Miyabi Hiyama

Akiyama Group, The Institute for Solid Stae Physics, The University of Tokyo

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Profile

Research Interest:: Theoretical Chemistry, Computational Chemistry, Biochemistry, Atomic and Molecular Physics

Education

1993-1996 :: Ph.D The Graduate University for Advances Studies, Japan
Thesis Title: Characteristics and dynamics of superexcited states of diatomic molecules
1991-1993 :: MA in Science , Keio University, Japan
Thesis Title: Theoretical Assignment of the Correlation bands observed in the near- threshold photoelectron spectra of N2, CO and HCl
1987-1991 :: BA in Science, Keio University, Japan
Thesis Title: The excimer emission spectra and the interaction potential energy of the ground and excited states of He and alkali metal systems

Employment History

2013- :: Project Researcher of The Institute for Solid State Physics, The University of Tokyo, Japan
: Part-time Lecturer of Nihon University, Japan
2012- :: Part-time Lecturer of The University of Electro-Communications, Japan
2012-2013:: Researcher of Nagoya University, Japan
2011-2013:: Part-time Lecturer of Chukyo University, Japan
2010-2013:: Part-time Lecturer of Nagoya University of Commerce and Business, Japan
2010-2012:: Technical assistant of Nagoya University, Japan
2010-2011:: Researcher of Nagoya Institute of Technology, Japan
Joint researcher of Nagoya University, Japan
2006-2010:: Joint researcher of Toyota Central R&D Labs., Inc., Japan
2004-2006:: Research associate of Institute for Molecular Science, Japan
2001-2004:: Research Fellow for Young Scientists (PD) of Japan Society for the Promotion of Science, The university of Tokyo, Japan
1999-2001:: Researcher of University of Oxford, UK
1996-1999:: Post doctoral Fellow of Japan Science and Technology Corporation, The University of Tokyo, Japan
1993-1996:: Research Fellow for Young Scientists (DC1) of Japan Society for the Promotion of Science, Institute for Molecular Science, Japan

Association and Memberships (Committee Work)

The Chemical Society of Japan
The Physical Society of Japan
The Society for Atomic Collision Research
The Society for Theoretical Chemistry
Japan Society for Molecular Science
Institute for Quantum Chemical Exploration

Award

2005 Incentive award for young scientist of The Society for Atomic Collision Research,
"Elucidation of mechanism for core excitation of molecules by R matrix / MQDT method"
2014 JPSJ Papers of Editors' Choice
" Fluctuation Local Recrystallization of Quati-Luquid Layer of Sub-micrometer- scaled Ice: A Molecular Dynamics Study" Y. Kajima, S. Ogata, R. Kobayashi, M. Hiyama, T. Tamura

Research Activity

Member of Steering Committee of field of Physics, The Physical Society of Japan, 2005~2006
Committee Member, The Society for Atomic Collision Research, 2006~2008
Member of selection committee for Poster Award, Annual Meeting of Japan Society for Molecular Science 2009

