The mitochondrial genome organization of the rice frog, Fejervarya limnocharis (Amphibia : Anura): a new gene order in the vertebrate mtDNA

The mitochondrial DNA of the rice frog, Fejervarya limnocharis (Amphibia, Anura), was obtained using long-and-accurate polymerase chain reaction (LA-PCR) combining with subcloning method. The complete nucleotide sequence (17,717 bp) of mitochondrial genome was determined subsequently. This mitochondrial genome is characterized by four distinctive features: the translocation of ND5 gene, a cluster of rearranged tRNA genes (tRNA(Thr), tRNA(Pro), tRNA(Leu) ((CUN))) a tandem duplication of tRNA(Mer) gene, and eight large 89-bp tandem repeats in the control region, as well as three short noncoding regions containing two repeated motifs existing in the gene cluster of ND5/tRNA(Thr)/tRNA(Pro)/tRNA(Leu)/tRNA(Phe). The tandem duplication of gene regions followed by deletions of supernumerary genes can be invoked to explain the shuffling of tRNAM(Met) and a cluster of tRNA and ND5 genes, as observed in this study. Both ND5 gene translocation and tandem duplication of tRNA(Met) were first observed in the vertebrate mitochondrial genomes. (c) 2004 Elsevier B.V. All rights reserved.

Structure and order of the discotic compound 2,3,6,7,10,11-hexakispentyloxytriphenylene as revealed by diffraction and molecular simulation studies

The aggregate structure of the discotic compound 2,3,6,7,10,11-hexakispentyloxytriphenylene (HPT) was studied both for the crystalline state and the liquid crystalline state by using electron crystallography and a molecular simulation approach. In the crystalline state, HPT was found to adopt an orthorhombic P-2212 space group with cell parameters a = 36.73 Angstrom, b = 27.99 Angstrom and c = 4.91 Angstrom. Molecular packing calculations were conducted to elucidate the molecular conformation and mutual orientational characteristics in the different states. Phase transitions and relationships are discussed from a structural point of view.

A novel line-order of InAs quantum dots on GaAs

A novel line-order of InAs quantum dots (QDs) along the [1, 1, 0] direction on GaAs substrate has been prepared by self-organized growth. After 2.5 monolayer InAs deposition, QDs in the first layer of multi-layer samples started to gather in a line. Owing to the action of strong stress between layers, almost all the dots of the fourth layer gathered in lines. The dots lining up tightly are actually one-dimensional superlattice of QDs, of which the density of electronic states is different from that of isolated QDs or quantum wires. The photoluminescence spectra of our multi-layer QD sample exhibited a feature of very broad band so that it is suitable for the active medium of super luminescent diode. The reason of dots lining up is attributed to the hill-and-valley structure of the buffer, anisotropy and different diffusion rates in the different directions on the buffer and strong stress between QD layers. (C) 2002 Published by Elsevier Science B. V.

APPLICATION OF ULTRAMICROELECTRODES IN STUDIES OF HOMOGENEOUS CATALYTIC REACTIONS .3. THE CONDITION FOR QUASI-1ST AND 2ND-ORDER HOMOGENEOUS CATALYTIC REACTIONS AT ULTRAMICRODISK ELECTRODES IN THE STEADY-STATE

The conditions for quasi-first and second order homogeneous catalytic reactions and their variation with each other at an ultramicrodisk electrode in the steady state are discussed in this paper. The order of reaction can be controlled by changing the dimension of the ultramicroelectrode: the second order reaction can be changed to quasi-first by decreasing the dimension of the ultramicroelectrode. An example of this is given. The main factor effect on the reaction order is the dimension of the ultramicroelectrode. The K4Fe(CN)6-aminopyrine system is selected to confirm the theory, the experiments showing that the system is a second order reaction at a 432 mum microelectrode, and a quasi-first order reaction at a 19 mum ultramicroelectrode. The kinetic constant of the system can be determined by applying the previous theory of homogeneous catalytic reaction.

Numerical simulation of an adaptive optics system with laser propagation in the atmosphere

A comprehensive model of laser propagation in the atmosphere with a complete adaptive optics (AO) system for phase compensation is presented, and a corresponding computer program is compiled. A direct wave-front gradient control method is used to reconstruct the wave-front phase. With the long-exposure Strehl ratio as the evaluation parameter, a numerical simulation of an AO system in a stationary state with the atmospheric propagation of a laser beam was conducted. It was found that for certain conditions the phase screen that describes turbulence in the atmosphere might not be isotropic. Numerical experiments show that the computational results in imaging of lenses by means of the fast Fourier transform (FFT) method agree well with those computed by means of an integration method. However, the computer time required for the FFT method is 1 order of magnitude less than that of the integration method. Phase tailoring of the calculated phase is presented as a means to solve the problem that variance of the calculated residual phase does not correspond to the correction effectiveness of an AO system. It is found for the first time to our knowledge that for a constant delay time of an AO system, when the lateral wind speed exceeds a threshold, the compensation effectiveness of an AO system is better than that of complete phase conjugation. This finding indicates that the better compensation capability of an AO system does not mean better correction effectiveness. (C) 2000 Optical Society of America.

