@LIST OF PUBLICATIONS@
- Aoi Taira, Ryuichi Okamoto, Tomonari Sumi, Kenichiro Koga, Takeshi Morita, Hiroshi Imamura,
"Solvation free energies of alcohols in water: temperature and pressure dependences" Physical Chemistry Chemical Physics 25, 31107–31117 (2023).
- Noa Nakata, Ryuichi Okamoto, Tomonari Sumi, Kenichiro Koga, Takeshi Morita, Hiroshi Imamura,
"Molecular mechanism of the common and opposing co-solvent effects of
fluorinated alcohol and urea on a coiled coil protein" Protein Science 32, e4763-1–e4763-15 (2023).
- Hidefumi Naito, Tomonari Sumi,
Kenichiro Koga, "How do water-mediated interactions and osmotic second
virial coefficients vary with particle size?" Faraday Discussions (2023) DOI:10.1039/D3FD00104K.
- Tomonari Sumi,
Kouji Harada,
"Muscarinic acetylcholine receptor-dependent and NMDA
receptor-dependent LTP and LTD share the common AMPAR trafficking
pathway" iScience 26, 106133-1–106133-23 (2023).
- Tomonari Sumi, Kouji Harada,
"Immune response to SARS-CoV-2 in severe disease and long COVID-19" iScience 25, 104723-1–104723-18 (2022).
- Hidefumi Naito, Ryuichi Okamoto, Tomonari Sumi, Kenichiro Koga, "Osmotic second virial coefficients for hydrophobic interactions as a function of solute size" J. Chem. Phys. 156, 221104-1|221104-5 (2022).
- Yasuhiro Isogai, Hiroshi Imamura, Tomonari Sumi, Tsuyoshi Shirai,
"Improvement of Protein Solubility in Macromolecular Crowding during
Myoglobin Evolution" Biochemistry 61, 1543–1547 (2022).
- Tomonari Sumi, Kouji Harada,
"Kinetics of the ancestral carbon metabolism pathways in deep-branching bacteria and archaea" Communications Chemistry 4, 149-1–149-9 (2021).
- Tomonari Sumi, Hiroshi Imamura,
"Water-mediated interactions destabilize proteins" Protein Science 30, 2132–2143 (2021).
- Yasuhiro Isogai, Hiroshi Imamura, Setsu Nakae, Tomonari Sumi,
Ken-ichi Takahashi, Tsuyoshi Shirai, "Common and unique strategies of
myoglobin evolution for deep-sea adaptation of diving mammals" iScience
24, 102920-1–102920-21 (2021).
- Hiroyuki Katsuto, Ryuichi Okamoto, Tomonari Sumi, Kenichiro Koga, "Ion Size Dependences of the Salting-Out Effect: Reversed Order of Sodium and Lithium Ions" J. Phys. Chem. B 125, 6296|6305 (2021).
- Kouji Harada and Tomonari Sumi,
"A mathematical study on the effects of a combination of an immune
checkpoint inhibitor and a mutagen for anti-HIV-1 therapy" Artificial
Life and Robotics 26 210–215 (2021).
- Takeshi Morita, Sayaka Mukaide, Ziqiao Chen, Kenjirou Higashi, Hiroshi Imamura, Kunikazu Moribe, Tomonari Sumi,
"Unveiling the Interaction Potential Surface between Drug-Entrapped
Polymeric Micelles Clarifying the High Drug Nanocarrier Efficiency"
Nano Lett. 21, 1303–1310 (2021).
- Hiroyo Ohgi, Hiroshi Imamura, Tomonari Sumi,
Keiko Nishikawa, Yoshikata Koga, Peter Westh, Takeshi Morita,
"Two different regimes in alcohol-induced coil–helix transition:
effects of 2,2,2-trifluoroethanol on proteins being either independent
of or enhanced by solvent structural fluctuations" Phys. Chem. Chem.
Phys. 23, 5760–5772 (2021).
- Tomonari Sumi
and Kouji Harada, "Mechanism underlying hippocampal long-term
potentiation and depression based on competition between endocytosis
and exocytosis of AMPA receptors" Sci. Rept. 10, 14711-1–14711-14 (2020).
