Updated on 2021/04/15

写真a

 
FUJIMOTO Kazushi
 
Organization
Graduate School of Engineering Materials Chemistry 1 Assistant Professor
Title
Assistant Professor
Contact information
メールアドレス

Degree 1

  1. 博士(工学) ( 2012.3   名古屋大学 ) 

Research Interests 3

  1. 生体分子関連

  2. 高分子

  3. 分子シミュレーション

Research Areas 3

  1. Nanotechnology/Materials / Fundamental physical chemistry

  2. Natural Science / Biophysics, chemical physics and soft matter physics

  3. Informatics / Computational science  / 分子動力学計算

Research History 2

  1. Ritsumeikan University   Assistant Professor

    2013.4 - 2014.9

  2. Nagoya University   Researcher

    2012.4 - 2013.3

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    Country:Japan

Education 3

  1. Nagoya University   Graduate School, Division of Engineering

    2009.4 - 2012.3

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    Country: Japan

  2. The Graduate University for Advanced Studies

    2007.4 - 2009.3

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    Country: Japan

  3. Ritsumeikan University   Faculty of Science and Engineering

    2003.4 - 2007.3

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    Country: Japan

Professional Memberships 5

  1. 日本化学会

  2. 溶液化学研究会

  3. 高分子学会

  4. 理論化学会

  5. THE MOLECULAR SIMULATION SOCIETY OF JAPAN

Committee Memberships 5

  1. 分子シミュレーション学会   学会誌編集委員  

    2020.10   

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    Committee type:学協会

  2. 溶液化学研究会若手の会オンラインシンポジウム   実行委員  

    2020.8 - 2020.10   

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    Committee type:学協会

  3. 溶液化学研究会若手の会   運営委員  

    2019.4   

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    Committee type:学協会

  4. 第33回 分子シミュレーション討論会   実行委員  

    2018.12 - 2019.12   

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    Committee type:学協会

  5. EMLG/JMLG2018   実行委員  

    2015.9 - 2018.10   

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    Committee type:学協会

Awards 2

  1. 36th International Conference on Solution Chemistry Poster Award

    2019.8   Molecular study of hepati solution tis B virus with pgRNA in the by molecular dynamics calculation

    Kazushi Fujimoto

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    Award type:Award from international society, conference, symposium, etc. 

  2. 溶液化学研究会奨励賞

    2017.10   分子動力学計算を用いた溶液内両親媒性分子の分子論的研究

    藤本和士

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    Award type:Award from Japanese society, conference, symposium, etc.  Country:Japan

 

Papers 26

  1. Position-Dependent Diffusion Constant of Molecules in Heterogeneous Systems as Evaluated by the Local Mean Squared Displacement Reviewed

    Tetsuro Nagai, Shuhei Tsurumaki, Ryo Urano, Kazushi Fujimoto, Wataru Shinoda, Susumu Okazaki

    Journal of Chemical Theory and Computation   Vol. 16 ( 12 ) page: 7239 - 7254   2020.12

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    Language:English   Publishing type:Research paper (scientific journal)   Publisher:American Chemical Society ({ACS})  

    DOI: 10.1021/acs.jctc.0c00448

    PubMed

  2. All-atom molecular dynamics study of impact fracture of glassy polymers. II: Microscopic origins of stresses in elasticity, yielding, and strain hardening Reviewed

    Zhiye Tang, Kazushi Fujimoto, Susumu Okazaki

    Polymer   Vol. 207 ( 20 ) page: 122908 - 122908   2020.10

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

    DOI: 10.1016/j.polymer.2020.122908

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  3. All-atom molecular dynamics study of impact fracture of glassy polymers. I: Molecular mechanism of brittleness of PMMA and ductility of PC Reviewed

    Kazushi Fujimoto, Zhiye Tang, Wataru Shinoda, Susumu Okazaki

    Polymer   Vol. 178   page: 121570 - 121570   2019.9

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    Authorship:Lead author   Language:English   Publishing type:Research paper (scientific journal)   Publisher:Elsevier {BV}  

    DOI: 10.1016/j.polymer.2019.121570

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  4. Free energy profile of permeation of Entecavir through Hepatitis B virus capsid studied by molecular dynamics calculation Reviewed

    Kazushi Fujimoto, Motohiro Fukai, Ryo Urano, Wataru Shinoda, Tetsuya Ishikawa, Katsumi Omagari, Yasuhito Tanaka, Atsushi Nakagawa, Susumu Okazaki

    Pure and Applied Chemistry   Vol. 92 ( 10 ) page: 1585-1594   2020

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

    ©2020 IUPAC & De Gruyter. This work is licensed under a Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International License. For more information, please visit: http://creativecommons.org/licenses/by-nc-nd/4.0/ 2020. Entecavir, triphosphorylated in liver cells, is an antiviral reagent against Hepatitis B virus (HBV). The reagent inhibits reverse transcription of RNA inside the virus capsid. In the present study, free energy profile of an Entecavir triphosphate (ETVTP) molecule has been calculated when it passes through pores of the capsid along two-and three-fold rotational symmetry axes in order to investigate permeation pathway of the reagent to the inside of the capsid. The calculations have been done based on thermodynamic integration (TI) method combined with all-Atomistic molecular dynamic (MD) calculations. A free energy minimum of-19 kJ/mol was found at the entrance of the pore from the outside along the three-fold symmetry axis. This stabilization is from the interaction of negatively charged ETVTP with positively charged capsid methionine residues. This excess free energy concentrates of the reagent at the entrance of the pore by a factor of about 2000. A free energy barrier of approximately 13 kJ/mol was also found near the exit of the pore to the inside of the capsid due to narrow space of the pore surrounded by hydrophobic wall made by proline residues and negatively charged wall by aspartic acid residues. There, ETVTP is partially dehydrated in order to pass through the narrow space, which causes the great free energy loss. Further, the negatively charged residues produce repulsive forces on the ETVTP molecule. In contrast, in the case of the pore along the two-fold symmetry axis, the calculated free energy profile showed shallower free energy minimum,-4 kJ/mol at the entrance in spite of the similarly high barrier, 7 kJ/mol, near the exit of the pore.

    DOI: 10.1515/pac-2020-0109

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    Scopus

  5. Molecular dynamics study of solubilization of cyclohexane, benzene, and phenol into mixed micelles composed of sodium dodecyl sulfate and octaethylene glycol monododecyl ether Reviewed

    Takeda Kosuke, Fujimoto Kazushi, Yoshii Noriyuki, Okazaki Susumu

    JOURNAL OF COMPUTATIONAL CHEMISTRY   Vol. 40 ( 31 ) page: 2722-2729   2019.12

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

    DOI: 10.1002/jcc.26047

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  6. Development of dissociative force field for all-atomistic molecular dynamics calculation of fracture of polymers Reviewed

    Fujimoto Kazushi, Payal Rajadeep Singh, Hattori Tomonori, Shinoda Wataru, Nakagaki Masayuki, Sakaki Shigeyoshi, Okazaki Susumu

    JOURNAL OF COMPUTATIONAL CHEMISTRY   Vol. 40 ( 29 ) page: 2571-2576   2019.11

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

    DOI: 10.1002/jcc.26034

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  7. Molecular Dynamics of Polyrotaxane in Solution Investigated by Quasi-Elastic Neutron Scattering and Molecular Dynamics Simulation: Sliding Motion of Rings on Polymer Reviewed

    Yasuda Yusuke, Hidaka Yuta, Mayumi Koichi, Yamada Takeshi, Fujimoto Kazushi, Okazaki Susumu, Yokoyama Hideaki, Ito Kohzo

    JOURNAL OF THE AMERICAN CHEMICAL SOCIETY   Vol. 141 ( 24 ) page: 9655-9663   2019.6

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

    DOI: 10.1021/jacs.9b03792

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  8. Molecular mechanism of material deformation and failure in butadiene rubber: Insight from all-atom molecular dynamics simulation using a bond breaking potential model Reviewed

    Rajdeep Singh Payal, Kazushi Fujimoto, Changwoon Jang, Wataru Shinoda, Yuki Takei, Hiroshi Shima, Katsuhiko Tsunoda, Susumu Okazaki

    Polymer   Vol. 170   page: 113 - 119   2019.4

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

    DOI: 10.1016/j.polymer.2019.03.006

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  9. Free energy change of micelle formation for sodium dodecyl sulfate from a dispersed state in solution to complete micelles along its aggregation pathways evaluated by chemical species model combined with molecular dynamics calculations Reviewed

    Noriyuki Yoshii, Mika Komori, Shinji Kawada, Hiroaki Takabayashi, Kazushi Fujimoto, Susumu Okazaki

    Wuli Huaxue Xuebao/ Acta Physico - Chimica Sinica   Vol. 34 ( 10 ) page: 1163 - 1170   2018.4

