Language：English   Publishing type：Research paper (scientific journal)   Publisher：AIP Publishing  

Polymer electrolyte membranes, for example, the Nafion (TM) membranes, used in the fuel cells are responsible for separating reactive gas molecules as well as for the efficient exchange of protons. Although control of the permeation of the gases is important to enhance the fuel cell performance, the mechanism by which hydrogen and oxygen molecules permeate through the membranes remains unclear. To clarify the mechanism, we investigated the three-dimensional free-energy landscape of hydrogen and oxygen molecules in Nafion membranes with various water contents focusing on relevant diffusion paths. Low-free-energy paths are found mainly in the polymer phase and the interfacial region between the polymer and water phases. Thus, the path of the transportation may be attributed to the polymer phase and interfacial phases. However, the free-energy value in the aqueous phase is only slightly higher (& SIM;1-2 k(B)T) than that in the other two phases, which indicates that a secondary contribution from the aqueous phase is expected. The free-energy landscape in the polymer and interfacial phases was found rugged, while it is comparatively flat in the water phase. We also found that an increase in water content brings about a smoother free-energy landscape in the polymer and interfacial phases. The decreased ruggedness may facilitate the gas diffusivity. These observations help understand the molecular mechanism of the gas diffusion in the membranes.

DOI： 10.1063/5.0075969

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Authorship：Lead author   Publishing type：Research paper (scientific journal)   Publisher：Wiley  

DOI： 10.1002/jcc.26742

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Other Link： https://onlinelibrary.wiley.com/doi/full-xml/10.1002/jcc.26742

Authorship：Lead author   Language：English   Publishing type：Research paper (scientific journal)   Publisher：{AIP} Publishing  

DOI： 10.1063/5.0065765

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Language：English   Publishing type：Research paper (scientific journal)   Publisher：Elsevier BV  

DOI： 10.1016/j.polymer.2021.123809

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Language：English   Publishing type：Research paper (scientific journal)   Publisher：American Chemical Society ({ACS})  

The authors propose a novel method to evaluate the position-dependent diffusion constant by analyzing unperturbed segments of a trajectory determined by the additional flat-bottom potential. The accuracy of this novel method is first established by studying homogeneous systems, where the reference value can be obtained by the Einstein relation. The applicability of this new method to heterogeneous systems is then demonstrated by studying a hydrophobic solute near a hydrophobic wall. The proposed method is also comprehensively compared with popular conventional methods, whereby the significance of the present method is illustrated. The novel method is powerful and useful for studying kinetics in heterogeneous systems based on molecular dynamics calculations.

DOI： 10.1021/acs.jctc.0c00448

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Language：English   Publishing type：Research paper (scientific journal)   Publisher：Elsevier BV  

DOI： 10.1016/j.polymer.2020.122908

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Language：English   Publishing type：Research paper (international conference proceedings)  

©2020 IUPAC & De Gruyter. This work is licensed under a Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International License. For more information, please visit: http://creativecommons.org/licenses/by-nc-nd/4.0/ 2020. Entecavir, triphosphorylated in liver cells, is an antiviral reagent against Hepatitis B virus (HBV). The reagent inhibits reverse transcription of RNA inside the virus capsid. In the present study, free energy profile of an Entecavir triphosphate (ETVTP) molecule has been calculated when it passes through pores of the capsid along two-and three-fold rotational symmetry axes in order to investigate permeation pathway of the reagent to the inside of the capsid. The calculations have been done based on thermodynamic integration (TI) method combined with all-Atomistic molecular dynamic (MD) calculations. A free energy minimum of-19 kJ/mol was found at the entrance of the pore from the outside along the three-fold symmetry axis. This stabilization is from the interaction of negatively charged ETVTP with positively charged capsid methionine residues. This excess free energy concentrates of the reagent at the entrance of the pore by a factor of about 2000. A free energy barrier of approximately 13 kJ/mol was also found near the exit of the pore to the inside of the capsid due to narrow space of the pore surrounded by hydrophobic wall made by proline residues and negatively charged wall by aspartic acid residues. There, ETVTP is partially dehydrated in order to pass through the narrow space, which causes the great free energy loss. Further, the negatively charged residues produce repulsive forces on the ETVTP molecule. In contrast, in the case of the pore along the two-fold symmetry axis, the calculated free energy profile showed shallower free energy minimum,-4 kJ/mol at the entrance in spite of the similarly high barrier, 7 kJ/mol, near the exit of the pore.

DOI： 10.1515/pac-2020-0109

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Language：English   Publishing type：Research paper (scientific journal)  

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Language：English   Publishing type：Research paper (scientific journal)   Publisher：Elsevier {BV}  

DOI： 10.1016/j.polymer.2019.121570

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Language：English   Publishing type：Research paper (scientific journal)   Publisher：Elsevier {BV}  

DOI： 10.1016/j.polymer.2019.03.006

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Language：English   Publishing type：Research paper (scientific journal)   Publisher：Beijing University Press  