Productivity

Publications

Peer-Reviewed Journals

M. Hiyama, Y. Noguchi, H. Akiyama, K. Yamada, N. Koga: Vibronic structures in absorption and fluorescence spectra of firefly oxyluciferin in aqueous solutions Photochem. Photobiol., 91, 819-827 (2015)
Y. Noguchi, M. Hiyama, H. Akiyama, Y. Harada, N. Koga: First-Principles Investigation of Strong Excitonic Effects in Oxygen 1s X-Ray Absorption Spectra J. Chem. Theo. Compt. 11, 1668-1673 (2015)
M. Hiyama, T. Mochizuki, H. Akiyama, N. Koga: Theoretical Study of Oxyluciferin Photoluminescence Pathways in Aqueous Solutions. Photochem. Photobiol., in press
Y. Noguchi, M. Hiyama, H. Akiyama, N. Koga: First-Principles Investigation on Rydberg excitations of Firefly Lu- ciferin Anion in Vacuum. J. Chem. Phys. 141, 044309 (2014)
T. Mochizuki, Y. Wang, M. Hiyama, H. Akiyama: Temperature-Sensitive Quantum Yields and Quantitative Spectra of Firefly Bioluminescence. Appl. Phys. Lett. 104, 213704 (2014)
M. Hiyama, H. Akiyama, T. Mochizuki, K. Yamada, N. Koga: Analysis of Photoexcitation Energy Dependence in the Photo Luminescence of Firefly Luciferin. Photochem. Photobiol.,90, 820-828 (2014)
M. Hiyama, H. Akiyama, K. Yamada, N. Koga: Theoretical Study of Fluorescence Spectra Utilizing the pKa Values of Acids in Their Excited States. Photochem. Photobiol., 90,35-44 (2014)
M. Hiyama, K. Yamada, T. Mochizuki, H. Akiyama, N. Koga: Theoretical study of pH dependence on photoluminescence of firefly luciferin. Luminescence 29, 70 (2014)
H. Akiyama, Y. Wang, M. Hiyama, T. Mochizuki, K. Terakado, T. Nakatsu: How can quantitative bioluminescence and in-situ fluorescence of firefly oxyluciferin in luciferase be compared with theoretical calculations? Luminescence 29, 7 - 8 (2014)
Y. Noguchi, M. Hiyama, H. Akiyama, K. Koga: First-Principles Investigation on Optical Properties of Firefly Luciferin Anion. Luminescence 29, 86 - 87 (2014)
Y. Kajima, S. Ogata, R. Kobayashi, M. Hiyama, T. Tamura, Fluctuation Local Recrystallization of Quati-Luquid Layer of Sub-micrometer- scaled Ice: A Molecular Dynamics Study. J. Phys. Soc. Japan, 83, 083601-1 - 083601-4 (2014)
M. Hiyama, H. Akiyama, Y. Wang, N. Koga: Theoretical Study of Oxyuciferin pKa Values; Relative Absorption Intensity in Aqueous Solutions. Chem. Phys. Lett., 577, 121-126 (2013)
M. Hiyama, H. Akiyama, K. Yamada, N. Koga: Theoretical Study of Firefly Luciferin pKa Values ż Relative Absorption Intensity in Aqueous Solutions. Photochem. Photobiol., 89, 571-578 (2013)
Y. Kajima, M. Hiyama, S. Ogata, T. Tamura, R. Kobayashi: Fast Time-Reversible Molecular Dynamics Algorithm for Rigid-Body Systems. J. Chem. Phys. 136, 234105-1-234105-8 (2012)
M. Hiyama, H. Akiyama, K. Yamada, N. Koga: Theoretical Study of Absorption and Fluorescence Spectra of Firefly Luciferin. Photochem. Photobiol., 88, 889-898 (2012)
M. Hiyama, N. Koga: Theoretical study of electron transfer in Rhodobacter sphaeroides reaction center. Photochem. Photobiol., 87, 1297-1307 (2011)
Y. Kajima, M. Hiyama, S. Ogata, T. Tamura: Exactly Time-Reversible Molecular Dynamics Algorithm for Rigid-Body Systems, J. Phys. Soc. Japan, 80, 114002-1 - 114002-7 (2011)
M. Hiyama, T. Kinjo, S-A. Hyodo: Angular Momentum Form of Verlet Algorithm for Rigid Molecules, J. Phys Soc. Japan, 77, 064001-1 - 064001-12 (2008)
M. S. Child, M. Hiyama: On the Choice of basis functions to eliminate false roots of the quantization condition in quantum defect theory, J. Phys., B40, 1233-1244 (2007)
M. Hiyama, N. Kosugi: Application of R matrix / MQDT method to valence and core excitations in NO, J. Phys. B39, 1797-1811 (2006)
M. Hiyama, N. Kosugi: Ab initio R-Matrix/Multi-channel quantum defect theory applied to molecular core excitation and ionization, J. Electron Spectroscopy and Related Phenomena, 144-147, 1223-1226 (2005)
S. Masuda, T. Gejo, M. Hiyama, N. Kosugi: Vibronic couplings in the C 1s-Rydberg and valence excitations of C2H2, revealed by angle-resolved photoion yield spectroscopy, J. Electron Spectroscopy and Related Phenomena, 144-147, 215-218 (2005)
M. Hiyama, N. Kosugi: Ab initio R-Matrix/Multi-channel Quantum Defect Theory Approach to Study Molecular Core Excitation and Ionization: GSCF4R, J. Theoretical and Computational Chemistry, 4, 35-47 (2005)
M. Hiyama, N. Kosugi: Ab initio R-Matrix/MQDT method for near-edge x-ray absorption fine structure, Physica. Scripta, T115, 136-139 (2005)
M. Hiyama, M. S. Child: Ab initio R-matrix/ MQDT study of nitric oxide II. Analysis of valence/ Rydberg interactions, J. Phys., B36 4547-4559 (2003)
M. Hiyama, K. Someda: Photoelectron spectra in intense laser fields: The effect of resonance with autoionizing Rydberg states, Physical Review, A68, 043402-1 ? 043402-8 (2003)
M. Hiyama, M. S. Child: Ab initio R-matrix/ multichannel quantum defect theory study of nitric oxide, J. Phys. B35, 1337-1351 (2002)
M. Hiyama, M. S. Child: Computation of negative energy Coulomb functions, J. Phys., B34, 3935-3950 (2001)
M. Hiyama, K. Someda: Stabilization of diatomic molecules against ionization in intense laser fields: Effects of overlapping resonance, Physical Review, A61, 023411-1-023411-8 (2000)
M. Hiyama, K. Someda: Ionization of atoms in intense laser fields. Strong mixing of auto- and photoionizations, Chem. Phys. Lett., 287, 613-619 (1998)
M. Hiyama, N. Kosugi, H. Nakamura: Characteristics and dynamics of superexcited states of diatomic molecules: General theoretical procedure, J. Chem. Phys. 107,9379-9381 (1997)
M. Hiyama, H. Nakamura: Two-center Coulomb functions, Comp. Phys. Comm., 103, 209 - 216 (1997)
M. Hiyama, H. Nakamura: Gaussian expansions of the two-center Coulomb functions, Comp. Phys. Comm., 103, 197-208 (1997)
M. Hiyama, H. Nakamura: Superexcited states of CO near the first ionization threshold, Chem. Phys. Lett., 248, 316-320 (1996)
M. Hiyama, S. Iwata: Theoretical assignment of the vibronic bands in the photoelectron spectra of N2 below 30 eV, Chem. Phys. Lett., 211, 319-327 (1993)
M. Hiyama, S. Iwata: Assignment of the photoelectron spectrum of HCl above 20 eV, Chem. Phys. Lett., 210, 187-192 (1993)
M. Hiyama, S. Nanbu, S. Iwata: The excimer emission spectra and the interaction potential energy of the ground and excited states of He and alkali metal systems, Chem. Phys. Lett. 192, 443-450 (1992)

