における非平衡過程

  TANAKA SHIGENORI

  バイオスーパーコンピューティング神戸2015, Nov. 2015, Japanese, 神戸, Domestic conference

  [Invited]

  Invited oral presentation


• 生命の起源分子生成に関する計算機シミュレーション

  TANAKA SHIGENORI, 島村 孝平

  広島大学地球惑星システム学セミナー, Oct. 2015, Japanese, 東広島, Domestic conference

  Public discourse


• Analysis of the effect of acute dose based on indicators taking account of cell survival and DNA damage

  YOSHINARI Kohei, TANAKA Shigenori, EBINA Kuniyoshi

  第1回放射線ワークショップ, Oct. 2015, Japanese, 富山大学五福キャンパス, Domestic conference

  Oral presentation


• フラグメント分子軌道法に基づくアカデミア創薬

  TANAKA SHIGENORI

  CBI学会2015年大会, Oct. 2015, Japanese, 東京, Domestic conference

  [Invited]

  Invited oral presentation


• 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

  TANAKA SHIGENORI

  スパコン入門セミナー, Sep. 2015, Japanese, 神戸, Domestic conference

  Public discourse


• 生体分子系における非平衡過程

  TANAKA SHIGENORI

  研究セミナー「環境変動の生態・生理学に関する研究会」, Sep. 2015, Japanese, 江別市, Domestic conference

  Public discourse


• Systems approach to the multi-timescale dynamics of photosynthesis

  MATSUOKA TAKESHI, TANAKA SHIGENORI, EBINA KUNIYOSHI

  The 53rd Annual Meeting of the Biophysical Society of Japan, Sep. 2015, English, Biophysical Society of Japan, Kanazawa University Kakuma Campus, 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, Domestic conference

  Poster presentation


• Nonequilibrium Processes in Biomolecular Systems

  TANAKA SHIGENORI

  Workshop on “Current Topics in Nano Simulations, Sep. 2015, English, Tsukuba, International conference

  [Invited]

  Nominated symposium


• タンパク質の量子化学計算の現状

  TANAKA SHIGENORI

  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, Jun. 2015, Japanese, 徳島, Domestic conference

  [Invited]

  Invited oral presentation


• Toward First-Principles Simulations for the Origin of Life

  TANAKA SHIGENORI

  Mini-Symposium on Functional and Biogenous Materials II, Mar. 2015, English, Okayama University, Okayama, International conference

  [Invited]

  Invited oral presentation


• Systems Approach to Excitation-Energy and Electron Transfer Reaction Networks in Thylakoid Membrane: Model Studies for Chlorophyll a Fluorescence Induction

  MATSUOKA TSUYOSHI, TANAKA SHIGENORI, EBINA KUNIYOSHI

  The 56th Annual Meeting of The Japanese Society of Plant Phisiologists, Mar. 2015, English, Tokyo, Domestic conference

  Poster presentation


• FMO Pharmaceutical Applications

  TANAKA SHIGENORI

  Workshop on Innovation and Pioneering Technology – Innovation by Synergy of Computational & Synchrotron Radiation Sciences (WINTech 2015), Mar. 2015, English, Kobe University, Kobe, International conference

  [Invited]

  Invited oral presentation


• 生体分子ダイナミクスにおける階層性と粗視化

  TANAKA SHIGENORI

  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」, Feb. 2015, Japanese, 神戸大学、神戸, Domestic conference

  [Invited]

  Invited oral presentation


• FMO法への期待

  TANAKA SHIGENORI

  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, Feb. 2015, Japanese, 神戸大学計算科学教育センター、神戸, Domestic conference

  [Invited]

  Invited oral presentation


• 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

  TANAKA SHIGENORI

  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）, Jan. 2015, Japanese, 甲南大学、神戸, Domestic conference

  [Invited]

  Invited oral presentation


• 高校生を軸に未来の社会を構想する

  TANAKA SHIGENORI

  第5回「咲いテク」情報交換会, Oct. 2014, Japanese, 神戸高校、神戸, Domestic conference

  [Invited]

  Invited oral presentation


• 大規模分子シミュレーション技術の医療・創薬への応用

  TANAKA SHIGENORI

  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」, Sep. 2014, Japanese, 大阪薬科大学、高槻, Domestic conference

  [Invited]

  Invited oral presentation


• 精度の高い相互作用エネルギー解析

  TANAKA SHIGENORI

  先進技術活用力養成講座・構造ベース創薬セミナー, Mar. 2014, Japanese, 神戸, Domestic conference

  Public discourse


• Multi-Scale Simulations for Complex Biomolecular Systems

  TANAKA SHIGENORI

  Workshop on Current Topics in Nano Simulations (CT-NanoSim2014), Mar. 2014, English, Tsukuba, International conference

  [Invited]

  Invited oral presentation


• Large-Scale Biomolecular Simulations on the Basis of Fragment Molecular Orbital Method

  TANAKA SHIGENORI

  International Workshop on Eigenvalue Problems: Algorithms, Software and Applications in Petascale Computing (EPASA2014), Mar. 2014, English, Tsukuba, International conference

  [Invited]

  Invited oral presentation


• Exploring Theoretical Models for Water

  TANAKA SHIGENORI

  The 5th JCS International Symposium on Theoretical Chemistry, Dec. 2013, English, Nara, International conference

  Poster presentation


• 大規模分子シミュレーションと創薬

  TANAKA SHIGENORI

  VINAS Users Conference 2013, Oct. 2013, Japanese, Domestic conference

  [Invited]

  Invited oral presentation


• 第一原理シミュレーションと創薬

  TANAKA SHIGENORI

  HPCIワークショップ2013, Sep. 2013, Japanese, Domestic conference

  [Invited]

  Invited oral presentation


• First-Principles Biomolecular Simulations for Drug Design

  TANAKA SHIGENORI

  医薬基盤研究所セミナー, Jul. 2013, English, Domestic conference

  Public discourse


• 大規模シミュレーションの意義

  TANAKA SHIGENORI

  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」, Jun. 2013, Japanese, Domestic conference

  [Invited]

  Invited oral presentation


• 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

  TANAKA SHIGENORI

  日本磁気学会第190回研究会「生体物質の物理」, May 2013, Japanese, Domestic conference

  [Invited]

  Invited oral presentation


• Possible Applications of Large-Scale Molecular Simulations toward the Understanding of Real World

  TANAKA SHIGENORI

  University of Southern California / Kobe University Joint Research Kick-off Symposium, Mar. 2013, English, Kobe, International conference

  [Invited]

  Nominated symposium


• Structure-Based Drug Design with the Fragment Molecular Orbital Method

  TANAKA SHIGENORI

  Workshop on Innovation and Pioneering Technology – Recent Development in Drug Discovery Sciences (WINPTech 2012), Feb. 2013, English, Kobe, International conference

