Localization of the Grover Walks on Spidernets and Free Meixner Laws

In the first part, we have constructed several families of interacting wedge-local nets of von Neumann algebras. In particular, we discovered a family of models based on the endomorphisms of the U(1)-current algebra ${\mathcal{A} ^{(0)}}$ of Longo-Witten. In this second part, we further investigate endomorphisms and interacting models. The key ingredient is the free massless fermionic net, which contains the U(1)-current net as the fixed point subnet with respect to the U(1) gauge action. Through the restriction to the subnet, we construct a new family of Longo-Witten endomorphisms on ${\mathcal{A} ^{(0)}}$ and accordingly interacting wedge-local nets in two-dimensional spacetime. The U(1)-current net admits the structure of particle numbers and the S-matrices of the models constructed here do mix the spaces with different particle numbers of the bosonic Fock space.     

Solvation dynamics of coumarin 153 in alcohols confined in silica nanochannels

Solvation dynamics in alcohols confined in silica nanochannels was examined by time-resolved fluorescence spectroscopy using coumarin 153 (C153) as a fluorescent probe. Surfactant-templated mesoporous silica was fabricated inside the pores of an anodic alumina membrane. The surfactant was removed by calcination to give mesoporous silica (Cal-NAM) containing one-dimensional (1D) silica nanochannels (diameter, 3.1 nm) whose inner surface was covered with silanol groups. By treating Cal-NAM with trimethylchlorosilane, trimethylsilyl (TMS) groups were formed on the inner surface of the silica nanochannels (TMS-NAM). Fluorescence dynamic Stokes shifts of C153 were measured in alcohols (ethanol, butanol, hexanol, and decanol) confined in the silica nanochannels of Cal- and TMS-NAMs, and the time-dependent fluorescence decay profiles could be best fitted by a biexponential function. The estimated solvent relaxation times were much larger than those observed in bulk alcohols for both Cal- and TMS-NAMs when ethanol or butanol was used as a solvent, indicating that the mobility of these alcohol molecules was restricted within the silica nanochannels. However, hexanol or decanol in Cal- and TMS-NAMs did not cause a remarkable increase in the solvent relaxation time in contrast to ethanol or butanol. Therefore, it was concluded that a relatively rigid assembly of alcohols (an alcohol chain) was formed within the silica nanochannels by hydrogen bonding interaction and van der Waals force between the surface functional groups of the silica nanochannels and alcohol molecules and by the successive interaction between alcohol molecules when alcohol with a short alkyl chain (ethanol or butanol) was used as a solvent.     

Synthesis, photophysical and electrochemical properties of perfluoroisopropyl substituted binuclear phthalocyanine conjugated with a butadiyne linker

Synthesis of 1,3-butadiyne-bridged perfluoroisopropyl binuclear phthalocyanine 2 has been successfully achieved from unsymmetrical A₃B-type iodo-perfluoroisopropyl phthalocyanine by palladium-catalyzed cross-coupling with trimethylsilylacetylene and copper-catalyzed Glaser homo-coupling as key reactions. The dyad 2 essentially remains non-aggregated irrespective of solvent and concentration. Electrochemical analysis suggests oxidation is not possible whereas the molecule is more easily reduced. All the results are advantages for photodynamic therapy (PDT).     

HELFIT: Helix fitting by a total least squares method

The problem of fitting a helix to data arises in analysis of protein structure, in nuclear physics, and in engineering. A continuous helix is described by five parameters: helix axis, helix radius, and helix pitch. One of these helix parameters is frequently predefined in the helix fitting. Other algorithms find only the helix axis or determine separately the helix axis, the helix radius, or the helix pitch. Here we describe a total least squares method, HELFIT, for helix fitting. HELFIT enables one to calculate simultaneously all five of the helix parameters with high accuracy. The minimum number of data points required for the analysis is only four. HELFIT is very insensitive to noise even in short helices. HELFIT also calculates a parameter, p = rmsd/(N − 1)^1/2, which estimates the regularity of helical structures independent of the number of data points, where rmsd is the root mean square distance from the best-fit helix to data points and N is the number of data points. It should become a basic tool of structural bioinformatics.     

