Extensive investigation of the influence of wall permeability on turbulence

application/pdfInternational Journal of Heat and Fluid Flow. 2019, 80, P.108465journal articl

飽和多孔媒体モデルにおけるDNAPL重力分散に関する実験的研究 <民間機関との共同研究>

Gravitational dispersion may play significant role in DNAPL (dense non-aqueous phase liquid) transport in groundwater. Fingering and droplet settlement are two examples on gravitational dispersion of DNAPL in groundwater environment. Gravitational dispersion of small spherical solid particles and TCE droplets through water-saturated porous medium models are dealt in this paper. The experimental 'set-up consisted of single-layered glass sphere media and visualizing equipments with high accuracy. The experimental results, based on ergodic theorem, are compared with analytical solution of one-dimensional gravitational dispersion equation. The results showed that dispersion of the particles and droplets could be well characterized by the present study. Values ofnon-dimensional ratio (Dz/v, v: kinematic viscosity) for solid particles and TCE droplets varied from 10 to 30, and 4 to 5.5, respectively. Particle and droplet Reynolds number varied between 74 and 230 in both cases..textapplication/pdfdepartmental bulletin pape

Investigation of Radiative Recombination of Semi-Polar (1-101)GaN Films Grown on Patterned (001)Si Substrate

We investigated the radiative recombination properties of semi-polar (11̅01)GaN films grown on patterned (001)Si substrate by using photoreflectance (PR) and photoluminescence (PL) spectroscopies. The X-ray diffraction (XRD) method was also used for investigating strain content. Estimated bandgap energy (Eg) by Kramers-Kronig transformation of PR spectrum showed about 35 meV lower energy side than that of polar (0001)GaN. It was found that the strain of growth direction (=[111]Si) did not exist from the XRD 2- scan. Therefore, reduction of Eg may be caused by the tensile strain along the [11̅0]Si or [112̅-]Si direction. From the low temperature PL and PR measurements, we could confirm the several radiative peaks caused by donor-bound exciton, acceptor-bound exciton, and donor-to-acceptor pair recombination.departmental bulletin pape

Observation of B̅0→DsJ*(2317)+K- Decay

journal articl

Solar neutrino measurements in Super-Kamiokande-II

The results of the second phase of the Super-Kamiokande solar neutrino measurement are presented and compared to the first phase. The solar neutrino flux spectrum and time variation as well as oscillation results are statistically consistent with the first phase and do not show spectral distortion. The timedependent flux measurement of the combined first and second phases coincides with the full period of solar cycle 23 and shows no correlation with solar activity. The measured 8B total flux is (2:38± 0.05(stat.)/begin+0.16 // -0.15/end (sys.)) × 10^6 cm^{-2} s^{-1} and the day-night difference is found to be (-6.3 ±4.2(stat.)±3.7(sys.))%.There is no evidence of systematic tendencies between the first and second phases.journal articl

Mechanism of DNA Threading Intercalation of Binuclear Ru Complexes: Uni- or Bimolecular Pathways Depending on Ligand Structure and Binding Density

In the long succession of small transition-metal compounds interacting reversibly with DNA, semirigid binuclear ruthenium complexes stand out by displaying exceptionally slow binding kinetics. To reach the final intercalated state, one of the bulky metal centers has to be threaded through the base stack, leading to a high level of structural discrimination. This makes the idea of utilizing binuclear complexes interesting in applications involving DNA sequence or conformation recognition. The finding that threading intercalation of the two structural analogues, Λ,Λ-[μ-(11,11‘-bidppz)X4Ru2]4+, X = 2,2‘-bipyridine (Λ,Λ-B4) and X = 1,10‘-phenanthroline (Λ,Λ-P4), into poly(dA-dT)2 can be described by surprisingly simple rate laws encouraged more extensive studies and analysis of these two systems. Kinetic measurements at different [basepair]/[complex] ratios show that Λ,Λ-B4 intercalates via a pseudo-first-order mechanism independent of binding density, whereas Λ,Λ-P4 displays a gradual transition from apparent first- to second-order kinetics when decreasing the [basepair]/[complex] mixing ratio. By employing the probabilistic method of McGhee and von Hippel, a rate law based on a supposed mechanism has been globally fitted and numerically integrated to describe threading of Λ,Λ-P4. In contrast to Λ,Λ-B4, the first-order mechanism of this analogue appears to require a long stretch of nonthreaded DNA. The results show that ancillary ligand structures indeed affect the mechanism of DNA threading, demonstrating the potential use of semirigid binuclear ruthenium complexes to target DNA

Stereoselectivity for DNA Threading Intercalation of Short Binuclear Ruthenium Complexes

