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Biomedical subjects

Ryoichi Yamamoto

Publications and source records attributed to Ryoichi Yamamoto.

9 recordsLinked to original sources
PubMed2006

Direct numerical simulations of electrophoresis of charged colloids.

We propose a numerical method to simulate electrohydrodynamic phenomena in charged colloidal dispersions. This method enables us to compute the time evolutions of colloidal particles, ions, and host fluids simultaneously by solving Newton, advection-diffusion, and Navier-Stokes equations so that the electrohydrodynamic couplings can be fully taken into account. The electrophoretic mobilities of charged spherical particles are calculated in several situations. The comparisons with approximation theories show quantitative agreements for dilute dispersions without any empirical parameters; however, our simulation predicts notable deviations in the case of dense dispersions.

Colloids↗
PubMed2006

Modification of chemical properties of cell walls by silicon and its role in regulation of the cell wall extensibility in oat leaves.

Effects of silicon on the mechanical and chemical properties of cell walls in the second leaf of oat (Avena sativa L.) seedlings were investigated. The cell wall extensibility in the basal region of the second leaf was considerably higher than that in the middle and subapical regions. Externally applied silicon increased the cell wall extensibility in the basal region, but it did not affect the extensibility in the middle and subapical regions. The amounts of cell wall polysaccharides and phenolic compounds, such as diferulic acid (DFA) and ferulic acid (FA), per unit length were lower in the basal region than in the middle and subapical regions of the leaf, and silicon altered these amounts in the basal region. In this region, silicon decreased the amounts of matrix polymers and cellulose per unit length and of DFA and FA, both per unit length and unit matrix polymer content. Silicon treatment also lowered the activity of phenylalanine ammonia-lyase (PAL, EC 4.3.1.5) in the basal region. In contrast, the amount of silicon in cell walls increased in response to silicon treatment in three regions. These results suggest that in the basal region, silicon reduces the net wall mass and the formation of phenolic acid-mediated cross-linkages between wall polysaccharides. Such modifications of wall architecture may be responsible for the silicon-induced increase in the cell wall extensibility in oat leaves.

Ammonia-Lyases↗
PubMed2005

Progressive inhibition by water deficit of cell wall extensibility and growth along the elongation zone of maize roots is related to increased lignin metabolism and progressive stelar accumulation of wall phenolics.

Water deficit caused by addition of polyethylene glycol 6000 at -0.5 MPa water potential to well-aerated nutrient solution for 48 h inhibited the elongation of maize (Zea mays) seedling primary roots. Segmental growth rates in the root elongation zone were maintained 0 to 3 mm behind the tip, but in comparison with well-watered control roots, progressive growth inhibition was initiated by water deficit as expanding cells crossed the region 3 to 9 mm behind the tip. The mechanical extensibility of the cell walls was also progressively inhibited. We investigated the possible involvement in root growth inhibition by water deficit of alterations in metabolism and accumulation of wall-linked phenolic substances. Water deficit increased expression in the root elongation zone of transcripts of two genes involved in lignin biosynthesis, cinnamoyl-CoA reductase 1 and 2, after only 1 h, i.e. before decreases in wall extensibility. Further increases in transcript expression and increased lignin staining were detected after 48 h. Progressive stress-induced increases in wall-linked phenolics at 3 to 6 and 6 to 9 mm behind the root tip were detected by comparing Fourier transform infrared spectra and UV-fluorescence images of isolated cell walls from water deficit and control roots. Increased UV fluorescence and lignin staining colocated to vascular tissues in the stele. Longitudinal bisection of the elongation zone resulted in inward curvature, suggesting that inner, stelar tissues were also rate limiting for root growth. We suggest that spatially localized changes in wall-phenolic metabolism are involved in the progressive inhibition of wall extensibility and root growth and may facilitate root acclimation to drying environments.

Blotting, Northern↗
PubMed2005

Simulation method to resolve hydrodynamic interactions in colloidal dispersions.

