The identification and quantification of highly stable 'common hairpin' in the dynamic process of co-transcriptional mRNA folding

In our studies, 88 human mRNA samples were collected from the Integrated Sequence-Structure database and then the dynamic process in co-transcriptional mRNA folding was simulated using the RNAstructure version 4.1 program. Through statistical analyses of the frequencies of occurrence of hairpins, a group of special folding structures-the 'common hairpins'-were identified. These 'common hairpins' have lower energies and occur in all the subsequent folding units that formed in the dynamic folding process. By applying the formulas (1)-(4) of the 'common hairpins' statistical model, 163 'common hairpins' were found, to make up about 7% of the total of 2286 hairpins. Classified studies further show that the 'common hairpins' that were studied may oscillate in the dynamic folding process. However, the hairpin loops of the 'common hairpins' and stems proximal to those 'common hairpins' loops maintain topologically stable structures, while other loops and stems distal to the 'common hairpins' loops are shown to be alterable structures. Strikingly, further studies indicate that the stable structures of these 'common hairpins' may have unbeknown effects on controlling the formation of protein structures in the translation process (unpublished results). (c) 2005 Elsevier B.V. All rights reserved.

CYCLIC PEPTIDE HEPATOTOXINS FROM FRESH-WATER CYANOBACTERIAL (BLUE-GREEN-ALGAE) WATERBLOOMS COLLECTED IN CENTRAL CHINA

Toxic cyanobacteria (blue-green algae) waterblooms have been found in several Chinese water bodies since studies began there in 1984. Waterbloom samples for this study contained Anabaena circinalis, Microcystis aeruginosa and Oscillatoria sp. Only those waterblooms dominated by Microcystis aeruginosa were toxic by the intraperitoneal (i.p.) mouse bioassay. Signs of poisoning were the same as with known hepatotoxic cyclic peptide microcystins. One toxic fraction was isolated from each Microcystis aeruginosa sample. Two hepatotoxic peptides were purified from each of the fractions by high-performance liquid chromatography and identified by amino acid analysis followed by low and high resolution fast-atom bombardment mass spectrometry (FAB-MS). LD50 i.p. mouse values for the two toxins were 245-mu-g/kg (Toxin A) and 53-mu-g/g (Toxin B). Toxin content in the cells was 0.03 to 3.95 mg/g (Toxin A) and 0.18 to 3.33 mg/kg (Toxin B). The amino acid composition of Toxin A was alanine [1], arginine [2], glutamic acid [1] and beta-methylaspartic acid [1]; for Toxin B it was the same, except one of the arginines was replaced with a leucine. Low- and high-resolution FAB-MS showed that the molecular weights were 1,037 m/z (Toxin A) and 994 m/z (Toxin B), with formulas of C49H76O12N13 (Toxin A) and C49H75O12N10 (Toxin B). It was concluded that Toxin A is microcystin-RR and Toxin B is microcystin-LR, both known cyclic heptapeptide hepatotoxins isolated from cyanobacteria in other parts of the world. Sodium borohydride reduction of microcystin-RR yielded dihydro-microcystin-RR (m/z = 1,039), an important intermediate in the preparation of tritium-labeled toxin for metabolism and fate studies.

The quantum tunnelling between two-component Bose-Einstein condensates in a double-well configuration

We examine in terms of exact solutions of the time-dependent Schrodinger equation, the quantum tunnelling process in Bose-Einstein condensates of two interacting species trapped in a double well configuration. Based on the two series of time-dependent SU(2) gauge transformations, we diagonalize the Hamilton operator and obtain analytic time-evolution formulas of the population imbalance and the berry phase. the particle population imbalance (a(L)(+)aL - a(R)(+)a(R)) of species A between the two wells is studied analytically.

The quantum tunneling between two-component Bose-Einstein condensates in a double-well configuration

In terms of exact solution of the time-dependent Schrodinger equation. we examine the quantum tunneling process in Bose condensates of two interacting species trapped in a double well configuration. We use the two series of time-dependent SU(2) gauge transformation to diagonalize the Hamilton operator obtain analytic time-evolution formulas of the population imbalance and the berry phase. The particle population imbalance (a(L)(+)a(L) - a(R)(+)a(R)) of species A between the two wells is studied analytically.