Surfactant molecules, when dispersed in solution, have been shown to spontaneously form aggregates. Our previous studies on molecular dynamics (MD) calculations have shown that ionic sodium dodecyl sulfate molecules quickly aggregated even when the aggregation number is small. The aggregation rate, however, decreased for larger aggregation numbers. In addition, studies have shown that micelle formation was not completed even after a 100 ns-long MD run (Chem. Phys. Lett. 2016, 646, 36). Herein, we analyze the free energy change of micelle formation based on chemical species model combined with molecular dynamics calculations. First, the free energy landscape of the aggregation, ∆G† i+j, where two aggregates with sizes i and j associate to form the (i + j)-mer, was investigated using the free energy of micelle formation of the i-mer, Gi†, which was obtained through MD calculations. The calculated ∆G† i+j was negative for all the aggregations where the sum of DS ions in the two aggregates was 60 or less. From the viewpoint of chemical equilibrium, aggregation to the stable micelle is desired. Further, the free energy profile along possible aggregation pathways was investigated, starting from small aggregates and ending with the complete thermodynamically stable micelles in solution. The free energy profiles, G(l, k), of † the aggregates at l-th aggregation path and k-th state were evaluated by the formation free energy Σ ni (l,k)Giand the i free energy of mixingΣ ni (l,k)kBTln(ni (l,k) / n(l,k)), where ni(l, k) is the number of i-mer in the system at the l-th i Σ i i aggregation path and k-th state, with n(l,k) (l,k) = n. All the aggregation pathways were obtained from the initial state of 12 pentamers to the stable micelle with i = 60. All the calculated G(l, k) values monotonically decreased with increasing k. This indicates that there are no free energy barriers along the pathways. Hence, the slowdown is not due to the thermodynamic stability of the aggregates, but rather the kinetics that inhibit the association of the fragments. The time required for a collision between aggregates, one of the kinetic factors, was evaluated using the fast passage time, tFPT. The calculated tFPT was about 20 ns for the aggregates with N = 31. Therefore, if aggregation is a diffusion-controlled process, it should be completed within the 100 ns-simulation. However, aggregation does not occur due to the free energy barrier between the aggregates, that is, the repulsive force acting on them. This may be caused by electrostatic repulsions produced by the overlap of the electric double layers, which are formed by the negative charge of the hydrophilic

DOI： 10.3866/PKU.WHXB201802271

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Language：English   Publishing type：Research paper (scientific journal)   Publisher：AMER INST PHYSICS  

In our previous study, all-atomistic molecular dynamics (MD) calculations have been carried out for the aggregation of ionic sodium dodecyl sulfate in water [S. Kawada et al., Chem. Phys. Lett. 646, 36 (2016)]. Aggregates of 20-30 dodecyl sulfate ions were formed within a short MD run for 10 ns. However, further aggregation did not occur despite a long MD calculation for more than 100 ns. This suggests that strong electrostatic repulsive interactions between the aggregates prevent the fusion of the aggregates. In the present study, mean force and potential of mean force acting between two aggregates with aggregation number N = 30 were evaluated as a function of their separation by MD calculations. The repulsive force becomes strong with decreasing distance between the two aggregates before they merge into one. An origin of the repulsive force is an electric double layer formed by the sulfate group and counter sodium ions. Strength of the repulsive force is in good agreement with the theoretical value given by the Derjaguin-Landau-Verwey-Overbeek (DLVO) theory. Once the aggregates establish contact, the force between them turns to be a large attractive force that can be explained by the interfacial tension. In order to form a single micelle from the two aggregates, it is necessary for them to climb over a free energy barrier of 23 kJ/mol. Once, the barrier is overcome, the micelle is stabilized by similar to 200 kJ/mol. The time constant of aggregation evaluated from the calculated free energy barrier was about 28 mu s at the concentration in our previous study. Published by AIP Publishing.

DOI： 10.1063/1.4998549

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Language：English   Publishing type：Research paper (scientific journal)   Publisher：AMER INST PHYSICS  

The surface structure and its fluctuation of spherical micelles were investigated using a series of density correlation functions newly defined by spherical harmonics and Legendre polynomials based on the molecular dynamics calculations. To investigate the influence of head-group charges on the micelle surface structure, ionic sodium dodecyl sulfate and nonionic octaethyleneglycol monododecylether (C12E8) micelles were investigated as model systems. Large-scale density fluctuations were observed for both micelles in the calculated surface static structure factor. The area compressibility of the micelle surface evaluated by the surface static structure factor was tens-of-times larger than a typical value of a lipid membrane surface. The structural relaxation time, which was evaluated from the surface intermediate scattering function, indicates that the relaxation mechanism of the long-range surface structure can be well described by the hydrostatic approximation. The density fluctuation on the two-dimensional micelle surface has similar characteristics to that of three-dimensional fluids near the critical point. Published by AIP Publishing.

DOI： 10.1063/1.4994698

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Language：English   Publishing type：Research paper (scientific journal)   Publisher：WILEY-V C H VERLAG GMBH  

Wide-angle X-ray scattering experiments and allatomistic molecular dynamics calculations were performed to elucidate the detailed structure of bilayer vesicles constructed by self-assembly of an amphiphilic palladium NCNpincer complex. We found an excellent agreement between the experimental and calculated X-ray spectra, and between the membrane thickness determined from a TEM image and that calculated from an electron-density profile, which indicated that the calculated structure was highly reliable. The analysis of the simulated bilayer structure showed that in general the membrane was softer than other phospholipid bilayer membranes. In this bilayer assemblage, the degree of alignment of complex molecules in the bilayer membrane was quite low. An analysis of the electron-density profile shows that the bilayer assemblage contains a space through which organic molecules can exit. Furthermore, the catalytically active center is near this space and is easily accessible by organic molecules, which permits the bilayer membrane to act as a nanoreactor. The free energy of permeation of water through the bilayer membrane of the amphiphilic complex was 12 kJmol(-1), which is much lower than that for phospholipid bilayer membranes in general. Organic molecules are expected to pass though the bilayer membrane. The self-assembled vesicles were shown to be catalytically active in a Miyaura-Michael reaction in water.

