Green-and-Red Photoluminescence from Si-Si and Ge-Ge Bonded Network Homopolymers and Copolymers

Recently, we found pure green photoluminescence (PL) at 540 nm (2.34 eV) in a vacuum, which is characteristic of a Si-Si bonded network polymer bearing n-butyl groups (organopolysilyne, SNP). SNP was carefully isolated as an orange-yellow solid by avoidance of contact with air and water in the polymer synthesis and PL measurement. This was in contrast with previous reports that SNPs carrying alkyl groups have a blue PL band around 450-480 nm. By applying the modified technique to a soluble Ge-Ge bonded network polymer carrying n-butyl groups (organopolygermyne, GNP), with much care in synthesising the polymer and measuring the PL, we found that GNP reveals a very brilliant red-coloured PL band at 690 nm (1.80 eV) in a vacuum at 77 K. This was in contrast with a previous report that GNP carrying n-hexyl groups has a green PL band at 560 nm (2.21 eV). On the other hand, soluble Si-Ge network copolymers (SGNPs) prepared in a similar way to SNP and GNP syntheses showed green-and-red dual PL bands at 540 nm and 690 nm. Based on analyses with IR, Raman, HR-TEM, XPS, EELS, UV-Vis and PL data, the dual emission was assumed to originate from the coexistence of Si and Ge domains (1-2 nm in diameter), possibly, in the same skeleton of SGNP.journal articl

Characteristics of turbulent square duct flows over porous media

application/pdfJournal of Fluid Mechanics. 2020, 884, P.A7journal articl

Observation of Initial Stage of Nano-Scale Au Thin Film on Si(111)7×7 Surface by the PLD Method

As an important information for fabrication of atomic scale Au thin film which is used for biosensors, we have observed morphology of Au particles absorbed on the Si(111)7x7 surface, which is supposed to be the initial stage of Au thin film formation. Au particles were adsorbed on the Si cleaned surface using PLD method, and the adsorbed particles were observed using the scanning tunneling microscope. As the number of laser shot was increased in the PLD method, size of the adsorbed particle became larger. The larger particle were seemed to form clusters which are aggregation of particles from which each particles are distinguished, so we call this type of clusters film-shaped clusters. In this work we have mainly analyzed this type of clusters. As a result the film-shaped clusters were found to have a structure of nearly monoatomic layer. The particles in the clusters were close gathered in nearly the 3-fold structure with an inter atomic distance of 0.864 nm. We proposed a model for the cluster structure by modifying Au(111) face so that the each observed particles consists of 3 Au atoms.departmental bulletin pape

損傷自己検知型デバイスの開発とそのシステム化に関する研究

textapplication/pdfdepartmental 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

Interpreting Oligonucleotide Microarray Data To Determine RNA Secondary Structure: Application to the 3‘ End of <i>Bombyx mori</i> R2 RNA^†

A method to deduce RNA secondary structure on the basis of data from microarrays of 2‘-O-methyl RNA 9-mers immobilized in agarose film on glass slides is tested with a 249 nucleotide RNA from the 3‘ end of the R2 retrotransposon from Bombyx mori. Various algorithms incorporating binding data and free-energy minimization calculations were compared for interpreting the data to provide possible secondary structures. Two different methods give structures with 100 and 87% of the base pairs determined by sequence comparison. In contrast, structures predicted by free-energy minimization alone by Mfold and RNAstructure contain 52 and 72% of the known base pairs, respectively. This combination of high throughput microarray techniques with algorithms using free-energy calculations has potential to allow for fast determination of RNA secondary structure. It should also facilitate the design of antisense and siRNA oligonucleotides

The Amber ff99 Force Field Predicts Relative Free Energy Changes for RNA Helix Formation