Review

L. Pichl, M. Hiyama, H. Nakamura: Analytical Treatment of the K matrix Integral Equation in the Dynamics of Superexcited Molecules, Dissociative Recombination of Molecular Ions with Electrons, (edited by S. L. Guberman, Kluwer Academic/Plenum Publishers) 167-176 (2003)
M. Hiyama, H. Nakamura: Characteristics and Dynamics of Superexcited States of Diatomic Molecules, Structure and Dynamics of Electronic Excited States, (edited by J. Laane, H. Takahashi, A. Bandrauk, Springer-Verlag) 296-317 (1998)
M. Hiyama, H. Nakamura: Characteristics and Dynamics of Superexcited States of CO, Dissociative Recombination: Theory, Experiment and Applications III, (edited by D. Zaifman, J. B. A. Mitchell, D. Schwalm, and B. R. Rowe, World Scientific), 212-215 (1995)

Invited talk

M. Hiyama, Y. Noguchi, T. Michizuki, K. Yamada, H. Akiyama, N. Koga: Theoretical study for photoluminescence of firefly-bioluminescence-related molecules Luciferin/Luciferase Engineering (# 410), THE INTERNATIONAL CHEMICAL CONGRESS OF PACIFIC BASIN SOCIETIES (Pacifichem 2015) Honolulu, Hawaii, USA, (2015.12.16)
H. Akiyama, M. Hiyama, T. Mochizuki, Y. Wang, Y. Ando: Quantitative Measurements, In-situ Spectroscopy, and Quantum-Chemistry Theoretical Studies on Firefly Bioluminescence.
M. Hiyama, K. Yamada, T. Mochizuki, H. Akiyama, N. Koga: Theoretical study for excited states of firefly-bioluminescence-related molecules 5th JCS International Symposium on Theoretical Chemistry, Todai-ji Culture Center, Nara, Japan, (2013.12.4)
Y. Wang, Y. Ando, T. Mochizuki, M. Hiyama, H. Akiyama: In-situ and Quantitative Spectroscopy of Firefly Bioluminescence, 18th International Conference on Dynamical Processes in Excited States of Solids (DPC'13), Fuzhou, China, (2013.8.7)
Y. Ando, Y. Wang, Y. Hayamizu, M. Hiyama, H. Kubota, N. Koga, H. Akiyama: What should we learn about concerning the color change of firefly bioluminescence? The 49st Annual Meeting of the Biophysical Society of Japan, Hyogo Univ., Japan, (2011.9.17)
M. Hiyama: R matrix/MQDT study for diatomic molecules, International Symposium on Spectroscopy, Reaction Dynamics and Manipulation of Atoms and Molecules, Tohoku Univ., Japan, (2007.2.27)
M. Hiyama: Calculation for cross section of photoionization in molecules, Core University Program Workshop on Atomic and Molecular Databases, National Institute for Fusion Science,Japan (2006.2.17)
M. Hiyama: Application of ab initio R matrix /Multi-channel quantum defect theory: valence and core excitations in NO molecule, IWP2005, Brazil (2005.7.29)
M. Hiyama, M. S. Child: An ab initio R-matrix/MQDT Study of Nitric Oxide, Sixth International Conference on Dissociative Recombination: Theory, Experiments and Applications, MosBach, Germany (2004.6.12)
M. Hiyama, H. Nakamura: Characteristics and Dynamics of Superexcited States of Diatomic Molecules, Dissociative Recombination: Theory, Experiment and Application, Weizmann Inst. Sci. Ein Gedi, Israel (1995.5.29)