Steady-state crack growth and fracture work based on the theory of mechanism-based strain gradient plasticity

Mode I steady-state crack growth is analyzed under plane strain conditions in small scale yielding. The elastic-plastic solid is characterized by the mechanism-based strain gradient (MSG) plasticity theory [J. Mech. Phys. Solids 47 (1999) 1239, J. Mech. Phys. Solids 48 (2000) 99]. The distributions of the normal separation stress and the effective stress along the plane ahead of the crack tip are computed using a special finite element method based on the steady-state fundamental relations and the MSG flow theory. The results show that during the steady-state crack growth, the normal separation stress on the plane ahead of the crack tip can achieve considerably high value within the MSG strain gradient sensitive zone. The results also show that the crack tip fields are insensitive to the cell size parameter in the MSG theory. Moreover, in the present research, the steady-state fracture toughness is computed by adopting the embedded process zone (EPZ) model. The results display that the steady-state fracture toughness strongly depends on the separation strength parameter of the EPZ model and the length scale parameter in the MSG theory. Furthermore, in order for the results of steady crack growth to be comparable, an approximate relation between the length scale parameters in the MSG theory and in the Fleck-Hutchinson strain gradient plasticity theory is obtained.

The Head-On Colliding Process Of Binary Liquid Droplets At Low Velocity: High-Speed Photography Experiments And Modeling

The experimental and theoretical studies are reported in this paper for the head-on collisions of a liquid droplet with another of the same fluid resting on a solid substrate. The droplet on the hydrophobic polydimethylsiloxane (PDMS) substrate remains in a shape of an approximately spherical segment and is isometric to an incoming droplet. The colliding process of the binary droplets was recorded with high-speed photography. Head-on collisions saw four different types of response in our experiments: complete rebound, coalescence, partial rebound With conglutination, and coalescence accompanied by conglutination. For a complete rebound, both droplets exhibited remarkable elasticity and the contact time of the two colliding droplets was found to be in the range of 10-20 ms. With both droplets approximately considered as elastic bodies, Hertz contact theory was introduced to estimate the contact time for the complete rebound case. The estimated result Was found to be on the same order of magnitude as the experimental data, which indicates that the present model is reasonable. (C) 2008 Elsevier Inc. All rights reserved.

Role Of Vertical Component Of Surface Tension Of The Droplet On The Elastic Deformation Of Pdms Membrane

Poly(dimethylsiloxane) (PDMS) has been widely used in lab-on-a-chip and micro- total analysis systems (mu-TAS), thus wetting and electrowetting behaviors of PDMS are of great importance in these devices. PDMS is a kind of soft polymer material, so the elastic deformation of PDMS membrane by a droplet cannot be neglected due to the vertical component of the interfacial tension between the liquid and vapor, and this vertical component of liquid-vapor surface tension is also balanced by the stress distribution within the PDMS membrane. Such elastic deformation and stress distribution not only affect the exact measurement of contact angle, but also have influence on the micro-fluidic behavior of the devices. Using ANSYS code, we simulated numerically the elastic deformation and stress distribution of PDMS membrane on a rigid substrate due to the liquid-vapor surface tension. It is found that the vertical elastic deformation of the PDMS membrane is on the order of several tens of nanometers due to the application of a droplet with a diameter of 2.31 mm, which is no longer negligible for lab-on-a-chip and mu-TAS. The vertical elastic deformation increases with the thickness of the PDMS membrane, and there exists a saturated membrane thickness, regarded as a semi-infinite membrane thickness, and the vertical elastic deformation reaches a limiting value when the membrane thickness is equal to or thicker than such saturated thickness. (C) Koninklijke Brill NV, Leiden, 2008.

Effect Of A Negative Poisson Ratio In The Tension Of Ceramics

The effect of a negative Poisson ratio is experimentally revealed in the tension deformation of a natural layered ceramic. This effect can increase the volume strain energy per unit volume by 1100% and, simultaneously, decrease the deformation strain energy per unit volume by about 44%, so that it effectively enhances the deformation capacity by about 1 order of magnitude in the tension of the material. The present study also shows that the physical mechanisms producing the effect are attributed to the climbing on one another of the nanostructures in the natural material, which provides a guide to the design of synthetic toughening composites.