The ability of the Amber ff99 force field to predict relative free energies of RNA helix formation was investigated. The test systems were three hexaloop RNA hairpins with identical loops and varying stems. The potential of mean force of stretching the hairpins from the native state to an extended conformation was calculated with umbrella sampling. Because the hairpins have identical loop sequence, the differences in free energy changes are only from the stem composition. The Amber ff99 force field was able to correctly predict the order of stabilities of the hairpins, although the magnitude of the free energy change is larger than that determined by optical melting experiments. The two measurements cannot be compared directly because the unfolded state in the optical melting experiments is a random coil, while the end state in the umbrella sampling simulations was an elongated chain. The calculations can be compared to reference data by using a thermodynamic cycle. By applying the thermodynamic cycle to the transitions between the hairpins using simulations and nearest-neighbor data, agreement was found to be within the sampling error of simulations, thus demonstrating that ff99 force field is able to accurately predict relative free energies of RNA helix formation

NMR-Assisted Prediction of RNA Secondary Structure: Identification of a Probable Pseudoknot in the Coding Region of an R2 Retrotransposon

As the rate of functional RNA sequence discovery escalates, high-throughput techniques for reliable structural determination are becoming crucial for revealing the essential features of these RNAs in a timely fashion. Computational predictions of RNA secondary structure quickly generate reasonable models but suffer from several approximations, including overly simplified models and incomplete knowledge of significant interactions. Similar problems limit the accuracy of predictions for other self-folding polymers, including DNA and peptide nucleic acid (PNA). The work presented here demonstrates that incorporating unassigned data from simple nuclear magnetic resonance (NMR) experiments into a dynamic folding algorithm greatly reduces the potential folding space of a given RNA and therefore increases the confidence and accuracy of modeling. This procedure has been packaged into an NMR-assisted prediction of secondary structure (NAPSS) algorithm that can produce pseudoknotted as well as non-pseudoknotted secondary structures. The method reveals a probable pseudoknot in the part of the coding region of the R2 retrotransposon from <i>Bombyx mori</i> that orchestrates second-strand DNA cleavage during insertion into the genome

Influence of Sequence and Covalent Modifications on Yeast tRNA Dynamics

Modified nucleotides are prevalent in tRNA. Experimental studies reveal that these covalent modifications play an important role in tuning tRNA function. In this study, molecular dynamics (MD) simulations were used to investigate how modifications alter tRNA dynamics. The X-ray crystal structures of tRNA­(Asp), tRNA­(Phe), and tRNA­(iMet), both with and without modifications, were used as initial structures for 333 ns explicit solvent MD simulations with AMBER. For each tRNA molecule, three independent trajectory calculations were performed, giving an aggregate of 6 μs of total MD across six molecules. The global root-mean-square deviations (RMSD) of atomic positions show that modifications only introduce significant rigidity to the global structure of tRNA­(Phe). Interestingly, RMSDs of the anticodon stem-loop (ASL) suggest that modified tRNA has a more rigid structure compared to the unmodified tRNA in this domain. The anticodon RMSDs of the modified tRNAs, however, are higher than those of corresponding unmodified tRNAs. These findings suggest that the rigidity of the anticodon stem-loop is finely tuned by modifications, where rigidity in the anticodon arm is essential for tRNA translocation in the ribosome, and flexibility of the anticodon is important for codon recognition. Sugar pucker and water residence time of pseudouridines in modified tRNAs and corresponding uridines in unmodified tRNAs were assessed, and the results reinforce that pseudouridine favors the 3′-endo conformation and has a higher tendency to interact with water. Principal component analysis (PCA) was used to examine correlated motions in tRNA. Additionally, covariance overlaps of PCAs were compared for trajectories of the same molecule and between trajectories of modified and unmodified tRNAs. The comparison suggests that modifications alter the correlated motions. For the anticodon bases, the extent of stacking was compared between modified and unmodified molecules, and only unmodified tRNA­(Asp) has significantly higher percentage of stacking time. Overall, the simulations reveal that the effect of covalent modification on tRNA dynamics is not simple, with modifications increasing flexibility in some regions of the structure and increasing rigidity in other regions