start-ver=1.4
cd-journal=joma
no-vol=10
cd-vols=
no-issue=1
article-no=
start-page=14711
end-page=
dt-received=
dt-revised=
dt-accepted=
dt-pub-year=2020
dt-pub=20200907
dt-online=
en-article=
kn-article=
en-subject=
kn-subject=
en-title=
kn-title=Mechanism underlying hippocampal long-term potentiation and depression based on competition between endocytosis and exocytosis of AMPA receptors
en-subtitle=
kn-subtitle=
en-abstract=
kn-abstract=N-methyl-D-aspartate (NMDA) receptor-dependent long-term potentiation (LTP) and long-term depression (LTD) of signal transmission form neural circuits and thus are thought to underlie learning and memory. These mechanisms are mediated by AMPA receptor (AMPAR) trafficking in postsynaptic neurons. However, the regulatory mechanism of bidirectional plasticity at excitatory synapses remains unclear. We present a network model of AMPAR trafficking for adult hippocampal pyramidal neurons, which reproduces both LTP and LTD. We show that the induction of both LTP and LTD is regulated by the competition between exocytosis and endocytosis of AMPARs, which are mediated by the calcium-sensors synaptotagmin 1/7 (Syt1/7) and protein interacting with C-kinase 1 (PICK1), respectively. Our result indicates that recycling endosomes containing AMPAR are always ready for Syt1/7-dependent exocytosis of AMPAR at peri-synaptic/synaptic membranes. This is because molecular motor myosin V-b constitutively transports the recycling endosome toward the membrane in a Ca2+-independent manner.
en-copyright=
kn-copyright=

en-aut-name=SumiTomonari
en-aut-sei=Sumi
en-aut-mei=Tomonari
kn-aut-name=
kn-aut-sei=
kn-aut-mei=
aut-affil-num=1
ORCID=

en-aut-name=HaradaKouji
en-aut-sei=Harada
en-aut-mei=Kouji
kn-aut-name=
kn-aut-sei=
kn-aut-mei=
aut-affil-num=2
ORCID=

affil-num=1
en-affil=Research Institute for Interdisciplinary Science, Okayama University
kn-affil=

affil-num=2
en-affil=Department of Computer Science and Engineering, Toyohashi University of Technology
kn-affil=
en-keyword=Biophysical models
kn-keyword=Biophysical models
en-keyword=Long-term depression
kn-keyword=Long-term depression
en-keyword=Long-term potentiation
kn-keyword=Long-term potentiation
END

start-ver=1.4
cd-journal=joma
no-vol=9
cd-vols=
no-issue=
article-no=
start-page=5186
end-page=
dt-received=
dt-revised=
dt-accepted=
dt-pub-year=2019
dt-pub=2019326
dt-online=
en-article=
kn-article=
en-subject=
kn-subject=
en-title=
kn-title=Theoretical analysis on thermodynamic stability of chignolin
en-subtitle=
kn-subtitle=
en-abstract=
kn-abstract=Understanding the dominant factor in thermodynamic stability of proteins remains an open challenge. Kauzmann's hydrophobic interaction hypothesis, which considers hydrophobic interactions between nonpolar groups as the dominant factor, has been widely accepted for about sixty years and attracted many scientists. The hypothesis, however, has not been verified or disproved because it is difficult, both theoretically and experimentally, to quantify the solvent effects on the free energy change in protein folding. Here, we developed a computational method for extracting the dominant factor behind thermodynamic stability of proteins and applied it to a small, designed protein, chignolin. The resulting free energy profile quantitatively agreed with the molecular dynamics simulations. Decomposition of the free energy profile indicated that intramolecular interactions predominantly stabilized collapsed conformations, whereas solvent-induced interactions, including hydrophobic ones, destabilized them. These results obtained for chignolin were consistent with the site-directed mutagenesis and calorimetry experiments for globular proteins with hydrophobic interior cores.
en-copyright=
kn-copyright=

en-aut-name=SumiTomonari
en-aut-sei=Sumi
en-aut-mei=Tomonari
kn-aut-name=
kn-aut-sei=
kn-aut-mei=
aut-affil-num=1
ORCID=

en-aut-name=KogaKenichiro
en-aut-sei=Koga
en-aut-mei=Kenichiro
kn-aut-name=
kn-aut-sei=
kn-aut-mei=
aut-affil-num=2
ORCID=