Sensitivity Analysis Of The Dimensionless Parameters In Scaling A Polymer Flooding Reservoir

A set of scaling criteria of a polymer flooding reservoir is derived from the governing equations, which involve gravity and capillary force, compressibility of water, oil, and rock, non-Newtonian behavior of the polymer solution, absorption, dispersion, and diffusion, etc. A numerical approach to quantify the dominance degree of each dimensionless parameter is proposed. With this approach, the sensitivity factor of each dimensionless parameter is evaluated. The results show that in polymer flooding, the order of the sensitivity factor ranges from 10(-5) to 10(0) and the dominant dimensionless parameters are generally the ratio of the oil permeability under the condition of the irreducible water saturation to water permeability under the condition of residual oil saturation, density, and viscosity ratios between water and oil, the reduced initial oleic phase saturation and the shear rate exponent of the polymer solution. It is also revealed that the dominant dimensionless parameters may be different from case to case. The effect of some physical variables, such as oil viscosity, injection rate, and permeability, on the dominance degree of the dimensionless parameters is analyzed and the dominant ones are determined for different cases.

Computation of turbulent-flow in a square duct - aspects of the secondary flow and its origin

A numerical study of turbulent flow in a straight duct of square cross-section is made. An order-of-magnitude analysis of the 3-D, time-averaged Navier-Stokes equations resulted in a parabolic form of the Navier-Stokes equations. The governing equations, expressed in terms of a new vector-potential formulation, are expanded as a multi-deck structure with each deck characterized by its dominant physical forces. The resulting equations are solved using a finite-element approach with a bicubic element representation on each cross-sectional plane. The numerical integration along the streamwise direction is carried out with finite-difference approximations until a fully-developed state is reached. The computed results agree well with other numerical studies and compare very favorably with the available experimental data. One important outcome of the current investigation is the interpretation analytically that the driving force of the secondary flow in a square duct comes mainly from the second-order terms of the difference in the gradients of the normal and transverse Reynolds stresses in the axial vorticity equation.

The mechanism of energy storage by shearing the solar magnetic field

In this paper, a complete set of MHD equations have been solved by numerical calculations in an attempt to study the dynamical evolutionary processes of the initial equilibrium configuration and to discuss the energy storage mechanism of the solar atmosphere by shearing the magnetic field. The initial equilibrium configuration with an arch bipolar potential field obtained from the numerical solution is similar to the configuration in the vicinity of typical solar flare before its eruption. From the magnetic induction equation in the set of MHD equations and dealing with the non-linear coupling effects between the flow field and magnetic field, the quantitative relationship has been derived for their dynamical evolution. Results show that plasma shear motion at the bottom of the solar atmosphere causes the magnetic field to shear; meanwhile the magnetic field energy is stored in local regions. With the increase of time the local magnetic energy increases and it may reach an order of 4×10^25 J during a day. Thus the local storage of magnetic energy is large enough to trigger a big solar flare and can be considered as the energy source of solar flares. The energy storage mechanism by shearing the magnetic field can well explain the slow changes in solar active regions.

The piston model of coronal transients

In the present paper, the piston model of the coronal transient (see Hu. 1983a, b is discssed in detail, and the quantitative results of unsteady gasdynamics are applied to the coronal transient processes. The piston model explains the major features of the transient observations, such as the density profile, the geometric configuration, the kinetic process and the classifications of the coronal transient. Based on the idea of piston model, the bright feature and the dark feature of the transient are the gasdynamical response of the dense plasma ejecting into the corona, and associate with the compressed and rarefied flows, respectively. The quantitative results show that the density increment in the compressed region and the density decrement in the rarefied region are one order of magnitude larger and smaller, respectively, to the density in the quiet corona, it agrees quantitatively with the observations, and both the bright feature and dark feature are explained at the same time.

The analysis of the transient temperature distribution of double-slab Nd:YAG laser medium

A novel double-slab Nd:YAG laser, which uses face-pumped slab medium cooled by liquid with different temperatures on both sides, is proposed. The thermal distortion of wavefront caused by the non-uniform temperature distribution in the laser gain media can be self-compensated. According to the method of operation, the models of the temperature distribution and stress are presented, and the analytic solutions for the model are derived. Furthermore, the numerical simulations with pulse pumping energy of 10 J and repetition frequencies of 500 and 1000 Hz are calculated respectively for Nd:YAG laser medium. The simulation results show that the temperature gradient remains the approximative linearity, and the heat stress is within the extreme range. Then the absorption coefficient is also discussed. The result indicates that the doping concentration cannot be too large for the high repetition frequency laser. It has been proved that the high repetition frequency, high laser beam quality, and high average output power of the order of kilowatt of Nd: YAG slab laser can be achieved in this structure.

New Insights into the Evolution of Intronic Sequences of the beta-fibrinogen Gene and Their Application in Reconstructing Mustelid Phylogeny

Mustelidae is the largest and most diverse family in the order Carnivora. The phylogenetic relationships among the subfamilies have especially long been a focus of study. Herein we are among the first to employ two new introns (4 and 7) of the nuclear P-f