DOI： 10.1002/chem.201603494

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Language：English   Publishing type：Research paper (scientific journal)   Publisher：TAYLOR & FRANCIS LTD  

We studied dynamic scaling law for the early stage domain growth in the micelle aggregation process of dispersed surfactant molecules in water for zwitterionic dodecyldimethylamine oxide (DDAO) and cationic dodecyltrimethylammonium chloride (DTAC) based on all-atomistic molecular dynamics calculations. For both surfactants, the aggregation number N increases in proportion to t(alpha)', where t and alpha' are the simulation time and exponent of the dynamic scaling, respectively. When the aggregation is controlled by diffusion, it follows the well-known Lifshitz-Slyozov (LS) law giving the exponent alpha' = 1. The values of a' obtained for DDAO and DTAC are 0.6 and 0.3, respectively, indicating that the aggregation rate is suppressed compared with purely diffusion controlled LS process. The aggregation of DDAO and DTAC may be partly controlled by electrostatic interaction between the aggregates.

DOI： 10.1080/08927022.2017.1328557

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Language：English   Publishing type：Research paper (scientific journal)   Publisher：AMER INST PHYSICS  

To obtain the radial (normal) and lateral (transverse) components of the local pressure tensor, P-N(R) and P-T(R), respectively, and the interfacial tension of micelles, molecular dynamics (MD) calculations were performed for spherical sodium dodecyl sulfate (SDS) micelles. The local pressure tensor was calculated as a function of radial distance R using the Irving-Kirkwood formula. Similar MD calculations were also carried out for an n-dodecane droplet in water to compare the differences in the local pressure and interfacial tension values with those of the micelles. The calculated interfacial tensions were 20 +/- 5 and 44 +/- 10 mN/m for the SDS micelles and dodecane droplets, respectively. The excess free energies due to the interfacial tension were 340 and 1331 kJ/mol for the SDS micelle and dodecane droplet, respectively. The micelles are stabilized by 991 kJ/mol by covering their hydrophobic cores with hydrophilic groups. The dodecane droplet has a large interfacial tension caused by the zero or positive values of P-N(R) - P-T(R) at all values of R. In contrast, the small interfacial tension in the SDS micelles comes from the negative P-N(R) - P-T(R) values over a wide range of R. The pressure difference between the inside and outside of the oil droplet and its interfacial tension well satisfies the Laplace equation. However, the hydrophobic core of the SDS micelle is quite different from the liquid alkane, and the SDS micelles do not follow Laplace's picture. Decomposing the interfacial tension into contributions from various interactions, it is found that those between charged and polar groups dominate the interfacial tension of the SDS micelles. The positive electrostatic potential (1.3 V) on the micelle surface and the negative potential (-0.15 V) on the oil droplet contribute to the interfacial tensions by 19 and 0.5 mN/m, respectively. Thus, the interfacial tension of the SDS micelles is produced by electrostatic interactions, in contrast to the dodecane droplet. Published by AIP Publishing.

DOI： 10.1063/1.4953405

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Language：English   Publishing type：Research paper (scientific journal)   Publisher：PUBLIC LIBRARY SCIENCE  

The efficacy and bias of signal transduction induced by a drug at a target protein are closely associated with the benefits and side effects of the drug. In particular, partial agonist activity and G-protein/beta-arrestin-biased agonist activity for the G-protein-coupled receptor (GPCR) family, the family with the most target proteins of launched drugs, are key issues in drug discovery. However, designing GPCR drugs with appropriate efficacy and bias is challenging because the dynamic mechanism of signal transduction induced by ligand-receptor interactions is complicated. Here, we identified the G-protein/beta-arrestin-linked fluctuating network, which initiates large-scale conformational changes, using sub-microsecond molecular dynamics (MD) simulations of the beta(2)-adrenergic receptor (beta(2)AR) with a diverse collection of ligands and correlation analysis of their G protein/beta-arrestin efficacy. The G-protein-linked fluctuating network extends from the ligand-binding site to the G-protein-binding site through the connector region, and the beta-arrestin-linked fluctuating network consists of the NPxxY motif and adjacent regions. We confirmed that the averaged values of fluctuation in the fluctuating network detected are good quantitative indexes for explaining G protein/beta-arrestin efficacy. These results indicate that short-term MD simulation is a practical method to predict the efficacy and bias of any compound for GPCRs.