affil-num=1
en-affil= Research Institute for Interdisciplinary Science, Okayama University
kn-affil=

affil-num=2
en-affil= Research Institute for Interdisciplinary Science, Okayama University
kn-affil=
END

start-ver=1.4
cd-journal=joma
no-vol=39
cd-vols=
no-issue=4
article-no=
start-page=202
end-page=217
dt-received=
dt-revised=
dt-accepted=
dt-pub-year=2017
dt-pub=20171108
dt-online=
en-article=
kn-article=
en-subject=
kn-subject=
en-title=
kn-title=Application of reference-modified density functional theory: Temperature and pressure dependences of solvation free energy
en-subtitle=
kn-subtitle=
en-abstract=
kn-abstract= Recently, we proposed a reference‐modified density functional theory (RMDFT) to calculate solvation free energy (SFE), in which a hard‐sphere fluid was introduced as the reference system instead of an ideal molecular gas. Through the RMDFT, using an optimal diameter for the hard‐sphere reference system, the values of the SFE calculated at room temperature and normal pressure were in good agreement with those for more than 500 small organic molecules in water as determined by experiments. In this study, we present an application of the RMDFT for calculating the temperature and pressure dependences of the SFE for solute molecules in water. We demonstrate that the RMDFT has high predictive ability for the temperature and pressure dependences of the SFE for small solute molecules in water when the optimal reference hard‐sphere diameter determined for each thermodynamic condition is used. We also apply the RMDFT to investigate the temperature and pressure dependences of the thermodynamic stability of an artificial small protein, chignolin, and discuss the mechanism of high‐temperature and high‐pressure unfolding of the protein. © 2017 Wiley Periodicals, Inc.
en-copyright=
kn-copyright=

en-aut-name=SumiTomonari
en-aut-sei=Sumi
en-aut-mei=Tomonari
kn-aut-name=
kn-aut-sei=
kn-aut-mei=
aut-affil-num=1
ORCID=

en-aut-name=MaruyamaYutaka
en-aut-sei=Maruyama
en-aut-mei=Yutaka
kn-aut-name=
kn-aut-sei=
kn-aut-mei=
aut-affil-num=2
ORCID=

en-aut-name=MitsutakeAyori
en-aut-sei=Mitsutake
en-aut-mei=Ayori
kn-aut-name=
kn-aut-sei=
kn-aut-mei=
aut-affil-num=3
ORCID=

en-aut-name=Mochizuki Kenji
en-aut-sei=Mochizuki 
en-aut-mei=Kenji
kn-aut-name=
kn-aut-sei=
kn-aut-mei=
aut-affil-num=4
ORCID=

en-aut-name=KogaKenichiro
en-aut-sei=Koga
en-aut-mei=Kenichiro
kn-aut-name=
kn-aut-sei=
kn-aut-mei=
aut-affil-num=5
ORCID=

affil-num=1
en-affil= Division of Superconducting and Functional Materials, Research Institute for Interdisciplinary Science, Okayama University
kn-affil=

affil-num=2
en-affil=Co-Design Team, FLAGSHIP 2020 Project, RIKEN Advanced Institute for Computational Science
kn-affil=

affil-num=3
en-affil= Department of Physics, Keio University
kn-affil=

affil-num=4
en-affil= Division of Superconducting and Functional Materials, Research Institute for Interdisciplinary Science, Okayama University
kn-affil=

affil-num=5
en-affil= Division of Superconducting and Functional Materials, Research Institute for Interdisciplinary Science, Okayama University
kn-affil=
en-keyword=3D-RISM theory
kn-keyword=3D-RISM theory
en-keyword=chignolin
kn-keyword=chignolin
en-keyword=classical density functional theory
kn-keyword=classical density functional theory
en-keyword=high-pressure unfolding
kn-keyword=high-pressure unfolding
en-keyword=hydrophobic solute
kn-keyword=hydrophobic solute
en-keyword=protein
kn-keyword=protein
en-keyword=temperature and pressure dependences of solvation free energy
kn-keyword=temperature and pressure dependences of solvation free energy
en-keyword=thermal denaturation
kn-keyword=thermal denaturation
END

