Papers - YAMATO, Takahisa
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Site-selective heat current analysis of & alpha;-helical protein with linear-homopolymer-like model
Wang Tingting, Yamato Takahisa, Sugiura Wataru
JOURNAL OF CHEMICAL PHYSICS Vol. 158 ( 21 ) 2023.6
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Computational study on the thermal conductivity of a protein Reviewed International coauthorship
Yamato, Takahisa; Wang, Tingting; Sugiura, Wataru; Laprévote, Olivier; Katagiri, Takahiro
Journal of Physical Chemistry B 2022.4
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Energy Transfer across Nonpolar and Polar Contacts in Proteins: Role of Contact Fluctuations Invited Reviewed International coauthorship
Poudel Humanath, Reid Korey M., Yamato Takahisa, Leitner David M.
JOURNAL OF PHYSICAL CHEMISTRY B Vol. 124 ( 44 ) page: 9852 - 9861 2020.11
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Variation of Energy Transfer Rates across Protein-Water Contacts with Equilibrium Structural Fluctuations of a Homodimeric Hemoglobin Reviewed International coauthorship
Reid Korey M., Yamato Takahisa, Leitner David M.
JOURNAL OF PHYSICAL CHEMISTRY B Vol. 124 ( 7 ) page: 1148 - 1159 2020.2
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Structure, dynamics and energy flow that govern heme protein functions: theory and experiments. Invited Reviewed International coauthorship
T. Yamato, D.M. Leitner
Biophysical Reviews Vol. 12 page: 291 - 292 2020
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Recent developments in the computational study of protein structural and vibrational energy dynamics Invited Reviewed International coauthorship
D. M. Leitner, T. Yamato
Biophysical Reviews Vol. 12 page: 317 - 322 2020
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Energy transport network in proteins Invited Reviewed
Takahisa YAMATO
Seibutsu Butsuri Vol. 60 ( 2 ) page: 94 - 97 2020
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Energy Exchange Network Model Demonstrates Protein Allosteric Transition: An Application to an Oxygen Sensor Protein
Ota Kunitaka, Yamato Takahisa
JOURNAL OF PHYSICAL CHEMISTRY B Vol. 123 ( 4 ) page: 768 - 775 2019.1
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Normal mode analysis and beyond
Yamato Takahisa, Laprevote Olivier
BIOPHYSICS AND PHYSICOBIOLOGY Vol. 16 page: 322 - 327 2019
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Scaling of Rates of Vibrational Energy Transfer in Proteins with Equilibrium Dynamics and Entropy
Reid Korey M., Yamato Takahisa, Leitner David M.
JOURNAL OF PHYSICAL CHEMISTRY B Vol. 122 ( 40 ) page: 9331-9339 2018.10
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Electron Transfer Pathways of Cyclobutane Pyrimidine Dimer Photolyase Revisited
Sato Ryuma, Kitoh-Nishioka Hirotaka, Ando Koji, Yamato Takahisa
JOURNAL OF PHYSICAL CHEMISTRY B Vol. 122 ( 27 ) page: 6912-6921 2018.7
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Characterization of mechanical unfolding intermediates of membrane proteins by coarse grained molecular dynamics simulation
Yamada Tatsuya, Mitaku Shigeki, Yamato Takahisa
CHEMICAL PHYSICS LETTERS Vol. 691 page: 276-282 2018.1
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MAPPING ENERGY TRANSPORT NETWORKS IN PROTEINS
Leitner David M., Yamato Takahisa
REVIEWS IN COMPUTATIONAL CHEMISTRY, VOL 31 Vol. 31 page: 63 - 113 2018
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Forced Unfolding Mechanism of Bacteriorhodopsin as Revealed by Coarse-Grained Molecular Dynamics Reviewed
T. Yamada, T. Yamato, S. Mitaku
Biophysical Journal Vol. 111 ( 10 ) page: 2986-2098 2016.11
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Forced unfolding mechanism of bacteriorhodopsin as revealed by coarse-grained molecular dynamics Reviewed
T. Yamada, T. Yamato, S. Mitaku
Biophysical Journal Vol. 111 page: 2086-2098 2016.11
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Energy exchange network of inter-residue interactions within a thermally fluctuating protein molecule: A computational study Reviewed
T. Ishikura, Y. Iwata, T. Hatano, T. Yamato
J. Comput. Chem. Vol. 36 page: 1709-1718 2015
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Computational study on the roles of amino acid residues in the active site formation mechanism of blue-light photoreceptors Reviewed
R. Sato, H. Kitoh-Nishioka, K. Ando, T. Yamato
Chem. Phys. Lett. Vol. 633 page: 247-251 2015
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Combinatorial approach of molecular dynamics simulations and database analysis for the studies of protein structure and function
T. Yamato and K. Yura
SEIKAGAKU Vol. 85 ( 8 ) page: 646-655 2013
