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Sumi, Tomonari

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The nature of the hydrophobic interaction varies as the solute size increases from methane’s to C60’s
FullText URL fulltext.pdf
Author Naito, Hidefumi| Sumi, Tomonari| Koga, Kenichiro|
Published Date 2024-12-02
Publication Title The Journal of Chemical Physics
Volume volume161
Issue issue21
Publisher AIP Publishing
Start Page 214501
ISSN 0021-9606
NCID AA00694991
Content Type Journal Article
language English
OAI-PMH Set 岡山大学
Copyright Holders © 2024 Author(s).
File Version publisher
PubMed ID 39620415
DOI 10.1063/5.0233808
Web of Science KeyUT 001368895000001
Related Url isVersionOf https://doi.org/10.1063/5.0233808
Vaccine and antiviral drug promise for preventing post-acute sequelae of COVID-19, and their combination for its treatment
FullText URL fulltext.pdf
Author Sumi, Tomonari| Harada, Kouji|
Keywords post-acute sequelae of SARS-CoV-2 infection PASC long Covid persistent viruses vaccine antiviral drug mathematical model immune response
Published Date 2024-08-09
Publication Title Frontiers in Immunology
Volume volume15
Publisher Frontiers Media
Start Page 1329162
ISSN 1664-3224
Content Type Journal Article
language English
OAI-PMH Set 岡山大学
Copyright Holders © 2024 Sumi and Harada.
File Version publisher
PubMed ID 39185419
DOI 10.3389/fimmu.2024.1329162
Web of Science KeyUT 001295899400001
Related Url isVersionOf https://doi.org/10.3389/fimmu.2024.1329162
Molecular mechanism of the common and opposing cosolvent effects of fluorinated alcohol and urea on a coiled coil protein
FullText URL fulltext.pdf
Author Nakata, Noa| Okamoto, Ryuichi| Sumi, Tomonari| Koga, Kenichiro| Morita, Takeshi| Imamura, Hiroshi|
Keywords 2,2,2-trifluoroethanol cosolvent effects preferential binding parameter protein folding stability urea
Published Date 2023-09-25
Publication Title Protein Science
Volume volume32
Issue issue10
Publisher Wiley
Start Page e4763
ISSN 0961-8368
NCID AA10829011
Content Type Journal Article
language English
OAI-PMH Set 岡山大学
Copyright Holders © 2023 The Authors.
File Version publisher
PubMed ID 37622187
DOI 10.1002/pro.4763
Web of Science KeyUT 001083988800003
Related Url isVersionOf https://doi.org/10.1002/pro.4763
How do water-mediated interactions and osmotic second virial coefficients vary with particle size?
FullText URL fulltext.pdf
Author Naito, Hidefumi| Sumi, Tomonari| Koga, Kenichiro|
Published Date 2024
Publication Title Faraday Discussions
Volume volume249
Publisher Royal Society of Chemistry (RSC)
Start Page 440
End Page 452
ISSN 1359-6640
NCID AA10836538
Content Type Journal Article
language English
OAI-PMH Set 岡山大学
Copyright Holders © The Royal Society of Chemistry 2024
File Version publisher
PubMed ID 37791511
DOI 10.1039/d3fd00104k
Web of Science KeyUT 001077081700001
Related Url isVersionOf https://doi.org/10.1039/d3fd00104k
Solvation free energies of alcohols in water: temperature and pressure dependences
FullText URL fulltext20231129-01.pdf
Author Taira, Aoi| Okamoto, Ryuichi| Sumi, Tomonari| Koga, Kenichiro|
Published Date 2023
Publication Title Physical Chemistry Chemical Physics
Volume volume25
Issue issue45
Publisher Royal Society of Chemistry (RSC)
Start Page 31107
End Page 31117
ISSN 1463-9076
NCID AA11301773
Content Type Journal Article
language English
OAI-PMH Set 岡山大学
Copyright Holders © the Owner Societies 2023
File Version publisher
PubMed ID 37947179
DOI 10.1039/d3cp03799a
Web of Science KeyUT 001099200400001
Related Url isVersionOf https://doi.org/10.1039/d3cp03799a
Immune response to SARS-CoV-2 in severe disease and long COVID-19
FullText URL fulltext.pdf
Author Sumi, Tomonari| Harada, Kouji|
Published Date 2022-08-19
Publication Title ISCIENCE
Volume volume25
Issue issue8
Publisher CELL PRESS
Start Page 104723
ISSN 2589-0042
Content Type Journal Article
language English
OAI-PMH Set 岡山大学
Copyright Holders © 2022 The Author(s).