start-ver=1.4
cd-journal=joma
no-vol=36
cd-vols=
no-issue=18
article-no=
start-page=1359
end-page=1369
dt-received=
dt-revised=
dt-accepted=
dt-pub-year=2015
dt-pub=20150531
dt-online=
en-article=
kn-article=
en-subject=
kn-subject=
en-title=
kn-title=A solvation-free-energy functional: A reference-modified density functional formulation
en-subtitle=
kn-subtitle=
en-abstract=
kn-abstract= The three-dimensional reference interaction site model (3D-RISM) theory, which is one of the most applicable integral equation theories for molecular liquids, overestimates the absolute values of solvation-free-energy (SFE) for large solute molecules in water. To improve the free-energy density functional for the SFE of solute molecules, we propose a reference-modified density functional theory (RMDFT) that is a general theoretical approach to construct the free-energy density functional systematically. In the RMDFT formulation, hard-sphere (HS) fluids are introduced as the reference system instead of an ideal polyatomic molecular gas, which has been regarded as the appropriate reference system of the interaction-site-model density functional theory for polyatomic molecular fluids. We show that using RMDFT with a reference HS system can significantly improve the absolute values of the SFE for a set of neutral amino acid side-chain analogues as well as for 504 small organic molecules. 
en-copyright=
kn-copyright=

en-aut-name=SumiTomonari
en-aut-sei=Sumi
en-aut-mei=Tomonari
kn-aut-name=
kn-aut-sei=
kn-aut-mei=
aut-affil-num=1
ORCID=

en-aut-name=MitsutakeAyori
en-aut-sei=Mitsutake
en-aut-mei=Ayori
kn-aut-name=
kn-aut-sei=
kn-aut-mei=
aut-affil-num=2
ORCID=

en-aut-name=MaruyamaYutaka
en-aut-sei=Maruyama
en-aut-mei=Yutaka
kn-aut-name=
kn-aut-sei=
kn-aut-mei=
aut-affil-num=3
ORCID=

affil-num=1
en-affil=Department of Chemistry, Faculty of Science, Okayama University,
kn-affil=

affil-num=2
en-affil=Department of Physics, Keio University,
kn-affil=

affil-num=3
en-affil=Department of Physics, Keio University,
kn-affil=
en-keyword=salvation-free-energy
kn-keyword=salvation-free-energy
en-keyword=classical density functional theory
kn-keyword=classical density functional theory
en-keyword=3D-RISM theory
kn-keyword=3D-RISM theory
en-keyword= water
kn-keyword= water
en-keyword=amino acid side-chain
kn-keyword=amino acid side-chain
en-keyword=chignolin
kn-keyword=chignolin
END

start-ver=1.4
cd-journal=joma
no-vol=144
cd-vols=
no-issue=22
article-no=
start-page=224104
end-page=
dt-received=
dt-revised=
dt-accepted=
dt-pub-year=2016
dt-pub=20160610
dt-online=
en-article=
kn-article=
en-subject=
kn-subject=
en-title=
kn-title=A reference-modified density functional theory: An application to solvation free-energy calculations for a Lennard-Jones solution
en-subtitle=
kn-subtitle=
en-abstract=
kn-abstract= In the conventional classical density functional theory (DFT) for simple fluids, an ideal gas is usually chosen as the reference system because there is a one-to-one correspondence between the external field and the density distribution function, and the exact intrinsic free-energy functional is available for the ideal gas. In this case, the second-order density functional Taylor series expansion of the excess intrinsic free-energy functional provides the hypernetted-chain (HNC) approximation. Recently, it has been shown that the HNC approximation significantly overestimates the solvation free energy (SFE) for an infinitely dilute Lennard-Jones (LJ) solution, especially when the solute particles are several times larger than the solvent particles [T. Miyata and J. Thapa, Chem. Phys. Lett. 604, 122 (2014)]. In the present study, we propose a reference-modified density functional theory as a systematic approach to improve the SFE functional as well as the pair distribution functions. The second-order density functional Taylor series expansion for the excess part of the intrinsic free-energy functional in which a hard-sphere fluid is introduced as the reference system instead of an ideal gas is applied to the LJ pure and infinitely dilute solution systems and is proved to remarkably improve the drawbacks of the HNC approximation. Furthermore, the third-order density functional expansion approximation in which a factorization approximation is applied to the triplet direct correlation function is examined for the LJ systems. We also show that the third-order contribution can yield further refinements for both the pair distribution function and the excess chemical potential for the pure LJ liquids.
en-copyright=
kn-copyright=

