Kyushu University Academic Staff Educational and Research Activities Database
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Ryo Akiyama Last modified date:2018.06.19

Associate Professor / Biochemistry Group
Department of Chemistry
Faculty of Sciences


Graduate School
Undergraduate School


E-Mail
Homepage
http://www.scc.kyushu-u.ac.jp/BioChemPhys/
Our Web page is administrated by students. The page has
the members' information, the research description and the
selected publications. Our recent discussion is shown on the
"White-board." .
Academic Degree
Ph.D. (Science)
Country of degree conferring institution (Overseas)
No
Field of Specialization
Chemical Physics, Biophysics, Solution Chemistry
Total Priod of education and research career in the foreign country
02years06months
Outline Activities
Biological and chemical phenomena is studied by statistical physics
and quantum mechanics in our research group. I give Lectures and has some labo-classes.
Research
Research Interests
  • Molecular Recognition in Biological System, Electron Transfer, Dielectric Behavior of Aqueous Solution,
    Solvation and Fluctuation, Crowding Problem in Cell, Effective attraction between like-charged macromolecules, Diffusion of Macromolecule
    keyword : Theory of Liquid, Crowding Problem, Molecular Recognition, Biomolecule, Spectroscopy, Soft matter, Polyelectrolyte
    2003.03The solvent effects on molecular recognitions in biological systems are studies by using liquid theory, especially OZ-HNC theory. In this study, we want to shed light on the excluded volume effect in the recognition mechanism..
Academic Activities
Reports
1. Hisashi Okumura, Masahiro Higashi, Yuichiro Yoshida, Hirofumi Sato, Ryo Akiyama, Theoretical approaches for dynamical ordering of biomolecular systems, Elsevier, 10.1016/j.bbagen.2017.10.001, BBA (Biochimica et Biophysica Acta) - General Subjects 1862 (2018) 212–228 (査読あり), 2018.02, Background Living systems are characterized by the dynamic assembly and disassembly of biomolecules. The dynamical ordering mechanism of these biomolecules has been investigated both experimentally and theoretically. The main theoretical approaches include quantum mechanical (QM) calculation, all-atom (AA) modeling, and coarse-grained (CG) modeling. The selected approach depends on the size of the target system (which differs among electrons, atoms, molecules, and molecular assemblies). These hierarchal approaches can be combined with molecular dynamics (MD) simulation and/or integral equation theories for liquids, which cover all size hierarchies. Scope of review We review the framework of quantum mechanical/molecular mechanical (QM/MM) calculations, AA MD simulations, CG modeling, and integral equation theories. Applications of these methods to the dynamical ordering of biomolecular systems are also exemplified. Major conclusions The QM/MM calculation enables the study of chemical reactions. The AA MD simulation, which omits the QM calculation, can follow longer time-scale phenomena. By reducing the number of degrees of freedom and the computational cost, CG modeling can follow much longer time-scale phenomena than AA modeling. Integral equation theories for liquids elucidate the liquid structure, for example, whether the liquid follows a radial distribution function. General significance These theoretical approaches can analyze the dynamic behaviors of biomolecular systems. They also provide useful tools for exploring the dynamic ordering systems of biomolecules, such as self-assembly. This article is part of a Special Issue entitled “Biophysical Exploration of Dynamical Ordering of Biomolecular Systems” edited by Dr. Koichi Kato..
2. The Asakura-Oosawa Model and the Difference of Thermodynamic Property between under Isobaric Condition and under Isochoric Condition.
3. The Young Person's Guide to the Asakura-Oosawa Theory.
4. Calorimetry and Macromolecular Interaction Arising from Translational Motion of Solvent Molecules.
Papers
1. 久保田 陽二, Akira Yoshimori, Nobuyuki Matubayasi, Makoto Suzuki, Ryo Akiyama, Molecular dynamics study of fast dielectric relaxation of water around a molecular-sized ion, JOURNAL OF CHEMICAL PHYSICS, 10.1063/1.4769972, 137, 22, 224502-1-224502-4, 2012.12.
2. Ryo Akiyama, and Ryo Sakata , An Integral Equation Study of Reentrant Behavior in Attractive Interactions between Like-Charged Macroions Immersed in an Electrolyte Solution, J. Phys. Soc. Jpn., 10.1143/JPSJ.80.123602, 80, 123602, 2011.12.
3. Yoji Kubota and Ryo Akiyama, Fine Structure of the Dielectric Response to a Molecular-Sized Ion in Water, J. Phys. Chem. Lett., 10.1021/jz200571f, 2, 13, 1588–1591, 2011.06, [URL].
4. Ryo Akiyama, Yasuhito Karino, Hokuto Obama, Ayako Yoshifuku, Adsorption of xenon on a protein arising from the translational motion of solvent molecules, Phys. Chem. Chem. Phys. , 10.1039/b921314g, 12, 3096-3101, 12, 3096-3101 (Communication), 2010.03, [URL].
5. Ryo Akiyama, Naohiko Fujino, Kouhei Kaneda, and Masahiro Kinoshita, Interaction between like-charged colloidal particles in aqueous electrolyte solution:
Attractive component arising from solvent granularity, Cond. Matt. Phys., 10, 587-596 , 2007.12, [URL].
6. Masahiro Kinoshita, Yuichi Harano, and Ryo Akiyama, Changes in thermodynamic quantities upon contact of two solutes in solvent under isochoric and isobaric conditions, J. Chem. Phys., 125, 244504-1-7 , 2006.12.
7. Ryo Akiyama, Yasuhito Karino, Yasuhiro Hagiwara, Masahiro Kinoshita, Remarkable Solvent Effects on Depletion Interaction in Crowding Media:
Analyses by the Integral Equation Theories, J. Phys. Soc. Jpn., 75, 064804-1-7 , 2006.05.
8. Merchant, K.A.; Noid, W.G.; Akiyama, R; Finkelstein, I.; Goun, A.; McClain, B.L.; Loring, R.F.; Fayer,M.D., Myoglobin-CO Substate Structures and Dynamics: Spectrally Resolved Stimulated Vibrational Echoes and Molecular Dynamics Simulations, J. Am. Chem. Soc., (2003) Vol.125, p.13804., 2003.11.
9. Ryo Akiyama and Roger F. Loring, Vibrational Echoes for Classical and Quantum Solutes,, J. Chem. Phys., Vol. 116, p.4655(2002)., 2002.01.
10. Ryo Akiyama, Masahiro Kinoshita, and Fumio Hirata:, Free energy profiles of electron transfer at water-electrode interface
studied by the reference interaction site model theory, Chem. Phys. Lett., Vol.305, p.251(1999)., 1999.01.
11. Ryo Akiyama and Fumio Hirata, Theoretical Study for Water Structure at Highly Ordered Surface: Effect of
Surface Structure, J. Chem. Phys., Vol.108, p.4904 (1998)., 1998.01.
12. Ryo Akiyama, Akira Yoshimori, Toshiaki Kakitani, Yasushi Imamoto, Yoshinori Shichida and Yasuyo Hatano, Analysis of Excited State Dynamics of 13-trans-Locked-Bacteriorhodopsin, J. Phys. Chem. A, Vol. 101, p.412 (1997)., 1997.01.
13. Ryo Akiyama, Toshiaki Kakitani, Yasushi Imamoto, Yoshinori Shichida and Yasuyo Hatano, Bacteriorhodopsin Analyzed by the Fourier Transform of Optical Absorption Spectra,, J. Phys. Chem., Vol. 99, 7147(1995)., 1995.01.
Presentations
1. Ryo Akiyama, Effective attraction between negatively charged sites on proteins and ordering of proteins in an electrolyte solution, The 4th International Symposium “Dynamical Ordering of Biomolecular Systems for creation of integrated functions”(新学術領域研究『動的秩序と機能』第4回国際シンポジウム), 2015.11.
2. Ryo Akiyama, Spatiotemporal dynamic ordering regulated by ATP hydrolysis and effective attraction between negatively charged sites in a biofluid, The 53rd Annual Meeting of the Biophysical Society of Japan, Formation of spatiotemporal dynamic ordering mediated by ATP hydrolysis (新学術 領域研究『動的秩序と機能』共催シンポジウム), 2015.09.
3. 秋山 良, Association of Actin Monomers and Effective Attraction between Like-Charged Colloidal Particles Mediated by Multivalent Cations, 第52回日本生物物理学会年会, 2014.09.
4. Ryo Akiyama, Shingo Fujihara, Takuto Sawayama, Akira Yoshimori, Interaction between like-charged particles and attractive patches on like-charged proteins, International Meeting on Application of Statistical Mechanics of Molecular Liquid on Soft Matter, 2014.09.
5. 秋山 良, Hydration dynamics and dielectric relaxation of water around an ion, Symposium on Hydrationand ATP Energy 2013, 2013.03.
6. 久保田 陽二, Akira Yoshimori, Nobuyuki Matubayasi, Makoto Suzuki, 秋山 良, Slow Rotational and Fast Dielectric Relaxation of Water around an Ion: A Molecular Dynamics Study, 4th France- Japan Joint Seminar, 2013.01.
7. Attractive interaction between like-charged macromolecules in an electrolyte solution and motion of amoeba, [URL].
8. Interaction between protein and biomolecule arising from translational motion of water molecules and thermodynamic quantities.
9. Effective interaction between like-charged colloidal particles in electrolyte solution: Attractive component arising from solvent granularity, [URL].
10. , [URL].
11. , [URL].
12. Crowding Problems in Cytoplasm and Interaction Arising from Translational Motion of Solvent Molecules, [URL].
13. Structure and dynamics of the A substates of MbCO:
molecular dynamics simulation study compared with infrared
vibrational echo experiments.
Educational
Educational Activities
I give lectures, "The nature of chemical bond", "Thermodynamics", "Biochemistry V", "Physical Chemistry IV", "labo-classes" and etc.

In our group, we study Chemical Physics and Biophysics, and students are learning the research,
discussion, reading and writing.
Other Educational Activities
  • 2012.08, I gave a lecture in Summer School of Biophysics 2012.
    Aug. 31st- Sep. 3rd, 2011, at Chitose, Hokkaido, Japan..
  • 2011.09, I gave two lectures in Summer School of Molecular Simulation 2011.
    Sep. 9-11th, 2011, at Ushimado, Okayama, Japan..
  • 2011.06, Title:Teaching statistical mechanics at UC Berkeley in the physical
    chemistry program at undergraduate and graduate level
    Speaker:Prof. David Chandler (Department of Chemistry, University of California Berkeley)
    14:30~15:00, June 27th, 2011.
    Lecture Room I, Department of Chemistry, Kyushu University.
    I prepared this talk as a lecture of EEP program..
  • 2009.03.
  • 2007.08.
  • 2007.08.
  • 2006.11.
  • 2006.11.