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Atomic stress tensor analysis of proteins Reviewed
T. Ishikura, T. Hatano, T. Yamato
Chemical Physics Letters Vol. 539-540 page: 144-150 2012.6
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Ligand migration in myoglobin: A combined study of computer simulation and X-ray crystallography Reviewed
T. Tsuduki, A. Tomita, S. Koshihara, S. Adachi, T. Yamato
Journal of Chemical Physics Vol. 136 ( 16 ) page: 16501 (9 pages) 2012.4
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Nonneutral evolution of volume fluctuation in lysozymes revealed by normal-mode analysis Reviewed
Shigefumi Miura, Takahisa Yamato, Tadashi Kamiyama, Kunihiko Gekko
Biophysical Chemistry Vol. 161 page: 39-45 2012.2
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Molecular mechanism of long-range synergetic color tuning between multiple amino acid residues in conger rhodopsin Reviewed
Biophysics Vol. 6 page: 67-78 2010.12
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Proteins at work: Computational biopolymer science of energy, electron, proton transfer and ligand migration Invited Reviewed
Vol. 67 ( 3 ) page: 179-186 2010.3
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*Visualizing breathing motion of internal cavities in concert with ligand migration in myoglobin Reviewed
Ayana Tomita, Tokushi Sato, Kouhei Ichiyanagi, Shunsuke Nozawa, Hirohiko Ichikawa, Matthieu Chollet, Fumihiro Kawai, Sam-Yong Park, Takayuki Tsuduki, Takahisa Yamato, Shin-ya Koshihara, and Shin-ichi Adachi
Proceedings of the National Academy of Sciences of U.S.A Vol. 106 ( 8 ) page: 2612-2616 2009
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Theoretical modeling of the O-intermediate structure of bacteriorhodopsin Reviewed
Hiroshi C. Watanabe, Takakazu Ishikura, and Takahisa Yamato
PROTEINS: Structure, Function, and Bioinformatics Vol. 75 ( 1 ) page: 53-61 2009
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Identification of Functional Residues of DNA Photolyase by BiophysicalComputation and Bioinformatics Invited Reviewed
Vol. 49 ( 4 ) page: 196-197 2009
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*Discrimination of class I CPD photolyase from blue light photoreceptors by single methionine residue Reviewed
Yuji Miyazawa, Hirotaka Nishioka, Kei Yura, and Takahisa Yamato
Biophysical Journal Vol. 94 page: 2194-2203 2008.3
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Stress tensor analysis of the proteinquake of photoactive yellow protein Reviewed
Kana Koike, Kazutomo Kawaguchi, and Takahisa Yamato
Phys. Chem. Chem. Phys. Vol. 10 ( 10 ) page: 1400-1405 2008
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Modulation of the absorption maximum of rhodopsin by amino acids in the C-terminus Invited Reviewed
"S. Yokoyama, T. Tada, T. Yamato"
Photochemistry and Photobiology Vol. 83 ( 2 ) page: 236-241 2007.3
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Spectral tuning of photoactive yellow protein Invited Reviewed
"T. Yamato, T. Ishikura, T. Kakitani, K. Kawaguchi, H. Watanabe"
Photochemistry and Photobiology Vol. 83 ( 2 ) page: 323-327 2007.3
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Non-Condon theory for the energy gap dependence of electron transfer rate
"H. Nishioka, T. Yamato, T. Kakitani"
Frontiers of Computational Science. Proceedings of the International Symposium on Frontiers of Computational Science 2005, Y. Kaneda, H. Kawamura, M. Sasai, Eds., Springer page: 293-297 2007
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*Energy transfer pathways relevant for long-range intramolecular signaling of photosensory protein revealed by microscopic energy conductivity analysis Reviewed
T. Ishikura, T. Yamato
Chemical Physics Letters Vol. 432 ( 4-6 ) page: 533-537 2006.12
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Theoretical prediction of optical absorption maxima for photosensory receptor mutants Reviewed
"Kazutomo Kawaguchi, and Takahisa Yamato"
Chemical Physics Letters Vol. 430 ( 4-6 ) page: 386-390 2006.10
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Temperature dependence of the inelastic electron tunneling Reviewed
"Hirotaka Nishioka, Takahisa Yamato, and Toshiaki Kakitani"
Molecular Simulation Vol. 32 ( 9 ) page: 727-734 2006.8
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Photochemical reaction of cyanobacterial BLUF domain protein PixD
"Fukushima Y, Murai Y, Okajima K, Shibata Y, Ikeuchi M, Yamato T, Itoh S"
PLANT AND CELL PHYSIOLOGY Vol. 47 page: S158-S158 Supple. S 2006
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"Interference, fluctuation, and alternation of electron tunneling in protein media. 2. Non-Condon theory for the energy gap dependence of electron transfer rate" Reviewed