Research Grant/Subsidy

1993-1996: Research Fellowship for Young Scientists(DC1) Grants-Aid for Scientific Research of JSPS
2001-2003: Research Fellowship for Young Scientists(PD) Grants-Aid for Scientific Research of JSPS
2006: Institute for Molecular Science
2004-2005: JST, Study of Spin-forbidden Ionization and Excitation via Inner-shell Excitation (Prof. Kosugi)
2014-2016: Institute for Quantum Chemical Exploration Grant
2015-2017: Grant-in-Aid for Scientific Research (C) of JSPS

Review of research

1990 - 1993 : Excited states of diatomic molecules

I studied the excimer emission spectra and the interaction potential energy of the ground and excited states of He and alkali, metal ion systems for graduation thesis. The rare gas-alkali molecular ions, HeLi+, HeNa+ and HeK+, are investigated with the ab initio MO CI method. The simulated theoretical emission spectra from the first excited state of these molecules were in good agreement with experimental spectra. Because a competitive pathway is found in the excited singlet state of HeK+, HeNa+ is the rare-gas-alkali-metal diatomic ion which shows the shortest wavelength emission among these possible candidates for VUV lasing systems. After that I studied theoretical assignment of the vibronic bands in the photoelectron spectra of N2, HCl, and CO below 30 eV for master thesis. The high-resolution photoelectron spectra of N2, HCl and CO up to 30 eV are analyzed with ab initio MO CI calculations. I was able to identify the vibrational quantum numbers of the spectra in the bands between 23 and 30 eV. From this, I discovered that previously unknown excited state had been hidden within the N2 photoelectron spectra. These days, these data are used to assign synchrotron radiation photoionization spectra.

1993 - 2006 : Super excited states of molecules

The super excited state is defined as the neutral molecule excited state of which energy is higher than the ionization threshold. There are two kinds of super exited state: one is the electronic excited state of neutral molecule and the other is vibrational excited state of Rydberg state.

Autoionization

I investigated the characteristics and dynamics of superexcited states of diatomic molecules using original general theoretical procedure for doctor thesis. I also studied the photoelectron spectra of atoms and molecules with an autoionizing state in intense laser fields. Strong mixing of auto- and photoionizations. Photoelectron spectra of an atom with an autoionizing state in intense laser fields are investigated theoretically. In intense fields, photoelectron spectra are found to have a profile totally different from that in weak fields. A 'phase transition' is found to take place at critical laser intensity and the spectral profile changes drastically at this critical point. This phenomenon originates from mixing of auto- and photoionizations in intense laser fields.

R matrix / multichannel quantum defect theory (R-matrix/MQDT)

To obtain the potential energy curves of both Rydberg and valence excited states, I have made the R-matrix/ multichannel quantum defect theory (R-matrix/MQDT) method by a combination of ab initio and multichannel quantum defect theories. I have shown that this method is used to calculate resonant changes in the MQDT scattering matrix arising from valence state interactions with the Rydberg channels of nitrogen monoxide. The resonant couplings between the Rydberg channels and four valence states are shown to vary sufficiently smoothly with both bond length and energy to allow easy interpolation. I have extended the range of application of R-matrix/MQDT, and this method cab be used to analyze core excitation spectra. Both valence and core excitations of the NO molecule were studied using the R matrix/ MQDT method. If we use the standard ab initio program code and R matrix/MQDT method, we can obtain not only the valence excited states but also core excited states of molecules and analyze the experimental spectra.