- Ken-ichi Amano, Ryosuke Sawazumi, Hiroshi Imamura, Tomonari Sumi, Kota Hashimoto, Kazuhiro Fukami, Haru Kitaoka, Naoya Nishi, Tetsuo Sakka,
"An Improved Model-potential-free Analysis of the Structure Factor
Obtained from a Small-angle Scattering: Acquisitions of the Pair
Distribution Function and the Pair Potential" Chem. Lett. 49, 1017–1021 (2020).
- Takeshi Morita, Yuki Ogawa, Hiroshi Imamura, Kouki Ookubo, Nobuo Uehara, and Tomonari Sumi,
"Interaction potential surface between Raman scattering enhancing
nanoparticles conjugated with a functional copolymer" Phys. Chem. Chem.
Phys. 21, 16889–16894 (2019).
- Tomonari Sumi and
Stefan Klumpp, "Is F1]ATPase a Rotary Motor with Nearly 100%
Efficiency? Quantitative Analysis of Chemomechanical Coupling and
Mechanical Slip" Nano Lett. 19, 3370–3379 (2019).
- Tomonari Sumi and Kenichiro Koga, "Theoretical analysis on thermodynamic stability of chignolin" Sci. Rept. 9, 5186-1–5186-9 (2019).
- Yasuhiro Isogai, Hiroshi Imamura, Setsu Nakae, Tomonari Sumi,
Ken-ichi Takahashi, Taro Nakagawa, Antonio Tsuneshige, and Tsuyoshi
Shirai, "Tracing whale myoglobin evolution by resurrecting ancient
proteins" Sci. Rept. 8, 16883-1–16883-14 (2018).
- TTomonari Sumi, Yutaka Maruyama, Ayori Mitsutake, Kenji Mochizuki, and Kenichiro Koga, "Application of
Reference-Modified Density Functional Theory: Temperature and Pressure
Dependences of Solvation Free Energy" J.
Comput. Chem. 39, 202–216 (2018).
- Tomonari Sumi, Atsushi Okumoto, Hitoshi Goto, and Hideo
Sekino, "Numerical calculation on a two-step subdiffusion behavior of
lateral protein movement in plasma membranes" Phys. Rev. E 96, 042410-1–042410-10 (2017).
- Tomonari Sumi, "Myosin V: Chemomechanical-coupling ratchet with load-induced mechanical slip" Sci. Rept. 7, 13489-1–13489-12 (2017).
- Tomonari Sumi, "Design principles governing chemomechanical coupling of kinesin" Sci. Rept. 7, 1163-1–1163-13 (2017).
- Kenji Mochizuki, Tomonari Sumi,
and Kenichiro Koga, "Influence of co-non-solvency on hydrophobic molecules driven by excluded volume effect" Phys. Chem. Chem.
Phys. 19, 23915–23918 (2017).
- Itaru Hatano, Kenji Mochizuki, Tomonari Sumi,
Kenichiro Koga, "Hydrophobic Polymer Chain in Water That Undergoes a
Coil-to-Globule Transition Near Room Temperature" J. Phys. Chem. B 120, 12127|12134 (2016).
- Takeshi Morita, Nobuo Uehara, Kenji Kuwahata, Hiroshi Imamura, Takeshi Shimada, Kouki Ookubo, Maki Fujita, and Tomonari Sumi,
"Interaction Potential between Biological Sensing Nanoparticles
Determined by Combining Small-Angle X‑ray Scattering and
Model-Potential-Free Liquid Theory" J. Phys. Chem. C 120, 25564|25571 (2016).
- Tomonari Sumi,
Ayori
Mitsutake, Yutaka Maruyama, and Kenichiro Koga, "A reference-modified
density functional theory: An application to solvation free energy
calculations for a Lennard-Jones solution" J. Chem. Phys. 144, 224104-1–1224104-15 (2016).
- Kenji Mochizuki, Tomonari Sumi,
and Kenichiro Koga, "Liquid–liquid phase separation of
N-isopropylpropionamide aqueous solutions above the lower critical
solution temperature" Sci. Rept. 6, 24657-1–24657-10 (2016)
- Kenji Mochizuki, Tomonari Sumi,
and Kenichiro Koga, "Driving forces for the pressure-induced
aggregation of poly(N-isopropylacrylamide) in water" Phys. Chem. Chem.
Phys. 18, 4697–4703 (2016).