"H. Nishioka, A. Kimura, T. Yamato, T. Kawatsu, T. Kakitani"
J. Phys. Chem. B. Vol. 109 page: 15621-15635 2005.8
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"Interference, fluctuation, and alternation of electron tunneling in protein media. 1. Two tunneling routes in photosynthetic reaction center alternate due to thermal fluctuation of protein conformation" Reviewed
"H. Nishioka, A. Kimura, T. Yamato, T. Kawatsu, T. Kakitani"
J. Phys. Chem. B. Vol. 109 ( 5 ) page: 1978-1987 2005.2
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Spectral tuning in photoactive yellow protein
"Kawaguchi K, Yamato T"
BIOPHYSICAL JOURNAL Vol. 88 ( 1 ) page: 508A-509A Part 2 Suppl. S 2005.1
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Prediction of Inelastic Tunneling Mechanism from Bacteriopheophytin to the Primary Quinone in Modified Bacterial Photosynthetic Reaction Centers
"H. Nishioka, T. Kawatsu, A. Kimura, T. Yamato, T. Kakitani"
"Photosynthesis: Fundamental Aspects to Global Perspectives, Proceedings of the 13th International Congress on Photosynthesis" Vol. 1 page: 327-328 2005
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*Role of protein in the primary step of the photoreaction of yellow protein Reviewed
"A. Yamada, T. Ishikura, T. Yamato"
"PROTEINS: Structure, Function and Bioinformatics" Vol. 55 ( 5 ) page: 1063-1069 2004.6
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Direct measure of functional importance visualized atom-by-atom for photoactive yellow protein: Application to photoisomerization reaction Reviewed
"A. Yamada, T. Ishikura, T. Yamato"
"PROTEINS: Structure, Function and Bioinformatics" Vol. 55 ( 4 ) page: 1070-1077 2004.6
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Torsion potential works in rhodopsin Reviewed
"A. Yamada, T. Yamato, S. Yamamoto, T. Kakitani"
Photochemistry and Photobiology Vol. 79 ( 5 ) page: 476-486 2004.5
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Protein driven photoisomerization reaction: Ab initio QM/MM study of photoactive yellow protein
"Yamada A, Ishikura T, Yamato T"
BIOPHYSICAL JOURNAL Vol. 84 ( 2 ) page: 270A-270A Part 2 Suppl. S 2003.2
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A Computational Study on the stability of the protonated Schiff base of retinal in rhodopsin Reviewed
"A. Yamada, T. Kakitani, S. Yamamoto, and T. Yamato"
Chem. Phys. Lett. Vol. 366 ( 5-6 ) page: 670-675 2002.12
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Destructive interference in the electron tunneling through protein media Reviewed
"T. Kawatsu, T. Kakitani, T. Yamato"
J. Phys. Chem. B. Vol. 106 ( 43 ) page: 11356-11366 2002.10
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On the anomaly of the tunneling matrix element in long-range electron transfer Reviewed
"T. Kawatsu, T. Kakitani, T. Yamato"
J. Phys. Chem. B. Vol. 106 ( 19 ) page: 5068-5074 2002.5
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Analysis of cis-trans photoisomerization mechanism of rhodopsin based on the tertiary structure of rhodopsin Reviewed
"A. Yamada, T. Yamato, T. Kakitani, S. Yamamoto"
J. Photoscience Vol. 9 page: 51-54 2002
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Unique mechanism of excitation energy transfer and photoisomerization in biological systems Reviewed
"T. Kakitani, T. Kawatsu, A. Kimura, A. Yamada, T. Yamato, S. Yamamoto"
J. Biol. Phys. Vol. 28 ( 3 ) page: 367-381 2002
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Theory of excitation energy transfer in the intermediate coupling case and its application to the photosynthetic antenna systems Reviewed
"Akihiro Kimura, Toshiaki Kakitani, Takahisa Yamato"
International Journal of Modern Physics B Vol. 15 ( 28-30 ) page: 3833-3836 2001.12
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Ab initio MO study on the potential energy surfaces for twisting around C15=N bond of protonated Schiff base of retinal Reviewed
"S. Yamamoto, H. Wasada, T. Kakitani, T. Yamato"
THEOCHEM Vol. 543 page: 79-87 2001.6
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Worm Model for Electron Tunneling in Proteins: Consolidation of the Pathway Model and the Dutton Plot Reviewed
"T. Kawatsu, T. Kakitani, T.Yamato"
J. Phys. Chem. B. Vol. 105 ( 19 ) page: 4424-4435 2001.5
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Ab initio MO study on potential energy surfaces for twisting around C7=C8 and C4-C7 bonds of coumaric acid Reviewed
"A. Yamada, S. Yamamoto, T. Yamato, T. Kakitani"
THEOCHEM Vol. 536 ( 2-3 ) page: 195-201 2001.2