  [Invited]

  Invited oral presentation


• 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

  TANAKA SHIGENORI

  平成24年度地球シミュレータ利用報告会, Jan. 2013, Japanese, 横浜, Domestic conference

  Oral presentation


• Towards the First-Principles and Coarse-Grained Descriptions for Charge and Energy Transfers in Biomolecular Systems

  TANAKA SHIGENORI

  Joint Dresden-Japan Workshop on Molecular Scale and Organic Electronic Materials, Dec. 2012, English, Dresden, Germany, International conference

  [Invited]

  Invited oral presentation


• Towards the First-Principles and Coarse-Grained Descriptions for Charge and Energy Transfers in Biomolecular Systems

  TANAKA SHIGENORI

  Indo-Japan Workshop on “Recent Advances in Spectroscopy and Microscopy: Fundamentals and Applications to Materials and Biology”, Nov. 2012, English, Hyderabad, India, International conference

  [Invited]

  Invited oral presentation


• フラグメント分子軌道（FMO）計算の現状と今後

  TANAKA SHIGENORI

  日本機械学会第25回計算力学講演会, Oct. 2012, Japanese, 神戸, Domestic conference

  [Invited]

  Invited oral presentation


• スーパーコンピュータによるドラッグデザイン

  TANAKA SHIGENORI

  KOBE工学サミットin Tokyoトライアル, Oct. 2012, Japanese, 東京, Domestic conference

  [Invited]

  Invited oral presentation


• FMO計算の今後

  TANAKA SHIGENORI

  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, Jul. 2012, Japanese, 東京, Domestic conference

  [Invited]

  Invited oral presentation


• Multi-Scale Simulations for Biomolecular Functions

  S. Tanaka

  2nd AICS International Symposium – Computer and Computational Sciences for Exascale Computing –, Mar. 2012, English, Kobe, International conference

  [Invited]

  Invited oral presentation


• Charge and Energy Transfers in Biomolecular Systems

  S. Tanaka

  NRI-TUD Joint Workshop for Organic Nanomaterials 2012, Mar. 2012, English, Tsukuba, International conference

  [Invited]

  Invited oral presentation


• 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

  中野 美紀, EBINA KUNIYOSHI, TANAKA SHIGENORI

  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－, Feb. 2012, Japanese, 神戸, Domestic conference

  Oral presentation


• 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

  田中 成典

  平成23年度地球シミュレータ利用報告会, Feb. 2012, Japanese, Yokohama, Domestic conference

  Invited oral presentation


• フラグメント分子軌道法のソフトウェア

  TANAKA SHIGENORI

  HPC産業利用スクール・ナノテクコース, Feb. 2012, Japanese, 柏, Domestic conference

  [Invited]

  Invited oral presentation


• コンピュータによる計算生命科学

  田中 成典

  洲本高校インスパイア・ハイスクール, Feb. 2012, Japanese, Sumoto, Domestic conference

  Invited oral presentation


• 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

  中野 美紀, 蛯名 邦禎, 田中 成典

  先端融合科学シンポジウム タンパク質アセンブリ, Jan. 2012, Japanese, Hyogo, Domestic conference

  Poster presentation


• タンパク質の電子状態計算から機能解析へ

  田中 成典

  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－」, Nov. 2011, Japanese, Toyonaka, Domestic conference

  [Invited]

  Invited oral presentation


• Aggregation mechanism of polyglutamine peptides in water by replica

  Miki Nakano, Kuniyoshi Ebina, Shigenori Tanaka

  FIBER International Symposium, FIBER FORUM 2011, Nov. 2011, English, Hyogo, International conference

  Poster presentation


• Aggregation mechanism of polyglutamine peptides in water by replica

  Miki Nakano, Kuniyoshi Ebina, Shigenori Tanaka

  CBI/JSBi 2001合同大会, Nov. 2011, English, Hyogo, International conference

  Poster presentation


• Comparison of Antigen-Antibody Binding by the Fragment Molecular Orbital Calculations for Swine-Origin Influenza Hemagglutinin Proteins

  吉岡 彬生, 田中 成典

  日本生物物理学会年会, Sep. 2011, English, 日本生物物理学会, Hyogo, International conference

  Oral presentation


• 蛋白質の電子状態計算と医療・創薬・環境科学への応用

  田中 成典

  第４回バイオナノシステムズ研究会, Aug. 2011, Japanese, Kobe, Domestic conference

  [Invited]

  Invited oral presentation


• 第一原理生体分子シミュレーションの展開

  田中 成典

  鳥取大学応用数理工学セミナー, Jun. 2011, Japanese, Tottori, Domestic conference

  [Invited]

  Invited oral presentation


• 創薬とシミュレーション

  田中 成典

  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, Jun. 2011, Japanese, Kobe, Domestic conference

  Invited oral presentation


• 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

  中野 美紀, 蛯名 邦禎, 田中 成典

  第11回日本蛋白質科学会年会, Jun. 2011, Japanese, 大阪, Domestic conference

  Poster presentation


• Large-Scale Ab Initio Simulations for Biomolecular Systems

  田中 成典

  Technische Universitat Dresden, Jun. 2011, English, Dresden, Germany, International conference

  [Invited]

  Invited oral presentation


• Large-Scale Ab Initio Simulations for Biomolecular Systems

  田中 成典

  Karlsruhe Institute of Technology, Jun. 2011, English, Karlsruhe, Germany, International conference

  [Invited]

  Invited oral presentation


• Large-Scale Ab Initio Simulations for Biomolecular Systems

  田中 成典

  th JCS Symposium on Theoretical Chemistry,, May 2011, English, Liblice, Czech Republic, International conference

  [Invited]

  Invited oral presentation


• Ab initio path integral molecular dynamics and Monte Carlo simulations for water trimer and oligopeptide

  Takatoshi Fujita, Masa-Aki Kusa, Takayuki Fujiwara, Yuji Mochizuki, Shigenori Tanaka

  Pacifichem2010, Dec. 2010, English, Honolulu, International conference

  Oral presentation


• スーパーコンピュータが変える医療の未来!?

