Several contributions to soil compactibility induced by cyclic loading test

To investigate the soil compactibility during the cyclic loading, three different kinds of paddy field soils were prepared so as to clarify interrelationships among stress amplitude ratio, bulk density, soil water content and pore water pressure. The presetting values of specimen include the soil water content(percent dry basis) and bulk density of 25% d.b. and 1.1 Mg/m³ respectively. The relation between the number of cyclic loading and axial strain exhibited an asymptotically increasing trend, converging toward a specific value for each experimental condition. Possible effect caused by elastic–plastic characteristics could be recognized, when axial strain for 0.5 Hz excitation becomes greater than the one of 1.0 Hz under same stress amplitude ratio. When the stress amplitude ratio took 0.1, the absolute value of axial strain of 0.5 Hz was greater than the one of 1.0 Hz, whereas its decreasing trend was recognized in the sequence of silt, clay and silty sand. The qualitative relations between pore water pressure and number of cyclic loading were also examined to scrutinize the effect of effective water pressure to the soil compactibility.     

Buffers to suppress sodium dodecyl sulfate adsorption to polyethylene oxide for protein separation on capillary polymer electrophoresis

Although polyethylene oxide (PEO) offers several advantages as a sieving polymer in SDS capillary polymer electrophoresis (SDS-CPE), solution properties of PEO cause deterioration in the electrophoresis because PEO in solution aggregates itself, degrades into smaller pieces, and forms polymer-micelle complexes with SDS. We examined protein separation on SDS-CPE with PEO as a sieving matrix in four individual buffer solutions: Tris-CHES, Tris-Gly, Tris-Tricine, and Tris-HCl buffers. The solution properties of PEO as a sieving matrix in those buffers were examined by dynamic light scattering (DLS) and by surface tension. Preferential SDS adsorption onto PEO disturbed protein-SDS complexation and impaired the protein separation efficiency. Substantial adsorption of SDS to PEO was particularly observed in Tris-Gly buffer. The Tris-CHES buffer prevented SDS from adsorbing onto the PEO. Only Tris-CHES buffer achieved separation of six proteins. This study demonstrated efficient protein separation on SDS-CPE with PEO.     

A free-energy perturbation method based on Monte Carlo simulations using quantum mechanical calculations (QM/MC/FEP method): application to highly solvent-dependent reactions

This study describes the framework of the quantum mechanical (QM)/Monte Carlo (MC)/free‐energy perturbation (FEP) method, a FEP method based on MC simulations using quantum chemical calculations. Because a series of structures generated by interpolating internal coordinates between transition state and reactant did not produce smooth free‐energy profiles, we used structures from the intrinsic reaction coordinate calculations. This method was first applied to the Diels–Alder reaction between methyl vinyl ketone and cyclopentadiene and produced ΔG values of 20.1 and 21.4 kcal mol^?1 in aqueous and methanol solutions, respectively. They are very consistent with the experimentally observed values. The other two applications were the free‐energy surfaces for the Cope elimination of N,N‐dimethyl‐3‐phenylbutan‐2‐amine oxide in aqueous, dimethyl sulfoxide, and tetrahydrofuran solutions, and the Kemp decarboxylation of 6‐hydroxybenzo‐isoxazole‐3‐carboxylic acid in aqueous, dimethyl sulfoxide, and CH₃CN solutions. The calculated activation free energies differed by less than 1.8 kcal mol^?1 from the experimental values for these reactions. Although we used droplet models for the QM/MC/FEP simulations, the calculated results for three reactions are very close to the experimental data. It was confirmed that most of the interactions between the solute and solvents can be described using small numbers of solvent molecules. This is because a few solvent molecules can produce large portions of the solute–solvent interaction energies at the reaction centers. When we confirmed the dependency on the droplet sizes of solvents, the QM/MC/FEP for a large droplet with 106 water molecules produced a ΔG value similar to the experimental values, as well as that for a small droplet with 34 molecules. © 2010 Wiley Periodicals, Inc. J Comput Chem, 2011     

Regulation of cellular responses to macroporous inorganic films prepared by the inverse-opal method

Regenerative medicine for repairing damaged body tissues has recently become critically important. Cell culture scaffolds are required for the control of cell attachment, proliferation, and differentiation in in vitro cell cultures. A new strategy to control cell adhesion, morphology, and proliferation was developed by culturing mouse osteoblast-like MC3T3-E1 cells on novel cell culture scaffolds fabricated using ordered nanometer-sized pores (100, 300, 500, and 1000 nm). Results of this study indicate that after 72 h of incubation, the number of cells cultured on a silica film with a pore size of 1000 nm was similar to or slightly lower than that cultured on a non-porous control silica film. Films with 100-500 nm pore sizes, however, resulted in the cell growth inhibition. Morphology of the cultured cells revealed increased elongation and the formation of actin stress fibers was virtually absent on macroporous silica films with 100-500 nm pore size. Vinculin molecules expressed in cells cultured on the non-porous silica films showed many clear focal adhesions, whereas focal contacts were insufficiently formed in cells cultured on macroporous films. The influence of hydroxyapatite (HAp) and alumina scaffolds on the behavior of MC3T3-E1 cells was also evaluated. The proliferation rate of MC3T3-E1 cells cultured on HAp films with 1000 nm pore size was increased to approximately 20% above than that obtained of cells cultured on non-porous HAp films. These results demonstrate that the pore size and constituents of films play a role in controlling the morphology and proliferation rate of MC3T3-E1 cells.     

