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Switching of the positive feedback for RAS activation by a concerted function of SOS membrane association domains
Yuki Nakamura1,2, Kayo Hibino3, Toshio Yanagida2, Yasushi Sako1,2
1Cellular Informatics Laboratory, RIKEN, 2Nanobiology Laboratories, Graduate School of Frontier Biosciences, Osaka University, 3Laboratory for Cell Signaling Dynamics, RIKEN QBiC
Biophysics and Physicobiology 13 1-11, 2016.
1Cellular Informatics Laboratory, RIKEN, 2Nanobiology Laboratories, Graduate School of Frontier Biosciences, Osaka University, 3Laboratory for Cell Signaling Dynamics, RIKEN QBiC
Biophysics and Physicobiology 13 1-11, 2016.
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Genetic analysis of revertants isolated from the rod-fragile fliF mutant of Salmonella
Hitomi Komatsu1, Fumio Hayashi2, Masahiro Sasa3, Koji Shikata3, Shigeru Yamaguchi4, Keiichi Namba1,5, Kenji Oosawa1,2,3
1Protonic NanoMachine Project, ERATO, JST, Seika, 2Division of Molecular Science, Faculty of Science and Technology Gunma University, 3Department of Biosciences, Teikyo University, 4Izumi Campus, Meiji University, 5Graduate School of Frontier Biosciences, Osaka University
Biophysics and Physicobiology 13 13-25, 2016.
1Protonic NanoMachine Project, ERATO, JST, Seika, 2Division of Molecular Science, Faculty of Science and Technology Gunma University, 3Department of Biosciences, Teikyo University, 4Izumi Campus, Meiji University, 5Graduate School of Frontier Biosciences, Osaka University
Biophysics and Physicobiology 13 13-25, 2016.
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Density functional study of molecular interactions in secondary structures of proteins
Yu Takano1,2,3, Ayumi Kusaka1, Haruki Nakamura1
1Institute for Protein Research, Osaka University, 2Graduate School of Information Sciences, Hiroshima City University, 3JST, CREST
Biophysics and Physicobiology 13 27-35, 2016.
1Institute for Protein Research, Osaka University, 2Graduate School of Information Sciences, Hiroshima City University, 3JST, CREST
Biophysics and Physicobiology 13 27-35, 2016.
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Operating principles of rotary molecular motors : differences between F1 and V1 motors
Ichiro Yamato1, Yoshimi Kakinuma2, Takeshi Murata3,4,5
1Department of Biological Science and Technology, Tokyo University of Science, 2Laboratory of Molecular Physiology and Genetics, Faculty of Agriculture, Ehime University, 3Department of Chemistry, Graduate School of Science, Chiba University, 4Molecular Chirality Research Center, Chiba University, 5JST, PRESTO
Biophysics and Physicobiology 13 37-44, 2016.
1Department of Biological Science and Technology, Tokyo University of Science, 2Laboratory of Molecular Physiology and Genetics, Faculty of Agriculture, Ehime University, 3Department of Chemistry, Graduate School of Science, Chiba University, 4Molecular Chirality Research Center, Chiba University, 5JST, PRESTO
Biophysics and Physicobiology 13 37-44, 2016.
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A unified statistical model of protein multiple sequence alignment integrating direct coupling and insertions
Akira R.Kinjo1
1Institute for Protein Research, Osaka University
Biophysics and Physicobiology 13 45-62, 2016.
1Institute for Protein Research, Osaka University
Biophysics and Physicobiology 13 45-62, 2016.
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Chaperonin GroEL uses asymmetric and symmetric reaction cycles in response to the concentration of non-native substrate proteins
Ryo Iizuka1, Takashi Funatsu1
1Graduate School of Pharmaceutical Sciences, The University of Tokyo
Biophysics and Physicobiology 13 63-69, 2016.
1Graduate School of Pharmaceutical Sciences, The University of Tokyo
Biophysics and Physicobiology 13 63-69, 2016.