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    Language:English   Publishing type:Research paper (scientific journal)   Publisher:Beijing University Press  

    Surfactant molecules, when dispersed in solution, have been shown to spontaneously form aggregates. Our previous studies on molecular dynamics (MD) calculations have shown that ionic sodium dodecyl sulfate molecules quickly aggregated even when the aggregation number is small. The aggregation rate, however, decreased for larger aggregation numbers. In addition, studies have shown that micelle formation was not completed even after a 100 ns-long MD run (Chem. Phys. Lett. 2016, 646, 36). Herein, we analyze the free energy change of micelle formation based on chemical species model combined with molecular dynamics calculations. First, the free energy landscape of the aggregation, ∆G† i+j, where two aggregates with sizes i and j associate to form the (i + j)-mer, was investigated using the free energy of micelle formation of the i-mer, Gi†, which was obtained through MD calculations. The calculated ∆G† i+j was negative for all the aggregations where the sum of DS ions in the two aggregates was 60 or less. From the viewpoint of chemical equilibrium, aggregation to the stable micelle is desired. Further, the free energy profile along possible aggregation pathways was investigated, starting from small aggregates and ending with the complete thermodynamically stable micelles in solution. The free energy profiles, G(l, k), of † the aggregates at l-th aggregation path and k-th state were evaluated by the formation free energy Σ ni (l,k)Giand the i free energy of mixingΣ ni (l,k)kBTln(ni (l,k) / n(l,k)), where ni(l, k) is the number of i-mer in the system at the l-th i Σ i i aggregation path and k-th state, with n(l,k) (l,k) = n. All the aggregation pathways were obtained from the initial state of 12 pentamers to the stable micelle with i = 60. All the calculated G(l, k) values monotonically decreased with increasing k. This indicates that there are no free energy barriers along the pathways. Hence, the slowdown is not due to the thermodynamic stability of the aggregates, but rather the kinetics that inhibit the association of the fragments. The time required for a collision between aggregates, one of the kinetic factors, was evaluated using the fast passage time, tFPT. The calculated tFPT was about 20 ns for the aggregates with N = 31. Therefore, if aggregation is a diffusion-controlled process, it should be completed within the 100 ns-simulation. However, aggregation does not occur due to the free energy barrier between the aggregates, that is, the repulsive force acting on them. This may be caused by electrostatic repulsions produced by the overlap of the electric double layers, which are formed by the negative charge of the hydrophilic

    DOI: 10.3866/PKU.WHXB201802271

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  10. Molecular dynamics study of the potential of mean force of SDS aggregates Reviewed

    Shinji Kawada, Kazushi Fujimoto, Noriyuki Yoshii, Susumu Okazaki

    JOURNAL OF CHEMICAL PHYSICS   Vol. 147 ( 8 )   2017.8

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    Language:English   Publishing type:Research paper (scientific journal)   Publisher:AMER INST PHYSICS  

    In our previous study, all-atomistic molecular dynamics (MD) calculations have been carried out for the aggregation of ionic sodium dodecyl sulfate in water [S. Kawada et al., Chem. Phys. Lett. 646, 36 (2016)]. Aggregates of 20-30 dodecyl sulfate ions were formed within a short MD run for 10 ns. However, further aggregation did not occur despite a long MD calculation for more than 100 ns. This suggests that strong electrostatic repulsive interactions between the aggregates prevent the fusion of the aggregates. In the present study, mean force and potential of mean force acting between two aggregates with aggregation number N = 30 were evaluated as a function of their separation by MD calculations. The repulsive force becomes strong with decreasing distance between the two aggregates before they merge into one. An origin of the repulsive force is an electric double layer formed by the sulfate group and counter sodium ions. Strength of the repulsive force is in good agreement with the theoretical value given by the Derjaguin-Landau-Verwey-Overbeek (DLVO) theory. Once the aggregates establish contact, the force between them turns to be a large attractive force that can be explained by the interfacial tension. In order to form a single micelle from the two aggregates, it is necessary for them to climb over a free energy barrier of 23 kJ/mol. Once, the barrier is overcome, the micelle is stabilized by similar to 200 kJ/mol. The time constant of aggregation evaluated from the calculated free energy barrier was about 28 mu s at the concentration in our previous study. Published by AIP Publishing.

    DOI: 10.1063/1.4998549

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  11. Spherical harmonics analysis of surface density fluctuations of spherical ionic SDS and nonionic C12E8 micelles: A molecular dynamics study Reviewed

    Noriyuki Yoshii, Yuki Nimura, Kazushi Fujimoto, Susumu Okazaki

    JOURNAL OF CHEMICAL PHYSICS   Vol. 147 ( 3 )   2017.7

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    Language:English   Publishing type:Research paper (scientific journal)   Publisher:AMER INST PHYSICS  

    The surface structure and its fluctuation of spherical micelles were investigated using a series of density correlation functions newly defined by spherical harmonics and Legendre polynomials based on the molecular dynamics calculations. To investigate the influence of head-group charges on the micelle surface structure, ionic sodium dodecyl sulfate and nonionic octaethyleneglycol monododecylether (C12E8) micelles were investigated as model systems. Large-scale density fluctuations were observed for both micelles in the calculated surface static structure factor. The area compressibility of the micelle surface evaluated by the surface static structure factor was tens-of-times larger than a typical value of a lipid membrane surface. The structural relaxation time, which was evaluated from the surface intermediate scattering function, indicates that the relaxation mechanism of the long-range surface structure can be well described by the hydrostatic approximation. The density fluctuation on the two-dimensional micelle surface has similar characteristics to that of three-dimensional fluids near the critical point. Published by AIP Publishing.

    DOI: 10.1063/1.4994698

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  12. Detailed Structural Analysis of a Self-Assembled Vesicular Amphiphilic NCN-Pincer Palladium Complex by Using Wide-Angle X-Ray Scattering and Molecular Dynamics Calculations Reviewed

    Go Hamasaka, Tsubasa Muto, Yoshimichi Andoh, Kazushi Fujimoto, Kenichi Kato, Masaki Takata, Susumu Okazaki, Yasuhiro Uozumi

    CHEMISTRY-A EUROPEAN JOURNAL   Vol. 23 ( 6 ) page: 1291 - 1298   2017.1

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    Language:English   Publishing type:Research paper (scientific journal)   Publisher:WILEY-V C H VERLAG GMBH  

    Wide-angle X-ray scattering experiments and allatomistic molecular dynamics calculations were performed to elucidate the detailed structure of bilayer vesicles constructed by self-assembly of an amphiphilic palladium NCNpincer complex. We found an excellent agreement between the experimental and calculated X-ray spectra, and between the membrane thickness determined from a TEM image and that calculated from an electron-density profile, which indicated that the calculated structure was highly reliable. The analysis of the simulated bilayer structure showed that in general the membrane was softer than other phospholipid bilayer membranes. In this bilayer assemblage, the degree of alignment of complex molecules in the bilayer membrane was quite low. An analysis of the electron-density profile shows that the bilayer assemblage contains a space through which organic molecules can exit. Furthermore, the catalytically active center is near this space and is easily accessible by organic molecules, which permits the bilayer membrane to act as a nanoreactor. The free energy of permeation of water through the bilayer membrane of the amphiphilic complex was 12 kJmol(-1), which is much lower than that for phospholipid bilayer membranes in general. Organic molecules are expected to pass though the bilayer membrane. The self-assembled vesicles were shown to be catalytically active in a Miyaura-Michael reaction in water.

    DOI: 10.1002/chem.201603494

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  13. Molecular dynamics study of the aggregation rate for zwitterionic dodecyldimethylamine oxide and cationic dodecyltrimethylammonium chloride micelles Reviewed

    Kazushi Fujimoto, Yousuke Kubo, Shinji Kawada, Noriyuki Yoshii, Susumu Okazaki

    MOLECULAR SIMULATION   Vol. 43 ( 13-16 ) page: 1331 - 1337   2017

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    Language:English   Publishing type:Research paper (scientific journal)   Publisher:TAYLOR & FRANCIS LTD  

    We studied dynamic scaling law for the early stage domain growth in the micelle aggregation process of dispersed surfactant molecules in water for zwitterionic dodecyldimethylamine oxide (DDAO) and cationic dodecyltrimethylammonium chloride (DTAC) based on all-atomistic molecular dynamics calculations. For both surfactants, the aggregation number N increases in proportion to t(alpha)', where t and alpha' are the simulation time and exponent of the dynamic scaling, respectively. When the aggregation is controlled by diffusion, it follows the well-known Lifshitz-Slyozov (LS) law giving the exponent alpha' = 1. The values of a' obtained for DDAO and DTAC are 0.6 and 0.3, respectively, indicating that the aggregation rate is suppressed compared with purely diffusion controlled LS process. The aggregation of DDAO and DTAC may be partly controlled by electrostatic interaction between the aggregates.

