Improvement of boundary conditions for non-planar boundaries represented by polygons with an initial particle arrangement technique

The boundary conditions represented by polygons in moving particle semi-implicit (MPS) method (Koshizuka and Oka, Nuclear Science and Engineering, 1996 Koshizuka, S., and Y. Oka. 1996. “Moving-Particle Semi-Implicit Method for Fragmentation of Incompressible Fluid.” Nuclear Science and Engineering 123: 421–434.[Taylor &; Francis Online], [Web of Science ®] , [Google Scholar]) have been widely used in the industry simulations since it can simply simulate complex geometry with high efficiency. However, the inaccurate particle number density near non-planar wall boundaries dramatically affects the accuracy of simulations. In this paper, we propose an initial boundary particle arrangement technique coupled with the wall weight function method (Zhang et al. Transaction of JSCES, 2015 Zhang, T.G., S. Koshizuka, K. Shibata, K. Murotani, and E. Ishii. 2015. “Improved Wall Weight Function With Polygon Boundary in Moving Particle Semi-Implicit Method.” Transaction of JSCES. No. 20150012. [Google Scholar]) to improve the particle number density near slopes and curved surfaces with boundary conditions represented by polygons in three dimensions. Two uniform grids are utilized in the proposed technique. The grid points in the first uniform grid are used to construct boundary particles, and the second uniform grid stores the same information as in the work by Zhang et al. The wall weight functions of the grid points in the second uniform grid are calculated by newly constructed boundary particles. The wall weight functions of the fluid particles are interpolated from the values stored on the grid points in the second uniform grid. Because boundary particles are located on the polygons, complex geometries can be accurately represented. The proposed method can dramatically improve the particle number density and maintain the high efficiency. The performance of the previously proposed wall weight function (Zhang et al.) with the boundary particle arrangement technique is verified in comparison with the wall weight function without boundary particle arrangement by investigating two example geometries. The simulations of a water tank with a wedge and a complex geometry show the general applicability of the boundary particle arrangement technique to complex geometries and demonstrate its improvement of the wall weight function near the slopes and curved surfaces.     

Heterogeneously catalyzed synthesis of primary amides directly from primary alcohols and aqueous ammonia

In the presence of a manganese oxide based octahedral molecular sieve (OMS-2), a range of primary amides could be synthesized directly from primary alcohols and ammonia. The observed catalysis was heterogeneous, and the recovered catalyst could be reused many times without an appreciable loss of its catalytic performance.     

Development of a fluorogenic probe with a transesterification switch for detection of histone deacetylase activity

Histone deacetylases (HDACs) are key enzymatic regulators of many cellular processes such as gene expression, cell cycle, and tumorigenesis. These enzymes are attractive targets for drug development. However, very few simple methods for monitoring HDAC activity have been reported. Here, we have developed a fluorogenic probe, K4(Ac)-CCB, which consists of the histone H3 peptide containing acetyl-Lys and a coumarin fluorophore with a carbonate ester. By the simple addition of the probe to a HDAC solution, enzyme activity was clearly detected through spontaneous intramolecular transesterification, which renders the probe fluorescent. In addition, K4(Ac)-CCB can be applied to the evaluation of HDAC inhibitor activity. This is the first report to demonstrate the monitoring of HDAC activity by using a one-step procedure. Thus, our novel fluorogenic probe will provide a powerful tool for epigenetic research and the discovery of HDAC-targeted drugs.     

No-wash protein labeling with designed fluorogenic probes and application to real-time pulse-chase analysis

Small molecule labeling techniques for cellular proteins under physiological conditions are very promising for revealing new biological functions. We developed a no-wash fluorogenic labeling system by exploiting fluorescence resonance energy transfer (FRET)-based fluorescein-cephalosporin-azopyridinium probes and a mutant β-lactamase tag. Fast quencher elimination, hydrophilicity, and high resistance against autodegradation were achieved by rational refinement of the structure. By applying the probe to real-time pulse-chase analysis, the trafficking of epidermal growth factor receptors between cell surface and intracellular region was imaged. In addition, membrane-permeable derivatization of the probe enabled no-wash fluorogenic labeling of intracellular proteins.     

Long-term observation of fluorescence of free single molecules to explore protein-folding energy landscapes

A method was developed to detect fluorescence intensity signals from single molecules diffusing freely in a capillary cell. A unique optical system based on a spherical mirror was designed to enable quantitative detection of the fluorescence intensity. Furthermore, "flow-and-stop" control of the sample can extend the observation time of single molecules to several seconds, which is more than 1000 times longer than the observation time available using a typical confocal method. We used this method to scrutinize the fluorescence time series of the labeled cytochrome c in the unfolded state. Time series analyses of the trajectories based on local equilibrium state analysis revealed dynamically differing substates on a millisecond time scale. This system presents a new avenue for experimental characterization of the protein-folding energy landscape.     

Strong two-photon absorption and its saturation of a self-organized dimer of an ethynylene-linked porphyrin tandem

The two-photon absorption properties of a self-organized dimer of a free-base and zinc(II) porphyrins tandem linked with an ethynylene group and terminated by imidazolyl and phenylethynyl groups were investigated. The self-organized dimer was found to exhibit strong two-photon absorption and furthermore the saturation of the two-photon absorption owing to the intense transition.     

Chemoselective reduction of nitrobenzenes to aminobenzenes having reducible groups by a titanium(IV) oxide photocatalyst under gas- and metal-free conditions

m-Nitrovinylbenzene was chemoselectively reduced to m-aminovinylbenzene in a suspension of a TiO(2) photocatalyst in the presence of a hole scavenger at room temperature under atmospheric pressure without the use of a precious metal or reducing gas, and nitrobenzenes having other reducible groups were also chemoselectively reduced to corresponding aminobenzenes.     

Synthesis of an insulated molecular wire by click polymerization

We developed a new method for the synthesis of an organic-soluble insulated molecular wire (IMW) with permethylated cyclodextrin (PMCD); this method involves click polymerization of linked [2]rotaxane containing azide and alkynyl groups at both ends of a π-conjugated guest.