DOI： 10.1371/journal.pone.0155816

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Language：English   Publishing type：Research paper (scientific journal)   Publisher：ELSEVIER SCIENCE BV  

Molecular dynamics calculations for anionic SOS, cationic DTAC, zwitterionic DDAO, nonionic C12E8 micelles, and dodecane droplets as a reference, were carried out in order to obtain the relation between the head group charges and structure of the micelle. The radial density profile of the carbon atom of hydrophobic tail shows a low-density region at the micelle center, where small hydrophobic solutes may be solubilized. This is commonly found among the micelles investigated in the present study. This indicates that the deep part of the micelle core is not influenced by the head group charges. In contrast, structure of surface of the hydrophobic core of the micelles is strongly influenced by the head groups. Fluctuation of the surface of the ionic SDS micelle is restricted by the strong Coulombic interaction between the charges of the sulfate groups and counter sodium ions. In the other micelles, this effect disappears so that a large fluctuation occurs on the micelle surface. The volume of solvent water decreases when the ionic SDS and DTAC micelles dissolved into water. Because of the strong electrostatic field around the micelle, orientation of water molecules has strong correlations with the micelles. Then, the tetrahedral water structure breaks. In particular, the density increases around the SDS micelles because of the strong attraction toward the sulfate groups. Thus, the volume shrinkage occurs. (C) 2015 Elsevier B.V. All rights reserved.

DOI： 10.1016/j.molliq.2015.12.062

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Language：English   Publishing type：Research paper (scientific journal)   Publisher：ELSEVIER SCIENCE BV  

In order to clarify the early-stage kinetics of micelle formation in concentrated surfactant solutions, all-atom molecular dynamics (MD) calculations of the aggregation of surfactant molecules dispersed in water were performed for ionic sodium dodecyl sulfate (SDS), nonionic octaethyleneglycol monododecyl ether (C12E8), and n-dodecane. The relationship between aggregate domain length and elapsed time from the beginning of the MD calculation obeyed the well-known Lifshitz-Slyozov (LS) law for C12E8 and n-dodecane. In contrast, the aggregation rate of SDS did not obey the LS law. This difference is likely due to the differences in strength of the electrostatic interactions between the aggregates. (C) 2016 Elsevier B.V. All rights reserved.

DOI： 10.1016/j.cplett.2015.12.062

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Language：English   Publishing type：Research paper (scientific journal)   Publisher：AMER INST PHYSICS  

In order to investigate shape of the micelles and its thermal fluctuations, molecular dynamics calculations have been performed for spherical ionic sodium dodecyl sulfate (SDS) and nonionic octaethyleneglycol monododecyl ether (C12E8) micelles. New statistical functions suitable for extracting the fluctuations of the shape of the spherical micelles were defined using spherical harmonics and Legendre polynomials. The breathing and deforming modes of the SDS and C12E8 micelles were analyzed in detail based on these new functions. The elastic nature of the micelle core was also discussed. The present analysis gives a new molecular picture that the micelle shape is a superposition of the various kinds of breathing and deforming modes, and each mode has a specific relaxation time of the shape fluctuation. (C) 2016 AIP Publishing LLC.

DOI： 10.1063/1.4940031

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Language：English   Publishing type：Research paper (scientific journal)   Publisher：WILEY-BLACKWELL  

A large number of molecular dynamics (MD) simulations have been carried out so far on personal computer clusters and conventional supercomputers using general-purpose MD software such as NAMD, GROMACS, CHARMM, and AMBER. The development of MD simulation program is closely related to the architecture of the computers. Recent trend of MD simulation is headed to large-scale calculation, long-time calculation of small systems, and calculation for large statistics. The most challenging one is the large-scale calculation. To realize the large-scale calculation, we have to efficiently control the massively parallel supercomputers with several 10 thousands of nodes. There, it is essential to develop software having a compatibility of such computer architecture. Recently, we have developed general-purpose MD software MODYLAS (MOlecular DYnamics simulation software for LArge Systems) for massively parallel supercomputers such as K-computer. Here, we describe the outline, important features, and computation of MODYLAS. An example result of the 200 ns-MD simulation of the viral capsid system consisting of about 6,500,000 atoms is also presented. (c) 2014 Wiley Periodicals, Inc.

DOI： 10.1002/qua.24841

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Language：English   Publishing type：Research paper (scientific journal)   Publisher：AMER INST PHYSICS  

Small viruses that belong, for example, to the Picornaviridae, such as poliovirus and foot-and-mouth disease virus, consist simply of capsid proteins and a single-stranded RNA (ssRNA) genome. The capsids are quite stable in solution to protect the genome from the environment. Here, based on longtime and large-scale 6.5 x 10(6) all-atom molecular dynamics calculations for the Mahoney strain of poliovirus, we show microscopic properties of the viral capsids at a molecular level. First, we found equilibrium rapid exchange of water molecules across the capsid. The exchange rate is so high that all water molecules inside the capsid (about 200 000) can leave the capsid and be replaced by water molecules from the outside in about 25 mu s. This explains the capsid's tolerance to high pressures and deactivation by exsiccation. In contrast, the capsid did not exchange ions, at least within the present simulation time of 200 ns. This implies that the capsid can function, in principle, as a semipermeable membrane. We also found that, similar to the xylem of trees, the pressure of the solution inside the capsid without the genome was negative. This is caused by coulombic interaction of the solution inside the capsid with the capsid excess charges. The negative pressure may be compensated by positive osmotic pressure by the solution-soluble ssRNA and the counter ions introduced into it. (C) 2014 AIP Publishing LLC.