Rashba spin-orbit coupling in InSb nanowires under transverse electric field

We investigate the Rashba spin-orbit coupling brought by transverse electric field in InSb nanowires. In small k(z) (k(z) is the wave vector along the wire direction) range, the Rashba spin-orbit splitting energy has a linear relationship with k(z), so we can define a Rashba coefficient similarly to the quantum well case. We deduce some empirical formulas of the spin-orbit splitting energy and Rashba coefficient, and compare them with the effective-mass calculating results. It is interesting to find that the Rashba spin-orbit splitting energy decreases as k(z) increases when k(z) is large due to the k(z)-quadratic term in the band energy. The Rashba coefficient increases with increasing electric field, and shows a saturating trend when the electric field is large. As the radius increases, the Rashba coefficient increases at first, then decreases. The effects of magnetic fields along different directions are discussed. The case where the magnetic field is along the wire direction or the electric field direction are similar. The spin state in an energy band changes smoothly as k(z) changes. The case where the magnetic field is perpendicular to the wire direction and the electric field direction is quite different from the above two cases, the k(z)-positive and negative parts of the energy bands are not symmetrical, and the energy bands with different spins cross at a k(z)-nonzero point, where the spin splitting energy and the effective g factor are zero.

Symmetry restrictions in the chirality dependence of physical properties of single-wall nanotubes

We investigate the chirality dependence of physical properties of nanotubes which are wrapped by the planar hexagonal lattice including graphite and boron nitride sheet, and reveal its symmetry origin. The observables under consideration are of scalar, vector, and tensor types. These exact chirality dependences obtained are useful to verify the experimental and numerical results and propose accurate empirical formulas. Some important features of physical quantities can also be extracted by considering the symmetry restrictions without complicated calculations.

A highly efficient beam propagation method for modeling step-index waveguides with tilt interface

Based on a new finite-difference scheme and Runge-Kutta method together with transparent boundary conditions (TBCs), a novel beam propagation method to model step-index waveguides with tilt interfaces is presented. The modified scheme provides an precies description of the tilt interface of the nonrectangular waveguide structure, showing a much better efficiency and accuracy comparing with the previously presented formulas.

New finite-difference scheme for simulations of step-index waveguides with tilt interfaces

A new finite-difference scheme is presented for the second derivative of a semivectorial field in a step-index optical waveguide with tilt interfaces. The present scheme provides an accurate description of the tilt interface of the nonrectangular structure. Comparison with previously presented formulas shows the effectiveness of the present scheme.

Calculation of the hourly and daily radiation incident on three step tracking planes

Mathematical formulas for estimating the hourly and daily radiation incident on planes of azimuth three step tracking and hour angle three step tracking have been derived in this paper. Based on the hourly solar radiation data of an average day in each month at Er-Lian-Hao-Te city, the hourly and monthly radiation received by planes of these two kinds of tracking have been calculated. The results show that in this district, one axis azimuth three step tracking and hour angle three step tracking could, respectively, obtain 66.5% and 63.3% higher radiation than that on the horizontal surface all year. Moreover, a two axis azimuth three step tracking plane could receive 72% more radiation than the horizontal surface. (C) 2002 Elsevier Science Ltd. All rights reserved.

Comparison of cooling rates for hot carriers in GaAs AlAs quantum wells based on macroscopic and microscopic phonon models

By using three analytical phonon models in quantum wells-the slab model, the guided-mode model, and the improved version of the Huang-Zhu model [Phys. Rev. B 38, 13 377 (1998)], -and the phonon modes in bulk, the energy-loss rates of hot carriers due to the Frohlich potential scattering in GaAs/AlAs multiple quantum wells (MQW's) are calculated and compared to those obtained based on a microscopic dipole superlattice model. In the study, a special emphasis is put on the effects of the phonon models on the hot-carrier relaxation process when taking the hot-phonon effect into account. Our numerical results show that, the calculated energy-loss rates based on the slab model and on the improved Huang-Zhu model are almost the same when ignoring the hot-phonon effect; however, with the hot phonon effect considered, the calculated cooling rate as well as the hot phonon occupation number do depend upon the phonon models to be adopted. Out of the four analytical phonon models investigated, the improved Huang-Zhu model gives the results most close to the microscopic calculation, while the guided-mode model presents the poorest results. For hot electrons with a sheet density around 10(12)/cm(2), the slab model has been found to overestimate the hot-phonon effect by more than 40% compared to the Huang-Zhu model, and about 75% compared to the microscopic calculation in which the phonon dispersion is fully included. Our calculation also indicates that Nash's improved version [J. Lumin. 44, 315 (1989)] is necessary for evaluating the energy-loss rates in quantum wells of wider well width, because Huang-Zhu's original analytical formulas an only approximately orthogonal for optical phonons associated with small in-plane wave numbers. [S0163-1829(99)08919-5].