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Cation-limited kinetic model for microbial extracellular electron transport via an outer membrane cytochrome C complex
Akihiro Okamoto1,2, Yoshihide Tokunou2, Junki Saito2
1Global Research Center for Environment and Energy based on Nanomaterials Science (GREEN), National Institute for Materials Science, 2Department of Applied Chemistry, School of Engineering, The University of Tokyo
Biophysics and Physicobiology 13 71-76, 2016.
1Global Research Center for Environment and Energy based on Nanomaterials Science (GREEN), National Institute for Materials Science, 2Department of Applied Chemistry, School of Engineering, The University of Tokyo
Biophysics and Physicobiology 13 71-76, 2016.
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Molecular mechanisms of substrate specificities of uridine-cytidine kinase
Wataru Tanaka1, Mitsuo Shoji1,2, Fumiaki Tomoike3, Yuzuru Ujiie1, Kyohei Hanaoka1, Ryuhei Harada1, Megumi Kayanuma1,2, Katsumasa Kamiya4, Toyokazu Ishida5, Ryoji Masui6,7, Seiki Kuramitsu6, Yasuteru Shigeta1,2
1Graduate School of Pure and Applied Sciences, University of Tsukuba, 2Center for Computational Sciences, University of Tsukuba, 3Graduate School of Frontier Biosciences, Osaka University, 4Center for Basic Education and Integrated Learning, Kanagawa Institute of Technology, 5Nanosystem Research Institute, National Institute of Advanced Industrial Science and Technology (AIST), 6Graduate School of Science, Osaka University, 7Graduate School of Science, Osaka City University
Biophysics and Physicobiology 13 77-84, 2016.
1Graduate School of Pure and Applied Sciences, University of Tsukuba, 2Center for Computational Sciences, University of Tsukuba, 3Graduate School of Frontier Biosciences, Osaka University, 4Center for Basic Education and Integrated Learning, Kanagawa Institute of Technology, 5Nanosystem Research Institute, National Institute of Advanced Industrial Science and Technology (AIST), 6Graduate School of Science, Osaka University, 7Graduate School of Science, Osaka City University
Biophysics and Physicobiology 13 77-84, 2016.
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Preface of Special Issue "Protein-Ligand Interactions"
Kei Yura1,2,3
1Graduate School of Humanities and Sciences, Ochanomizu University, 2Center for Informational Biology, Ochanomizu University, 3National Institute of Genetics
Biophysics and Physicobiology 13 85-86, 2016.
1Graduate School of Humanities and Sciences, Ochanomizu University, 2Center for Informational Biology, Ochanomizu University, 3National Institute of Genetics
Biophysics and Physicobiology 13 85-86, 2016.
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Mass spectrometric analysis of protein-ligand interactions
Kentaro Ishii1, Masanori Noda2, Susumu Uchiyama1,2
1Okazaki Institute for Integrative Bioscience, National Institutes of Natural Sciences, 2Department of Biotechnology, Graduate School of Engineering, Osaka University
Biophysics and Physicobiology 13 87-95, 2016.
1Okazaki Institute for Integrative Bioscience, National Institutes of Natural Sciences, 2Department of Biotechnology, Graduate School of Engineering, Osaka University
Biophysics and Physicobiology 13 87-95, 2016.
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Determination of locked interfaces in biomolecular complexes using Haptimol_RD
Georgios Iakovou1, Stephen Laycock1, Steven Hayward1
1School of Computing Sciences, University of East Anglia
Biophysics and Physicobiology 13 97-103, 2016.
1School of Computing Sciences, University of East Anglia
Biophysics and Physicobiology 13 97-103, 2016.
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Specificity of broad protein interaction surfaces for proteins with multiple binding partners
Nobuyuki Uchikoga1, Yuri Matsuzaki2, Masahito Ohue3, Yutaka Akiyama2,3
1Department of Physics, Faculty of Science and Engineering, Chuo University, 2Education Academy of Computational Life Sciences, Tokyo Institute of Technology, 3Department of Computer Science, Graduate School of Information Science and Engineering, Tokyo Institute of Technology
Biophysics and Physicobiology 13 105-115, 2016.
1Department of Physics, Faculty of Science and Engineering, Chuo University, 2Education Academy of Computational Life Sciences, Tokyo Institute of Technology, 3Department of Computer Science, Graduate School of Information Science and Engineering, Tokyo Institute of Technology
Biophysics and Physicobiology 13 105-115, 2016.