DOI： 10.1063/1.4897557

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Language：English   Publishing type：Research paper (scientific journal)   Publisher：AMER CHEMICAL SOC  

The origin of high solubility of poly(oxyethylene) in water has been an open question. Although it is thought that the high solubility of poly(oxyethylene) arises from an increase of the trans-gauche-trans (tgt) conformer in water, the relationship between the increase of the tgt conformer and the solubility is unclear. In this study, we have investigated the conformational equilibria of 1,2-dimethoxyethane, which is a model molecule for poly(oxyethylene), by using Raman spectroscopy, and determined the change in the population and the free energy of each conformer with the aid of density functional theory calculations. The free energy of transfer of the tgt conformer from the pure liquid to the water phase is -6.1 +/- 0.2 kJ mol(-1). Furthermore, the fraction of the tgt conformer increases from 0.37 to 0.78. Thus, the net contribution of the tgt conformer is -4.8 +/- 0.2 kJ mol(-1), which is 79% of the total free energy of transfer (-6.07 kJ mol(-1)). This demonstrates that the high solubility of 1,2-dimethoxyethane originates from the lowest free energy and the highest fraction of the tgt conformer in water. We also successfully explain the thermodynamic mechanism of the low solubility of dimethoxymethane, which is the model molecule for poly(oxymethylene).

DOI： 10.1021/jp5048997

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Language：English   Publishing type：Research paper (scientific journal)   Publisher：AMER CHEMICAL SOC  

Our new molecular dynamics (MD) simulation program, MODYLAS, is a general-purpose program appropriate for very large physical, chemical, and biological systems. It is equipped with most standard MD techniques. Long-range forces are evaluated rigorously by the fast multipole method (FMM) without using the fast Fourier transform (FFT). Several new methods have also been developed for extremely fine-grained parallelism of the MD calculation. The virtually buffering-free methods for communications and arithmetic Operations, the minimal communication latency algorithm, and the parallel bucket-relay communication algorithm for the upper-level multipole moments in the FMM realize excellent scalability. The methods for blockwise arithmetic operations avoid data reload, attaining very small cache miss rates. Benchmark tests for MODYLAS using 65 536 nodes of the K-computer showed that the overall calculation time per MD step including communications is as short as about 5 ins for a 10 million-atom system; that is, 35 ns of simulation time can be computed per day. The program enables investigations of large-scale real systems such as viruses, liposomes, assemblies of proteins and micelles, and polymers.

DOI： 10.1021/ct400203a

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Language：English   Publishing type：Research paper (scientific journal)   Publisher：AMER INST PHYSICS  

Free energy of transfer of methylamine, octylamine, methanol, and octanol from water phase to sodium dodecyl sulfate (SI)S) micelle has been calculated using thermodynamic integration method combined with molecular dynamics calculations. Together with the results for alkanes obtained in our previous study [K. Fujimoto, N. Yoshii, and S. Okazaki, J. Chem. Phys. 133, 074511 (2010)], the effect of polar group on the partition of hydrophilic solutes between water phase and the micelle has been investigated in detail at a molecular level. The calculations showed that the molecules with octyl group are more stable in the SDS micelle than in the water phase due to their hydrophobicity of long alkyl chain. In contrast, methanol and methylamine are stable in the water phase as well as in the micelle because of their high hydrophilicity. The spatial distribution of methylamine, octylamine, methanol, and octanol has also been evaluated as a function of the distance, R, from the center of mass of SDS micelle to the solutes. The distribution shows that the methylamine molecule is adsorbed on the SDS micelle surface, while the methanol molecule is delocalized among the whole system, i.e., in the water phase, on the surface of the micelle, and in the hydrophobic core of the micelle. The octylamine and octanol molecules are solubilized in the SDS micelle with palisade layer structure and are not found in the water phase. (C) 2012 American Institute of Physics. [http://dx.doi.org/10.1063/1.4747491]

DOI： 10.1063/1.4747491

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Language：English   Publishing type：Research paper (scientific journal)   Publisher：AMER INST PHYSICS  

The free energy profiles, Delta G(r), for penetration of methane and water molecules into sodium dodecyl sulfate (SDS) micelles have been calculated as a function of distance r from the SDS micelle to the methane and water molecules, using the thermodynamic integration method combined with molecular dynamics calculations. The calculations showed that methane is about 6-12 kJ mol(-1) more stable in the SDS micelle than in the water phase, and no Delta G(r) barrier is observed in the vicinity of the sulfate ions of the SDS micelle, implying that methane is easily drawn into the SDS micelle. Based on analysis of the contributions from hydrophobic groups, sulfate ions, sodium ions, and solvent water to Delta G(r), it is clear that methane in the SDS micelle is about 25 kJ mol(-1) more stable than it is in the water phase because of the contribution from the solvent water itself. This can be understood by the hydrophobic effect. In contrast, methane is destabilized by 5-15 kJ mol(-1) by the contribution from the hydrophobic groups of the SDS micelle because of the repulsive interactions between the methane and the crowded hydrophobic groups of the SDS. The large stabilizing effect of the solvent water is higher than the repulsion by the hydrophobic groups, driving methane to become solubilized into the SDS micelle. A good correlation was found between the distribution of cavities and the distribution of methane molecules in the micelle. The methane may move about in the SDS micelle by diffusing between cavities. In contrast, with respect to the water, Delta G(r) has a large positive value of 24-35 kJ mol(-1), so water is not stabilized in the micelle. Analysis showed that the contributions change in complex ways as a function of r and cancel each other out. Reference calculations of the mean forces on a penetrating water molecule into a dodecane droplet clearly showed the same free energy behavior. The common feature is that water is less stable in the hydrophobic core than in the water phase because of the energetic disadvantage of breaking hydrogen bonds formed in the water phase. The difference between the behaviors of the SDS micelles and the dodecane droplets is found just at the interface; this is caused by the strong surface dipole moment formed by sulfate ions and sodium ions in the SDS micelles. (C) 2012 American Institute of Physics. [doi:10.1063/1.3671997]