- Kiharu Abe, Tomonari Sumi,
and Kenichiro Koga, "Mean-Field Approximation to the Hydrophobic
Hydration in the Liquid|Vapor Interface of Water" J. Phys. Chem. B 120, 2012|2019 (2016).
- Tomonari Sumi,
Ayori
Mitsutake, and Yutaka Maruyama, "Erratum: gA solvation-Free-Energy
Functional: A Reference-Modified Density Functional Formulation" [J.
Comput. Chem. 2015, 36, 1359–1369]" J. Comput. Chem. 36, 2009–2011 (2015).
- Tomonari Sumi,
Ayori Mitsutake, and Yutaka Maruyama, "A Solvation-Free-Energy
Functional: A Reference-Modified Density Functional Formulation" J.
Comput. Chem. 36, 1359–1369 (2015).
- Tomonari Sumi, Hiroshi
Imamura, Takeshi Morita, Yasuhiro Isogai, and Keiko Nishikawa, "Model-potential-free analysis of small angle
scattering of proteins in solution: insights into solvent effects on
protein–protein interaction" Phys. Chem. Chem. Phys. 16, 25492–25497 (2014).
- Kiharu Abe, Tomonari Sumi,
and Kenichiro Koga, "Temperature dependence of local solubility of
hydrophobic molecules in the liquid-vapor interface of water" J. Chem.
Phys. 141, 18C516-1–18C516-8 (2014).
- Tomonari Sumi, Hiroshi Imamura, Takeshi Morita, Yasuhiro Isogai, and Keiko Nishikawa, "A model-free method for extracting interaction
potential between protein molecules using small-angle X-ray scattering"
J. Mol. Liq. 200, 42–46 (2014).
- A. Okumoto, T. Akiyama, H. Sekino, and T. Sumi, "Time series data analysis using DFA" AIP Cof. Proc. 1585, 175-180 (2014).
- Hiroshi Imamura, Takeshi Morita, Tomonari Sumi, Yasuhiro Isogai, Minoru Kato, and Keiko Nishikawa, and K. Nishikawa, "Modulation of the intermolecular
interaction of myoglobin by removal of the heme" J. Sync. Rad. 20, 919–922 (2013).
- Tomonari Sumi
and Hideo Sekino, "Effects of Hydrophobic Hydration on Polymer Chain Immersed in Supercooled Water" RSC Advances 3, 12743–12750 (2013).
- Tomonari Sumi
and Hideo Sekino, "Possible mechanism underlying high-pressure
unfolding of proteins: Formation of short-period high-density hydration
shell" Phys. Chem. Chem. Phys. (Communication) 13, 15829–15832 (2011).
- Tadanori Koga, Peter Gin, Hiroki Yamaguch, Maya Endoh, Mitsunori
Asada, Levent Sendogdular, Motoyasu Kobayashi, Atsushi Takahara, Bulent
Akgun, Sushil Satija, and Tomonari
Sumi, "Generality of Anomalous Expansion of Polymer Chains in
Supercritical Fluids" Polymer 52,
4331–4336 (2011).
- Tomonari Sumi,
Nobuyuki Imazaki,
and Hideo Sekino, "Erratum: gDewetting-induced globule-coil transitions
of model polymersand possible implications high-temperature and
low-pressure unfolding of proteinsh [J. Chem. Phys. 132, 165101 (2010)]" J. Chem. Phys. 132, 229901, 1-1,
(2010).
- Tomonari Sumi,
Nobuyuki Imazaki, and Hideo Sekino, "Dewetting-induced globule-coil
transitions of model polymers and possible implications
high-temperature and low-pressure unfolding of proteins" J. Chem. Phys.
132, 165101, 1-8,
(2010). This paper has been selected for the Vir. J. Bio. Phys.
Res. 19 (2010).
- Tomonari Sumi,
Chiaki Suzuki, and Hideo Sekino, "Hydrophobic effects on
multivalent-salt-induced self-condensation of DNA" J. Chem. Phys. 131, 161103, 1-4, (Communication)
(2009). This paper has been selected for the Vir. J. Bio. Phys.
Res. 18 (2009).
- Tomonari Sumi,
Nobuyuki Imazaki, and Hideo Sekino, "Critical Casimir effect in a
polymer chain in supercritical solvents" Phys. Rev. E 79, 030801(R), 1-4 (2009).
