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Ryo Akiyama Last modified date:2020.06.19

Associate Professor / Biochemistry Group
Department of Chemistry
Faculty of Sciences


Graduate School
Undergraduate School


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Homepage
https://kyushu-u.pure.elsevier.com/en/persons/ryo-akiyama
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http://www.scc.kyushu-u.ac.jp/BioChemPhys/
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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, Selective Absorption in Confined Space
    keyword : Theory of Liquid, Crowding Problem, Molecular Recognition, Biomolecule, Spectroscopy, Soft matter, Polyelectrolyte, Selective Absorption
    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. Y. Tamura1, A. Yoshimori, A. Suematsu and R. Akiyama, Reentrant crystallization of like-charged colloidal particles in an electrolyte solution: Relationship between the shape of the phase diagram and the effective potential of colloidal particles, EPL (Europhys Letter), 10.1209/0295-5075/129/66001, 129, 66001-p1-66001-p7, 2020.04, The reentrant crystallization of like-charged colloidal particles in electrolyte solutions was studied to clarify the relationship between the shape of the phase diagram and the particle-particle effective potential. Coexisting densities were calculated at various electrolyte concentrations using the thermodynamic perturbation expansion method with effective one-component models. The effective potentials were obtained using an integral equation theory for liquids. Some model effective potentials were examined. The calculated results indicated that the reentrant behaviors of various acidic protein solutions observed in the experiments required not only the nonmonotonic dependence of the short-range attraction on the electrolyte concentration, but also the absence of a long repulsive tail..
2. Yuka Nakamura, Shota Arai, Masahiro Kinoshita, Akira Yoshimori, Ryo Akiyama, Reduced density profile of small particles near a large particle
Results of an integral equation theory with an accurate bridge function and a Monte Carlo simulation, Journal of Chemical Physics, 10.1063/1.5100040, 151, 4, 044506-1-044506-10, 2019.07, Solute-solvent reduced density profiles of hard-sphere fluids were calculated by using several integral equation theories for liquids. The traditional closures, Percus-Yevick (PY) and the hypernetted-chain (HNC) closures, as well as the theories with bridge functions, Verlet, Duh-Henderson, and Kinoshita (named MHNC), were used for the calculation. In this paper, a one-solute hard-sphere was immersed in a one-component hard-sphere solvent and various size ratios were examined. The profiles between the solute and solvent particles were compared with those calculated by Monte Carlo simulations. The profiles given by the integral equations with the bridge functions were much more accurate than those calculated by conventional integral equation theories, such as the Ornstein-Zernike (OZ) equation with the PY closure. The accuracy of the MHNC-OZ theory was maintained even when the particle size ratio of solute to solvent was 50. For example, the contact values were 5.7 (Monte Carlo), 5.6 (MHNC), 7.8 (HNC), and 4.5 (PY), and the first minimum values were 0.48 (Monte Carlo), 0.46 (MHNC), 0.54 (HNC), and 0.40 (PY) when the packing fraction of the hard-sphere solvent was 0.38 and the size ratio was 50. The asymptotic decay and the oscillation period for MHNC-OZ were also very accurate, although those given by the HNC-OZ theory were somewhat faster than those obtained by Monte Carlo simulations..
3. Ken Tokunaga, Ryo Akiyama, Molecular dynamics study of a solvation motor in a Lennard-Jones solvent, Physical Review E, 10.1103/PhysRevE.100.062608, 100, 6, 062608-1-062608-8, 2019.12, The motions of a solvation motor in a Lennard-Jones solvent were calculated by using molecular dynamics simulation. The results were analyzed considering the large spatial scale effects caused by the motion of the solvation motor. A reaction site was located on the surface of the solvation motor and the attraction between the reaction site and the solvent molecules was varied for 100 fs. The motion of the motor was driven by solvation changes near the reaction site on the motor. Two finite-size effects were observed in the motion. One was the hydrodynamic effect and the other was the increase in solvent viscosity caused by heat generation. The latter affected not only the displacement of the motor caused by the reaction but also the wave propagation phenomena. Both effects reduced the motor displacement. Heat generation affects the displacement, in particular for small systems. By contrast, the hydrodynamic effect remained even for large systems. An extrapolation method was proposed for the displacement..
4. Ayano Chiba, Akio Oshima, Ryo Akiyama, Confined Space Enables Spontaneous Liquid Separation by Molecular Size