DOI： 10.1063/1.3671997

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Language：English   Publishing type：Research paper (scientific journal)   Publisher：TAYLOR & FRANCIS LTD  

Enthalpy and entropy of transfer from water phase to a sodium dodecyl sulphate (SDS) micelle core Delta H-w -> m and T Delta S-w -> m, respectively, have been investigated by molecular dynamics calculation for a series of hydrophobic solutes originally immiscible with water. It is found that both thermodynamic quantities decrease as a function of number of carbon atoms of the alkanes. Structural behaviour of the solubilised alkane molecules in the micelle has been analysed too. The calculated distribution functions show that methane moves around the whole core, whereas the alkane molecules larger than methane are localised in the centre of the core, i.e. the low-density region of the alkyl chains of SDS.

DOI： 10.1080/08927022.2010.533275

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Language：English   Publishing type：Research paper (scientific journal)   Publisher：AMER INST PHYSICS  

Free energy of transfer, Delta G(w -> m), from water phase to a sodium dodecyl sulfate (SDS) micelle core has been calculated for a series of hydrophobic solutes originally immiscible with water by thermodynamic integration method combined with molecular dynamics calculations. The calculated free energy of transfer is in good correspondence to the experiment as well as the theoretical free energy of transfer. The calculated Delta G(w -> m)'s are all negative, implying that the alkane molecules are more stable in the micelle than in the water phase. It decreases almost linearly as a function of the number of carbon atoms of the alkanes longer than methane with a decrement of 3.3 kJ mol(-1) per one methylene group. The calculated free energy of transfer indicates that, for example, at the micelle concentration of 50 CMC (critical micelle concentration), about only 1 of 6 micelles or 1 of 32 000 micelles does not contain a solute methane or n-octane molecule, respectively. (C) 2010 American Institute of Physics. [doi:10.1063/1.3469772]

DOI： 10.1063/1.3469772

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Authorship：Lead author   Language：Japanese   Publishing type：Article, review, commentary, editorial, etc. (other)  

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J-GLOBAL

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Authorship：Lead author,　Last author,　Corresponding author   Language：Japanese   Publishing type：Article, review, commentary, editorial, etc. (trade magazine, newspaper, online media)  

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Authorship：Lead author,　Last author,　Corresponding author   Language：Japanese   Publishing type：Article, review, commentary, editorial, etc. (other)  

CiNii Books

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Authorship：Lead author,　Last author,　Corresponding author   Language：Japanese   Publishing type：Article, review, commentary, editorial, etc. (other)  

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Event date： 2024.12

Language：Japanese   Presentation type：Poster presentation  

Venue：アクリエひめじ, 兵庫県姫路市   Country：Japan  

学生優秀発表賞受賞

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Event date： 2024.12

Language：Japanese   Presentation type：Poster presentation  

Venue：アクリエひめじ, 兵庫県姫路市   Country：Japan  

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Event date： 2024.11

Language：English   Presentation type：Oral presentation (invited, special)  

Venue：Tohoku University Katahira Campus, Sendai, Miyagi   Country：Japan  

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Event date： 2024.11

Language：Japanese   Presentation type：Oral presentation (general)  

Venue：京都府京都市左京区, 国立京都国際会館   Country：Japan  

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Event date： 2024.11

Language：Japanese   Presentation type：Oral presentation (general)  

Venue：京都府京都市左京区 国立京都国際会館   Country：Japan  

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Event date： 2024.11

Language：Japanese   Presentation type：Oral presentation (general)  

Country：Japan  

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Event date： 2024.11

Language：English   Presentation type：Poster presentation  

Venue：the Bankoku Shinryokan at The Busena Terrace, Nago-shi, Okinawa   Country：Japan  

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Event date： 2024.11

Language：Japanese   Presentation type：Oral presentation (invited, special)  

Venue：愛媛大学城北キャンパス 理学部本館, 愛媛県松山市   Country：Japan  

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Event date： 2024.10 - 2024.11

Language：Japanese   Presentation type：Oral presentation (general)  

Venue：名古屋市工業研究所, 愛知県名古屋市熱田区   Country：Japan  

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Event date： 2024.9

Language：Japanese   Presentation type：Poster presentation  

Country：Japan  

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Event date： 2024.9

Language：Japanese   Presentation type：Poster presentation  

Country：Japan  

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Event date： 2024.8

Language：Japanese   Presentation type：Oral presentation (general)  

Venue：愛知県名古屋市天白区 名城大学天白キャンパス   Country：Japan  

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Event date： 2023.12

Language：Japanese   Presentation type：Oral presentation (general)  

Venue：福井県   Country：Japan  

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Event date： 2023.11

Language：Japanese   Presentation type：Oral presentation (general)  

Venue：福井県   Country：Japan  

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Event date： 2023.11

Language：Japanese   Presentation type：Oral presentation (general)  

Venue：福井県   Country：Japan  

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Event date： 2023.10

Language：Japanese   Presentation type：Public lecture, seminar, tutorial, course, or other speech  

Venue：名古屋   Country：Japan  

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Event date： 2023.10

Language：English   Presentation type：Oral presentation (invited, special)  