  S. Tanaka

  サイエンスカフェ鳥取, Nov. 2010, Japanese, 鳥取, Domestic conference

  Invited oral presentation


• Support to Science Activities by Citizens for Sustainable Society in Hyogo Prefecture

  Masayuki Itoh, Yoshiaki Takeda, Kuniyoshi Ebina, Shigenori Tanaka, Emiko Maekawa, Ikumi Dohzono

  日本科学教育学会年会, Sep. 2010, Japanese, 日本科学教育学会, University of Hiroshima, Domestic conference

  Oral presentation


• 周期境界条件フラグメント分子軌道法の開発

  藤田 貴敏, 中野 達也, 田中 成典

  第4回分子科学討論会, Sep. 2010, Japanese, 大阪, Domestic conference

  Poster presentation


• Energy analysis of polyglutamine peptides by MM-GB/SA method

  Miki Nakano, Shigenori Tanaka

  CBI学会2010年大会, Sep. 2010, English, 東京, International conference

  Poster presentation


• 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

  中野 美紀, 渡邉 博文, 田中 成典

  第10回蛋白質科学会, Jun. 2010, Japanese, 札幌, Domestic conference

  Poster presentation


• 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

  吉岡 彬生, 栗崎 以久男, 渡邉 博文, 田中 成典

  日本コンピュータ化学会2010春季年会, May 2010, Japanese, 東京, Domestic conference

  Poster presentation


• 周期境界条件フラグメント分子軌道法の開発

  藤田 貴敏, 中野 達也, 田中 成典

  第13回理論化学討論会, May 2010, Japanese, 北海道, Domestic conference

  Poster presentation


• 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

  中野 美紀, 蛯名 邦禎, 田中 成典

  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, Feb. 2010, Japanese, 神戸, Domestic conference

  Poster presentation


• 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

  S. Tanaka

  第23回KOBE工学サミット, 2010, English, 第23回KOBE工学サミット, Kobe, International conference

  Invited oral presentation


• 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

  S. Tanaka

  九州大学第10回化学・材料研究セミナー, 2010, Japanese, 九州大学, 九州大学国際ホール, Domestic conference

  Invited oral presentation


• 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

  S. Tanaka

  平成22年度地球シミュレータ利用報告会, 2010, Japanese, 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, Domestic conference

  Invited oral presentation


• 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

  S. Tanaka

  地球シミュレータ産業利用シンポジウム2010, 2010, English, 地球シミュレータ産業利用シンポジウム, 鳥取, Domestic conference

  Invited oral presentation


• コンピュータによる計算生命科学

  S. Tanaka

  洲本高校インスパイア・ハイスクール, 2010, Japanese, 兵庫県立洲本高校, Sumoto, Domestic conference

  Others


• Large-Scale Biomolecular Calculations on the Basis of Fragment Molecular Orbital Method

  S. Tanaka

  Indo-Japan Joint Workshop on “New Frontiers of Molecular Spectroscopy: From Gas Phase to Proteins, 2010, English, Indo-Japan Joint Workshop on “New Frontiers of Molecular Spectroscopy: From Gas Phase to Proteins, 神戸, International conference

  Invited oral presentation


• Ab Initio Path Integral Molecular Dynamics and Monte Carlo Simulations for Water Trimer and Oligopeptides” (Symposium “Advances in Quantum Monte Carlo”

  T. Fujita, M. Kusa, T. Fujiwara, Y. Mochizuki, S. Tanaka

  Pacifichem 2010, 2010, English, Symposium “Advances in Quantum Monte Carlo” in the 2010 International Chemical Congress of Pacific Basin Societies, Honolulu, Hawaii, International conference

  Oral presentation


• Ab Initio FMO Approach to Biomolecular Reactions

  S. Tanaka

  Quantum Systems in Chemistry and Physics Workshop (QSCP-XV), 2010, English, Quantum Systems in Chemistry and Physics Workshop (QSCP-XV), Magdalene College, Cambridge, England, International conference

  Invited oral presentation


• 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

  Shigenori Tanaka

  地球シミュレータ利用報告会, Jan. 2010, Japanese, 海洋研究開発機構横浜研究所三好記念講堂, Domestic conference

  Invited oral presentation


• 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

  Shigenori Tanaka

  徳島大学創薬理論化学セミナー, Jan. 2010, Japanese, 徳島大学, Domestic conference

  Invited oral presentation


• 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

  S. Tanaka

  第23回分子シミュレーション討論会, Dec. 2009, Japanese, 名古屋市中小企業振興会館, Domestic conference

  Invited oral presentation


• 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

  I. Kurisaki

  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」, Dec. 2009, Japanese, 大阪大学, Domestic conference

  Invited oral presentation


• Possibility of the Prediction for Mutations of Influenza Hemagglutinin by a Combination of Ab initio Molecular Simulation and Hemadsorption Experiment

  K. Takematsu, K. Fukuzawa, K. Nakajima, Y. Mochizuki, T. Nakano, S. Tanaka

  International Symposium of Electronic Structure Calculations -Theory, Correlated and Large Scale Systems and Numerical Methods-, Dec. 2009, English, The university Tokyo, International conference

  Poster presentation


• Ab Initio Quantum Simulation Based

  T. Fujita, H. Watanabe, S. Tanaka

  International Symposium of Electronic Structure Calculations -Theory, Correlated and Large Scale Systems and Numerical Methods-, Dec. 2009, English, 東京大学, International conference

  Poster presentation


• Ab Initio Biomolecular Simulations Based on the Fragment Molecular Orbital Method

  S. Tanaka

  International Symposium of Electronic Structure Calculations – Theory, Correlated and Large Scale Systems and Numerical Methods –, Dec. 2009, English, The University of Tokyo, International conference

  Invited oral presentation


• 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

  S. Tanaka

  第７回地球シミュレータシンポジウム, Nov. 2009, Japanese, 日本科学未来館, Domestic conference

  Invited oral presentation


• Incorporation of solvation effect with Poisson-Boltzmann equation into FMO method

  H. Watanabe, T. Nakano, S. Tanaka

  CBI KSBSB Joint Conference, BIOINFO 2009, Nov. 2009, English, Busan, Korea, International conference

  Poster presentation


• Fragment Molecular Orbital (FMO) Method: Application to Drug Discovery

  H. Watanabe

  CBI KSBSB Joint Conference, BIOINFO 2009, Nov. 2009, English, Busan, International conference

  Invited oral presentation


• Ab Initio Biomolecular Simulations Based on the Fragment Molecular Orbital Method

  S. Tanaka

  Institute of Chemistry, Academia Sinica, Nov. 2009, English, Taipei, International conference

  Invited oral presentation


• 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

  S. Tanaka

  「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, Oct. 2009, Japanese, 東京大学弥生講堂, Domestic conference

  Invited oral presentation


• 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

  栗崎 以久男, 松本 淳, 由良 敬, 田中 成典

  日本生物物理学会第47回年会, Oct. 2009, Japanese, 徳島, Domestic conference

  Poster presentation


• Possibility of Mutation Prediction of Influenza Hemagglutinin by Combination of Hemadsorption Experiment and Quantum Chemical Calculation for Antibody Binding