- Tomonari Sumi
and Hideo Sekino, "A Self-Consistent
Density-Functional
Approach for Homogeneous and Inhomogeneous Classical Fluids" J. Phys.
Soc. Jpn. 77,
034605, 1-8, (2008).
- Tomonari Sumi
and Hideo Sekino, "Metal-nonmetal transition in dense fluid hydrogen"
J. Chem. Phys. 128, 044712,
1-7 (2008).
- Tomonari Sumi,
Kazuhiko Kobayashi, and Hideo Sekino, "Behavior of a polymer chain
immersed in a binary mixture of solvents" J. Chem. Phys. 127, 164904,
1-7 (2007).
- Tomonari Sumi and Hideo Sekino, "Integral equation study
of
hydrophobic interaction: A comparison between the simple point charge
model for water and a Lennard-Jones model for solvent" J. Chem. Phys. 126, 144508, 1-7 (2007). This paper
has been selected for the Vir. J. Bio. Phys. Res. 13 (2007).
- Tomonari Sumi and Hideo Sekino, "A crossover from metal to
plasma in dense fluid hydrogen" J. Chem. Phys. 125, 194526, 1-10 (2006).
- Tomonari Sumi and Hideo Sekino, "An interaction site model
integral equation study of molecular fluids explicitly considering the
molecular orientation" J. Chem. Phys. 125,
034509, 1-9 (2006).
- Tomonari Sumi, Chiaki Suzuki, and Hideo Sekino, "Entropy-
or enthalpy-driven collapse of strongly charged polymer chains in a
one-component
charged fluid of counterions or coions" J. Chem. Phys. 123,
204907, 1-6 (2005).
- Tomonari Sumi and Hideo Sekino, "Anomalous behavior of a
polymer chain in supercritical solvents:A remarkable expansion of
solvophobic polymer" Chem. Phys. Lett. 407, 322 (2005).
- Tomonari Sumi and Hideo Sekino, "A remarkable
increase of positron annihilation rate in supercritical fluid xenon"
Chem. Phys. Lett. 407, 294 (2005).
- Tomonari Sumi and Hideo Sekino, "A Cooperative phenomenon
between polymer chain and supercritical solvents: Remarkable expansions
of solvophiric and solvophobic polymers" J. Chem. Phys. 122,
194910 (2005).
- Tomonari Sumi and Hideo Sekino, "A Path-integral
Influence Functional for Excess Electron in Fluids: Density-functional
Formulation" J. Chem. Phys. 120, 8157-8165 (2004).
- Tomonari Sumi, Hideaki Shirahama, and Hideo Sekino, "A
Density-functional Study for the Liquid-vapor Coexistence Curve of
Nitrogen fluid" J. Chem. Phys. 121, 1014-1019 (2004).
- Tomonari Sumi and Fumio Hirata, "A density-functional
theory for polymer liquids based on the interaction site model" J.
Chem. Phys. 118, 2431-2442 (2003).
- Tomonari Sumi, Takashi Imai, and Fumio Hirata, "Integral
equations for molecular fluids based on interaction site model:
Density-functional formulation" J. Chem. Phys. 115, 6653-6662
(2001).
- Tomonari Sumi, Eisaku Miyoshi, and Kiyoshi Tanaka,
"Molecular-dynamics study of liquid mercury in the density region
between
metal and nonmetal" Phys. Rev. B 59, 6153-6158 (1999).
- Tomonari Sumi, Eisaku Miyoshi, Yoshiko Sakai, and Osamu
Matsuoka, "Molecular-orbital and molecular-dynamics study of
mercury" Phys. Rev. B 57, 914-918 (1998).
- Eisaku Miyoshi, Tetsuya Ichikawa, Tomonari Sumi, Yoshiko
Sakai, and Norihiro Shida, "Ab initio CASSCF and MRSDCI
calculations of the (C6H6)2+ radical" Chem. Phys. Lett. 275,
404-408 (1997).
- Tomonari Sumi, Yoshiko Sakai, and Eisaku Miyoshi, "Molecular-orbital study of Li and LiOH adsorption on a Cu(001) surface
II. Cluster-model calculations with image charges." Phys. Rev. B 55,
4755-4760 (1997).
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