    DOI: 10.1080/08927022.2017.1328557

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  14. A molecular dynamics study of local pressures and interfacial tensions of SDS micelles and dodecane droplets in water Reviewed

    Masahiro Kitabata, Kazushi Fujimoto, Noriyuki Yoshii, Susumu Okazaki

    JOURNAL OF CHEMICAL PHYSICS   Vol. 144 ( 22 ) page: 224701-1-9   2016.6

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    Language:English   Publishing type:Research paper (scientific journal)   Publisher:AMER INST PHYSICS  

    To obtain the radial (normal) and lateral (transverse) components of the local pressure tensor, P-N(R) and P-T(R), respectively, and the interfacial tension of micelles, molecular dynamics (MD) calculations were performed for spherical sodium dodecyl sulfate (SDS) micelles. The local pressure tensor was calculated as a function of radial distance R using the Irving-Kirkwood formula. Similar MD calculations were also carried out for an n-dodecane droplet in water to compare the differences in the local pressure and interfacial tension values with those of the micelles. The calculated interfacial tensions were 20 +/- 5 and 44 +/- 10 mN/m for the SDS micelles and dodecane droplets, respectively. The excess free energies due to the interfacial tension were 340 and 1331 kJ/mol for the SDS micelle and dodecane droplet, respectively. The micelles are stabilized by 991 kJ/mol by covering their hydrophobic cores with hydrophilic groups. The dodecane droplet has a large interfacial tension caused by the zero or positive values of P-N(R) - P-T(R) at all values of R. In contrast, the small interfacial tension in the SDS micelles comes from the negative P-N(R) - P-T(R) values over a wide range of R. The pressure difference between the inside and outside of the oil droplet and its interfacial tension well satisfies the Laplace equation. However, the hydrophobic core of the SDS micelle is quite different from the liquid alkane, and the SDS micelles do not follow Laplace's picture. Decomposing the interfacial tension into contributions from various interactions, it is found that those between charged and polar groups dominate the interfacial tension of the SDS micelles. The positive electrostatic potential (1.3 V) on the micelle surface and the negative potential (-0.15 V) on the oil droplet contribute to the interfacial tensions by 19 and 0.5 mN/m, respectively. Thus, the interfacial tension of the SDS micelles is produced by electrostatic interactions, in contrast to the dodecane droplet. Published by AIP Publishing.

    DOI: 10.1063/1.4953405

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  15. Molecular dynamics study of the structure of anionic SDS, cationic DTAC, zwitterionic DDAO, and nonionic C12E8 spherical micelles in solution Reviewed

    Noriyuki Yoshii, Kazushi Fujimoto, Susumu Okazaki

    JOURNAL OF MOLECULAR LIQUIDS   Vol. 217   page: 99 - 102   2016.5

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

    Molecular dynamics calculations for anionic SOS, cationic DTAC, zwitterionic DDAO, nonionic C12E8 micelles, and dodecane droplets as a reference, were carried out in order to obtain the relation between the head group charges and structure of the micelle. The radial density profile of the carbon atom of hydrophobic tail shows a low-density region at the micelle center, where small hydrophobic solutes may be solubilized. This is commonly found among the micelles investigated in the present study. This indicates that the deep part of the micelle core is not influenced by the head group charges. In contrast, structure of surface of the hydrophobic core of the micelles is strongly influenced by the head groups. Fluctuation of the surface of the ionic SDS micelle is restricted by the strong Coulombic interaction between the charges of the sulfate groups and counter sodium ions. In the other micelles, this effect disappears so that a large fluctuation occurs on the micelle surface. The volume of solvent water decreases when the ionic SDS and DTAC micelles dissolved into water. Because of the strong electrostatic field around the micelle, orientation of water molecules has strong correlations with the micelles. Then, the tetrahedral water structure breaks. In particular, the density increases around the SDS micelles because of the strong attraction toward the sulfate groups. Thus, the volume shrinkage occurs. (C) 2015 Elsevier B.V. All rights reserved.

    DOI: 10.1016/j.molliq.2015.12.062

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  16. G-Protein/beta-Arrestin-Linked Fluctuating Network of G-Protein-Coupled Receptors for Predicting Drug Efficacy and Bias Using Short-Term Molecular Dynamics Simulation Reviewed

    Osamu Ichikawa, Kazushi Fujimoto, Atsushi Yamada, Susumu Okazaki, Kazuto Yamazaki

    PLOS ONE   Vol. 11 ( 5 ) page: e0155816   2016.5

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    Language:English   Publishing type:Research paper (scientific journal)   Publisher:PUBLIC LIBRARY SCIENCE  

    The efficacy and bias of signal transduction induced by a drug at a target protein are closely associated with the benefits and side effects of the drug. In particular, partial agonist activity and G-protein/beta-arrestin-biased agonist activity for the G-protein-coupled receptor (GPCR) family, the family with the most target proteins of launched drugs, are key issues in drug discovery. However, designing GPCR drugs with appropriate efficacy and bias is challenging because the dynamic mechanism of signal transduction induced by ligand-receptor interactions is complicated. Here, we identified the G-protein/beta-arrestin-linked fluctuating network, which initiates large-scale conformational changes, using sub-microsecond molecular dynamics (MD) simulations of the beta(2)-adrenergic receptor (beta(2)AR) with a diverse collection of ligands and correlation analysis of their G protein/beta-arrestin efficacy. The G-protein-linked fluctuating network extends from the ligand-binding site to the G-protein-binding site through the connector region, and the beta-arrestin-linked fluctuating network consists of the NPxxY motif and adjacent regions. We confirmed that the averaged values of fluctuation in the fluctuating network detected are good quantitative indexes for explaining G protein/beta-arrestin efficacy. These results indicate that short-term MD simulation is a practical method to predict the efficacy and bias of any compound for GPCRs.

    DOI: 10.1371/journal.pone.0155816

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  17. Molecular dynamics study of the formation mechanisms of ionic SDS and nonionic C12E8 micelles and n-dodecane droplets Reviewed

    Shinji Kawada, Mika Komori, Kazushi Fujimoto, Noriyuki Yoshii, Susumu Okazaki

    CHEMICAL PHYSICS LETTERS   Vol. 646   page: 36 - 40   2016.2

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

    In order to clarify the early-stage kinetics of micelle formation in concentrated surfactant solutions, all-atom molecular dynamics (MD) calculations of the aggregation of surfactant molecules dispersed in water were performed for ionic sodium dodecyl sulfate (SDS), nonionic octaethyleneglycol monododecyl ether (C12E8), and n-dodecane. The relationship between aggregate domain length and elapsed time from the beginning of the MD calculation obeyed the well-known Lifshitz-Slyozov (LS) law for C12E8 and n-dodecane. In contrast, the aggregation rate of SDS did not obey the LS law. This difference is likely due to the differences in strength of the electrostatic interactions between the aggregates. (C) 2016 Elsevier B.V. All rights reserved.

    DOI: 10.1016/j.cplett.2015.12.062

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  18. A molecular dynamics study of the breathing and deforming modes of the spherical ionic SDS and nonionic C12E8 micelles Reviewed

    Lin Wang, Kazushi Fujimoto, Noriyuki Yoshii, Susumu Okazaki

    JOURNAL OF CHEMICAL PHYSICS   Vol. 144 ( 3 ) page: 034903-1-7   2016.1

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    Language:English   Publishing type:Research paper (scientific journal)   Publisher:AMER INST PHYSICS  

    In order to investigate shape of the micelles and its thermal fluctuations, molecular dynamics calculations have been performed for spherical ionic sodium dodecyl sulfate (SDS) and nonionic octaethyleneglycol monododecyl ether (C12E8) micelles. New statistical functions suitable for extracting the fluctuations of the shape of the spherical micelles were defined using spherical harmonics and Legendre polynomials. The breathing and deforming modes of the SDS and C12E8 micelles were analyzed in detail based on these new functions. The elastic nature of the micelle core was also discussed. The present analysis gives a new molecular picture that the micelle shape is a superposition of the various kinds of breathing and deforming modes, and each mode has a specific relaxation time of the shape fluctuation. (C) 2016 AIP Publishing LLC.