  K. Takematsu, K. Fukuzawa, K. Omagari, K. Nakajima, S. Nakajima, Y. Mochizuki, T. Nakano, H. Watanabe, S. Tanaka

  第47回日本生物物理学会, Oct. 2009, English, アスティ徳島, International conference

  Invited oral presentation


• Characterization of monomeric polyglutamine peptides by replica exchange molecular dynamics simulation

  中野 美紀, 渡邉 博文, 田中 成典

  第４７回日本生物物理学会年会, Oct. 2009, English, 徳島, Domestic conference

  Poster presentation


• 大規模シミュレーションによる生体反応の理解

  S. Tanaka

  日本物理学会2009年秋季大会, Sep. 2009, Japanese, 熊本大学, Domestic conference

  Invited oral presentation


• 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

  S. Tanaka

  第58回高分子討論会, Sep. 2009, Japanese, Domestic conference

  Invited oral presentation


• Understanding Protein Functions through First-Principles Molecular Simulations

  S. Tanaka

  Institute of Atomic and Molecular Sciences, Academia Sinica, Sep. 2009, English, National Taiwan University, International conference

  Invited oral presentation


• Ab Initio Biomolecular Simulations Based on the Fragment Molecular Orbital Method

  S. Tanaka

  National Chiao Tung Tung University, Sep. 2009, English, Hsinchu, International conference

  Invited oral presentation


• Creation of a system to support civil science activities in regional community

  Masayuki Itoh, Kuniyoshi Ebina, Yoshiaki Takeda, Shigenori Tanaka

  日本科学教育学会年会, Aug. 2009, Japanese, 日本科学教育学会, 同志社女子大学, Domestic conference

  Oral presentation


• 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

  S. Tanaka

  第318回「医学研究の基礎を語り合う集い」, Jul. 2009, Japanese, 東京慈恵会医科大学, Domestic conference

  Invited oral presentation


• Large-Scale Biomolecular Simulations Based on the Fragment Molecular Orbital Method

  S. Tanaka

  CREST International Symposium on Theory and Simulations of Complex Molecular Systems, Jul. 2009, English, Fukui Institute for Fundamental Chemistry, International conference

  Invited oral presentation


• 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

  竹松 和友, 福澤 薫, 尾曲 克己, 中島 節子, 中島 捷久, 望月 祐志, 中野 達也, 渡邉 博文, 田中 成典

  第12回理論化学討論会, May 2009, Japanese, 東京, Domestic conference

  Poster presentation


• 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

  S. Tanaka

  大阪大学サイバーメディアセンター・セミナー, May 2009, Japanese, 大阪大学サイバーメディアセンター, Domestic conference

  Invited oral presentation


• 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.

  中野 美紀, 渡邉 博文, 田中 成典

  第9回日本蛋白質科学会年会, May 2009, Japanese, 熊本, Domestic conference

  Poster presentation


• Poisson-Boltzmann方程式によるFMO法への溶媒効果の取り込み

  渡邉 博文, 中野 達也, 田中 成典

  日本コンピュータ化学会春季年会2009年春季年会, May 2009, Japanese, 東京, Domestic conference

  Poster presentation


• Fragment Molecular Orbital Method for Large-Scale Biomolecular Systems

  S. Tanaka

  International Conference on Computational & Experimental Engineering & Sciences 2009 (ICCES’09), Apr. 2009, English, Phuket, International conference

  Invited oral presentation


• 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

  渡邉 千鶴, 渡邉 博文, 田中 成典

  日本物理学会第６４回年次大会, Mar. 2009, Japanese, 東京, Domestic conference

  Oral presentation


• 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

  藤田 貴敏, 渡邉 博文, 田中 成典

  日本物理学会第64回年次大会, Mar. 2009, Japanese, 東京, Domestic conference

  Oral presentation


• 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

  栗崎 以久男, Stuart Rothstein, 渡邉 博文, 田中 成典

  第８回蛋白質科学会, Feb. 2009, Japanese, 東京, Domestic conference

  Poster presentation


• Relationship between Structural Fluctuation and Positions of Helix 12 in Nuclear Receptors Studied by Molecular Dynamics Simulation

  C. Watanabe, H. Watanabe, S. Tanaka

  Supercomputing in Solid State Physics (SciSSP) 2009, Feb. 2009, English, 柏, International conference

  Poster presentation


• 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

  竹松 和友, 福澤 薫, 尾曲 克巳, 中島 捷久, 中島 節子, 中野 達也, 望月 祐志, 渡邉 博文, 田中 成典

  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」, Jan. 2009, Japanese, 岡崎, Domestic conference

  Poster presentation


• 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

  藤田 貴敏, 渡邉 博文, 田中 成典

  スーパーコンピュータワークショップ2009, Jan. 2009, Japanese, 愛知, Domestic conference

  Poster presentation


• 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

  沖山 佳生, 渡邉 博文, 石川 岳志, 福澤 薫, 望月 祐志, 中野 達也, 蛯名 邦禎, 田中 成典

  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」, Jan. 2009, Japanese, 岡崎, Domestic conference

  Poster presentation


• 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

  竹松 和友, 福澤 薫, 尾曲 克巳, 中島 捷久, 中島 節子, 中野 達也, 望月 祐志, 渡邉 博文, 田中 成典

  バイオスーパーコンピューティングシンポジウム(BSCS)2008, Dec. 2008, Japanese, 東京, Domestic conference

  Poster presentation


• 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

  沖山 佳生, 渡邉 博文, 福澤 薫, 中野 達也, 望月 祐志, 石川 岳志, 蛯名 邦禎, 田中 成典

  バイオスーパーコンピューティングシンポジウム(BSCS)2008, Dec. 2008, Japanese, 東京, Domestic conference

  Poster presentation


• 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

  渡邉 博文, 田中 成典

  バイオスーパーコンピューティングシンポジウム(BSCS)2008, Dec. 2008, Japanese, 東京, Domestic conference

  Poster presentation


• 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

  中野 美紀, 渡邉 博文, 田中 成典

  第22回分子シミュレーション討論会, Nov. 2008, Japanese, 岡山, Domestic conference

  Poster presentation


• 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

  沖山 佳生, 渡邉 博文, 福澤 薫, 中野 達也, 望月 祐志, 田中 成典

  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, Nov. 2008, Japanese, 東京, Domestic conference

  Poster presentation


• FMO法による生体高分子の第一原理計算

  田中 成典

  第11回スーパーコンピューティング・セミナー, Nov. 2008, Japanese, スーパーコンピューティング技術産業応用協議会, 東京, Domestic conference