2006-2014 : Molecular Dynamics Simulations for Rigid-Body Systems

For dynamics simulation including enough water molecules in biological systems, an approximation for water molecules will be needed. Although some water molecules in biological systems play important roles in the reactions, the others work as a filed. The latter kind water molecules can be approximate as rigid molecules.

Angular Momentum Verlet (AMV) algorithm

A new simple algorithm named 'the angular momentum Verlet (AMV) algorithm ' was presented for solving the equations of motion for rigid molecules. For obtaining a high accuracy in molecular dynamics simulations, the scaling method with the constraint by Lagrange's method of undetermined multipliers was introduced in this algorithm.

Fast Time-Reversible Molecular Dynamics Algorithm (FT)

In association with AMV algorithm, a new algorithm for molecular dynamic simulation for rigid molecules was made with Prof. Kajima and Prof. Ogata's gourp in Nagoya Institute of Technology. We developed a remarkable algorithm in the molecular dynamics to numerically enforce the complete time-reversal symmetry

2010 - : Mechanisms of Photochemistry in Biomolecules

To elucidate the mechanism of photochemistry in biomolecules theoretically, we need the information about the electronic states of biomolecules, the nuclear dynamics of them, and the effects from the environment around them. I pay attention to the electron transition in the photochemistry of photosynthesis and bioluminescences. These processes are considered as essential processes in each biological system.

Electron Transfer in Photochemical Reaction Center of Bacterial Photosystems

Photosynthesis is a biochemical reaction that transforms solar energy into chemical energy. The essence of light-dependent reactions in the early stages of photo- synthesis is the transformation of the absorbed excitation energy into the electron transfer energy. There are two light-dependent reaction systems in plants and algae, photosystem I (PSI) and photosystem II (PSII). Bacterial photosystems are suitable for investigating the electron transfer in these reaction centers because they are categorized as either PSI or PSII. A typical example for PSI systems is the reaction center of purple bacteria. I investigated that the electron transfer in the reaction centers of purple bacteria using ab initio method with Prof. Koga of Nagoya University. We found that the presence of the longest substitution on porphyrin rings play rules of promoting the electron transition in the reaction center of purple bacteria.

Emission Color in Firefly Bioluminescence

To understand the mechanism of firefly bioluminescence, the spectroscopic property has been paid attention to and investigated over the past few decades. In the firefly bioluminescence, not only its substrate and emitter but also the effects from proteins may decide the emission color. However, the spectroscopic characteristics of firefly luciferin (luciferin here after) and oxyluciferin, which are substrate and emitter of firefly bioluminesccence, were unclear.

Firefly Luciferin

To understand the mechanism of firefly bioluminescence, the spectroscopic property has been paid attention to Because of unstable of oxyluciferin in aqueous solutions, its experimental spectra were quite few. On the other hand, there are many experimental data for luciferin in aqueous solutions. Therefore, first of all we paid attention to the spectroscopic characteristics of luciferin. We studied the photoluminescence of luciferin and clarified its ground and excited states with the quantum chemical calculations. These results are in good agreement with its experimental spectra. We found that the main peak position in photoluminescence spectra was changed with the pH value of its solution because the kinds of most abundant chemical species were changed. Recently, the photo absorption spectra of lucifein in gas phase were reported. Then, we analyzed these photo absorption spectra of luciferin in gas phase using the first-principles GW+Bethe-Salpeter method made by Dr. Noguchi of ISSP and compared with the results obtained using a recent experiment in vacuum. This method well reproduces the line shape at the photon energy corresponding to the Rydberg and resonance excitations.

Firefly Oxyluciferin

Next, we studied the theoretical absorption spectra of oxyluciferin using similar methods for luciferin. The absorption spectra and photoluminescence pathway of oxylucifein in aqueous solutions were estimated. We also determined the full width at half maximum of absorption and emission spectra from vibrational analysis. The pH dependence of theoretical molar concentration is in good agreement with experimental one. We elucidated the photoluminescence process for green emissions above and below pH 8, the photoluminescence process for blue emission, and the photoluminescence process for red emission in strong acidic conditions.

2014 - : Core Absorption Spectra

Recent developments in experimental techniques enable us to obtain sufficiently accurate X-ray absorption spectra (XAS) and discuss the electronic and atomic properties of a wide range of materials under various experimental conditions. The oxygen 1s XAS of acetone and acetic acid molecules in vacuum were calculated by utilizing the first-principles GW+Bethe-Salpeter method with an all-electron mixed basis. The theoretical excitation energies show good agreement with the available experimental data without an artificial shift. Our method reproduces the first and second isolated peaks and broad peaks at higher photon energies, corresponding to Rydberg excitations.