    DOI: 10.1063/1.4940031

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  19. MODYLAS: A Highly Parallelized General-Purpose Molecular Dynamics Simulation Program Invited Reviewed

    Noriyuki Yoshii, Yoshimichi Andoh, Kazushi Fujimoto, Hidekazu Kojima, Atsushi Yamada, Susumu Okazaki

    INTERNATIONAL JOURNAL OF QUANTUM CHEMISTRY   Vol. 115 ( 5 ) page: 342 - 348   2015.3

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    Language:English   Publishing type:Research paper (scientific journal)   Publisher:WILEY-BLACKWELL  

    A large number of molecular dynamics (MD) simulations have been carried out so far on personal computer clusters and conventional supercomputers using general-purpose MD software such as NAMD, GROMACS, CHARMM, and AMBER. The development of MD simulation program is closely related to the architecture of the computers. Recent trend of MD simulation is headed to large-scale calculation, long-time calculation of small systems, and calculation for large statistics. The most challenging one is the large-scale calculation. To realize the large-scale calculation, we have to efficiently control the massively parallel supercomputers with several 10 thousands of nodes. There, it is essential to develop software having a compatibility of such computer architecture. Recently, we have developed general-purpose MD software MODYLAS (MOlecular DYnamics simulation software for LArge Systems) for massively parallel supercomputers such as K-computer. Here, we describe the outline, important features, and computation of MODYLAS. An example result of the 200 ns-MD simulation of the viral capsid system consisting of about 6,500,000 atoms is also presented. (c) 2014 Wiley Periodicals, Inc.

    DOI: 10.1002/qua.24841

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  20. Why Is Poly(oxyethylene) Soluble in Water? Evidence from the Thermodynamic Profile of the Conformational Equilibria of 1,2-Dimethoxyethane and Dimethoxymethane Revealed by Raman Spectroscopy Reviewed

    Ryoichi Wada, Kazushi Fujimoto, Minoru Kato

    JOURNAL OF PHYSICAL CHEMISTRY B   Vol. 118 ( 42 ) page: 12223 - 12231   2014.10

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    Language:English   Publishing type:Research paper (scientific journal)   Publisher:AMER CHEMICAL SOC  

    The origin of high solubility of poly(oxyethylene) in water has been an open question. Although it is thought that the high solubility of poly(oxyethylene) arises from an increase of the trans-gauche-trans (tgt) conformer in water, the relationship between the increase of the tgt conformer and the solubility is unclear. In this study, we have investigated the conformational equilibria of 1,2-dimethoxyethane, which is a model molecule for poly(oxyethylene), by using Raman spectroscopy, and determined the change in the population and the free energy of each conformer with the aid of density functional theory calculations. The free energy of transfer of the tgt conformer from the pure liquid to the water phase is -6.1 +/- 0.2 kJ mol(-1). Furthermore, the fraction of the tgt conformer increases from 0.37 to 0.78. Thus, the net contribution of the tgt conformer is -4.8 +/- 0.2 kJ mol(-1), which is 79% of the total free energy of transfer (-6.07 kJ mol(-1)). This demonstrates that the high solubility of 1,2-dimethoxyethane originates from the lowest free energy and the highest fraction of the tgt conformer in water. We also successfully explain the thermodynamic mechanism of the low solubility of dimethoxymethane, which is the model molecule for poly(oxymethylene).

    DOI: 10.1021/jp5048997

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  21. All-atom molecular dynamics calculation study of entire poliovirus empty capsids in solution Reviewed

    Y. Andoh, N. Yoshii, A. Yamada, K. Fujimoto, H. Kojima, K. Mizutani, A. Nakagawa, A. Nomoto, S. Okazaki

    JOURNAL OF CHEMICAL PHYSICS   Vol. 141 ( 16 ) page: 16501 1-11   2014.10

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    Language:English   Publishing type:Research paper (scientific journal)   Publisher:AMER INST PHYSICS  

    Small viruses that belong, for example, to the Picornaviridae, such as poliovirus and foot-and-mouth disease virus, consist simply of capsid proteins and a single-stranded RNA (ssRNA) genome. The capsids are quite stable in solution to protect the genome from the environment. Here, based on longtime and large-scale 6.5 x 10(6) all-atom molecular dynamics calculations for the Mahoney strain of poliovirus, we show microscopic properties of the viral capsids at a molecular level. First, we found equilibrium rapid exchange of water molecules across the capsid. The exchange rate is so high that all water molecules inside the capsid (about 200 000) can leave the capsid and be replaced by water molecules from the outside in about 25 mu s. This explains the capsid's tolerance to high pressures and deactivation by exsiccation. In contrast, the capsid did not exchange ions, at least within the present simulation time of 200 ns. This implies that the capsid can function, in principle, as a semipermeable membrane. We also found that, similar to the xylem of trees, the pressure of the solution inside the capsid without the genome was negative. This is caused by coulombic interaction of the solution inside the capsid with the capsid excess charges. The negative pressure may be compensated by positive osmotic pressure by the solution-soluble ssRNA and the counter ions introduced into it. (C) 2014 AIP Publishing LLC.

    DOI: 10.1063/1.4897557

    Web of Science

    PubMed

  22. MODYLAS: A Highly Parallelized General-Purpose Molecular Dynamics Simulation Program for Large-Scale Systems with Long-Range Forces Calculated by Fast Multipole Method (FMM) and Highly Scalable Fine-Grained New Parallel Processing Algorithms Reviewed

    Yoshimichi Andoh, Noriyuki Yoshii, Kazushi Fujimoto, Keisuke Mizutani, Hidekazu Kojima, Atsushi Yamada, Susumu Okazaki, Kazutomo Kawaguchi, Hidemi Nagao, Kensuke Iwahashi, Fumiyasu Mizutani, Kazuo Minami, Shin-ichi Ichikawa, Hidemi Komatsu, Shigeru Ishizuki, Yasuhiro Takeda, Masao Fukushima

    JOURNAL OF CHEMICAL THEORY AND COMPUTATION   Vol. 9 ( 7 ) page: 3201 - 3209   2013.7

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    Language:English   Publishing type:Research paper (scientific journal)   Publisher:AMER CHEMICAL SOC  

    Our new molecular dynamics (MD) simulation program, MODYLAS, is a general-purpose program appropriate for very large physical, chemical, and biological systems. It is equipped with most standard MD techniques. Long-range forces are evaluated rigorously by the fast multipole method (FMM) without using the fast Fourier transform (FFT). Several new methods have also been developed for extremely fine-grained parallelism of the MD calculation. The virtually buffering-free methods for communications and arithmetic Operations, the minimal communication latency algorithm, and the parallel bucket-relay communication algorithm for the upper-level multipole moments in the FMM realize excellent scalability. The methods for blockwise arithmetic operations avoid data reload, attaining very small cache miss rates. Benchmark tests for MODYLAS using 65 536 nodes of the K-computer showed that the overall calculation time per MD step including communications is as short as about 5 ins for a 10 million-atom system; that is, 35 ns of simulation time can be computed per day. The program enables investigations of large-scale real systems such as viruses, liposomes, assemblies of proteins and micelles, and polymers.

    DOI: 10.1021/ct400203a

    Web of Science

    PubMed

  23. Molecular dynamics study of free energy of transfer of alcohol and amine from water phase to the micelle by thermodynamic integration method Reviewed

    K. Fujimoto, N. Yoshii, S. Okazaki

    JOURNAL OF CHEMICAL PHYSICS   Vol. 137 ( 9 ) page: 094902 1-6   2012.9

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    Free energy of transfer of methylamine, octylamine, methanol, and octanol from water phase to sodium dodecyl sulfate (SI)S) micelle has been calculated using thermodynamic integration method combined with molecular dynamics calculations. Together with the results for alkanes obtained in our previous study [K. Fujimoto, N. Yoshii, and S. Okazaki, J. Chem. Phys. 133, 074511 (2010)], the effect of polar group on the partition of hydrophilic solutes between water phase and the micelle has been investigated in detail at a molecular level. The calculations showed that the molecules with octyl group are more stable in the SDS micelle than in the water phase due to their hydrophobicity of long alkyl chain. In contrast, methanol and methylamine are stable in the water phase as well as in the micelle because of their high hydrophilicity. The spatial distribution of methylamine, octylamine, methanol, and octanol has also been evaluated as a function of the distance, R, from the center of mass of SDS micelle to the solutes. The distribution shows that the methylamine molecule is adsorbed on the SDS micelle surface, while the methanol molecule is delocalized among the whole system, i.e., in the water phase, on the surface of the micelle, and in the hydrophobic core of the micelle. The octylamine and octanol molecules are solubilized in the SDS micelle with palisade layer structure and are not found in the water phase. (C) 2012 American Institute of Physics. [http://dx.doi.org/10.1063/1.4747491]

    DOI: 10.1063/1.4747491

    Web of Science

  24. Free energy profiles for penetration of methane and water molecules into spherical sodium dodecyl sulfate micelles obtained using the thermodynamic integration method combined with molecular dynamics calculations Reviewed