  Invited oral presentation


• 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

  藤田 貴敏, 渡邉 博文, 田中 成典

  第2回分子科学討論会, Oct. 2008, Japanese, 福岡, Domestic conference

  Poster presentation


• 「奪われし未来」と環境ホルモン

  田中 成典

  大学連携「ひょうご講座」, Oct. 2008, Japanese, 神戸, Domestic conference

  Invited oral presentation


• Relationship between Structural Fluctuation and Positions of Helix 12 in the Nuclear Receptors Studied by Molecular Dynamics Simulation

  C. Watanabe, H. Watanabe, S. Tanaka

  CBI学会2008 年大会, Oct. 2008, English, 東京, International conference

  Poster presentation


• Determination of ESP charges on polypeptides using the fragment molecular orbital method and the applications for molecular simulations

  Y. Okiyama, H. Watanabe, T. Ishikawa, K. Fukuzawa, Y. Mochizuki, T. Nakano, K. Ebina, S. Tanaka

  CBI学会2008 年大会, Oct. 2008, English, 東京, International conference

  Poster presentation


• 実用を目指した生体高分子の第一原理計算

  田中 成典

  第2回分子科学討論会, Sep. 2008, Japanese, 福岡, Domestic conference

  Invited oral presentation


• 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

  竹松 和友, 福澤 薫, 中島 捷久, 尾曲 克巳, 望月 祐志, 渡邉 博文, 田中 成典

  第2回分子科学討論会, Sep. 2008, Japanese, 福岡, Domestic conference

  Poster presentation


• 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

  近藤 洋隆, 中村 卓, 山口 梓, 渡邉 博文, 田中 成典

  第二回分子科学討論会2008福岡, Sep. 2008, Japanese, 福岡, Domestic conference

  Poster presentation


• Theoretical Study on Isotope Effects in Polypeptides Based on Path Integral Molecular Dynamics and Fragment Molecular Orbital Method

  T. Fujita, H. Watanabe, S. Tanaka

  WATOC 2008, Sep. 2008, English, Sydney, International conference

  Poster presentation


• Applications of the Fragment Molecular Orbital Method to Biomolecular Systems

  S. Tanaka

  The International Conference on Theory and Applications of Computational Chemistry 2008, Sep. 2008, English, China, International conference

  Invited oral presentation


• 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―

  田中 成典

  生物物理若手の会・関西３支部合同セミナー, Aug. 2008, Japanese, 神戸, Domestic conference

  Invited oral presentation


• 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

  田中 成典

  岐阜大学人獣感染防御研究センターセミナー, Aug. 2008, Japanese, 岐阜, Domestic conference

  Invited oral presentation


• Simulation study of the RNA binding protein, NOVA-2, by Fragment molecular orbital (FMO) method

  I. Kurisaki, K. Fukuzawa, T. Nakano, Y. Mochizuki, H. Watanabe, S. Tanaka

  236th ACS National Meeting, Aug. 2008, English, アメリカ, International conference

  Poster presentation


• Quantum Monte Carlo Combined with Fragment Molecular Orbital Method

  S. Tanaka

  6th Congress of the International Society for Theoretical Chemical Physics, Jul. 2008, English, Canada, International conference

  Invited oral presentation


• 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

  中野 美紀, 渡邉 博文, 田中 成典

  第8回蛋白質科学会年会, Jun. 2008, Japanese, 東京, Domestic conference

  Poster presentation


• 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

  竹松 和友, 福澤 薫, 中島 捷久, 望月 祐志, 渡邉 博文, 田中 成典

  第８回日本蛋白質科学会年会, Jun. 2008, Japanese, 東京, Domestic conference

  Poster presentation


• 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

  渡邉 博文, 竹松 和友, 福澤 薫, 望月 祐志, 中野 達也, Irina Kufareva, Ruben Abagyan, 田中 成典

  第11回理論化学討論会, May 2008, Japanese, 横浜, Domestic conference

  Poster presentation


• 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

  中野 美紀, 渡邉 博文, 田中 成典

  第11回理論化学討論会, May 2008, Japanese, 横浜, Domestic conference

  Poster presentation


• 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

  藤田 貴敏, 渡邉 博文, 田中 成典

  第11回理論化学討論会, May 2008, Japanese, 横浜, Domestic conference

  Poster presentation


• 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

  沖山 佳生, 渡邉 博文, 石川 岳志, 福澤 薫, 望月 祐志, 中野 達也, 蛯名 邦禎, 田中 成典

  第11回理論化学討論会, May 2008, Japanese, 横浜, Domestic conference

  Poster presentation


• 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

  竹松 和友, 福澤 薫, 中島 捷久, 望月 祐志, 渡邉 博文, 田中 成典

  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, May 2008, Japanese, 横浜, Domestic conference

  Poster presentation


• Developments and Applications of Fragment Molecular Orbital Method

  S. Tanaka

  University of Aarhus, May 2008, English, Denmark, International conference

  Invited oral presentation


• 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

  田中 成典

  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, Mar. 2008, Japanese, 神戸, Domestic conference

  Invited oral presentation


• 「生体分子第一原理計算における電子相関の役割」

  S. Tanaka

  第３回「電子状態計算における電子相関の諸問題」研究会, Dec. 2007, Japanese, 北陸先端科学技術大学院大学, 石川県能美市, Domestic conference

  Invited oral presentation


• 「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」

  S. Tanaka

  神戸大学理学部・物性セミナー, Dec. 2007, Japanese, 神戸大学理学部, Domestic conference

  Invited oral presentation


• Theoretical study on the physicochemical properties of Pumilio RNA-binding domain by Fragment Molecular Orbital (FMO) method

  栗崎 以久男, 福澤 薫, 中野 達也, 望月 祐志, 渡邉 博文, 田中 成典

  第45回生物物理学会, Dec. 2007, Japanese, パシフィコ横浜, Domestic conference

  Poster presentation


• 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

  S. Tanaka

  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, Nov. 2007, Japanese, 独立行政法人科学技術振興機構（JST）, 慶応義塾大学（三田）, Domestic conference

  Invited oral presentation


• 「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」

  S. Tanaka

  徳島大学薬学部・薬品物理化学特論集中講義, Oct. 2007, Japanese, 徳島大学薬学部, 徳島大学薬学部, Domestic conference

  Invited oral presentation


• Molecular dynamics simulation study on the structural stabilities of polyglutamine peptides

  M. Nakano, H. Watanabe, H. Ogawa, S. Tanaka

  CBI学会2007年大会, Oct. 2007, English, 広島大学, International conference

  Poster presentation


• Computational Evalution of Binding Energy of Mutated Estrogen Receptors with the Fragment Molecular Orbital Method

