Kobe University

Graduate School of System Informatics

Department of Computational Science

1-1, Rokkodai, Nada, Kobe 657-8501, Japan

TEL: +81-78-803-6620

FAX: +81-78-803-6620

E-MAIL: tanaka2[at]kobe-u.ac.jp

We are developing computational methodologies for ab initio calculations of biomolecular systems on the basis of fragment molecular orbital (FMO) method. The FMO method currently provides a state-of-the-art tool for the electronic structure calculations of proteins and nucleic acids, and has enabled us to perform a variety of first-principles biomolecular simulations. Examples for target systems include nuclear receptors, influenza viral proteins, SARS-CoV-2 viral proteins, bioluminescent proteins, and DNA-protein complexes.

[Selected Publications]

・K. Fukuzawa, Y. Komeiji, Y. Mochizuki, T. Nakano, and S. Tanaka,
“Intra- and Inter-Molecular Interactions between Cyclic-AMP Receptor
Protein and DNA: Ab Initio Fragment Molecular Orbital Study”, J. Comput.
Chem. 27 (2006) pp. 948-960.

・M. Ito, K. Fukuzawa, Y. Mochizuki, T.
Nakano, and S. Tanaka, “Ab Initio Fragment Molecular Orbital Study of
Molecular Interactions between Liganded Retinoid X Receptor and Its
Coactivator. Part II: Influence of Mutations in Transcriptional
Activation Function 2 Activating Domain Core on the Molecular
Interactions”, J. Phys. Chem. A 112 (2008) pp. 1986-1998.

・A. Tagami,
N. Ishibashi, D. Kato, N. Taguchi, Y. Mochizuki, H. Watanabe, M. Ito,
and S. Tanaka, “Ab Initio Quantum-Chemical Study on Emission Spectra of
Bioluminescent Luciferases by Fragment Molecular Orbital Method”, Chem.
Phys. Lett. 472 (2009) pp. 118-123.

・T. Iwata, K. Fukuzawa, K.
Nakajima, S. Aida-Hyugaji, Y. Mochizuki, H. Watanabe, and S. Tanaka,
“Theoretical Analysis of Binding Specificity of Influenza Viral
Hemagglutinin to Avian and Human Receptors Based on the Fragment
Molecular Orbital Method”, Comput. Biol. Chem. 32 (2008) pp. 198-211.

・K.
Takematsu, K. Fukuzawa, K. Omagari, S. Nakajima, K. Nakajima, Y.
Mochizuki, T. Nakano, H. Watanabe, and S. Tanaka, “Possibility of
Mutation Prediction of Influenza Hemagglutinin by Combination of
Hemadsorption Experiment and Quantum Chemical Calculation for Antibody
Binding”, J. Phys. Chem. B 113 (2009) pp. 4991-4994.

・A. Yoshioka, K.
Fukuzawa, Y. Mochizuki, K. Yamashita, T. Nakano, Y. Okiyama, E.
Nobusawa, K. Nakajima, and S. Tanaka, “Prediction of Probable Mutations
in Influenza Virus Hemagglutinin Protein Based on Large-Scale Ab Initio
Fragment Molecular Orbital Calculations”, J. Mol. Graph. Model. 30
(2011) pp. 110-119.

・S. Tanaka, Y. Mochizuki, Y. Komeiji, Y. Okiyama,
and K. Fukuzawa, “Electron-Correlated Fragment-Molecular-Orbital
Calculations for Biomolecular and Nano Systems”, Phys. Chem. Chem. Phys.
16 (2014) pp. 10310-10344.

・R. Hatada, K. Okuwaki, Y. Mochizuki, Y. Handa,
K. Fukuzawa, Y. Komeiji, Y. Okiyama, and S. Tanaka, “Fragment Molecular Orbital
Based Interaction Analyses on COVID-19 Main Protease - Inhibitor N3 Complex
(PDB ID: 6LU7)”. J. Chem. Inf. Model. 60 (2020) pp. 3593-3602.

・K. Fukuzawa and S. Tanaka, “Fragment Molecular Orbital Calculations for
Biomolecules”, Curr. Opin. Struct. Biol. 72 (2022) pp. 127-134.

Structure-based simulation is a promising approach to rational drug design. We have developed a variety of multi-scale computational schemes on the basis of fragment molecular orbital, molecular dynamics, and coarse-grained methods.

[Selected Publications]

・Y. Okiyama, H. Watanabe, K. Fukuzawa, T. Nakano, Y. Mochizuki, T. Ishikawa,
K. Ebina, and S. Tanaka, “Application of the Fragment Molecular Orbital
Method for Determination of Atomic Charges on Polypeptides. II. Toward
an Improvement of Force Fields Used for Classical Molecular Dynamics
Simulations”, Chem. Phys. Lett. 467 (2009) pp. 417-423.