    K. Fujimoto, N. Yoshii, S. Okazaki

    JOURNAL OF CHEMICAL PHYSICS   Vol. 136 ( 1 ) page: 014511, 1-9   2012.1

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    The free energy profiles, Delta G(r), for penetration of methane and water molecules into sodium dodecyl sulfate (SDS) micelles have been calculated as a function of distance r from the SDS micelle to the methane and water molecules, using the thermodynamic integration method combined with molecular dynamics calculations. The calculations showed that methane is about 6-12 kJ mol(-1) more stable in the SDS micelle than in the water phase, and no Delta G(r) barrier is observed in the vicinity of the sulfate ions of the SDS micelle, implying that methane is easily drawn into the SDS micelle. Based on analysis of the contributions from hydrophobic groups, sulfate ions, sodium ions, and solvent water to Delta G(r), it is clear that methane in the SDS micelle is about 25 kJ mol(-1) more stable than it is in the water phase because of the contribution from the solvent water itself. This can be understood by the hydrophobic effect. In contrast, methane is destabilized by 5-15 kJ mol(-1) by the contribution from the hydrophobic groups of the SDS micelle because of the repulsive interactions between the methane and the crowded hydrophobic groups of the SDS. The large stabilizing effect of the solvent water is higher than the repulsion by the hydrophobic groups, driving methane to become solubilized into the SDS micelle. A good correlation was found between the distribution of cavities and the distribution of methane molecules in the micelle. The methane may move about in the SDS micelle by diffusing between cavities. In contrast, with respect to the water, Delta G(r) has a large positive value of 24-35 kJ mol(-1), so water is not stabilized in the micelle. Analysis showed that the contributions change in complex ways as a function of r and cancel each other out. Reference calculations of the mean forces on a penetrating water molecule into a dodecane droplet clearly showed the same free energy behavior. The common feature is that water is less stable in the hydrophobic core than in the water phase because of the energetic disadvantage of breaking hydrogen bonds formed in the water phase. The difference between the behaviors of the SDS micelles and the dodecane droplets is found just at the interface; this is caused by the strong surface dipole moment formed by sulfate ions and sodium ions in the SDS micelles. (C) 2012 American Institute of Physics. [doi:10.1063/1.3671997]

    DOI: 10.1063/1.3671997

    Web of Science

  25. Enthalpy and entropy of transfer of alkanes from water phase to the micelle core Reviewed

    K. Fujimoto, N. Yoshii, S. Okazaki

    MOLECULAR SIMULATION   Vol. 38 ( 5 ) page: 342 - 345   2012

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    Language:English   Publishing type:Research paper (scientific journal)   Publisher:TAYLOR & FRANCIS LTD  

    Enthalpy and entropy of transfer from water phase to a sodium dodecyl sulphate (SDS) micelle core Delta H-w -> m and T Delta S-w -> m, respectively, have been investigated by molecular dynamics calculation for a series of hydrophobic solutes originally immiscible with water. It is found that both thermodynamic quantities decrease as a function of number of carbon atoms of the alkanes. Structural behaviour of the solubilised alkane molecules in the micelle has been analysed too. The calculated distribution functions show that methane moves around the whole core, whereas the alkane molecules larger than methane are localised in the centre of the core, i.e. the low-density region of the alkyl chains of SDS.

    DOI: 10.1080/08927022.2010.533275

    Web of Science

  26. Molecular dynamics study of solubilization of immiscible solutes by a micelle: Free energy of transfer of alkanes from water to the micelle core by thermodynamic integration method Reviewed

    K. Fujimoto, N. Yoshii, S. Okazaki

    JOURNAL OF CHEMICAL PHYSICS   Vol. 133 ( 7 ) page: 074511 1-6   2010.8

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    Language:English   Publishing type:Research paper (scientific journal)   Publisher:AMER INST PHYSICS  

    Free energy of transfer, Delta G(w -> m), from water phase to a sodium dodecyl sulfate (SDS) micelle core has been calculated for a series of hydrophobic solutes originally immiscible with water by thermodynamic integration method combined with molecular dynamics calculations. The calculated free energy of transfer is in good correspondence to the experiment as well as the theoretical free energy of transfer. The calculated Delta G(w -> m)'s are all negative, implying that the alkane molecules are more stable in the micelle than in the water phase. It decreases almost linearly as a function of the number of carbon atoms of the alkanes longer than methane with a decrement of 3.3 kJ mol(-1) per one methylene group. The calculated free energy of transfer indicates that, for example, at the micelle concentration of 50 CMC (critical micelle concentration), about only 1 of 6 micelles or 1 of 32 000 micelles does not contain a solute methane or n-octane molecule, respectively. (C) 2010 American Institute of Physics. [doi:10.1063/1.3469772]

    DOI: 10.1063/1.3469772

    Web of Science

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Books 1

  1. ポリマーの強靭化技術最前線 破壊機構、分子結合制御、しなやかタフポリマーの開発

    藤本和士、湯之也、岡崎進( Role: Contributor)

    株式会社エヌ・ティー・エス  2020.5  ( ISBN:978-4-86043-668-1

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    Language:Japanese Book type:Scholarly book

MISC 6

  1. 全原子分子動力学計算法による高分子破壊シミュレーション Invited

    藤本和士

    アンサンブル   Vol. 22 ( 4 ) page: 289-293   2020.10

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    Language:Japanese  

  2. 全原子分子動力学計算によるガラス状高分子衝撃破壊の分子論 Invited

    藤本 和士

    日本化学会情報化学部会誌   Vol. 37 ( 4 ) page: 99   2019.12

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    Language:Japanese   Publishing type:Article, review, commentary, editorial, etc. (scientific journal)  

    DOI: 10.11546/cicsj.37.99

  3. 生体高分子-タンパク質-の分子動力学シミュレーション Invited

    藤本和士、岡崎進

    高分子   Vol. 66 ( 10 )   2017.9

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    Authorship:Lead author   Language:Japanese   Publishing type:Article, review, commentary, editorial, etc. (other)  

  4. GPUマシンでシミュレーション タンパク質のフォールディング計算がより手軽に Invited

    藤本和士

    化学   Vol. 70 ( 6 )   2015.6

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    Authorship:Lead author, Last author, Corresponding author   Language:Japanese   Publishing type:Article, review, commentary, editorial, etc. (trade magazine, newspaper, online media)  

  5. ミセル水溶液中の溶質の可溶化に関する計算機シミュレーション Invited Reviewed

    藤本和士

    熱測定   Vol. 40 ( 3 )   2013.7

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    Authorship:Lead author, Last author, Corresponding author   Language:Japanese   Publishing type:Article, review, commentary, editorial, etc. (other)  

  6. 分子動力学法に基づいた自由エネルギー計算によるSDSミセル可溶化の理論的研究

    藤本和士

    アンサンブル   Vol. 15 ( 1 )   2013.1

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    Authorship:Lead author, Last author, Corresponding author   Language:Japanese   Publishing type:Article, review, commentary, editorial, etc. (other)  

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Presentations 61

  1. 全原子分子動力学法による衝撃破壊のミクロ描像 Invited

    藤本和士

    20-2高分子学会講演会 高分子材料による接着とその破壊  2021.2.5 

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    Event date: 2021.2.5

    Language:English   Presentation type:Oral presentation (invited, special)  

  2. Free Energy Calculation of the Permeation of Ortho-silicic Acid through a Model Cell Membrane

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    Event date: 2020.10.29 - 2020.10.30

    Language:Japanese   Presentation type:Oral presentation (general)  

    Country:Japan  

  3. 全原子分子動力学計算による、ガラス状高分子の延伸及び圧縮破壊の分子論的研究

    藤本和士、石川博章、湯之也、岡崎進

    第69回高分子科学討論会 

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    Event date: 2020.9.16 - 2020.9.18

    Language:Japanese   Presentation type:Oral presentation (general)  

    Venue:webex   Country:Japan  

  4. Dynamics of Rings and Polymer in Polyrotaxane Studied by Molecular Dynamics Simulations and Quasi-Elastic Neutron Scattering Experiments International conference

    Yusuke Yasuda, Yuta Hidaka, Koichi Mayumi, Takeshi Yamada, Kazushi Fujimoto, Susumu Okazaki, Hideaki Yokoyama, Kohzo Ito

    Materials Research Meeting 2019 

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    Event date: 2019.12.10 - 2019.12.14

    Language:English   Presentation type:Oral presentation (general)  

    Venue:Yokohama, Japan   Country:Japan  

  5. All-atom Molecular Dynamics Study of Impact Fracture of Glassy Polymers International conference

    K. Fujimoto, Z. Tang, S. Okazaki

    Materials Research Meeting 2019 

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    Event date: 2019.12.10 - 2019.12.14

    Language:English   Presentation type:Oral presentation (general)  