en-aut-name=SumiTomonari
en-aut-sei=Sumi
en-aut-mei=Tomonari
kn-aut-name=
kn-aut-sei=
kn-aut-mei=
aut-affil-num=1
ORCID=

en-aut-name=MaruyamaYutaka
en-aut-sei=Maruyama
en-aut-mei=Yutaka
kn-aut-name=
kn-aut-sei=
kn-aut-mei=
aut-affil-num=2
ORCID=

en-aut-name=MitsutakeAyori
en-aut-sei=Mitsutake
en-aut-mei=Ayori
kn-aut-name=
kn-aut-sei=
kn-aut-mei=
aut-affil-num=3
ORCID=

en-aut-name=KogaKenichiro
en-aut-sei=Koga
en-aut-mei=Kenichiro
kn-aut-name=
kn-aut-sei=
kn-aut-mei=
aut-affil-num=4
ORCID=

affil-num=1
en-affil=Department of Chemistry, Faculty of Science, Okayama University
kn-affil=

affil-num=2
en-affil=Co-Design Team, Exascale Computing Project, RIKEN Advanced Institute for Computational Science
kn-affil=

affil-num=3
en-affil=Co-Design Team, Exascale Computing Project, RIKEN Advanced Institute for Computational Science
kn-affil=

affil-num=4
en-affil=Department of Chemistry, Faculty of Science, Okayama University
kn-affil=
END

start-ver=1.4
cd-journal=joma
no-vol=16
cd-vols=
no-issue=46
article-no=
start-page=25492
end-page=25497
dt-received=
dt-revised=
dt-accepted=
dt-pub-year=2014
dt-pub=20141017
dt-online=
en-article=
kn-article=
en-subject=
kn-subject=
en-title=
kn-title=Model-potential-free analysis of small angle scattering of proteins in solution: insights into solvent effects on protein-protein interaction
en-subtitle=
kn-subtitle=
en-abstract=
kn-abstract= To extract protein-protein interaction from experimental small-angle scattering of proteins in solutions using liquid state theory, a model potential consisting of a hard-sphere repulsive potential and the excess interaction potential has been introduced. In the present study, we propose a model-potential-free integral equation method that extracts the excess interaction potential by using the experimental small-angle scattering data without specific model potential such as the Derjaguin-Landau-Verwey-Overbeek (DLVO)-type model. Our analysis of experimental small-angle X-ray scattering data for lysozyme solution shows both the stabilization of contact configurations of protein molecules and a large activation barrier against the formation of the contact configurations in addition to the screened Coulomb repulsion. These characteristic features, which are not well-described by the DLVO-type model, are interpreted as solvent effects.
en-copyright=
kn-copyright=

en-aut-name=SumiTomonari
en-aut-sei=Sumi
en-aut-mei=Tomonari
kn-aut-name=
kn-aut-sei=
kn-aut-mei=
aut-affil-num=1
ORCID=

en-aut-name=ImamuraHiroshi
en-aut-sei=Imamura
en-aut-mei=Hiroshi
kn-aut-name=
kn-aut-sei=
kn-aut-mei=
aut-affil-num=2
ORCID=

en-aut-name=MoritaTakeshi
en-aut-sei=Morita
en-aut-mei=Takeshi
kn-aut-name=
kn-aut-sei=
kn-aut-mei=
aut-affil-num=3
ORCID=

en-aut-name=IsogaiYasuhiro
en-aut-sei=Isogai
en-aut-mei=Yasuhiro
kn-aut-name=
kn-aut-sei=
kn-aut-mei=
aut-affil-num=4
ORCID=

en-aut-name=NishikawaKeiko
en-aut-sei=Nishikawa
en-aut-mei=Keiko
kn-aut-name=
kn-aut-sei=
kn-aut-mei=
aut-affil-num=5
ORCID=

affil-num=1
en-affil=Department of Chemistry, Faculty of Science, Okayama University
kn-affil=

affil-num=2
en-affil=Graduate School of Advanced Integration Science, Chiba University
kn-affil=