Selective Absorption of Alkanes into a Polyolefin Cast Film, Langmuir, 10.1021/acs.langmuir.9b02509, 35, 52, 17177-17184, 2019.12, The depletion force has been used to explain phase separation phenomena in colloidal systems. Here, we showed that depletion force can explain not only phase separation of large and small colloidal particles but also preferential absorption of larger molecules from a mixture of large and small molecules in a liquid state. When a polyolefin cast film was immersed in a mixture of long and short normal alkanes, the longer molecules were selectively absorbed into the film. This experimental result was explained from the viewpoint of depletion force. The main finding was the use of confined space to emphasize the separation tendency caused by the force. In general, the increase in entropy may serve as a driving force to mix molecules. However, if sufficiently narrow pores are present, large and small molecules are separated naturally by size as the entropy increases. This finding will lead to size exclusion chromatography of low-mass molecules, similar to gel permeation chromatography of macromolecules. In order to demonstrate the effect of depletion force, we selected and experimented with a system based on a polyolefin isotactic poly(4-methyl-1-pentene) (P4MP1) film and a normal alkane mixture and realized high molecular selectivity. The P4MP1 film we used can be prepared simply by evaporating the solvent from the solution and casting the film. On the basis of the Asakura-Oosawa theory, we concluded that spontaneous and high molecular selectivity is attributed to the depletion force provided by the small sub-nanopores with uniform size in the film..
5. Ayumi Suematsu, Takuto Sawayama, and Ryo Akiyama, Effective potential between negatively charged patches on acidic proteins immersed in various electrolyte solutions, The Journal of Chemical Physics, doi: 10.1063/1.5038912, 149, 074105-1-8, 2018.08, Effective interactions between O-sized anions in various electrolyte solutions were calculated by using
the integral equation theory with some simple models. The results indicated that only multivalent
cations mediated a strong effective attraction between O-sized anions at a certain concentration. The
effective interaction turned from repulsive to attractive as the electrolyte concentration increased,
and the effective attraction decreased when more electrolyte was added. Moreover, the effective interactions between O-sized anions in the electrolyte solution did not present a long repulsive tail, although the effective attraction caused by the divalent cations appeared. By contrast, the effective attraction mediated by monovalent cations and the reentrant behavior did not appear and the effective interaction was basically repulsive. These behaviors agree with the experimental results for reentrant condensation of acidic proteins in various electrolyte solutions. The calculated results suggest that the dissociated carboxylic acidic groups on the proteins form attractive patches between proteins under certain concentration conditions..
6. 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.
7. 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.
8. 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].
9. 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].
10. 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].
11. 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.
12. 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.
13. 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.
14. Ryo Akiyama and Roger F. Loring, Vibrational Echoes for Classical and Quantum Solutes,, J. Chem. Phys., Vol. 116, p.4655(2002)., 2002.01.
15. 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.
16. 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.
17. 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.
18. 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. Ayano Chiba, Akio Oshima, Kenzaburo Okubo, and Ryo Akiyama, Separation of inert solvent mixtures accentuated by confined spaces, 6th Japan-Korea International Symposium on Material Science and Technology 2019 (JKMST2019), 2019.08.
2. Ryo Akiyama, Asakura-Oosawa theory: On the Origin of Excluded Volume Effects in a Crowding Media and the Progress, the 5th International Conference on Molecular Simulation (ICMS2019), 2019.11.
3. Ryo Akiyama, Statistical Mechanics Study of Separation of Inert Solvent Mixtures by a Porous Material, The 2nd International Conference on Material Research and Innovation (ICMARI 2019), 2019.12.
4. 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.
5. 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.
6. 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.
7. 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.
8. 秋山 良, Hydration dynamics and dielectric relaxation of water around an ion, Symposium on Hydrationand ATP Energy 2013, 2013.03.
9. 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.
10. Attractive interaction between like-charged macromolecules in an electrolyte solution and motion of amoeba, [URL].
11. Interaction between protein and biomolecule arising from translational motion of water molecules and thermodynamic quantities.
12. Effective interaction between like-charged colloidal particles in electrolyte solution: Attractive component arising from solvent granularity, [URL].
13. , [URL].
14. , [URL].
15. Crowding Problems in Cytoplasm and Interaction Arising from Translational Motion of Solvent Molecules, [URL].
16. 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.
Social
Professional and Outreach Activities
Presenter for general science such as Science Cafe..