    Country:Japan  

  6. Molecular Dynamics Study of Compressive Fracture of Glassy Polymers International conference

    H. Ishikawa, K. Fujimoto, Z. Tang, S. Okazaki

    Materials Research Meeting 2019 

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    Event date: 2019.12.10 - 2019.12.14

    Language:English   Presentation type:Poster presentation  

    Country:Japan  

  7. 次期スパコン「富岳」での大規模・長時間分子動力学計算実現のためのソフトウェアMODYLASの性能向上

    安藤嘉倫、 坂下達哉、 張家超、 朱喆、 浦野諒、 藤本和士、 吉井範行、 岡崎進

    第33回分子シミュレーション討論会 

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    Event date: 2019.12.9 - 2019.12.11

    Language:Japanese   Presentation type:Oral presentation (general)  

    Venue:名古屋市公会堂   Country:Japan  

  8. 非晶高分子の衝撃破壊に関する分子論的研究

    藤本和士、湯 之也、 岡崎 進

    第33回分子シミュレーション討論会 

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    Event date: 2019.12.9 - 2019.12.11

    Language:Japanese   Presentation type:Oral presentation (general)  

    Venue:名古屋市公会堂   Country:Japan  

  9. Molecular Dynamics of Polyrotaxane in Solution

    Yusuke Yasuda, Yuta Hidaka, Koichi Mayumi, Takeshi Yamada, Kazushi Fujimoto, Susumu Okazaki, Hideaki Yokoyama, and Kohzo Ito

    2nd GLowing Polymer Symposium in KANTO 

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    Event date: 2019.11.30

    Language:English   Presentation type:Oral presentation (general)  

    Country:Japan  

  10. 全原子分子動力学法による高分子衝撃破壊の分子論 Invited

    藤本和士

    2019年度高分子シミュレーション技術セミナー討論会(11月度例会) 

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    Event date: 2019.11.11 - 2019.11.12

    Language:Japanese   Presentation type:Oral presentation (invited, special)  

    Venue:静岡   Country:Japan  

  11. 高分子衝撃破壊の分子論 Invited

    藤本和士

    JSOL CAEフォーラム 2019 

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    Event date: 2019.11.6 - 2019.11.8

    Language:Japanese   Presentation type:Oral presentation (invited, special)  

    Country:Japan  

  12. A new method to obtain position dependent-diffusion constant with flat-bottom potential International conference

    T. Nagai, S. Tsurumaki, K. Fujimoto, S. Okazaki

    The 5th International Conference on Molecular Simulation 

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    Event date: 2019.11.3 - 2019.11.6

    Language:English   Presentation type:Poster presentation  

    Country:Korea, Republic of  

  13. Molecular Dynamics Study of Impact Fracture of Glassy Polymers : Compressive Fracture International conference

    H. Ishikawa, K. Fujimoto, Z. Tang, S. Okazaki

    The 5th International Conference on Molecular Simulation 

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    Event date: 2019.11.3 - 2019.11.6

    Language:English   Presentation type:Poster presentation  

    Country:Korea, Republic of  

  14. All-atom Molecular Dynamics Study of Impact Fracture of Glassy Polymers: On the Yielding Phenomenon International conference

    Z. Tang, K. Fujimoto, S. Okazaki

    The 5th International Conference on Molecular Simulation 

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    Event date: 2019.11.3 - 2019.11.6

    Language:English   Presentation type:Poster presentation  

    Country:Korea, Republic of  

  15. 高分子材料の全原子計算 Invited

    藤本和士

    第8回材料系ワークショップ〜「富岳」時代の 材料系シミュレーションの最前線 

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    Event date: 2019.10.18

    Language:Japanese   Presentation type:Oral presentation (invited, special)  

    Venue:品川, 東京   Country:Japan  

  16. 一本鎖ポリロタキサンの分子ダイナミクス

    保田侑亮,日高悠太,眞弓晧一, 山田武, 藤本和士,岡崎進, 横山英明, 伊藤耕三

    第67回レオロジー討論会 

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    Event date: 2019.10.16 - 2019.10.18

    Language:Japanese   Presentation type:Oral presentation (general)  

    Country:Japan  

  17. ポリロタキサンの内部運動モード

    保田 侑亮, 日高 悠太, 眞弓 晧一, 山田 武, 藤本 和士, 岡崎 進, 横山 英明, 伊藤 耕三

    第68回高分子討論会 

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    Event date: 2019.9.25 - 2019.9.27

    Language:Japanese   Presentation type:Oral presentation (general)  

    Venue:福井   Country:Japan  

  18. 非晶高分子の衝撃破壊に関する分子論的研究

    藤本 和士、湯 之也、岡崎 進

    第68回高分子討論会 

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    Event date: 2019.9.25 - 2019.9.27

    Language:Japanese   Presentation type:Oral presentation (general)  

    Venue:福井大学文京キャンパス   Country:Japan  

  19. 非晶高分子衝撃破壊に関する分子論的研究Ⅲ:圧縮破壊

    石川博章、藤本和士、湯之也、岡崎進

    第68回高分子討論会 

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    Event date: 2019.9.25 - 2019.9.27

    Language:Japanese   Presentation type:Poster presentation  

    Venue:福井大学文京キャンパス   Country:Japan  

  20. 非晶高分子の衝撃破壊に関する分子論的研究:ミクロの視点における降伏現象の解明

    湯 之也、藤本 和士、篠田 渉、岡崎 進

    第68回高分子討論会 

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    Event date: 2019.9.25 - 2019.9.27

    Language:Japanese   Presentation type:Oral presentation (general)  

    Venue:福井大学文京キャンパス   Country:Japan  

  21. Calculation of free energy of transfer of a reverse transcription inhibitor to the inside of HepatitisB Virus (HBV) capsid

    R.Urano, K. Fujimoto, Y. Andoh, N. Yoshii, W. Shinoda, S. Okazaki

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    Event date: 2019.9.24 - 2019.9.26

    Language:English   Presentation type:Poster presentation  

    Country:Japan  

  22. Calculation of free energy of transfer of a nucleotide reverse transcription inhibitor from bulk liver cell to the inside of Hepatitis B Virus (HBV) capsid

    R. Urano, K. Fujimoto, Y. Andoh, N. Yoshii, W. Shinoda, S. Okazaki

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    Event date: 2019.9.17 - 2019.9.20

    Language:Japanese   Presentation type:Oral presentation (general)  

    Country:Japan  

  23. Molecular study of hepatitis B virus with pgRNA in the solution by all-atom molecular dynamics calculation International conference

    K. Fujimoto,Y. Yamaguchi,R. Urano, W. Shinoda,T. Ishikawa, K. Omagari, Y. Tanaka,A. Nakagawa,S. Okazaki

    Joint EMLG/JMLG conference 2019 

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    Event date: 2019.9.8 - 2019.9.13

    Language:English   Presentation type:Poster presentation  

    Venue:GASK(Kutna Hora,Czech Republic)   Country:Japan  

  24. Novel method to evaluate position-dependent diffusion constant of small molecules in heterogeneous systems International conference

    T. Nagai, S. Tsurumaki, R. Urano, K. Fujimoto, W. Shinoda, S. Okazaki

    the 36th International Conference on Solution Chemistry (ICSC2019) 

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    Event date: 2019.8.4 - 2019.8.8

    Language:English   Presentation type:Oral presentation (general)  

    Country:Japan  

  25. Molecular study of hepatitis B virus with pgRNA in the solution by molecular dynamics calculation International conference

    K. Fujimoto, Y. Yamaguchi, R. Urano, W. Shinoda, T.Ishikawa, K. Omagari, Y. Tanaka, A. Nakagawa, S. Okazakia

    the 36th International Conference on Solution Chemistry (ICSC2019) 

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    Event date: 2019.8.4 - 2019.8.8

    Language:English   Presentation type:Poster presentation  

    Country:Japan  

  26. ポリロタキサンの溶液中における分子ダイナミクス

    保田侑亮, 日高悠太, 眞弓晧一, 山田武, 藤本和士, 岡崎進, 横山英明, 伊藤耕三

    第68回高分子年次大会 

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    Event date: 2019.5.29 - 2019.5.31

    Language:Japanese   Presentation type:Oral presentation (general)  

    Country:Japan  

  27. 全原子分子動力学計算による純ブタジエンゴム破壊の分子機構の研究

    パヤル ラジディープ 、藤本和士、ジャン チャンウーン、篠田渉、武井祐樹、島広志、角田克彦、岡崎進

    第68回高分子学会年次大会 

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    Event date: 2019.5.29 - 2019.5.31

    Language:Japanese   Presentation type:Oral presentation (general)  

    Country:Japan  

  28. 非晶高分子の衝撃破壊に関する分子論的研究 I:延性と脆性

    藤本和士、湯之也、篠田渉、岡崎進

    第68回高分子学会年次大会 

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    Event date: 2019.5.29 - 2019.5.31