Venue：Taipei   Country：Taiwan, Province of China  

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Event date： 2023.9

Language：Japanese   Presentation type：Oral presentation (general)  

Venue：香川県   Country：Japan  

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Event date： 2023.9

Language：Japanese   Presentation type：Oral presentation (invited, special)  

Venue：北海道   Country：Japan  

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Event date： 2023.9

Language：English   Presentation type：Poster presentation  

Venue：Bordeaux   Country：France  

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Event date： 2022.10

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Event date： 2022.9

Language：Japanese   Presentation type：Oral presentation (general)  

Venue：徳島   Country：Japan  

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Event date： 2022.9

Language：Japanese   Presentation type：Oral presentation (general)  

Venue：徳島   Country：Japan  

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Event date： 2022.9

Language：Japanese   Presentation type：Oral presentation (general)  

Venue：徳島   Country：Japan  

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Event date： 2022.9

Language：Japanese   Presentation type：Oral presentation (general)  

Venue：徳島   Country：Japan  

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Event date： 2022.9

Language：Japanese   Presentation type：Oral presentation (general)  

Venue：北海道   Country：Japan  

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Event date： 2022.9

Language：Japanese   Presentation type：Oral presentation (general)  

Venue：北海道   Country：Japan  

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Event date： 2022.9

Language：Japanese   Presentation type：Oral presentation (general)  

Venue：北海道   Country：Japan  

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Event date： 2022.9

Language：Japanese   Presentation type：Poster presentation  

Venue：北海道   Country：Japan  

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Event date： 2022.9

Language：Japanese   Presentation type：Poster presentation  

Venue：北海道   Country：Japan  

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Event date： 2022.5

Presentation type：Oral presentation (invited, special)  

Venue：オンライン   Country：Japan  

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Event date： 2021.12

Language：English   Presentation type：Oral presentation (general)  

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Event date： 2021.9

Language：Japanese   Presentation type：Oral presentation (general)  

Country：Japan  

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Event date： 2021.9

Language：Japanese   Presentation type：Oral presentation (general)  

Venue：北海道大学   Country：Japan  

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Event date： 2021.9

Language：Japanese   Presentation type：Oral presentation (general)  

Country：Japan  

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Event date： 2021.9

Language：Japanese   Presentation type：Oral presentation (general)  

Venue：北海道大学   Country：Japan  

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Event date： 2021.9

Language：Japanese   Presentation type：Oral presentation (general)  

Country：Japan  

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Event date： 2021.9

Language：Japanese   Presentation type：Poster presentation  

Country：Japan  

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Event date： 2021.9

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Event date： 2021.9

Language：Japanese   Presentation type：Oral presentation (general)  

Venue：オンライン   Country：Japan  

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Event date： 2021.9

Language：Japanese   Presentation type：Oral presentation (general)  

Venue：オンライン   Country：Japan  

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Event date： 2021.9

Language：Japanese   Presentation type：Oral presentation (general)  

Venue：オンライン   Country：Japan  

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Event date： 2021.6

Language：Japanese   Presentation type：Public lecture, seminar, tutorial, course, or other speech  

Venue：オンライン  

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Event date： 2021.5

Language：Japanese   Presentation type：Oral presentation (general)  

Venue：オンライン  

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Event date： 2021.5

Language：Japanese   Presentation type：Poster presentation  

Venue：オンライン  

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Event date： 2021.2

Language：English   Presentation type：Oral presentation (invited, special)  

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Event date： 2020.10

Language：Japanese  

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Event date： 2020.9

Language：Japanese   Presentation type：Oral presentation (general)  

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Event date： 2019.11

Language：English   Presentation type：Poster presentation  

Country：Korea, Republic of  

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Event date： 2019.11

Language：English   Presentation type：Poster presentation  

Country：Korea, Republic of  

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Event date： 2019.11

Language：English   Presentation type：Oral presentation (invited, special)  

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Event date： 2019.11

Language：English   Presentation type：Poster presentation  

Country：Korea, Republic of  

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Event date： 2019.9

Language：Japanese   Presentation type：Oral presentation (general)  

Venue：福井大学文京キャンパス   Country：Japan  

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Event date： 2019.5

Language：Japanese   Presentation type：Poster presentation  

Country：Japan  

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Event date： 2019.5

Language：Japanese   Presentation type：Poster presentation  

Country：Japan  

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Event date： 2018.11

Language：English   Presentation type：Poster presentation  

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Event date： 2018.9

Presentation type：Oral presentation (general)  

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Event date： 2018.9

Presentation type：Oral presentation (general)  

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Event date： 2017.11

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Event date： 2016.11 - 2016.12

Presentation type：Oral presentation (general)  

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Event date： 2016.11 - 2016.12

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Event date： 2016.11 - 2016.12

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Event date： 2016.11

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Event date： 2016.11

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Event date： 2016.10

Language：English   Presentation type：Poster presentation  

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Event date： 2016.9

Language：English   Presentation type：Poster presentation  

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Event date： 2016.5

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Event date： 2016.5

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Event date： 2014.11

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Event date： 2014.5

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Event date： 2013.11

Presentation type：Poster presentation  

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Event date： 2013.11

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Event date： 2013.11

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Event date： 2013.11

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Event date： 2013.11

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Event date： 2013.11

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Event date： 2013.11

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Event date： 2013.11

Presentation type：Poster presentation  

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Event date： 2013.10

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Event date： 2013.9

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Event date： 2013.9

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Event date： 2013.9

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Event date： 2013.9

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Event date： 2013.9

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Event date： 2013.5

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Event date： 2012.11

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Event date： 2012.11

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Event date： 2012.11

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Event date： 2012.10

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Event date： 2012.7

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Event date： 2011.12

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Language：Japanese   Presentation type：Oral presentation (invited, special)  