・C. Watanabe,
H. Watanabe, and S. Tanaka, “An Interpretation of Positional
Displacement of the Helix12 in Nuclear Receptors: Preexistent Swing-up
Motion Triggered by Ligand Binding”, Biochim. Biophys. Acta 1804 (2010)
pp. 1832-1840.

・T. Nakano, Y. Mochizuki, K. Yamashita, C. Watanabe, K. Fukuzawa, K.
Segawa, Y. Okiyama, T. Tsukamoto, and S. Tanaka, “Development of the
Four-Body Corrected Fragment Molecular Orbital (FMO4) Method”, Chem.
Phys. Lett. 523 (2012) pp. 128-133.

・C. Watanabe, K. Fukuzawa, Y.
Okiyama, T. Tsukamoto, A. Kato, S. Tanaka, Y. Mochizuki, and T. Nakano,
“Three- and Four-Body Corrected Fragment Molecular Orbital Calculations
with a Novel Subdividing Fragmentation Method Applicable to
Structure-Based Drug Design”, J. Mol. Graph. Model. 41 (2013) pp. 31-42.

・S. Uehara and S. Tanaka, “AutoDock-GIST: Incorporating Thermodynamics of
Active-Site Water into Scoring Function for Accurate Protein-Ligand Docking”,
Molecules 21 (2016) 1604.

・S. Uehara and S. Tanaka, “Cosolvent-Based Molecular
Dynamics for Ensemble Docking: Practical Method for Generating Druggable Protein
Conformations”, J. Chem. Inf. Model. 57 (2017) pp. 742-756.

・Y. Okiyama, T. Nakano,
C. Watanabe, K. Fukuzawa, Y. Mochizuki, and S. Tanaka, “Fragment Molecular Orbital
Calculations with Implicit Solvent Based on the Poisson–Boltzmann Equation: Implementation
and DNA Study”, J. Phys. Chem. B 122 (2018) pp. 4457-4471.

・Y. Okiyama, C. Watanabe,
K. Fukuzawa, Y. Mochizuki, T. Nakano, and S. Tanaka, “Fragment Molecular Orbital Calculations
with Implicit Solvent Based on the Poisson–Boltzmann Equation: II. Protein and Its
Ligand-Binding System Studies”, J. Phys. Chem. B 123 (2019) pp 957-973.

・S. Nakata,
Y. Mori, and S. Tanaka, “End-to-End Protein-Ligand Complex Structure Generation with
Diffusion-Based Generative Models”, BMC Bioinformatics 24 (2023) 233.

Protein systems contain a variety of interesting dynamical behaviors intimately associated with their functions. Some of them play essential roles for high-efficiency energy conversions or signal transductions in bio-systems. We have developed analytical and computational tools for describing protein dynamics such as vibrational energy transfer, excitation energy transfer and charge transfer.

[Selected Publications]

・S. Tanaka, “Renormalization-Group Inspired Approach to Vibrational
Energy Transfer in Protein”, J. Phys. Soc. Jpn. 81 (2012) 033801.

・S.
Tanaka, “Modulation of Excitation Energy Transfer by Conformational
Oscillations in Biomolecular Systems”, Chem. Phys. Lett. 508 (2011) pp.
139-143.

・Y. Suzuki and S. Tanaka, “Excitation Energy Transfer
Modulated by Oscillating Electronic Coupling of a Dimeric System
Embedded in a Molecular Environment”, Phys. Rev. E 86 (2012) 021914.

・S.
Tanaka and E.B. Starikov, “Analysis of Electron-Transfer Rate Constant
in Condensed Media with Inclusion of Inelastic Tunneling and Nuclear
Quantum Effects”, Phys. Rev. E 81 (2010) 027101.

・T. Matsuoka, S.
Tanaka, and K. Ebina, “Hierarchical Coarse-Graining Model for
Photosystem II Including Electron and Excitation-Energy Transfer
Processes”, BioSystems 117 (2014) pp. 15-29.

・Y. Suzuki, K. Ebina,
and S. Tanaka, “Four-Electron Model for Singlet and Triplet Excitation Energy
Transfers with Inclusion of Coherence Memory, Inelastic Tunneling and Nuclear
Quantum Effects”, Chem. Phys. 474 (2016) pp. 18-24.

We have developed a theoretical method to describe correlational properties of liquid water on the basis of integral equation approach in which triplet correlations and associated bridge functions are taken into account in the framework of density functional theory.