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Theory of excitation energy transfer in the intermediate coupling case. II. Criterion for intermediate coupling excitation energy transfer mechanism and application to the photosynthetic antenna system Reviewed
"A. Kimura, T. Kakitani, T. Yamato"
J. Phys. Chem. B. Vol. 104 ( 39 ) page: 9276-9287 2000.10
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Theory of excitation transfer in the intermediate coupling case Reviewed
"A. Kimura, T. Kakitani, T. Yamato"
J. Luminescence Vol. 87-89 page: 815-817 2000.5
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A novel method for determining electron tunneling pathway in protein Reviewed
"T. Kawatsu, T. Kakitani, T. Yamato"
Inorganica Chimica Acta Vol. 300-302 page: 862-868 2000.4
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Monte Carlo simulation study on the structure and reaction at metal-electrolyte interface. II. Mechanism of nonlinear electrode reactions Reviewed
"N. Goto, T. Kakitani, T. Yamato, Y. Hatano"
J. Phys. Soc. Jpn. Vol. 68 ( 11 ) page: 3729-3737 1999.11
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Ab initio MO study on the potential energy surfaces for twisting around the C11=C12 bond of the protonated Schiff base of retinal Reviewed
"Yamamoto, S., Wasada, H., Kakitani, T., Yamato, T"
THEOCHEM Vol. 461-462 page: 463-471 1999.4
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Molecular Dynamics of a 15-Residue Poly(L-alanine)in Water : Helix Formation and Energetics Reviewed
"M. Takano, T. Yamato, J. Higo, A. Suyama, K. Nagayama"
Journal of the American Chemical Society Vol. 121 ( 4 ) page: 605-612 1999.2
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Molecular dynamics simulation of the excited-state dynamics of bacteriorhodopsin
"T. Yamato, T. Kakitani"
"Photosynthesis: Mechanisms and Effects, Vol. III, G. Garab, ed., Kluwer Academic Publishers, Netherlands" page: 1771-1774 1999
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Novel method to detect a motif of local structures in different protein conformations Reviewed
"H. Wako, T. Yamato"
Protein Engineering Vol. 11 ( 11 ) page: 981-990 1998.11
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Molecular Dynamics Study of Femtosecond Events in Photoactive Yellow Protein After Photocexcitation of the Chromophore Reviewed
"T. Yamato, N. Niimura, N. Go"
"PROTEINS : Structure, Function, and Genetics" Vol. 32 ( 3 ) page: 268-275 1998.8
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Molecular Dynamics Simulation of the Excited-State Dynamics of Bacteriorhodopsin Reviewed
"T. Yamato, T. Kakitani"
Photochemistry and Photobiology Vol. 66 ( 6 ) page: 735-740 1997.12
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Mechanical Property of a TIM-Barrel Protein Reviewed
"N. Kobayashi, T. Yamato, N. Go"
"Proteins : Structure, Function, and Genetics" Vol. 28 page: 109-116 1997
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Strain Tensor Field in Proteins Reviewed
T. Yamato
Journal of Molecular Graphics Vol. 14 page: 105-107 1996
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Finite element study of protein structure under high pressure
T. Yamato
"High Pressure Bioscience and Biotechnology Progress in Biotechnology, 13. Elsevier, Amsterdam," page: 157-162 1996
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Computer simulation approach
"T. Yamato, N. Go"
( 24 ) page: 25-29 1995
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Topographical metric to analyze the theumal flucfuations of protein conformation Reviewed
"T. Yamato, M. Saito, J. Higo"
Chemical Physics Lelters Vol. 219 page: 155-159 1994
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Dynamical properties of a beta-sheet in a tim barrel
"N. Kobayashi, T. Yamato, N. Go"
Protein Eng. Vol. 7 ( 9 ) page: 1163-1164 1994
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有限要素と歪みテンソル解析を用いた球状蛋白質の圧力変形の研究(共著)
第45回タンパク質構造討論会 大阪 1994
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Computational Study of Mechanical Constructions of Protein
T. Yamato
BUTSURI Vol. 49 ( 4 ) page: 305-307 1994
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Conformational Deformation in Deoxymyoglobin by Hydrostafic Pressure Reviewed
"T. Yamato, J. Higo, Y. Seno, and N. Go"
"Proteins : Structure, Function and Gentics" Vol. 16 ( 4 ) page: 327-340 1993.8
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Conformational Deformation in Deoxymyoglobin by Hydrostafic Pressure
T.Yamato and N. Go
"Computer Aided innovation of New Materials II, Elsevier Science Publishers B. V." page: 1215-1218 1993
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Glass state of Proteins
"T. Yamato, N. Go"
BUSSEI KENKYU Vol. 59 ( 5 ) page: 672-677 1993