File Version publisher
PubMed ID 35813874
DOI 10.1016/j.isci.2022.104723
Web of Science KeyUT 000843628600010
Related Url isVersionOf https://doi.org/10.1016/j.isci.2022.104723
Osmotic second virial coefficients for hydrophobic interactions as a function of solute size
FullText URL fulltext20220810-2.pdf
Author Naito, Hidefumi| Okamoto, Ryuichi| Sumi, Tomonari| Koga, Kenichiro|
Note This article may be downloaded for personal use only. Any other use requires prior permission of the author and AIP Publishing. This article appeared in (Hidefumi Naito, Ryuichi Okamoto, Tomonari Sumi, Kenichiro Koga; Osmotic second virial coefficients for hydrophobic interactions as a function of solute size. J. Chem. Phys. 14 June 2022; 156 (22): 221104. https://doi.org/10.1063/5.0097547) and may be found at (https://doi.org/10.1063/5.0097547).
This fulltext is available in June 2023.|
Published Date 2022-06-14
Publication Title The Journal of Chemical Physics
Volume volume156
Issue issue22
Publisher AIP Publishing
Start Page 221104
ISSN 0021-9606
Content Type Journal Article
language English
OAI-PMH Set 岡山大学
Copyright Holders © 2022 Author(s).
File Version publisher
PubMed ID 35705398
DOI 10.1063/5.0097547
Web of Science KeyUT 000832682400001
Related Url isVersionOf https://doi.org/10.1063/5.0097547
Kinetics of the ancestral carbon metabolism pathways in deep-branching bacteria and archaea
FullText URL fulltext.pdf
Author Sumi, Tomonari| Harada, Kouji|
Published Date 2021-10-22
Publication Title Communications Chemistry
Volume volume4
Issue issue1
Publisher Nature Portfolio
Start Page 149
ISSN 2399-3669
Content Type Journal Article
language English
OAI-PMH Set 岡山大学
Copyright Holders © The Author(s) 2021
File Version publisher
DOI 10.1038/s42004-021-00585-0
Web of Science KeyUT 000710351300002
Related Url isVersionOf https://doi.org/10.1038/s42004-021-00585-0
Ion Size Dependences of the Salting-Out Effect: Reversed Order of Sodium and Lithium Ions
FullText URL fulltext20210803-3.pdf
Author Katsuto, Hiroyuki| Okamoto, Ryuichi| Sumi, Tomonari| Koga, Kenichiro|
Note This document is the Accepted Manuscript version of a Published Work that appeared in final form in [The Journal of Physical Chemistry B], copyright © American Chemical Society after peer review and technical editing by the publisher. To access the final edited and published work see https://doi.org/10.1021/acs.jpcb.1c03388|
Published Date 2021-6-8
Publication Title The Journal of Physical Chemistry B
Volume volume125
Issue issue23
Publisher American Chemical Society (ACS)
Start Page 6296
End Page 6305
ISSN 1520-6106
Content Type Journal Article
language English
OAI-PMH Set 岡山大学
Copyright Holders © 2021 American Chemical Society
File Version author
PubMed ID 34102058
DOI 10.1021/acs.jpcb.1c03388
Web of Science KeyUT 000664303000026
Related Url isVersionOf https://doi.org/10.1021/acs.jpcb.1c03388
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
FullText URL PCCP_2021.pdf ESI_PCCP_2021.pdf
Author Ohgi, Hiroyo| Imamura, Hiroshi| Sumi, Tomonari| Nishikawa, Keiko| Koga, Yoshikata| Westh, Peter| Morita, Takeshi|
Published Date 2021-03-23
Publication Title Physical Chemistry Chemical Physics
Volume volume23
Issue issue10
Publisher Royal Society of Chemistry (RSC)
Start Page 5760
End Page 5772
ISSN 1463-9076
NCID AA11301773
Content Type Journal Article
language English
OAI-PMH Set 岡山大学
Copyright Holders the Owner Societies 2021
File Version author
PubMed ID 33481971
DOI 10.1039/d0cp05103a
Web of Science KeyUT 000630207300062
Related Url isVersionOf https://doi.org/10.1039/d0cp05103a
Unveiling the Interaction Potential Surface between Drug-Entrapped Polymeric Micelles Clarifying the High Drug Nanocarrier Efficiency
FullText URL Manuscript_NanoLett.pdf SI_NanoLett.pdf