Theoretical study on singlet oxygen adsorption onto surface of graphene-like aromatic hydrocarbon molecules

Recently, graphene sheet is one of interesting systems to realize novel electronic properties. Especially, interaction between graphene and adsorbed oxygen molecule is very important to control electronic condition. In this paper, we employed some aromatic hydrocarbons as simple systems of graphene sheet and ab initio MO calculations were carried out to investigate inter-molecular interaction. It is found that not triplet but singlet O₂ molecule have potential of chemisorption onto graphene surface. From the calculated potential energy surface (PES) for distance between benzene and O₂ molecules, meta-stable structure is found at about 1.5 Å with potential barrier. In the optimized structure of its meta-stable state, structural strain can be relaxed through bending of planer benzene ring. Its energy is estimated at 70.10 kcal/mol for benzene. We also estimated the strain effects for naphthalene and pyrene molecules as larger case of graphene and they were 80.85 and 72.45 kcal/mol, respectively.     

Real-time measurements of protein dynamics using fluorescence activation-coupled protein labeling method

We present a fluorescence activation-coupled protein labeling (FAPL) method, which employs small-molecular probes that exhibit almost no basal fluorescence but acquire strong fluorescence upon covalent binding to tag-proteins. This method enables real-time imaging of protein labeling without any washout process and is uniquely suitable for real-time imaging of protein dynamics on the cell surface. We applied this method to address the spatiotemporal dynamics of the EGF receptor during cell migration.     

Interlaboratory study of DNA extraction from multiple ground samples, multiplex real-time PCR, and multiplex qualitative PCR for individual kernel detection system of genetically modified maize

In many countries, the labeling of grains, feed, and foodstuff is mandatory if the genetically modified (GM) organism content exceeds a certain level of approved GM varieties. We previously developed an individual kernel detection system consisting of grinding individual kernels, DNA extraction from the individually ground kernels, GM detection using multiplex real-time PCR, and GM event detection using multiplex qualitative PCR to analyze the precise commingling level and varieties of GM maize in real sample grains. We performed the interlaboratory study of the DNA extraction with multiple ground samples, multiplex real-time PCR detection, and multiplex qualitative PCR detection to evaluate its applicability, practicality, and ruggedness for the individual kernel detection system of GM maize. DNA extraction with multiple ground samples, multiplex real-time PCR, and multiplex qualitative PCR were evaluated by five laboratories in Japan, and all results from these laboratories were consistent with the expected results in terms of the commingling level and event analysis. Thus, the DNA extraction with multiple ground samples, multiplex real-time PCR, and multiplex qualitative PCR for the individual kernel detection system is applicable and practicable in a laboratory to regulate the commingling level of GM maize grain for GM samples, including stacked GM maize.     

Potential energy curve for ring-opening reactions: comparison between broken-symmetry and multireference coupled cluster methods

The spin-unrestricted Hartree-Fock (UHF)-based coupled cluster singles and doubles (UHF-CCSD) and Mukherjee's state-specific multireference CCSD (MkCCSD) methods are applied to four ring-opening reactions. The spin-restricted Hartree-Fock (RHF)-based CCSD (RHF-CCSD) calculations are also performed for comparison. In the case of the UHF-CCSD method, an approximate spin-projection (AP) method is applied to the broken-symmetry (BS) singlet solution to remove the spin contamination effect. For potential energy curves (PECs) of all reactions presented in this study, the results of RHF-CCSD and UHF-CCSD are substantially different from those of MkCCSD, while the results after the AP method (AP-UCCSD) reproduce the MkCCSD results well. It strongly suggests that the spin contamination effect should be removed by the AP correction even at the UHF-CCSD level to predict reliable energetics of these reactions.     

Synthesis of oxosumanenes through benzylic oxidation

Oxosumanenes were synthesized through benzylic oxidation. The electronic and redox properties were revealed to exhibit the expanded π-conjugation compared to sumanene. Single-crystal X-ray analysis of monooxosumanene showed columnar π-stacking in a concave-convex fashion. Stereoselective trimethylation of the trioxo derivative was performed via 1,2-addition to the carbonyl groups.