A computational method is presented to resolve hydrodynamic interactions acting on solid particles immersed in incompressible host fluids. In this method, boundaries between solid particles and host fluids are replaced with a continuous interface by assuming a smoothed profile. This enabled us to calculate hydrodynamic interactions both efficiently and accurately, without neglecting many-body interactions. The validity of the method was tested by calculating the drag force acting on a single cylindrical rod moving in an incompressible Newtonian fluid. This method was then applied in order to simulate sedimentation process of colloidal dispersions.

Journal Article↗
PubMed2005

Molecular dynamics simulation of heat conduction in near-critical fluids.

Using molecular dynamics simulations we study supercritical fluids near the gas-liquid critical point under heat flow in two dimensions. We calculate the steady-state temperature and density profiles. The resultant thermal conductivity exhibits critical singularity in agreement with the mode-coupling theory in two dimensions. We also calculate distributions of the momentum and heat fluxes at fixed density. They indicate that liquidlike (entropy-poor) clusters move toward the warmer boundary and gaslike (entropy-rich) regions move toward the cooler boundary in a temperature gradient. This counterflow results in critical enhancement of the thermal conductivity.

Journal Article↗
PubMed2004

Entanglements in quiescent and sheared polymer melts.

We visualize entanglements in polymer melts using molecular dynamics simulation. A bead at an entanglement interacts persistently for long times with the nonbonded beads (those excluding the adjacent ones in the same chain). The interaction energy of each bead with the nonbonded beads is averaged over a time interval tau much longer than microscopic times but shorter than the onset time of tube constraints tau e. Entanglements can then be detected as hot spots consisting of several beads with relatively large values of the time-averaged interaction energy. We next apply a shear flow with rate much faster than the disengagement motion of entangled chains. With increasing strain the chains take zigzag shapes and one-half of the hot spots become bent. The chains are first stretched as a network but, as the bends approach the chain ends, disentanglements subsequently occur, leading to stress overshoot observed experimentally.

Journal Article↗
PubMed2004

Supercooled liquids under shear: theory and simulation.

We analyze the behavior of supercooled fluids under shear both theoretically and numerically. Theoretically, we generalize the mode-coupling theory of supercooled fluids to systems under stationary shear flow. Our starting point is the set of generalized fluctuating hydrodynamic equations with a convection term. A nonlinear integrodifferential equation for the intermediate scattering function is constructed. This theory is applied to a two-dimensional colloidal suspension. The shear rate dependence of the intermediate scattering function and the shear viscosity is analyzed. We have also performed extensive numerical simulations of a two-dimensional binary liquid with soft-core interactions near, but above, the glass transition temperature. Both theoretical and numerical results show the following. (i) A drastic reduction of the structural relaxation time and the shear viscosity due to shear. Both the structural relaxation time and the viscosity decrease as gamma(-nu) with an exponent nu< or =1, where gamma; is the shear rate. (ii) Almost isotropic dynamics regardless of the strength of the anisotropic shear flow.

Journal Article↗
PubMed2002

Growth promotion and an increase in cell wall extensibility by silicon in rice and some other Poaceae seedlings.

The effect of silicon on organ growth and its mechanisms of action were studied in rice ( Oryza sativa L. cv. Koshihikari), oat ( Avena sativa L. cv. Victory), and wheat ( Triticum aestivum L. cv. Daichino-Minori) seedlings grown in the dark. Applying silicon in the form of silicic acid to these seedlings via culture solution resulted in growth promotion of third (rice) or second (oat and wheat) leaves. The optimal concentration of silicon was 5-10 mM. No growth promotion was observed in early organs, such as coleoptiles or first leaves. In silicon-treated rice third leaves, the epidermal cell length increased, especially in the basal regions, without any effect on the number of cells, showing that silicon promoted cell elongation but not cell division. Silicon also increased the cell wall extensibility significantly in the basal regions of rice third leaves. These results indicate that silicon stimulates growth of rice and some other Poaceae leaves by increasing cell wall extensibility.

Journal Article↗