Author Morita, Takeshi| Mukaide, Sayaka| Chen, Ziqiao| Higashi, Kenjirou| Imamura, Hiroshi| Moribe, Kunikazu| Sumi, Tomonari|
Keywords polymeric micelle drug entrapment nanocarrier interaction potential surface small-angle X-ray scattering model-potential-free liquid-state theory
Note This document is the Accepted Manuscript version of a Published Work that appeared in final form in Nano Letters, copyright © American Chemical Society after peer review and technical editing by the publisher. To access the final edited and published work see https://doi.org/10.1021/acs.nanolett.0c03978 .|
Published Date 2021-01-22
Publication Title Nano Letters
Volume volume21
Issue issue3
Publisher American Chemical Society (ACS)
Start Page 1303
End Page 1310
ISSN 1530-6984
NCID AA11511812
Content Type Journal Article
language English
OAI-PMH Set 岡山大学
Copyright Holders 2021 American Chemical Society
File Version author
PubMed ID 33480258
DOI 10.1021/acs.nanolett.0c03978
Web of Science KeyUT 000619638600015
Related Url isVersionOf https://doi.org/10.1021/acs.nanolett.0c03978
Mechanism underlying hippocampal long-term potentiation and depression based on competition between endocytosis and exocytosis of AMPA receptors
FullText URL fulltext.pdf
Author Sumi, Tomonari| Harada, Kouji|
Keywords Biophysical models Long-term depression Long-term potentiation
Published Date 2020-09-07
Publication Title Scientific Reports
Volume volume10
Issue issue1
Publisher Nature
Start Page 14711
ISSN 2045-2322
Content Type Journal Article
language English
OAI-PMH Set 岡山大学
Copyright Holders © The Author(s) 2020
File Version publisher
PubMed ID 32895399
DOI 10.1038/s41598-020-71528-3
Web of Science KeyUT 000570970200006
Related Url isVersionOf https://doi.org/10.1038/s41598-020-71528-3
Theoretical analysis on thermodynamic stability of chignolin
FullText URL SR9_1_5186.pdf
Author Sumi, Tomonari| Koga, Kenichiro|
Published Date 2019-3-26
Publication Title Scientific Reports
Volume volume9
Publisher Nature Publishing Group
Start Page 5186
ISSN 2045-2322
Content Type Journal Article
language English
OAI-PMH Set 岡山大学
Copyright Holders © The Author(s) 2019
File Version publisher
PubMed ID 30914684
DOI 10.1038/s41598-019-41518-1
Web of Science KeyUT 000462298600073
Related Url isVersionOf https://doi.org/10.1038/s41598-019-41518-1
Application of reference-modified density functional theory: Temperature and pressure dependences of solvation free energy
FullText URL J_ComputChem_39_4_202.pdf SI_J_ComputChem_39_4_202.pdf
Author Sumi, Tomonari| Maruyama, Yutaka| Mitsutake, Ayori| Mochizuki , Kenji| Koga, Kenichiro|
Keywords 3D-RISM theory chignolin classical density functional theory high-pressure unfolding hydrophobic solute protein temperature and pressure dependences of solvation free energy thermal denaturation
Published Date 2017-11-08
Publication Title Journal of Computational Chemistry
Volume volume39
Issue issue4
Publisher Wiley
Start Page 202
End Page 217
ISSN 01928651
NCID AA00257341
Content Type Journal Article
language English
OAI-PMH Set 岡山大学
File Version author
PubMed ID 29116647
DOI 10.1002/jcc.25101
Web of Science KeyUT 000417850400002
Related Url isVersionOf https://doi.org/10.1002/jcc.25101
A solvation-free-energy functional: A reference-modified density functional formulation
FullText URL J_Comput_Chem_36_18_135.pdf
Author Sumi, Tomonari| Mitsutake, Ayori| Maruyama, Yutaka|
Keywords salvation-free-energy classical density functional theory 3D-RISM theory water amino acid side-chain chignolin
Published Date 2015-05-31
Publication Title Journal of Computational Chemistry
Volume volume36
Issue issue18
Start Page 1359
End Page 1369
ISSN 01928651
NCID AA00257341
Content Type Journal Article
language English
OAI-PMH Set 岡山大学
File Version author
PubMed ID 26032201