  H. Watanabe, I. Kufareva, R. Abagyan, K. Fukuzawa, T. Nakano, Y. Mochiduki, S. Tanaka

  CBI学会2007年大会, Oct. 2007, English, 広島大学, International conference

  Poster presentation


• 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

  中野 美紀, 小川 肇, 渡邉 博文, 田中 成典

  第１回分子科学討論会, Sep. 2007, Japanese, 東北大学, Domestic conference

  Poster presentation


• 「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」

  S. Tanaka

  神戸大学自然科学先端融合研究環・材料物理コロキウム, Sep. 2007, Japanese, 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, Domestic conference

  Invited oral presentation


• 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

  伊藤 三香, 福澤 薫, 望月 祐志, 中野 達也, 田中 成典

  第１回分子科学討論会, Sep. 2007, Japanese, 東北大学, Domestic conference

  Poster presentation


• 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

  沖山 佳生, 渡邉 博文, 福澤 薫, 中野 達也, 望月 祐志, 石川 岳志, 田中 成典, 蛯名 邦禎

  第１回分子科学討論会, Sep. 2007, Japanese, 東北大学, Domestic conference

  Poster presentation


• 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

  渡邉 博文, 福澤 薫, 中野 達也, 望月 祐志, 田中 成典

  第１回分子科学討論会, Sep. 2007, Japanese, 東北大学, Domestic conference

  Poster presentation


• 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

  岩田 達則, 竹松 和友, 福澤 薫, 中島 捷久, 日向寺 祥子, 望月 祐志, 栗崎 以久男, 渡邉 博文, 田中 成典

  第１回分子科学討論会, Sep. 2007, Japanese, 東北大学, Domestic conference

  Poster presentation


• 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

  栗崎 以久男, 福澤 薫, 中野 達也, 望月 裕志, 渡邉 博文, 田中 成典

  第１回分子科学討論会, Sep. 2007, Japanese, 東北大学, Domestic conference

  Poster presentation


• Effects of non-thermal radiative electromagnetic field on dispersion forces

  Yosuke Suzuki, Kuniyoshi Ebina, Shigenori Tanaka, Toshiyuki Morii

  Asia Pacific Physics Conference 10, Aug. 2007, English, Pohang, Korea, International conference

  Poster presentation


• Biomolecular Calculations Based on Electron-Correlated Fragment Molecular Orbital Methods

  S. Tanaka

  ISSP International Workshop and Symposium on Foundations and Applications of the Density Functional Theor, Aug. 2007, English, Institute for Solid State Physics, University of Tokyo, International conference

  Invited oral presentation


• AB INITIO FRAGMENT MOLECULAR ORBITAL STUDY OF MOLECULAR INTERACTIONS BETWEEN LIGANDED RETINOID X RECEPTOR AND ITS COACTIVATOR

  M. Ito, K. Fukuzawa, Y. Mochizuki, Tatsuya Nakano, S. Tanaka

  The 22nd International Course & Conference on the Interfaces among Mathematics, Jun. 2007, English, Chemistry & Computer Sciences, International conference

  Poster presentation


• 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

  伊藤 三香, 福澤 薫, 望月 祐志, 中野 達也, 田中 成典

  第１０回理論化学討論会, May 2007, Japanese, 名古屋大学, Domestic conference

  Poster presentation


• 「DNAの電子状態」

  S. Tanaka

  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」, Apr. 2007, Japanese, 理化学研究所, 理化学研究所、和光市, Domestic conference

  Invited oral presentation


• 分子間力は振動電場の下で増大するか

  鈴木 洋介, 蛯名 邦禎, 田中 成典, 森井 俊行

  日本物理学会春季大会, Mar. 2007, Japanese, 鹿児島大学, Domestic conference

  Oral presentation


• 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－

  菊地 大輔, 蛯名 邦禎, 田中 成典, 渡邉 博文

  日本物理学会 2007年春季大会, Mar. 2007, Japanese, 鹿児島大学, Domestic conference

  Oral presentation


• Quantum Monte Carlo Calculations of Biomolecules Based on Fragment Molecular Orbital Method

  S. Tanaka, H. Watanabe, R. Maezono, M.D. Towler, R.J. Needs

  Symposium in Honor of Professor William A. Lester Jr’s 70th Birthday, Mar. 2007, English, Berkeley, CA, USA, International conference

  [Invited]

  Invited oral presentation


• Applications of the Fragment Molecular Orbital Method to Biomolecular Systems

  S. Tanaka

  University of California, Mar. 2007, English, San Diego, CA, USA, International conference

  [Invited]

  Invited oral presentation


• A New Approach for the Electron Correlation in Biological Molecules: Combination of Quantum Monte Carlo Method and Fragment Molecular Orbital Method

  渡邉 博文, 前園 涼, 田中 成典

  第二回「電子状態計算における電子相関の諸問題 」研究会, Feb. 2007, English, 北海道大学(ファカルティハウスエンレイソウ), International conference

  Oral presentation


• 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

  栗崎 以久男, 福澤 薫, 中野 達也, 望月 祐志, 田中 成典

  「シミュレーション技術の革新と実用化基盤の構築」, Jan. 2007, Japanese, Tokyo, Domestic conference

  Poster presentation


• 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

  Shigenori Tanaka

  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, Jan. 2007, Japanese, Tokyo, Domestic conference

  Invited oral presentation


• Theoretical study on the physicochemical properties of Pumilio RNA-binding domain by quantum chemical calculations

  I. Kurisaki, K. Fukuzawa, T. Nakano, H. Watanabe, S. Tanaka

  Theory and simulation of biomolecular nano-machines, Dec. 2006, English, Hyogo, Japan, International conference

  Poster presentation


• 生体高分子の第一原理シミュレーションの最近の展開

  Shigenori Tanaka

  第7回先端医療セミナー, Nov. 2006, Japanese, Kobe, Domestic conference

  Invited oral presentation


• 生体高分子ドッキング解析システムMIZUHO/BioStationの開発

  田中 成典, 佐藤 智之, 加藤 昭史, 福澤 薫, 中野 達也

  第34回構造活性相関シンポジウム, Nov. 2006, Japanese, Kobe, Domestic conference

  Others


• Theoretical study on the physicochemical properties of Pumilio RNA-binding domain by quantum chemical calculations

  I. Kurisaki, K. Fukuzawa, T. Nakano, H. Watanabe, S. Tanaka

  Fifth East Asian Biophysics Symposium & Forty-Fourth Annual Meeting of the Biophysical Society of Japan, Nov. 2006, English, Okinawa, Japan, International conference

  Poster presentation


• 生体電子物性と環境応答

  Shigenori Tanaka

  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－」, Oct. 2006, Japanese, Kyoto, Domestic conference

  Invited oral presentation


• 「奪われし未来」をめぐって

  Shigenori Tanaka

  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, Oct. 2006, Japanese, Kobe, Domestic conference