Threading intercalation is an unusual DNA binding mode with significantly slower association and dissociation rates compared with classical intercalation. The latter has been shown to correlate well with cytotoxicity, and therefore, threading intercalating compounds are of great interest in the search for new DNA binding drugs. Thus, there is a need for better understanding of the mechanisms behind this type of binding. In this work, we have investigated the threading intercalation ability of the four stereoisomers of the AT-specific binuclear ruthenium complex [μ-dppzip(phen)4Ru2]4+ using different spectroscopic techniques. This complex contains an unsymmetrical bridging ligand consisting of a dipyridophenazine and an imidazophenanthroline ring system, in which the photophysical properties of the Ru-dipyridophenazine complex moiety make it possible to distinguish the intercalating part from the nonintercalating part. We have found that Δ geometry around the ruthenium on the intercalating dipyridophenazine moiety and Λ geometry on the nonintercalating imidazophenanthroline moiety is the optimal configuration for threading intercalation of this complex and that the chirality on the ruthenium of the nonintercalating half dominates the stereospecificity in the threaded state. This is the cause of the reversed enantioselectivity compared with the parent threading intercalating complex [μ-bidppz(phen)4Ru2]4+, in which the enantioselectivity is controlled by the chirality on the intercalating half. The differences in the interactions with DNA between the two complexes are most likely due to the fact that [μ-dppzip(phen)4Ru2]4+ has a slightly shorter bridging ligand than the parent complex

Enantioselective DNA Threading Dynamics by Phenazine-Linked [Ru(phen)₂dppz]²⁺ Dimers

The interactions between the stereoisomers of the chiral bis-intercalator [μ-C4(cpdppz)2-(phen)4Ru2]4+ and DNA reveal interesting dynamic discrimination properties. The two enantiomers Δ-Δ and Λ-Λ both form very strong complexes with calf thymus DNA with similar thermodynamic affinities. By contrast, they display considerable variations in their binding kinetics. The Δ-Δ enantiomer has higher affinity for calf thymus DNA than for [poly(dA-dT)]2, and the association kinetics of the dimer to DNA, as well as to polynucleotides, requires a multiexponential fitting function. The dissociation reaction, on the other hand, could be described by a single exponential for [poly(dA-dT)]2, whereas two exponentials were required for mixed-sequence DNA. To understand the key mechanistic steps of the reaction, the kinetics was studied at varied salt concentration for different choices of DNA and chirality of the threading complex. The enantiomers were found to have markedly different dissociation rates, the Λ-Λ enantiomer dissociating about an order of magnitude faster than the Δ-Δ enantiomer. Also, the salt dependence of the dissociation rate constants differed between the enantiomers, being stronger for the Λ-Λ enantiomer than for the Δ-Δ enantiomer. Since the dissociation reaction requires unthreading of bulky parts of the bis-intercalator through the DNA helix, a considerable conformational change of the DNA must be involved, possibly defining the rate-limiting step

Mechanical Control of ATP Synthase Function: Activation Energy Difference between Tight and Loose Binding Sites

Despite exhaustive chemical and crystal structure studies, the mechanistic details of how FoF1-ATP synthase can convert mechanical energy to chemical, producing ATP, are still not fully understood. On the basis of quantum mechanical calculations using a recent high-resolution X-ray structure, we conclude that formation of the P−O bond may be achieved through a transition state (TS) with a planar PO3− ion. Surprisingly, there is a more than 40 kJ/mol difference between barrier heights of the loose and tight binding sites of the enzyme. This indicates that even a relatively small change in active site conformation, induced by the γ-subunit rotation, may effectively block the back reaction in βTP and, thus, promote ATP

Another step toward understanding the binding mode of other derivatives of [Ru(phen)₂L] complexes

Linear dichroism (LD), UV-Vis and fluorescence spectroscopy were used to investigate the interaction of the Δ- and Λ-enantiomers of the two complexes of [Ru(phen)2 2-phenylimidazophenanthroline]+2 (referred to as B-complex) and [Ru(phen)2 2-(1-pyrenyl)limidazophenanthroline]+2 (named as P-complex), with ct-DNA. Absorption titration experiments of the enantiomers showed significant hypochromism with red shift indicating a strong perturbation of the DNA on the intra-ligand (IL) and the metal-to-ligand charge transfer (MLCT) transitions of the complexes, and fluorescence titration curves indicate strong binding. LD spectra for the B-enantiomers bound to DNA were qualitatively similar to spectra for the well-studied intercalator [Ru(phen)2dppz]+2, indicating intercalation of the phenyl-imidazophenanthroline part of the complex. However, for Λ-P, the LD-spectrum resembled Δ-B, and Δ-P resembled Λ-B, indicating a mirror image relationship of the transition moment directions relative to the helix axis when going from B to P. For interpretation of the data, and clarifying the nature of the binding mode of the P-complexes, a model was proposed based on the crystal structure previously presented by the Cardin group. The reversed LD is suggested to be due to partial intercalation of the pyrene moiety, pushing the Ru(phen)2-moiety out from the opposite groove and allowing it to rotate anticlockwise around the pyrene-imidazole bond. Communicated by Ramaswamy H. Sarma</p