Generalized Viscoplastic Modeling of Debris Flow

Various concepts have been proposed or used in the development of rheological models for debris flow. The earliest model developed by Bagnold was based on the concept of the “dispersive” pressure generated by grain collisions. Bagnold’s concept appears to be theoretically sound, but his empirical model has been found to be inconsistent with most theoretical models developed from non-Newtonian fluid mechanics. Although the generality of Bagnold’s model is still at issue, debris-flow modelers in Japan have generally accepted Takahashi’s formulas derived from Bagnold’s model. Some efforts have recently been made by theoreticians in non-Newtonian fluid mechanics to modify or improve Bagnold’s concept or model. A viable rheological model should consist both of a rate-independent part and a rate-dependent part. A generalized viscoplastic fluid (GVF) model that has both parts as well as two major rheological properties (i.e., the normal stress effect and soil yield criterion) is shown to be sufficiently accurate, yet practical, for general use in debris-flow modeling. In fact, Bagnold’s model is found to be only a particular case of the GVF model. Analytical solutions for (steady) uniform debris flows in wide channels are obtained from the GVF model based on Bagnold’s simplified assumption of constant grain concentration.

由一阶逻辑公式得到命题逻辑可满足性问题实例

命题逻辑可满足性(SAT)问题是计算机科学中的一个重要问题.近年来许多学者在这方面进行了大量的研究,提出了不少有效的算法.但是,很多实际问题如果用一组一阶逻辑公式来描述,往往更为自然.当解释的论域是一个固定大小的有限集合时,一阶逻辑公式的可满足性问题可以等价地归约为 SAT 问题.为了利用现有的高效 SAT工具,提出了一种从一阶逻辑公式生成 SAT 问题实例的算法,并描述了一个自动的转换工具,给出了相应的实验结果.还讨论了通过增加公式来消除同构从而减小搜索空间的一些方法.实验表明,这一算法是有效的,可以用来解决数学研究和实际应用中的许多问题.

Spectroscopic ellipsometry study of In2O3 thin films

In2O3 films grown by helicon magnetron sputtering with different thicknesses were characterized by spectroscopic ellipsometry in the energy range from 1.5 to 5.0 eV. Aside from one amorphous sample prepared at room substrate temperature, polycrystalline In2O3 films with cubic crystal structure were confirmed for other four samples prepared at the substrate temperature of 450 A degrees C. Excellent SE fittings were realized by applying 1 and/or 2 terms F&B amorphous formulations, building double layered film configuration models, and further taking account of void into the surface layer based on Bruggeman effective medium approximation for thinner films. Spectral dependent refractive indices and extinction coefficients were obtained for five samples. The curve shapes were well interpreted according to the applied dispersion formulas. Almost similar optical band gap values from 3.76 to 3.84 eV were obtained for five samples by Tauc plot calculation using extinction coefficients under the assumption of direct allowed optical transition mode.

Principle of the moving-mirror-pair interferometer and the tilt tolerance of the double moving mirror

A novel type of interferometer, the moving-mirror-pair interferometer, is presented, and its principle and properties are studied. The new interferometer is built with three flat mirrors, which include two flat moving mirrors fixed as a single moving part by a rigid structure and one flat fixed mirror. The optical path difference (OPD) is obtained by the straight reciprocating motion of the double moving mirror, and the OPD value is four times the physical shift value of the double moving mirror. The tilt tolerance of the double moving mirror of the novel interferometer is systematically analyzed by means of modulation depth and phase error. Where the square aperture is concerned, the formulas of the tilt tolerance were derived. Due to the novel interferometer's large OPD value and low cost, it is very applicable to the high-spectral-resolution Fourier-transform spectrometers for any wavenumber region from the far infrared to the ultraviolet. (C) 2008 Optical Society of America.

Analysis of the lateral displacement and optical path difference in wide-field-of-view polarization interference imaging spectrometer

The mechanism of beam splitting and principle of wide-field-of-view compensation of modified Savart polariscope in the wide-field-of-view polarization interference imaging spectrometer (WPIIS) are analyzed and discussed. Formulas for the lateral displacement and optical path difference (OPD) produced by the modified Savart polariscope are derived by ray-tracing method. The theoretical and practical guidance is thereby provided for the study, design, modulation, experiment and engineering of the polarization interference imaging spectrometers and other birefringent Fourier-transform spectrometers based on Savart polariscopes. (c) 2006 Elsevier B.V. All rights reserved.