  Invited oral presentation


• 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

  渡邉 博文, 田中 成典, 杉村 乾次, 武石 祥史, 榎本 平

  分子構造総合討論会, Sep. 2006, Japanese, Shizuoka, Domestic conference

  Poster presentation


• 疎水性相互作用へのイオンによる影響の検討

  藤田 貴敏, 渡邉 博文, 田中 成典

  分子構造総合討論会, Sep. 2006, Japanese, Shizuoka, Domestic conference

  Poster presentation


• 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

  鈴木 洋介, 蛯名 邦禎, 田中 成典, 森井 俊行

  日本物理学会秋季大会, Sep. 2006, Japanese, 千葉大学, Domestic conference

  Oral presentation


• 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−

  菊地 大輔, 蛯名 邦禎, 田中 成典, 渡邉 博文

  日本物理学会秋季大会, Sep. 2006, Japanese, 千葉大学, Domestic conference

  Oral presentation


• 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

  田中 成典, 伊藤 三香, 福澤 薫, 石川 岳志, 望月 祐志, 中野 達也

  分子構造総合討論会, Sep. 2006, Japanese, Shizuoka, Domestic conference

  Poster presentation


• Molecular Interactions Between Estrogen Receptor and its Ligand studied by the ab initio fragment molecular orbital method

  K. Fukuzawa, Y. Mochizuki, S. Tanaka, K. Kitaura, T. Nakano

  XIIth International Congress of Quantum Chemistry, Sep. 2006, English, Kyouto, International conference

  Poster presentation


• FMO法へのMCPの導入と生体分子系への適用

  田中 成典, 石川 岳志, 望月 祐志, 中野 達也, 甘利 真司, 森 寛敏, 本田 宏明, 藤田 貴俊, 常盤 広明, 古明地 勇人, 福澤 薫, 田中 皓, 三好 栄作

  分子構造総合討論会, Sep. 2006, Japanese, Shizuoka, Domestic conference

  Poster presentation


• Intra- and intermolecular interactions between cyclic-AMP receptor protein and DNA: Ab initio fragment molecular orbital study

  K. Fukuzawa, Y. Komeiji, Y. Mochizuki, A. Kato, T. Nakano, S. Tanaka

  2006 Annual meeting of CBI society, Jul. 2006, English, Tokyo, International conference

  Poster presentation


• 疎水性相互作用へのイオンによる影響の検討

  藤田 貴敏, 渡邉 博文, 田中 成典

  東京工業大学, Jun. 2006, Japanese, Tokyo, Domestic conference

  Oral presentation


• Ab initio Studies on electronic structure of DNA

  H. Watanabe, T. Fujita, E. B. Starikov, W. Wenzel, R. Maezono, K. Fukuzawa, T. Nakano, S. Tanaka

  Charge Migration in DNA, University of Manitoba, Jun. 2006, English, Winnipeg, Canada, International conference

  Poster presentation


• Intra- and intermolecular interactions between cyclic-amp receptor protein and DNA: Ab initio fragment molecular orbital study

  K. Fukuzawa, Y. Komeiji, Y. Mochizuki, A. Kato, T. Nakano, S. Tanaka

  XIIth International Congress of Quantum Chemistry, May 2006, English, Kyoto, International conference

  Poster presentation


• Computational Study for Improvement of Carbon Fixation Enzyme, Rubisco, with Fragment Molecular Orbital Method

  H. Watanabe, S. Tanaka, K. Sugiura, Y. Takeishi, T. Enomoto

  The XIIth International Congress of Quantum Chemistry, May 2006, English, Kyoto, International conference

  Poster presentation


• A Combinatorial Approach of Quantum Monte Carlo Method and Fragment Molecular Orbital Method

  H. Watanabe, R. Maezono, S. Tanaka

  The XIIth International Congress of Quantum Chemistry, May 2006, English, Kyoto, International conference

  Public symposium


• 「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」

  TANAKA

  日本コンピューター化学会2005春季年会・特別講演, May 2005, 日本コンピューター化学会, 東京工業大学（東京）,, Domestic conference

  Oral presentation


• "Application of MQEq (Modified Charge Equilibration) to the Biological System"

  OGAWA, NAKANO, TANAKA

  QEq2005; The state of the arts of QEq (Charge Equilibration), May 2005, 奈良県新公会堂（奈良市）,, Domestic conference

  Oral presentation


• 「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」

  田中 成典

  日本コンピューター化学会2005春季年会, 2005, Japanese, 東京工業大学、東京, Domestic conference

  Invited oral presentation


• 「FMO法による核内受容体へのアプローチ」

  田中 成典

  第250回CBI学会研究講演会, 2005, Japanese, 日本化学会化学会館、東京, Domestic conference

  Invited oral presentation


• 「DNAのナノ領域ダイナミクスの第一原理的解析」

  田中 成典

  「生命量子科学」研究会, 2005, Japanese, 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, Domestic conference

  Invited oral presentation


• バイオインフォマティクスと環境科学

  Shigenori Tanaka

  「情報」の視点からの環境科学へのアプローチ, 2005, Japanese, 大学連携「ひょうご講座」, 兵庫県立神戸学習プラザ、神戸, Domestic conference

  Invited oral presentation


• Biomolecular Calculations Using Ab Initio Quantum Monte Carlo Technique Combined with Fragment Molecular Orbital Method

  R. Maezono, S Tanaka

  Symposium “Advances in Quantum Monte Carlo” in the 2005, 2005, English, International Chemical Congress of Pacific Basin Societie, Honolulu, Hawaii, USA, International conference

  Invited oral presentation


• Application of MQEq (Modified Charge Equilibration) to the Biological System

  T. Ogawa, T. Nakano, S. Tanaka

  QEq2005; The state of the arts of QEq (Charge Equilibration, 2005, English, 奈良県新公会堂、奈良市, International conference

  Invited oral presentation


• 「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」

  TANAKA

  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, Dec. 2004, 独立行政法人科学技術振興機構（JST）, JST東京本部（東京）,, Domestic conference

  Oral presentation


• 「DNAのナノ領域ダイナミクスの第一原理的解析」

  TANAKA

  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, Oct. 2004, 独立行政法人科学技術振興機構（JST）, TEPIAホール（東京）,, Domestic conference

  Oral presentation


• CD spectra of glycine and polyglycine

  OKIYAMA, EBINA, TANAKA

  The Ninth Asia Pacific Physics Conference (9th APPC), Oct. 2004, English, Association of Asia Pacific Physics Societies, Hanoi, ヴェトナム, International conference

  [Invited]

  Invited oral presentation


• 「新しい時代に皆で考えたいこと」

  TANAKA

  CBI学会人材育成シンポジウム, Aug. 2004, 日本化学会, 日本化学会化学会館（東京）,, Domestic conference

  Oral presentation


• 「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」

  TANAKA

  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－」, Jul. 2004, 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）,, Domestic conference