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Dynamic profile analysis to characterize dynamics-driven allosteric sites in enzymes
Junko Taguchi1, Akio Kitao2
1Tsukuba Research Center, Taiho Pharmaceutical Co., Ltd, 2Institute of Molecular and Cellular Biosciences, The University of Tokyo
Biophysics and Physicobiology 13 117-126, 2016.
1Tsukuba Research Center, Taiho Pharmaceutical Co., Ltd, 2Institute of Molecular and Cellular Biosciences, The University of Tokyo
Biophysics and Physicobiology 13 117-126, 2016.
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Conformational shift in the closed state of GroEL induced by ATP-binding triggers a transition to the open state
Yuka Suzuki1,5, Kei Yura2,3,4
1Department of Biology, Ochanomizu University, 2Graduate School of Humanities and Sciences, Ochanomizu University, 3Center for Informational Biology, Ochanomizu University, 4National Institute of Genetics, 5Present address:Okinawa Institute of Science and Technology
Biophysics and Physicobiology 13 127-134, 2016.
1Department of Biology, Ochanomizu University, 2Graduate School of Humanities and Sciences, Ochanomizu University, 3Center for Informational Biology, Ochanomizu University, 4National Institute of Genetics, 5Present address:Okinawa Institute of Science and Technology
Biophysics and Physicobiology 13 127-134, 2016.
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Effects of substrate conformational strain on binding kinetics of catalytic antibodies
Masayuki Oda1, Takeshi Tsumuraya2, Ikuo Fujii2
1Graduate School of Life and Environmental Sciences, Kyoto Prefectural University, 2Graduate School of Science, Osaka Prefecture University
Biophysics and Physicobiology 13 135-138, 2016.
1Graduate School of Life and Environmental Sciences, Kyoto Prefectural University, 2Graduate School of Science, Osaka Prefecture University
Biophysics and Physicobiology 13 135-138, 2016.
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Effects of the difference in similarity measures on the comparison of ligand-binding pockets using a reduced vector representation of pockets
Tsukasa Nakamura1,2, Kentaro Tomii1,2,3
1Department of Computational Biology and Medical Sciences, Graduate School of Frontier Sciences, The University of Tokyo, 2Artificial Intelligence Research Center, National Institute of Advanced Industrial Science and Technology (AIST), 3Biotechnology Research Institute for Drug Discovery National Institute of Advanced Industrial Science and Technology (AIST)
Biophysics and Physicobiology 13 139-147, 2016.
1Department of Computational Biology and Medical Sciences, Graduate School of Frontier Sciences, The University of Tokyo, 2Artificial Intelligence Research Center, National Institute of Advanced Industrial Science and Technology (AIST), 3Biotechnology Research Institute for Drug Discovery National Institute of Advanced Industrial Science and Technology (AIST)
Biophysics and Physicobiology 13 139-147, 2016.
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Importance of consensus region of multiple-ligand templates in a virtual screening method
Tatsuya Okuno1,2, Koya Kato3, Shintaro Minami4, Tomoki P. Terada3, Masaki Sasai3, George Chikenji3
1Department of Applied Physics, Nagoya University, 2Division of Neurogenetics, Center for Neurological Diseases and Cancer, Nagoya University Graduate School of Medicine, 3Department of Computational Science and Engineering, Nagoya University, 4Department of Complex Systems Science, Nagoya University
Biophysics and Physicobiology 13 149-156, 2016.
1Department of Applied Physics, Nagoya University, 2Division of Neurogenetics, Center for Neurological Diseases and Cancer, Nagoya University Graduate School of Medicine, 3Department of Computational Science and Engineering, Nagoya University, 4Department of Complex Systems Science, Nagoya University
Biophysics and Physicobiology 13 149-156, 2016.
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Structural characterization of single nucleotide variants at ligand binding sites and enzyme active sites of human proteins
Kazunori D. Yamada1, Hafumi Nishi1, Junichi Nakata2, Kengo Kinoshita1,2,3
1Graduate School of Information Sciences, Tohoku University, 2Tohoku Medical Megabank Organization, Tohoku University, 3Institute of Development, Aging, and Cancer, Tohoku University
Biophysics and Physicobiology 13 157-163, 2016.