    Language:Japanese   Presentation type:Oral presentation (general)  

    Country:Japan  

  29. 非晶高分子の衝撃破壊に関する分子論的研究 II:分子論的解釈

    湯之也、藤本和士、篠田渉、岡崎進

    第68回高分子学会年次大会 

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    Event date: 2019.5.29 - 2019.5.31

    Language:Japanese   Presentation type:Oral presentation (general)  

    Country:Japan  

  30. 非晶高分子衝撃破壊に関する分子論的研究Ⅲ:圧縮破壊

    石川博章、藤本和士、湯之也、岡崎進

    第68回高分子学会年次大会 

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    Event date: 2019.5.29 - 2019.5.31

    Language:Japanese   Presentation type:Poster presentation  

    Country:Japan  

  31. For Understanding of Mass Transport in Heterogeneous System, Establishment of Position-dependent Self-diffusion Coefficient Evaluation Method for Small Molecule

    S. Tsurumaki, R. Urano, K. Fujimoto, W. Shinoda, S. Okazaki

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    Event date: 2019.5.27 - 2019.5.29

    Language:Japanese   Presentation type:Poster presentation  

    Country:Japan  

  32. 抗B型肝炎ウイルス(HBV)薬剤分子のカプシド内部への吸収の自由エネルギー

    浦野諒、藤本和士、安藤嘉倫、吉井範行、篠田渉、岡崎進

    第22回理論化学討論会 

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    Event date: 2019.5.27 - 2019.5.29

    Language:Japanese   Presentation type:Oral presentation (general)  

    Country:Japan  

  33. All-atom Molecular Dynamics Study of Impact Fracture of Glassy Polymers

    K. Fujimoto, Z. Tang, W. Shinoda, S. Okazaki

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    Event date: 2019.5.27 - 2019.5.29

    Language:Japanese   Presentation type:Oral presentation (general)  

    Country:Japan  

  34. All-atom Molecular Dynamics Study of Compressive Fracture of Glassy Polymers

    H. Ishikawa, K. Fujimoto, T. Zhiye, S. Okazaki

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    Event date: 2019.5.27 - 2019.5.29

    Language:Japanese   Presentation type:Poster presentation  

    Country:Japan  

  35. A molecular dynamics study of the molecular origin of the ductile rupture of PC International conference

    Zhiye Tang, Kazushi Fujimoto, Wataru Shinoda and Susumu Okazaki

    28th Annual Meeting of MRS-Japan 2018 

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    Event date: 2018.12.18 - 2018.12.20

    Language:English   Presentation type:Poster presentation  

    Country:Japan  

  36. Molecular Study of Impact Fracture of Amorphous Polymer Ⅰ: Brittle Material - PMMA International conference

    Kazushi Fujimoto, Zhiye Tang, Rajdeep Payal, Wataru Shinoda and Susumu Okazaki

    28th Annual Meeting of MRS-Japan 2018 

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    Event date: 2018.12.18 - 2018.12.20

    Language:English   Presentation type:Oral presentation (general)  

    Country:Japan  

  37. Empirical Valence BondのMODYALSへの実装

    藤本和士

    ポスト「京」重点課題5「エネルギーの高効率な創出,変換・貯蔵,利用の新規基盤技術の開発」第5回公開シンポジウム 

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    Event date: 2018.12.12 - 2018.12.13

    Language:Japanese   Presentation type:Poster presentation  

    Venue:北海道大学(北海道札幌市)   Country:Japan  

  38. 分子動力学計算によるポリスチレンの衝撃破壊における分子論

    伊藤直紀 , 藤本和士 , 湯之也, 篠田 渉 , 岡崎 進

    第32回分子シミュレーション討論会 

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    Event date: 2018.11.28 - 2018.11.30

    Language:Japanese   Presentation type:Poster presentation  

    Venue:産業技術総合研究所(茨城県つくば市)   Country:Japan  

  39. 非晶高分子の衝撃破壊に関する分子論的研究II:分子論的解釈

    湯之也、藤本和士、篠田渉、岡崎進

    第32回分子シミュレーション討論会 

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    Event date: 2018.11.28 - 2018.11.30

    Language:Japanese   Presentation type:Oral presentation (general)  

    Venue:産業技術総合研究所(茨城県つくば市)   Country:Japan  

  40. 非晶高分子の衝撃破壊に関する分子論的研究I:延性と脆性

    藤本和士、湯之也、Rajdeep Payal篠田渉、岡崎進

    第32回分子シミュレーション討論会 

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    Event date: 2018.11.28 - 2018.11.30

    Language:Japanese   Presentation type:Oral presentation (general)  

    Venue:産業技術総合研究所(茨城県つくば市)   Country:Japan  

  41. 不均一系の物質輸送の理解に向けて、位置に依存する自己拡散係数の再検討

    弦巻周平,浦野諒,藤本和士,篠田渉,岡崎進

    第32回分子シミュレーション討論会 

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    Event date: 2018.11.28 - 2018.11.30

    Language:Japanese   Presentation type:Poster presentation  

    Venue:産業技術総合研究所(茨城県つくば市)   Country:Japan  

  42. 分子動力学法を用いた pregenome RNA を内包したB型肝炎ウイルスの物性解明

    山口陽平, 今井甫, 藤本和士, 浦野諒, 篠田渉 , 尾曲克己, 田中靖人, 石川哲也, 中川敦史, 岡崎進

    第32回分子シミュレーション討論会 

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    Event date: 2018.11.28 - 2018.11.30

    Language:Japanese   Presentation type:Poster presentation  

    Venue:産業技術総合研究所(茨城県つくば市)   Country:Japan  

  43. 大規模分子動力学計算-生体分子から高分子材料まで Invited

    藤本和士

    近畿化学協会 コンピュータ化学部会 第103回例会 

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    Event date: 2018.10.26

    Language:Japanese   Presentation type:Oral presentation (invited, special)  

    Venue:大阪   Country:Japan  

  44. 非晶性高分子材料の破壊の分子シミュレーション Invited International conference

    藤本和士

    高分子計算機科学研究会 

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    Event date: 2018.10.15

    Language:Japanese   Presentation type:Oral presentation (invited, special)  

    Venue:東京   Country:Japan  

  45. 高分子の衝撃破壊に関する分子論的研究

    藤本和士、湯 之也、篠田 渉、岡崎 進

    第12回分子科学討論会 

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    Event date: 2018.9.10 - 2018.9.13

    Language:Japanese   Presentation type:Oral presentation (general)  

    Venue:福岡国際会議場(福岡県福岡市)   Country:Japan  

  46. All-Atomistic Molecular Dynamics Calculation of Impact Fracture of Glassy Polymers

    K. Fujimoto, W. Shinoda, S. Okazaki

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    Event date: 2018.8.26 - 2018.8.30

    Language:English   Presentation type:Oral presentation (invited, special)  

    Country:Japan  

  47. ガラス状高分子PMMAの衝撃破壊に関する分子論的研究

    藤本和士,服部智成,篠田 渉,岡崎 進

    第21回理論化学討論会 

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    Event date: 2018.5.15 - 2018.5.17

    Language:Japanese   Presentation type:Oral presentation (general)  

    Venue:岡崎カンファレンスセンター(岡崎市)   Country:Japan  

  48. 分子動力学計算を用いた溶液内両親媒性分子の分子論的研究 Invited

    藤本和士

    電気化学会第85回大会 

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    Event date: 2018.3.9 - 2018.3.11

    Language:Japanese   Presentation type:Oral presentation (invited, special)  

    Country:Japan  

  49. 分子動力学計算を用いたガラス状高分子衝撃破壊の分子論的研究

    藤本和士,服部智成,篠田渉,岡崎進

    第31回分子シミュレーション討論会 

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    Event date: 2017.11.29 - 2017.12.1

    Language:Japanese   Presentation type:Oral presentation (general)  

    Venue:金沢商工会議所   Country:Japan  

  50. pg-RNAを内包したB型肝炎ウイルスの全原子分子動力学シミュレーション

    山口陽平,今井甫,藤本和士,浦野諒,尾曲克己,田中靖人,石川哲也,中川敦史,篠田渉,岡崎進

    第31回分子シミュレーション討論会 

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    Event date: 2017.11.29 - 2017.12.1

    Language:Japanese   Presentation type:Poster presentation  

    Venue:金沢商工会議所   Country:Japan  

  51. 分子動力学法による電解質水溶液中の一様に帯電した球殻内に生成される負圧の分子論的解明

    島航平,藤本和士,篠田渉,岡崎進

    第31回分子シミュレーション討論会 

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    Event date: 2017.11.29 - 2017.12.1