affil-num=3
en-affil=Graduate School of Advanced Integration Science, Chiba University
kn-affil=

affil-num=4
en-affil=Department of Biotechnology, Toyama Prefectural University
kn-affil=

affil-num=5
en-affil=Graduate School of Advanced Integration Science, Chiba University
kn-affil=
END

start-ver=1.4
cd-journal=joma
no-vol=200
cd-vols=
no-issue=Part.A
article-no=
start-page=42
end-page=46
dt-received=
dt-revised=
dt-accepted=
dt-pub-year=2014
dt-pub=20140401
dt-online=
en-article=
kn-article=
en-subject=
kn-subject=
en-title=
kn-title=A model-free method for extracting interaction potential between protein molecules using small-angle X-ray
en-subtitle=
kn-subtitle=
en-abstract=
kn-abstract= A small-angle X-ray scattering has been used to probe protein–protein interaction in solution. Conventional methods need to input modeled potentials with variable/invariable parameters to reproduce the experimental structure factor. In the present study, a model-free method for extracting the excess part of effective interaction potential between protein molecules in solutions over an introduced hard-sphere potential by using experimental data of small-angle X-ray scattering is presented on the basis of liquid-state integral equation theory. The reliability of the model-free method is tested by the application to experimentally derived structure factors for dense lysozyme solutions with different solution conditions [Javid et al., Phys. Rev. Lett. 99, 028101 (2007), Schroer et al., Phys. Rev. Lett. 106, 178102 (2011)]. The structure factors calculated from the model-free method agree well with the experimental ones. The model-free method provides the following picture of the lysozyme solution: these are the stabilization of contact-pair configurations, large activation barrier against their formations, and screened Coulomb repulsion between the charged proteins. In addition, the model-free method will be useful to verify whether or not a model for colloidal system is acceptable to describing protein–protein interaction.
en-copyright=
kn-copyright=

en-aut-name=SumiTomonari
en-aut-sei=Sumi
en-aut-mei=Tomonari
kn-aut-name=
kn-aut-sei=
kn-aut-mei=
aut-affil-num=1
ORCID=

en-aut-name=ImamuraHiroshi
en-aut-sei=Imamura
en-aut-mei=Hiroshi
kn-aut-name=
kn-aut-sei=
kn-aut-mei=
aut-affil-num=2
ORCID=

en-aut-name=MoritaTakeshi
en-aut-sei=Morita
en-aut-mei=Takeshi
kn-aut-name=
kn-aut-sei=
kn-aut-mei=
aut-affil-num=3
ORCID=

en-aut-name=NishikawaKeiko
en-aut-sei=Nishikawa
en-aut-mei=Keiko
kn-aut-name=
kn-aut-sei=
kn-aut-mei=
aut-affil-num=4
ORCID=

affil-num=1
en-affil=Department of Chemistry, Faculty of Science, Okayama University
kn-affil=

affil-num=2
en-affil=Graduate School of Advanced integration Science, Chiba University
kn-affil=

affil-num=3
en-affil=Graduate School of Advanced integration Science, Chiba University
kn-affil=

affil-num=4
en-affil=Graduate School of Advanced integration Science, Chiba University
kn-affil=
en-keyword=Protein solutions
kn-keyword=Protein solutions
en-keyword=Lysozyme
kn-keyword=Lysozyme
en-keyword=Protein-protein interaction
kn-keyword=Protein-protein interaction
en-keyword=Liquid state theory
kn-keyword=Liquid state theory
en-keyword=Integral equation
kn-keyword=Integral equation
en-keyword=DLVO model
kn-keyword=DLVO model
END

start-ver=1.4
cd-journal=joma
no-vol=96
cd-vols=
no-issue=4-1
article-no=
start-page=042410
end-page=
dt-received=
dt-revised=
dt-accepted=
dt-pub-year=2017
dt-pub=20171019
dt-online=
en-article=
kn-article=
en-subject=
kn-subject=
en-title=
kn-title=Numerical calculation on a two-step subdiffusion behavior of lateral protein movement in plasma membranes
en-subtitle=
kn-subtitle=
en-abstract=
kn-abstract= A two-step subdiffusion behavior of lateral movement of transmembrane proteins in plasma membranes has been observed by using single-molecule experiments. A nested double-compartment model where large compartments are divided into several smaller ones has been proposed in order to explain this observation. These compartments are considered to be delimited by membrane-skeleton "fences" and membrane-protein "pickets" bound to the fences. We perform numerical simulations of a master equation using a simple two-dimensional lattice model to investigate the heterogeneous diffusion dynamics behavior of transmembrane proteins within plasma membranes. We show that the experimentally observed two-step subdiffusion process can be described using fence and picket models combined with decreased local diffusivity of transmembrane proteins in the vicinity of the pickets. This allows us to explain the two-step subdiffusion behavior without explicitly introducing nested double compartments.
en-copyright=
kn-copyright=