1Graduate School of Information Sciences, Tohoku University, 2Tohoku Medical Megabank Organization, Tohoku University, 3Institute of Development, Aging, and Cancer, Tohoku University
Biophysics and Physicobiology 13 157-163, 2016.
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Amino acid residues of bitter taste receptor TAS2R16 that determine sensitivity in primates to β-glycosides
Hiroo Imai1, Nami Suzuki-Hashido1, Yoshiro Ishimaru2, Takanobu Sakurai2, Lijie Yin3, Wenshi Pan3, Masaji Ishiguro4, Katsuyoshi Masuda5, Keiko Abe2, Takumi Misaka2, Hirohisa Hirai1
1Primate Research Institute, Kyoto University, 2Graduate School of Agricultural and Life Sciences, The University of Tokyo, 3Center for Nature and Society School of Life Sciences, Peking University, 4Department of Applied Life Sciences, Niigata University of Pharmacy and Applied Life Sciences, 5Suntory Institute for Bioorganic Research
Biophysics and Physicobiology 13 165-171, 2016.
1Primate Research Institute, Kyoto University, 2Graduate School of Agricultural and Life Sciences, The University of Tokyo, 3Center for Nature and Society School of Life Sciences, Peking University, 4Department of Applied Life Sciences, Niigata University of Pharmacy and Applied Life Sciences, 5Suntory Institute for Bioorganic Research
Biophysics and Physicobiology 13 165-171, 2016.
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In silico studies for the interaction of tumor necrosis factor-alpha (TNF-α) with different saponins from Vietnamese ginseng (Panax vietnamensis)
Oanh T. P. Kim1, Manh D. Le2, Hoang X. Trinh2, Hai V. Nong1
1Institute of Genome Research, Vietnam Academy of Science and Technology, 2Center for Computational Physics, Institute of Physics, Vietnam Academy of Science and Technology
Biophysics and Physicobiology 13 173-180, 2016.
1Institute of Genome Research, Vietnam Academy of Science and Technology, 2Center for Computational Physics, Institute of Physics, Vietnam Academy of Science and Technology
Biophysics and Physicobiology 13 173-180, 2016.
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Molecular dynamics analysis to evaluate docking pose prediction
Takako Sakano1, Md. Iqbal Mahamood1, Takefumi Yamashita1, Hideaki Fujitani1
1Laboratory for Systems Biology and Medicine, Research Center for Advanced Science and Technology, the University of Tokyo
Biophysics and Physicobiology 13 181-194, 2016.
1Laboratory for Systems Biology and Medicine, Research Center for Advanced Science and Technology, the University of Tokyo
Biophysics and Physicobiology 13 181-194, 2016.
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Metabolic pathway reconstruction strategies for central metabolism and natural product biosynthesis
Masaaki Kotera1, Susumu Goto2
1School of Life Science and Technology Tokyo Institute of Technology, 2Bioinformatics Center, Institute for Chemical Research, Kyoto University
Biophysics and Physicobiology 13 195-205, 2016.
1School of Life Science and Technology Tokyo Institute of Technology, 2Bioinformatics Center, Institute for Chemical Research, Kyoto University
Biophysics and Physicobiology 13 195-205, 2016.
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myPresto/omegagene : a GPU-accelerated molecular dynamics simulator tailored for enhanced conformational sampling methods with a non-Ewald electrostatic scheme
Kota Kasahara1, Benson Ma2, Kota Goto3, Bhaskar Dasgupta4,5, Junichi Higo4, Ikuo Fukuda4, Tadaaki Mashimo5, Yutaka Akiyama3,6, Haruki Nakamura4
1College of Life Sciences, Ritsumeikan University, 2College of Engineering, University of Illinois, 3School of Computing, Tokyo Institute of Technology, 4Institute for Protein Research, Osaka University, 5Technology Research Association for Next Generation Natural Products Chemistry, 6Molecular Profiling Research Center for Drug Discovery, National Institute of Advanced Industrial Science and Technology
Biophysics and Physicobiology 13 209-216, 2016.