    Language:Japanese   Presentation type:Poster presentation  

    Venue:金沢商工会議所   Country:Japan  

  52. 分子動力学法を用いた抗B型肝炎薬のウイルスカプシド透過機構の研究

    深井基裕,浦野諒,藤本和士,篠田渉,岡崎進

    第31回分子シミュレーション討論会 

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    Event date: 2017.11.29 - 2017.12.1

    Language:Japanese   Presentation type:Poster presentation  

    Venue:金沢商工会議所   Country:Japan  

  53. 分子動力学計算を用いた溶液内両親媒性分子の分子論的研究 Invited

    藤本和士

    第40回溶液化学シンポジウム 

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    Event date: 2017.10.18 - 2017.10.20

    Language:Japanese   Presentation type:Oral presentation (invited, special)  

    Venue:イーグレひめじ(あいめっせホール)(兵庫県姫路市)   Country:Japan  

  54. 分子動力学法を用いた抗B型肝炎薬のウイルスカプシド透過機構解明

    深井基裕,藤本和士,篠田渉,岡崎進

    第40回溶液化学シンポジウム 

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    Event date: 2017.10.18 - 2017.10.20

    Language:Japanese   Presentation type:Poster presentation  

    Venue:イーグレひめじ(あいめっせホール)(兵庫県姫路市)   Country:Japan  

  55. 電解質水溶液中の一様に帯電した球殻内に生成される負圧の分子論的解明

    島航平,小嶋秀和,藤本和士,篠田渉,岡崎進

    第40回溶液化学シンポジウム 

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    Event date: 2017.10.18 - 2017.10.20

    Language:Japanese   Presentation type:Poster presentation  

    Venue:イーグレひめじ(あいめっせホール)(兵庫県姫路市)   Country:Japan  

  56. 分子動力学計算を用いた非晶性高分子衝撃破壊の分子論的研究

    藤本和士,服部智成,篠田渉,岡崎進

    第66回高分子討論会 

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    Event date: 2017.9.19 - 2017.9.22

    Language:Japanese   Presentation type:Oral presentation (general)  

    Venue:愛媛大学城北キャンパス   Country:Japan  

  57. 電解質水溶液中の一様に帯電した球殻内に生成される負圧の分子論的解明

    島航平,藤本和士,篠田渉,岡崎進

    第11回分子科学討論会 

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    Event date: 2017.9.15 - 2017.9.18

    Language:Japanese   Presentation type:Poster presentation  

    Venue:東北大学   Country:Japan  

  58. Molecular Mechanism of Impact Fracture in Polymers Materials: Glassy Polymers

    Kazushi Fujimoto, Tomonari Hattori, Wataru Shinoda, Susumu Okazaki

    Hokkaido University-ImPACT Joint Symposium on Advanced Soft Matter: From Single Molecule to Tough Polymers 

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    Event date: 2017.8.7 - 2017.8.8

    Language:English   Presentation type:Poster presentation  

    Country:Japan  

  59. 分子動力学計算による高分子破壊現象の分子論的研究:ガラス性高分子

    藤本和士,埜﨑寛雄,パヤル ラジディープ,服部智成,伊藤直紀,中垣雅之,榊茂好,篠田渉,岡崎進

    第66回高分子学会年次大会 

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    Event date: 2017.5.29 - 2017.5.31

    Language:Japanese   Presentation type:Oral presentation (general)  

    Venue:幕張メッセ   Country:Japan  

  60. Molecular Modeling of Stress Failure in Polymer Materials: Butadiene Rubber

    Rajdeep Singh Payal, Kazushi Fujimoto, Yuki Takei, Hiroshi Shima, Wataru Shinoda, Susumu Okazaki

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    Event date: 2017.5.29 - 2017.5.31

    Language:English   Presentation type:Oral presentation (general)  

    Country:Japan  

  61. ウィルスカプシドをモデル化した荷電球殻内における電解質水溶液の物理化学的研究

    藤本 和士,Faten Hakim,小嶋 秀和,安藤 嘉倫,吉井 範行,篠田 渉,岡崎 進

    第18回理論化学討論会 

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    Event date: 2015.5.20 - 2015.5.22

    Language:Japanese   Presentation type:Poster presentation  

    Venue:大阪、大阪大学   Country:Japan  

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Research Project for Joint Research, Competitive Funding, etc. 2

  1. 長時間全原子分子動力学(AA-MD)計算による、自己修復性高分子の自己修 復能に関連する物理量の探索および、自己修復現象の分子論的解明

    2020.12 - 2021.12

    日東学術振興財団研究助成 

    藤本和士

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    Grant type:Competitive

  2. 環境適合型機能性化学品

    2020.04 - 2023.03

    「富岳」成果創出加速プログラム 

    松林伸幸

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    Grant type:Competitive

KAKENHI (Grants-in-Aid for Scientific Research) 3

  1. 分子ダイナミクス計測による架橋高分子材料の強靭化メカニズム解明

    Grant number:20K05627  2020.04 - 2023.03

    眞弓 皓一

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    Authorship:Coinvestigator(s) 

    本研究では、変形した高分子ゲル中における高分子鎖の分子ダイナミクスを中性子準弾性散乱法および全原子分子動力学(MD)シミュレーションによって解析することで、高分子鎖の形態分布(局所歪み分布)を定量し、材料の破壊を支配している応力集中鎖(伸び切り鎖)を検出する。高分子ゲルの架橋構造と変形下における応力集中、およびマクロスケールにおける破壊挙動の相関を調べることで、高分子架橋材料の破壊メカニズムを明らかにし、強靭化に向けた分子設計指針の確立を目指す。

  2. Elucidation of nano-mechanical properties of a highly adhesive and highly extensible protein and creation of mechanochemical materials

    Grant number:20H00319  2020.04 - 2023.03

    Japan Society for the Promotion of Science  Grants-in-Aid for Scientific Research Grant-in-Aid for Scientific Research (A)  Grant-in-Aid for Scientific Research (A)

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    Authorship:Coinvestigator(s) 

  3. 非晶性高分子への溶剤の影響に関する分子論的解明

    Grant number:20K05631  2020.04 - 2023.03

    藤本 和士

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    Authorship:Principal investigator 

    Grant amount:\4420000 ( Direct Cost: \3400000 、 Indirect Cost:\1020000 )

    特定の高分子に特定の溶剤が作用する時、破壊現象が起こる。この現象は実学的な調査が先行しており、化学的・物理的な理解は解明されたとは言い難い。この現象は明らかに分子性が効いており、ミクロな描像に基づいた研究が必要となってくる。そこで、本研究課題では全原子分子動力学計算を用いて、(1) 溶剤分子の高分子中への溶解挙動、(2) 溶剤分子の高分子中での拡散挙動、(3) 高分子破壊時における溶剤分子の応答を計算することにより、分子レベルから高分子破壊への溶剤影響の解明を目指す。

 

Teaching Experience (On-campus) 8

  1. Chemistry/Biotechnology Tutorial I

    2020

  2. 量子化学Iおよび演習

    2020

  3. 化学生命工学実験IV

    2020

  4. 化学生命工学実験I

    2020

  5. 無機物理化学実験

    2015

  6. 無機物理化学演習

    2015

  7. 無機物理化学実験

    2014

  8. 無機物理化学演習

    2014

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Social Contribution 7

  1. 西宮市立西宮東高等学校自然科学系コース講演

    Lecturer

    西宮市立西宮東高等学校  2020.11.11

  2. 西宮市立西宮東高等学校自然科学系コース講演

    Lecturer

    西宮市立西宮東高等学校  2019.10.23

  3. 西宮市立西宮東高等学校自然科学系コース講演

    Lecturer

    2018.10

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    Audience: High school students

    Type:Lecture

  4. 西宮市立西宮東高等学校自然科学系コース講演

    Lecturer

    西宮市立西宮東高等学校  自然科学系コース講演  2017.8

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    Audience: High school students

    Type:Lecture

  5. 西宮市立西宮東高等学校自然科学系コース講演

    Lecturer

    西宮市立西宮東高等学校  自然科学系コース講演  2016.6

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    Audience: High school students

    Type:Lecture

  6. 西宮市立西宮東高等学校自然科学系コース講演

    2015.5

  7. 西宮市立西宮東高等学校自然科学系コース講演

    2014.6

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Academic Activities 3

  1. 分子シミュレーション学会 学会誌編集委員

    Planning, management, etc.

    分子シミュレーション学会   2020.10 - Now

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    Type:Academic society, research group, etc. 

  2. 溶液化学研究会若手の会

    Planning, management, etc.

    2019.4 - Now

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    Type:Academic society, research group, etc. 

  3. EMLG/JMLG2018 International contribution

    Planning, management, etc.

    2015.9 - 2018.10

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    Type:Competition, symposium, etc.