  Oral presentation


• 「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」

  TANAKA

  第102回自然環境論セミナー, May 2004, 神戸大学発達科学部（神戸）,, Domestic conference

  Oral presentation


• Ab Initio Approach to Nanoscale Dynamics of DNA

  TANAKA

  Oct. 2003, 産業技術総合研究所生命情報科学研究センター（東京）,, Domestic conference

  Oral presentation


• "Quantum Monte Carlo Descriptions of Molecular Interactions Relevant to Biopolymers"

  TANAKA

  226th American Chemical Society National Meeting, Sep. 2003, ***（New York City, USA),, Domestic conference

  Oral presentation


• "Ab Initio Approach to Nanoscale Dynamics of DNA"

  TANAKA

  Sep. 2003, Brock University（St. Catharines, Canada),, Domestic conference

  Oral presentation


• "Theoretical Modeling for Electron Transfer and Transport in DNA"

  TANAKA

  The 7th World Multi-Conference on Systemics, Cybernetics and Informatics (SCI 2003), Jul. 2003, ***(Orlando, Florida, USA),, Domestic conference

  Oral presentation


• 「DNA・蛋白質の電子構造とダイナミクス」

  TANAKA

  企業研究会第16期CAMMフォーラム５月例会, May 2003, 企業研究会, 虎ノ門パストラル（東京）,, Domestic conference

  Oral presentation


• 「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」

  TANAKA

  「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, Apr. 2003, 技術情報協会, 五反田ゆうぽうと（東京）,, Domestic conference

  Oral presentation


• 「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」

  TANAKA

  第229回CBI学会研究講演会, Mar. 2003, CBI学会, 日本化学会化学会館（東京）,, Domestic conference

  Oral presentation


• Ab Initio Approach to Nanoscale Dynamics of DNA

  TANAKA

  Mar. 2003, 山口大学（宇部市）,, Domestic conference

  Oral presentation


• 「色素増感型太陽電池の開発・設計と実用化への課題」

  TANAKA

  「太陽電池の開発と高効率化および応用」技術セミナー, Jan. 2003, 日本テクノセンター, 九段ポンピアンビル（東京）,, Domestic conference

  Oral presentation

• Computational study on thermal relaxation processes in biomolecular systems

  田中 成典

  Japan Society for the Promotion of Science, Grants-in-Aid for Scientific Research, Grant-in-Aid for Scientific Research (C), Kobe University, 01 Apr. 2021 - 31 Mar. 2024

  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。


• 水を通して見る生体分子夾雑系の情報熱力学

  田中 成典

  科学研究費補助金／新学術領域研究, Apr. 2017 - Mar. 2022, Principal investigator

  Competitive research funding


• 生命の起源物質生成の計算機シミュレーション：アミノ酸・核酸とその重合化

  田中 成典

  学術研究助成基金助成金／基盤研究(C), Apr. 2018 - Mar. 2021, Principal investigator

  Competitive research funding


• Development of analysis method of transition state for improvement of enzymatic function

  Nakamura Takashi

  Japan Society for the Promotion of Science, Grants-in-Aid for Scientific Research, Grant-in-Aid for Scientific Research (C), Nagahama Institute of Bio-Science and Technology, 19 Jul. 2016 - 31 Mar. 2019

  We would like to develop a computational method by which experimental researchers can improve the function of a target enzyme easily and efficiently, and thus performed the search of transition structure that is necessary to estimate an activation energy of the enzymatic reaction and the calculation of the activation energy by quantum chemical calculation. We then compared the calculation results with the experimental results. As a result, we found that to obtain comparable result between experiment and calculation, reaction path of the target enzyme should be calculated quite accurately even though the reaction coordinate is complex.


• Development of super-resolution structure analysis techniques for bio-macromolecules based on a quantum chemical calculation

  Fukuzawa Kaori, HONMA Teruki, TANAKA Shigenori, TSURUTA Hiroki, WATANABE Chiduru

  Japan Society for the Promotion of Science, Grants-in-Aid for Scientific Research, Grant-in-Aid for Scientific Research (C), 01 Apr. 2015 - 31 Mar. 2018

  In this study, we are developing a new precise structure determination method of protein - ligand complex by using X-ray crystal structure analysis and quantum chemical calculation. Based on the fragment molecular orbital method, we attempted to use the energy calculation, structure optimization, interaction analysis, and electron density analysis to substantially increase the resolution of structural analysis by experiment. t was shown that quantum chemical calculations are quite useful in predicting high-precision activity of Pim 1 kinase inhibitors, hydration of anti-influenza drugs, prediction of high-resolution structures from low-resolution crystal structures of estrogen receptors.


• 創薬への応用に向けたrasがん遺伝子産物の構造ダイナミクスの分子機構の解明

  島 扶美

  科学研究費補助金／基盤研究(B), Apr. 2014 - Mar. 2017

  Competitive research funding


• 計算創薬のための蛋白質複合系の精密構造・相互作用解析手法の開発

  田中 成典

  学術研究助成基金助成金／基盤研究(C), Apr. 2014 - Mar. 2017, Principal investigator

  Competitive research funding


• 量子モンテカルロ－フラグメント分子軌道法による水の第一原理シミュレーション

  田中 成典

  学術研究助成基金助成金／基盤研究(C), 2011, Principal investigator

  Competitive research funding


• 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」

  田中 成典

  2010, Principal investigator

  Competitive research funding


• 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

  田中 成典

  2007, Principal investigator

  Competitive research funding


• 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

  田中 成典

  2006, Principal investigator

  Competitive research funding


• Analysis of charge transfer and I-V property for the DNA chip by quantum chemical calculations

  KURITA Noriyuki, TANAKA Shigenori

  Japan Society for the Promotion of Science, Grants-in-Aid for Scientific Research, Grant-in-Aid for Scientific Research (B), Toyohashi University of Technology, 2003 - 2005

  Electrochemical DNA chips determine the sequence of DNA bases by detecting the change in charge conductivity through single- or double-strand DNA. Experimentally, double-strand DNAs were found to conduct much greater electric current than single-strand DNAs. To gain insight into the underlying mechanism leading to such a disparity in charge conductivity, the hole/electron conductivities in single- and double-strand DNAs were theoretically examined by molecular dynamics and molecular orbital (MO) calculations. The hole/electron transfer integrals between the neighboring DNA bases were estimated from the frontier MO energy levels. The current-voltage characteristics of single- and double-strand DNAs, derived from the transfer integrals and the site energy of each DNA base, are qualitatively in agreement with experiment.


• フラグメント分子軌道法による生体系の応用計算

  田中 成典

  2005, Principal investigator

  Competitive research funding