[Selected Publications]

・S. Tanaka and M. Nakano, “Triplet Correlations and Bridge Functions
in Classical Density Functional Theory for Liquid Water”, Chem. Phys.
Lett. 572 (2013) pp. 38-43.

・S. Tanaka and M. Nakano, “Classical
Density Functional Calculation of Radial Distribution Functions of
Liquid Water”, Chem. Phys. 430 (2014) pp. 18-22.

We have developed novel methods for quantum Monte Carlo (QMC) calculations for molecular and condensed-matter systems. Variational and path-integral QMC methods have been implemented and applied to water molecule, NiO, and small peptides.

[Selected Publications]

・S. Tanaka, S.M. Rothstein, and W.A. Lester, Jr., ed., “Advances in
Quantum Monte Carlo” (ACS Symposium Series 1094, American Chemical
Society, Washington, DC, 2012).

・W.A. Lester, Jr., S.M. Rothstein,
and S. Tanaka, ed., “Recent Advances in Quantum Monte Carlo Methods ,
Part II” (World Scientific, Singapore, 2002).

・S. Tanaka, “Cohesive Energy of NiO: A Quantum Monte Carlo Approach”, J. Phys. Soc. Jpn. 62, No. 6 (1993) pp. 2112-2119.

・S.
Tanaka, “Variational Quantum Monte Carlo Approach to the Electronic
Structure of NiO”, J. Phys. Soc. Jpn. 64, No. 11 (1995) pp. 4270-4277.

・S. Tanaka, “Structural Optimization in Variational Quantum Monte Carlo”, J. Chem. Phys. 100, No. 10 (1994) pp. 7416-7420.

・R.
Maezono, H. Watanabe, S. Tanaka, M.D. Towler, and R.J. Needs,
“Fragmentation Method Combined with Quantum Monte Carlo Calculations”,
J. Phys. Soc. Jpn. 76, No.6 (2007) 064301.

・T. Fujita, S. Tanaka, T.
Fujiwara, M. Kusa, Y. Mochizuki, and M. Shiga, “Ab Initio Path Integral
Monte Carlo Simulations for Water Trimer with Electron Correlation
Effects”, Comput. Theor. Chem. 997 (2012) pp. 7-13.

・S. Tanaka, “Variational Quantum Monte Carlo with Inclusion of Orbital Correlations”, J. Phys. Soc. Jpn. 82, No.7 (2013) 075001.

One of my longstanding interests is laid on quantum many-body problems. Examples include the theoretical analyses of correlational, thermodynamic and transport properties of electron liquids and hydrogen plasmas over wide ranges of density and temperature. I have also calculated the multiparticle distribution functions for ideal Fermi gas system in the ground state for any spatial dimension. The N-particle distribution function is expressed in terms of a determinant form in which a correlation kernel plays a vital role. The expression obtained for the one-dimensional Fermi gas is essentially equivalent to that known for the distribution of the eigenvalues of random unitary matrices, which, in turn, has a mathematical structure analogous to the distribution of non-trivial zeros of the Riemann zeta function.

[Selected Publications]

・S. Tanaka and S. Ichimaru, “Thermodynamics and Correlational Properties
of Finite-Temperature Electron Liquids in the Singwi-Tosi-Land-Sjolander Approximation”,
J. Phys. Soc. Jpn. 55, No. 7 (1986) pp. 2278-2289.

・S. Ichimaru, H. Iyetomi, and
S. Tanaka, “Statistical Physics of Dense Plasmas: Thermodynamics, Transport Coefficients
and Dynamic Correlations”, Phys. Rep. 149, Nos. 2-3 (1987) pp. 91-205.

・S. Tanaka
and S. Ichimaru, “Spin-Dependent Correlations and
Thermodynamic Functions for Electron Liquids at Arbitrary Degeneracy and Spin
Polarization”, Phys. Rev. B39 (1989) pp. 1036-1051.

・S. Tanaka,
X.-Z. Yan, and S. Ichimaru, “Equation of State and Conductivities of
Dense Hydrogen Plasmas near the Metal-Insulator Transition”, Phys. Rev.
A41 (1990) pp. 5616-5625.

・S. Tanaka, “Multiparticle Distributions of
Ideal Fermi Gas: Analogy to Random Matrices and the Riemann Zeros”, J.
Phys. Soc. Jpn. 80 (2011) 034001.

・S. Tanaka, “Correlational and Thermodynamic
Properties of Finite-Temperature Electron Liquids in the Hypernetted-Chain Approximation”,
J. Chem. Phys. 145 (2016) 214104.