1College of Life Sciences, Ritsumeikan University, 2College of Engineering, University of Illinois, 3School of Computing, Tokyo Institute of Technology, 4Institute for Protein Research, Osaka University, 5Technology Research Association for Next Generation Natural Products Chemistry, 6Molecular Profiling Research Center for Drug Discovery, National Institute of Advanced Industrial Science and Technology
Biophysics and Physicobiology 13 209-216, 2016.
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Model simulation of the SPOC wave in a bundle of striated myofibrils
Koutaro Nakagome1, Katsuhiko Sato2, Seine A.Shintani3, Shin'ichi Ishiwata1
1Department of Physics, Faculty of Science and Engineering, Waseda University, 2Research Institute for Electronic Science (RIES), Hokkaido University, 3Department of Physics, Faculty of Science, The University of Tokyo
Biophysics and Physicobiology 13 217-226, 2016.
1Department of Physics, Faculty of Science and Engineering, Waseda University, 2Research Institute for Electronic Science (RIES), Hokkaido University, 3Department of Physics, Faculty of Science, The University of Tokyo
Biophysics and Physicobiology 13 217-226, 2016.
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Domain-based biophysical characterization of the structural and thermal stability of FliG, an essential rotor component of the Nat-driven flagellar motor
Yasuhiro Onoue1, Rei Abe-Yoshizumi†,1, Mizuki Gohara1, Yuuki Nishino1, Shiori Kobayashi1, Yasuo Asami2, Michio Homma1
1Division of Biological Science, Graduate School of Science, Nagoya University, 2TA Instruments Japan Inc., †Present address:Department of Frontier Materials, Nagoya Institute of Technology
Biophysics and Physicobiology 13 227-233, 2016.
1Division of Biological Science, Graduate School of Science, Nagoya University, 2TA Instruments Japan Inc., †Present address:Department of Frontier Materials, Nagoya Institute of Technology
Biophysics and Physicobiology 13 227-233, 2016.
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Accelerating in vitro studies on circadian clock systems using an automated sampling device
Yoshihiko Furuike1,2, Jun Abe1, Atsushi Mukaiyama1,2, Shuji Akiyama1,2
1Research Center of Integrative Molecular Systems, Institute for Molecular Science, NINS, 2Department of Functional Molecular Science, SOKENDAI (The Graduate University for Advanced Studies)
Biophysics and Physicobiology 13 235-241, 2016.
1Research Center of Integrative Molecular Systems, Institute for Molecular Science, NINS, 2Department of Functional Molecular Science, SOKENDAI (The Graduate University for Advanced Studies)
Biophysics and Physicobiology 13 235-241, 2016.
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Memorial Issue for Professor Nobuhiko Saito
Kei Yura1,2,3, Hiroshi Wako4
1Graduate School of Humanities and Sciences, Ochanomizu University, 2Center for Informational Biology, Ochanomizu University, 3National Institute of Genetics, 4School of Social Sciences, Waseda University
Biophysics and Physicobiology 13 243-243, 2016.
1Graduate School of Humanities and Sciences, Ochanomizu University, 2Center for Informational Biology, Ochanomizu University, 3National Institute of Genetics, 4School of Social Sciences, Waseda University
Biophysics and Physicobiology 13 243-243, 2016.
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Obituary : Nobuhiko Saito, a man who understood protein folding in his own way
Kei Yura1,2
1Center for Informational Biology, Ochanomizu University, 2National Institute of Genetics
Biophysics and Physicobiology 13 245-247, 2016.
1Center for Informational Biology, Ochanomizu University, 2National Institute of Genetics
Biophysics and Physicobiology 13 245-247, 2016.
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Professor Nobuhiko Saito's contribution to statistical mechanics of biopolymers
Mitiko Go1,2
1Administration, Nagoya University, 2Department of Bio-Science, Nagahama Institute of Bio-Science and Technology
Biophysics and Physicobiology 13 249-250, 2016.
1Administration, Nagoya University, 2Department of Bio-Science, Nagahama Institute of Bio-Science and Technology
Biophysics and Physicobiology 13 249-250, 2016.
