@LIST OF PUBLICATIONS@

  1. 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).
  2. 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).
  3. 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).
  4. 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).
  5. 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).
  6. 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).
  7. 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).
  8. Tomonari Sumi and Kenichiro Koga, "Theoretical analysis on thermodynamic stability of chignolin" Sci. Rept. 9, 5186-1–5186-9 (2019).
  9. 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).
  10. 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).
  11. 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).
  12. Tomonari Sumi, "Myosin V: Chemomechanical-coupling ratchet with load-induced mechanical slip" Sci. Rept. 7, 13489-1–13489-12 (2017).
  13. Tomonari Sumi, "Design principles governing chemomechanical coupling of kinesin" Sci. Rept. 7, 1163-1–1163-13 (2017).
  14. 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).
  15. 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).
  16. 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).
  17. 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).
  18.  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)
  19. 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).
  20. 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).
  21. 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).
  22. 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).
  23. 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).
  24. 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).
  25. 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).
  26. A. Okumoto, T. Akiyama, H. Sekino, and T. Sumi, "Time series data analysis using DFA" AIP Cof. Proc. 1585, 175-180 (2014).
  27. 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).
  28. Tomonari Sumi and Hideo Sekino, "Effects of Hydrophobic Hydration on Polymer Chain Immersed in Supercooled Water" RSC Advances 3, 12743–12750 (2013).
  29. 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).
  30. 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).
  31. 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).
  32. 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).
  33. 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).
  34. 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).
  35. 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).
  36. Tomonari Sumi and Hideo Sekino, "Metal-nonmetal transition in dense fluid hydrogen" J. Chem. Phys. 128, 044712, 1-7 (2008).
  37. 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).
  38. 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).
  39. Tomonari Sumi and Hideo Sekino, "A crossover from metal to plasma in dense fluid hydrogen" J. Chem. Phys. 125, 194526, 1-10 (2006).
  40. 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).
  41. 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).
  42. 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).
  43. Tomonari Sumi and Hideo Sekino, "A remarkable increase of positron annihilation rate in supercritical fluid xenon" Chem. Phys. Lett. 407, 294 (2005).
  44. 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).
  45. 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).
  46. 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).
  47. 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).
  48. 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).
  49. 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).
  50. Tomonari Sumi, Eisaku Miyoshi, Yoshiko Sakai, and Osamu Matsuoka, "Molecular-orbital and molecular-dynamics study of mercury" Phys. Rev. B 57, 914-918 (1998).
  51. 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).
  52. 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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