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Anufriev R.,University of Tokyo | Maire J.,University of Tokyo | Maire J.,Tokyo Science and Industrial Research Institute | Nomura M.,University of Tokyo | Nomura M.,Japan Science and Technology Agency
Physical Review B - Condensed Matter and Materials Physics | Year: 2016

We investigate the impact of various phonon-scattering mechanisms on the in-plane thermal conductivity of suspended silicon thin films with two-dimensional periodic arrays of holes, i.e., phononic crystal (PnC) nanostructures. A large amount of data on the PnC structures with square, hexagonal, and honeycomb lattices reveals that the thermal conductivity is mostly determined by the surface-to-volume ratio. However, as the characteristic size of the structure is reduced down to several tens of nanometers, thermal conductivity becomes independent of the surface-to-volume ratio, lattice type, and other geometrical parameters, being controlled solely by the distance between adjacent holes (neck size). © 2016 American Physical Society.

Hirano A.,Japan National Institute of Advanced Industrial Science and Technology | Kameda T.,Tokyo Science and Industrial Research Institute | Shinozaki D.,University of Tsukuba | Arakawa T.,Alliance Protein Laboratories | Shiraki K.,University of Tsukuba
Journal of Physical Chemistry B | Year: 2013

We have previously demonstrated that arginine increases the solubility of aromatic compounds that have poor water solubility, an effect referred to as the "arginine-assisted solubilization system (AASS)". In the current study, we utilized a molecular dynamics simulation to examine the solubilization effects of arginine on caffeic acid, which has a tendency to aggregate in aqueous solution. Caffeic acid has a hydrophobic moiety containing a π-conjugated system that includes an aromatic ring and a hydrophilic moiety with hydroxyl groups and a carboxyl group. While its solubility increases at higher pH values due to the acquisition of a negative charge, the solubility was greatly enhanced by the addition of 1 M arginine hydrochloride at any pH. The results of the simulation indicated that the caffeic acid aggregates were dissociated by the arginine hydrochloride, which is consistent with the experimental data. The binding free energy calculation for two caffeic acid molecules in an aqueous 1 M arginine hydrochloride solution indicated that arginine stabilized the dissociated state due to the interaction between its guanidinium group and the π-conjugated system of the caffeic acid. The binding free energy of two caffeic acid molecules in the arginine hydrochloride solution exhibited a local minimum at approximately 8 Å, at which the arginine intervened between the caffeic acid molecules, causing a stabilization of the dissociated state of caffeic acid. Such stabilization by arginine likely led to the caffeic acid solubilization, as observed in both the experiment and the MD simulation. The results reported in this paper suggest that AASS can be attributed to the stabilization resulting from the intervention of arginine in the interaction between the aromatic compounds. © 2013 American Chemical Society.

Nomura M.,University of Tokyo | Nomura M.,Albert Ludwigs University of Freiburg | Nakagawa J.,University of Tokyo | Kage Y.,University of Tokyo | And 4 more authors.
Applied Physics Letters | Year: 2015

Thermal phonon transport in silicon nanowires (Si NWs) and two-dimensional phononic crystal (2D PnC) nanostructures was investigated by measuring thermal conductivity using a micrometer-scale time-domain thermoreflectance. The impact of nanopatterning on thermal conductivity strongly depends on the geometry, specularity parameter, and thermal phonon mean free path (MFP) distribution. Thermal conductivities for 2D PnC nanostructures were found to be much lower than that for NWs with similar characteristic length and surface-to-volume ratio due to stronger phonon back scattering. In single-crystalline Si, PnC patterning has a stronger impact at 4 K than at room temperature due to a higher specularity parameter and a longer thermal phonon MFP. Nanowire patterning has a stronger impact in polycrystalline Si, where thermal phonon MFP distribution is biased longer by grain boundary scattering. © 2015 AIP Publishing LLC.

Daiyasu H.,Osaka University | Nemoto W.,Tokyo Denki University | Toh H.,Tokyo Science and Industrial Research Institute
Frontiers in Microbiology | Year: 2012

Chemokine receptors (CKRs) function in the inflammatory response and in vertebrate homeostasis. Decoy and viral receptors are two types of CKR homologs with modified functions from those of the typical CKRs. The decoy receptors are able to bind ligands without signaling. On the other hand, the viral receptors show constitutive signaling without ligands. We examined the sites related to the functional difference. At first, the decoy and viral receptors were each classified into five groups, based on the molecular phylogenetic analysis. A multiple amino acid sequence alignment between each group and the CKRs was then constructed. The difference in the amino acid composition between the group and the CKRs was evaluated as the Kullback-Leibler (KL) information value at each alignment site.The KL information value is considered to reflect the difference in the functional constraints at the site. The sites with the top 5% of KL information values were selected and mapped on the structure of a CKR. The comparisons with decoy receptor groups revealed that the detected sites were biased on the intracellular side. In contrast, the sites detected from the comparisons with viral receptor groups were found on both the extracellular and intracellular sides. More sites were found in the ligand binding pocket in the analyses of the viral receptor groups, as compared to the decoy receptor groups. Some of the detected sites were located in the GPCR motifs. For example, the DRY motif of the decoy receptors was often degraded, although the motif of the viral receptors was basically conserved. The observations for the viral receptor groups suggested that the constraints in the pocket region are loose and that the sites on the intracellular side are different from those for the decoy receptors, which may be related to the constitutive signaling activity of the viral receptors.© 2012 Daiyasu, Nemoto and Toh.

Hirano A.,University of Tsukuba | Kameda T.,Tokyo Science and Industrial Research Institute | Arakawa T.,Alliance Protein Laboratories | Shiraki K.,University of Tsukuba
Journal of Physical Chemistry B | Year: 2010

The poor aqueous solubility of drug substances hampers their broader applications. This paper describes a de novo strategy to increase the aqueous solubility of drug substances using an arginine-assisted solubilization system (AASS) with alkyl gallates as model drug substances. Solubility experiments of alkyl gallates showed that arginine greatly increases the aqueous solubility of different alkyl gallates, whose aqueous solubilities differ widely. In contrast, lysine showed marginal effects on alkyl gallates solubility. Molecular dynamic simulation indicated a greater interaction of arginine with alkyl gallates than that of lysine, which reflects favorable interaction between the guanidinium group of arginine and the aromatic ring of alkyl gallates. Such interaction apparently disrupts association of alkyl gallate molecules, leading to solubilization. These results indicate AASS as a promising approach to solubilize poorly soluble drug substances containing aromatic ring structures. © 2010 American Chemical Society.

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