en-aut-name=SumiTomonari
en-aut-sei=Sumi
en-aut-mei=Tomonari
kn-aut-name=
kn-aut-sei=
kn-aut-mei=
aut-affil-num=1
ORCID=

en-aut-name=OkumotoAtsushi
en-aut-sei=Okumoto
en-aut-mei=Atsushi
kn-aut-name=
kn-aut-sei=
kn-aut-mei=
aut-affil-num=2
ORCID=

en-aut-name=GotoHitoshi
en-aut-sei=Goto
en-aut-mei=Hitoshi
kn-aut-name=
kn-aut-sei=
kn-aut-mei=
aut-affil-num=3
ORCID=

en-aut-name=SekinoHideo
en-aut-sei=Sekino
en-aut-mei=Hideo
kn-aut-name=
kn-aut-sei=
kn-aut-mei=
aut-affil-num=4
ORCID=

affil-num=1
en-affil=Research Institute for Interdisciplinary Science and Department of Chemistry, Faculty of Science, Okayama University
kn-affil=

affil-num=2
en-affil= Department of Computer Science and Engineering, Graduate School of Engineering, Toyohashi University of Technology
kn-affil=

affil-num=3
en-affil= Department of Computer Science and Engineering, Graduate School of Engineering, Toyohashi University of Technology
kn-affil=

affil-num=4
en-affil= Department of Computer Science and Engineering, Graduate School of Engineering, Toyohashi University of Technology
kn-affil=
END

start-ver=1.4
cd-journal=joma
no-vol=19
cd-vols=
no-issue=5
article-no=
start-page=3370
end-page=3378
dt-received=
dt-revised=
dt-accepted=
dt-pub-year=2019
dt-pub=20190424
dt-online=
en-article=
kn-article=
en-subject=
kn-subject=
en-title=
kn-title=Is F-1-ATPase a Rotary Motor with Nearly 100% Efficiency? Quantitative Analysis of Chemomechanical Coupling and Mechanical Slip
en-subtitle=
kn-subtitle=
en-abstract=
kn-abstract= We present a chemomechanical network model of the rotary molecular motor F1-ATPase which quantitatively describes not only the rotary motor dynamics driven by ATP hydrolysis but also the ATP synthesis caused by forced reverse rotations. We observe a high reversibility of F1-ATPase, that is, the main cycle of ATP synthesis corresponds to the reversal of the main cycle in the hydrolysis-driven motor rotation. However, our quantitative analysis indicates that torque-induced mechanical slip without chemomechanical coupling occurs under high external torque and reduces the maximal efficiency of the free energy transduction to 40–80% below the optimal efficiency. Heat irreversibly dissipates not only through the viscous friction of the probe but also directly from the motor due to torque-induced mechanical slip. Such irreversible heat dissipation is a crucial limitation for achieving a 100% free-energy transduction efficiency with biological nanomachines because biomolecules are easily deformed by external torque.
en-copyright=
kn-copyright=

en-aut-name=SumiTomonari
en-aut-sei=Sumi
en-aut-mei=Tomonari
kn-aut-name=
kn-aut-sei=
kn-aut-mei=
aut-affil-num=1
ORCID=

en-aut-name=KlumppStefan
en-aut-sei=Klumpp
en-aut-mei=Stefan
kn-aut-name=
kn-aut-sei=
kn-aut-mei=
aut-affil-num=2
ORCID=

affil-num=1
en-affil=Research Institute for Interdisciplinary Science, Department of Chemistry, Faculty of Science, Okayama University
kn-affil=