DOI 10.1002/jcc.23942
Web of Science KeyUT 000356310800002
Related Url isVersionOf https://doi.org/10.1002/jcc.23942
A reference-modified density functional theory: An application to solvation free-energy calculations for a Lennard-Jones solution
FullText URL J_ChemPhys_144_22_224104.pdf
Author Sumi, Tomonari| Maruyama, Yutaka| Mitsutake, Ayori| Koga, Kenichiro|
Published Date 2016-06-10
Publication Title Journal of Chemical Physics
Volume volume144
Issue issue22
Publisher American Institute of Physics
Start Page 224104
ISSN 00219606
NCID AA00694991
Content Type Journal Article
language English
OAI-PMH Set 岡山大学
File Version author
PubMed ID 27305993
DOI 10.1063/1.4953191
Web of Science KeyUT 000378926100007
Related Url isVersionOf https://doi.org/10.1063/1.4953191
Model-potential-free analysis of small angle scattering of proteins in solution: insights into solvent effects on protein-protein interaction
FullText URL PhysChemChemPhys_16_46_25492.pdf
Author Sumi, Tomonari| Imamura, Hiroshi| Morita, Takeshi| Isogai, Yasuhiro| Nishikawa, Keiko|
Published Date 2014-10-17
Publication Title Physical Chemistry Chemical Physics
Volume volume16
Issue issue46
Publisher Royal Society of Chemistry
Start Page 25492
End Page 25497
ISSN 14639076
NCID AA11301773
Content Type Journal Article
language English
OAI-PMH Set 岡山大学
File Version author
PubMed ID 25343423
DOI 10.1039/c4cp03606a
Web of Science KeyUT 000344989500036
Related Url isVersionOf https://doi.org/10.1039/c4cp03606a
A model-free method for extracting interaction potential between protein molecules using small-angle X-ray
FullText URL J_MoleculLiq_200_42.pdf
Author Sumi, Tomonari| Imamura, Hiroshi| Morita, Takeshi| Nishikawa, Keiko|
Keywords Protein solutions Lysozyme Protein-protein interaction Liquid state theory Integral equation DLVO model
Published Date 2014-04-01
Publication Title Journal of Molecular Liquids
Volume volume200
Issue issuePart.A
Publisher Elsevier Science
Start Page 42
End Page 46
ISSN 01677322
NCID AA10636062
Content Type Journal Article
language English
OAI-PMH Set 岡山大学
File Version author
DOI 10.1016/j.molliq.2014.03.014
Web of Science KeyUT 000347592900010
Related Url isVersionOf https://doi.org/10.1016/j.molliq.2014.03.014
Numerical calculation on a two-step subdiffusion behavior of lateral protein movement in plasma membranes
FullText URL PhysRevE_96_4_042410_a.pdf
Author Sumi, Tomonari| Okumoto, Atsushi| Goto, Hitoshi| Sekino, Hideo|
Published Date 2017-10-19
Publication Title Physical review. E.
Volume volume96
Issue issue4-1
Publisher American Physical Society
Start Page 042410
ISSN 24700045
NCID AA11558033
Content Type Journal Article
language English
OAI-PMH Set 岡山大学
File Version publisher
PubMed ID 29347488
DOI 10.1103/PhysRevE.96.042410
Web of Science KeyUT 000413293200004
Related Url isVersionOf https://doi.org/10.1103/PhysRevE.96.042410
Is F-1-ATPase a Rotary Motor with Nearly 100% Efficiency? Quantitative Analysis of Chemomechanical Coupling and Mechanical Slip
FullText URL Nanolett_19_5_3370.pdf SI_Nanolett_19_5_3370.pdf
Author Sumi, Tomonari| Klumpp, Stefan|
Keywords F-1-ATPase rotary molecular motor chemomechanical network model free-energy transduction efficiency ATP synthesis torque-induced mechanical slip
Published Date 2019-04-24
Publication Title Nano Letters
Volume volume19
Issue issue5
Publisher American Chemical Society
Start Page 3370
End Page 3378
ISSN 15306984
NCID AA11511812
Content Type Journal Article
language English
OAI-PMH Set 岡山大学
Copyright Holders Copyright © 2019 American Chemical Society
File Version author
PubMed ID 31017791
DOI 10.1021/acs.nanolett.9b01181
Web of Science KeyUT 000467781900078
Related Url isVersionOf https://doi.org/10.1021/acs.nanolett.9b01181
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