Venue：兵庫県立大学 姫路工学キャンパス, 兵庫県姫路市   Country：Japan  

依頼講演

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Language：Japanese   Presentation type：Oral presentation (invited, special)  

Venue：オンライン   Country：Japan  

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Language：English   Presentation type：Poster presentation  

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Language：English   Presentation type：Oral presentation (general)  

Venue：Yokohama, Japan  

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Language：English   Presentation type：Oral presentation (general)  

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Language：Japanese   Presentation type：Oral presentation (general)  

Venue：名古屋市公会堂  

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Language：Japanese   Presentation type：Oral presentation (general)  

Venue：名古屋市公会堂  

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Language：English   Presentation type：Oral presentation (general)  

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Language：Japanese  

Venue：静岡  

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Language：Japanese  

Venue：東京  

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Presentation type：Poster presentation  

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Language：Japanese  

Venue：東京  

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Language：Japanese   Presentation type：Oral presentation (general)  

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Language：Japanese   Presentation type：Poster presentation  

Venue：福井大学文京キャンパス  

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Language：Japanese   Presentation type：Oral presentation (general)  

Venue：福井  

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Language：Japanese   Presentation type：Oral presentation (general)  

Venue：福井大学文京キャンパス  

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Language：English   Presentation type：Poster presentation  

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Language：Japanese   Presentation type：Oral presentation (general)  

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Language：English   Presentation type：Poster presentation  

Venue：GASK(Kutna Hora,Czech Republic)  

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Language：English   Presentation type：Poster presentation  

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Language：English   Presentation type：Oral presentation (general)  

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Language：Japanese   Presentation type：Oral presentation (general)  

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Language：Japanese   Presentation type：Oral presentation (general)  

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Language：Japanese   Presentation type：Oral presentation (general)  

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Language：Japanese   Presentation type：Poster presentation  

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Language：Japanese   Presentation type：Oral presentation (general)  

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Language：Japanese   Presentation type：Oral presentation (general)  

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Language：Japanese   Presentation type：Oral presentation (general)  

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Language：English   Presentation type：Oral presentation (general)  

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Language：English   Presentation type：Poster presentation  

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Language：Japanese   Presentation type：Poster presentation  

Venue：北海道大学（北海道札幌市）  

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Language：Japanese   Presentation type：Poster presentation  

Venue：産業技術総合研究所（茨城県つくば市）  

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Language：Japanese   Presentation type：Poster presentation  

Venue：産業技術総合研究所（茨城県つくば市）  

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Language：Japanese   Presentation type：Oral presentation (general)  

Venue：産業技術総合研究所（茨城県つくば市）  

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Language：Japanese   Presentation type：Poster presentation  

Venue：産業技術総合研究所（茨城県つくば市）  

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Language：Japanese   Presentation type：Oral presentation (general)  

Venue：産業技術総合研究所（茨城県つくば市）  

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Language：Japanese   Presentation type：Oral presentation (invited, special)  

Venue：大阪  

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Language：Japanese   Presentation type：Oral presentation (invited, special)  

Venue：東京  

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Language：Japanese   Presentation type：Oral presentation (general)  

Venue：福岡国際会議場（福岡県福岡市）  

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Language：English   Presentation type：Oral presentation (invited, special)  

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Language：Japanese   Presentation type：Oral presentation (general)  

Venue：岡崎カンファレンスセンター（岡崎市）  

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Language：Japanese   Presentation type：Oral presentation (invited, special)  

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Language：Japanese   Presentation type：Poster presentation  

Venue：金沢商工会議所  

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Language：Japanese   Presentation type：Oral presentation (general)  

Venue：金沢商工会議所  

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Language：Japanese   Presentation type：Poster presentation  

Venue：金沢商工会議所  

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Language：Japanese   Presentation type：Poster presentation  

Venue：金沢商工会議所  

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Language：Japanese   Presentation type：Poster presentation  

Venue：イーグレひめじ(あいめっせホール)（兵庫県姫路市）  

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Language：Japanese   Presentation type：Oral presentation (invited, special)  

Venue：イーグレひめじ(あいめっせホール)（兵庫県姫路市）  

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Language：Japanese   Presentation type：Poster presentation  

Venue：イーグレひめじ(あいめっせホール)（兵庫県姫路市）  

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Language：Japanese   Presentation type：Oral presentation (general)  

Venue：愛媛大学城北キャンパス  

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Language：Japanese   Presentation type：Poster presentation  

Venue：東北大学  

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Language：English   Presentation type：Poster presentation  

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Language：English   Presentation type：Oral presentation (general)  

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Language：Japanese   Presentation type：Oral presentation (general)  

Venue：幕張メッセ  

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Language：Japanese   Presentation type：Poster presentation  

Venue：大阪、大阪大学  

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Audience： High school students

Type：Visiting lecture

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Audience： High school students

Type：Lecture

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Type：Visiting lecture

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Type：Visiting lecture

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