Rupture and regeneration of colloidal crystals as studied by two-dimensional ultra-small-angle X-ray scattering

The structure of colloidal crystals of silica particles in water was studied by using the two-dimensional (2D) ultra-small-angle X-ray scattering (USAXS) technique. By violent shaking of the dispersion, large (body-centered cubic, bcc) crystals were broken into microcrystals while the lattice structure and lattice constant were preserved. The 2D-USAXS profiles revealed that the [111] direction of bcc microcrystals was parallel to the capillary axis and their orientational distribution with respect to the capillary axis was random. While a prepeak was observed in the one-dimensional USAXS measurements, no such peak was detected by the 2D-USAXS technique. The prepeak was concluded to be due to {110} being rotated by 54.7 degrees (the angle between [001] and [111]) from the capillary axis. The diffraction from the plane was out of the horizontal plane and was observed at a lower angle as a prepeak by detector scanning in the horizontal direction.     

Synthesis and evaluation of fluorogenic reagents for simultaneous detection of peptides and proteins by HPLC in two different samples

To find the pairs of fluorogenic reagents having similar retention times in HPLC but with different fluorescent characteristics, six fluorogenic reagents bearing benzoxadiazole or benzoselenadiazole skeletons were synthesized. The resultant derivatives obtained from the reaction of peptides and proteins with reagents which have a benzoselenadiazole skeleton showed different fluorescence characteristics from those with a benzoxadiazole skeleton. Since each corresponding derivatives of trypsin inhibitor and BSA with DAABD-Cl and 7-fluoro-N-[2-(diethylamino)ethyl]-2,1,3-benzoselenadiazole-4-sulfonamide (DEAEABSeD-F) have similar retention times, the pair of reagents was adopted for the sensitive simultaneous detection of proteins in two different samples. When the soluble fraction of mouse hippocampus was divided into the two samples (A and B), each was reacted with DEAEABSeD-F for A and DAABD-Cl for B, respectively. The two reaction solutions were combined and subjected to HPLC analysis with two fluorescent detectors in series (excitation and emission at different wavelengths for A and B, respectively). The resultant two chromatograms had quite similar patterns for each other. The new pair of fluorogenic reagents (DAABD-Cl and DEAEABSeD-F) would be applicable to proteomics studies using the previously reported FD-LC-MS/MS method.     

8-Endo selective Friedel-Crafts cyclization of vinyloxiranes with Co2(CO)6-complexed acetylene

An 8-endo selective Friedel-Crafts cyclization of vinyloxirane 8 with Co₂(CO)₆-complexed benzeneacetylene was found to give poly-functional eight-membered cyclic compound 9 in high yields.     

In situ ATR-IR investigation of L-lysine adsorption on montmorillonite

The adsorption behavior of lysine on montmorillonite in aqueous solution was investigated by in situ attenuated total reflectance infrared (ATR-IR) spectroscopy. To distinguish the protonation states of α-amino group, side-chain amino group and carboxyl group in lysine structure using ATR-IR spectra (i.e., NH₂ versus and COO⁻ versus COOH), pH-induced spectral changes of dissolved lysine were firstly measured and correlated with the thermodynamically calculated dissociation states of lysine (di-cationic, cationic, zwitterionic and anionic states). The obtained result was applied to interpret the ATR-IR spectra of lysine adsorbed on montmorillonite. We found that the adsorbed lysine was dominantly present as cationic state over the whole range of tested pH (pH = 4.9–9.7). This indicates that the adsorption is mainly driven by electrostatic interaction between the negatively charged montmorillonite surface and positively charged cationic lysine. We also found that lysine interacts with montmorillonite surface through the protonated side-chain amino group. This result suggests that lysine has a preferred vertical orientation, with the side-chain amino group pointing toward the surface.     

Label-free molecular beacon system based on DNAs containing abasic sites and fluorescent ligands that bind abasic sites

A new class of label-free molecular beacon (MB) system based on DNA strands that contain abasic (AP) sites (AP-DNA) and adopt stem-loop structures, in combination with fluorescent ligands that bind these AP sites, has been developed. Unlike a conventional MB, which requires covalent labeling of the MB with a fluorophore and a quencher, the developed system (APMB) does not require covalent attachment of signal transduction units. Detailed sensing functions of a series of APMB systems were examined with the aid of the fluorescent ligand named ATMND to provide insight into the design strategy for APMB systems. The effects of the stem length and the position of the AP site in the stem moiety on the fluorescence response of the APMB system were examined. Genotyping of a G/C SNP of PCR amplification products was successfully demonstrated with the APMB system and blue-fluorescent ATMND as a ligand. The APMB system was further extended to a system that utilized green-fluorescent lumiflavin.