affil-num=2
en-affil=Department Theory and Bio-Systems, Max Planck Institute of Colloids and Interfaces
kn-affil=
en-keyword=F-1-ATPase
kn-keyword=F-1-ATPase
en-keyword=rotary molecular motor
kn-keyword=rotary molecular motor
en-keyword=chemomechanical network model
kn-keyword=chemomechanical network model
en-keyword=free-energy transduction efficiency
kn-keyword=free-energy transduction efficiency
en-keyword=ATP synthesis
kn-keyword=ATP synthesis
en-keyword=torque-induced mechanical slip
kn-keyword=torque-induced mechanical slip
END

start-ver=1.4
cd-journal=joma
no-vol=36
cd-vols=
no-issue=26
article-no=
start-page=2009
end-page=2011
dt-received=
dt-revised=
dt-accepted=
dt-pub-year=2015
dt-pub=20150731
dt-online=
en-article=
kn-article=
en-subject=
kn-subject=
en-title=
kn-title=Erratum: "A solvation-free-energy functional: A reference-modified density functional formulation" [J. Comput. Chem. 2015, 36, 1359-1369].
en-subtitle=
kn-subtitle=
en-abstract=
kn-abstract=
en-copyright=
kn-copyright=

en-aut-name=SumiTomonari
en-aut-sei=Sumi
en-aut-mei=Tomonari
kn-aut-name=
kn-aut-sei=
kn-aut-mei=
aut-affil-num=1
ORCID=

en-aut-name=Mitsutake Ayori
en-aut-sei=Mitsutake
en-aut-mei= Ayori
kn-aut-name=
kn-aut-sei=
kn-aut-mei=
aut-affil-num=2
ORCID=

en-aut-name=Maruyama  Yutaka
en-aut-sei=Maruyama
en-aut-mei=  Yutaka
kn-aut-name=
kn-aut-sei=
kn-aut-mei=
aut-affil-num=3
ORCID=

affil-num=1
en-affil= Department of Chemistry, Faculty of Science, Okayama University
kn-affil=

affil-num=2
en-affil=Department of Physics, Keio University
kn-affil=

affil-num=3
en-affil=Department of Physics, Keio University
kn-affil=
END

start-ver=1.4
cd-journal=joma
no-vol=3
cd-vols=
no-issue=31
article-no=
start-page=12743
end-page=12750
dt-received=
dt-revised=
dt-accepted=
dt-pub-year=2013
dt-pub=20130507
dt-online=
en-article=
kn-article=
en-subject=
kn-subject=
en-title=
kn-title=Effects of hydrophobic hydration on polymer chains immersed in supercooled water
en-subtitle=
kn-subtitle=
en-abstract=
kn-abstract= A multiscale simulation of a hydrophobic polymer chain immersed in water including the supercooled region is presented. Solvent effects on the polymer conformation were taken into account via liquid–state density functional theory in which a free-energy functional model was constructed using a density response function of bulk water, determined from a molecular dynamics (MD) simulation. This approach overcomes sampling problems in simulations of high-viscosity polymer solutions in the deeply supercooled region. Isobars determined from the MD simulations of 4000 water molecules suggest a liquid–liquid transition in the deeply supercooled region. The multiscale simulation reveals that a hydrophobic polymer chain exhibits swelling upon cooling along isobars below a hypothesized second critical pressure; no remarkable swelling is observed at higher pressures. These observations agree with the behavior of a polymer chain in a Jagla solvent model that qualitatively reproduces the thermodynamics and dynamics of liquid water. A theoretical analysis of the results obtained from the multiscale simulation show that a decrease in entropy due to the swelling arises from the formation of a tetrahedral hydrogen bond network in the hydration shell.
en-copyright=
kn-copyright=

en-aut-name=SumiTomonari
en-aut-sei=Sumi
en-aut-mei=Tomonari
kn-aut-name=
kn-aut-sei=
kn-aut-mei=
aut-affil-num=1
ORCID=

en-aut-name=SekinoHideo
en-aut-sei=Sekino
en-aut-mei=Hideo
kn-aut-name=
kn-aut-sei=
kn-aut-mei=
aut-affil-num=2
ORCID=

affil-num=1
en-affil=Department of Chemistry, Okayama University
kn-affil=

affil-num=2
en-affil=Department of Computer Science and Engineering, Toyohashi University of Technology
kn-affil=
END