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Statistical mechanics of protein structural transitions : Insights from the island model
Yukio Kobayashi1
1Department of Information Systems Science, Faculty of Science and Engineering, Soka Univeristy
Biophysics and Physicobiology 13 251-262, 2016.
1Department of Information Systems Science, Faculty of Science and Engineering, Soka Univeristy
Biophysics and Physicobiology 13 251-262, 2016.
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Characterization of protein folding by a Φ-value calculation with a statistical-mechanical model
Hiroshi Wako1, Haruo Abe2
1School of Social Sciences, Waseda University, 2Department of Electrical Engineering, Nishinippon Institute of Technology
Biophysics and Physicobiology 13 263-279, 2016.
1School of Social Sciences, Waseda University, 2Department of Electrical Engineering, Nishinippon Institute of Technology
Biophysics and Physicobiology 13 263-279, 2016.
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Cooperativity and modularity in protein folding
Masaki Sasai1, George Chikenji1, Tomoki P.Terada1
1Department of Computational Science and Engineering and Department of Applied Physics, Nagoya University
Biophysics and Physicobiology 13 281-293, 2016.
1Department of Computational Science and Engineering and Department of Applied Physics, Nagoya University
Biophysics and Physicobiology 13 281-293, 2016.
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Itinerary profiling to analyze a large number of protein-folding trajectories
Motonori Ota1, Mitsunori Ikeguchi2, Akinori Kidera2
1Graduate School of Information Science, Nagoya University, 2Graduate School of Medical Life Science, Yokohama City University
Biophysics and Physicobiology 13 295-304, 2016.
1Graduate School of Information Science, Nagoya University, 2Graduate School of Medical Life Science, Yokohama City University
Biophysics and Physicobiology 13 295-304, 2016.
- アブストラクト： 従量制は110円（税込）、基本料金制は基本料金に含まれます。
- 全文ダウンロード： 従量制、基本料金制の方共に770円(税込) です。
What parameters characterize "life"?
Shigeki Mitaku1, Ryusuke Sawada2
1Emeritus Professor of Nagoya University, 2Division of System Cohort, Medical Institute of Bioregulation, Kyushu University
Biophysics and Physicobiology 13 305-310, 2016.
1Emeritus Professor of Nagoya University, 2Division of System Cohort, Medical Institute of Bioregulation, Kyushu University
Biophysics and Physicobiology 13 305-310, 2016.
- アブストラクト： 従量制は110円（税込）、基本料金制は基本料金に含まれます。
- 全文ダウンロード： 従量制、基本料金制の方共に770円(税込) です。
Theoretical analyses on a flipping mechanism of UV-induced DNA damage
Ryuma Sato1, Ryuhei Harada1, Yasuteru Shigeta1
1Center for Computational Sciences, University of Tsukuba
Biophysics and Physicobiology 13 311-319, 2016.
1Center for Computational Sciences, University of Tsukuba
Biophysics and Physicobiology 13 311-319, 2016.
- アブストラクト： 従量制は110円（税込）、基本料金制は基本料金に含まれます。
- 全文ダウンロード： 従量制、基本料金制の方共に770円(税込) です。
Actin binding domain of filamin distinguishes posterior from anterior actin filaments in migrating Dictyostelium cells
Keitaro Shibata1,4, Akira Nagasaki1, Hiroyuki Adachi2, Taro Q.P.Uyeda1,3
1Biomedical Research Institute, National Institute of Advanced Industrial Science and Technology, 2Department of Biotechnology, University of Tokyo, 3Department of Physics, Faculty of Science and Engineering, Waseda University, 4Present address: Department of Biology, University of Padova
Biophysics and Physicobiology 13 321-331, 2016.
1Biomedical Research Institute, National Institute of Advanced Industrial Science and Technology, 2Department of Biotechnology, University of Tokyo, 3Department of Physics, Faculty of Science and Engineering, Waseda University, 4Present address: Department of Biology, University of Padova
Biophysics and Physicobiology 13 321-331, 2016.
- アブストラクト： 従量制は110円（税込）、基本料金制は基本料金に含まれます。
- 全文ダウンロード： 従量制、基本料金制の方共に770円(税込) です。
