Duplication and independent selection of cell-wall invertase genes GIF1 and OsCIN1 during rice evolution and domestication

Background: Various evolutionary models have been proposed to interpret the fate of paralogous duplicates, which provides substrates on which evolution selection could act. In particular, domestication, as a special selection, has played important role in crop cultivation with divergence of many genes controlling important agronomic traits. Recent studies have indicated that a pair of duplicate genes was often sub-functionalized from their ancestral functions held by the parental genes. We previously demonstrated that the rice cell-wall invertase (CWI) gene GIF1 that plays an important role in the grain-filling process was most likely subjected to domestication selection in the promoter region. Here, we report that GIF1 and another CWI gene OsCIN1 constitute a pair of duplicate genes with differentiated expression and function through independent selection. Results: Through synteny analysis, we show that GIF1 and another cell-wall invertase gene OsCIN1 were paralogues derived from a segmental duplication originated during genome duplication of grasses. Results based on analyses of population genetics and gene phylogenetic tree of 25 cultivars and 25 wild rice sequences demonstrated that OsCIN1 was also artificially selected during rice domestication with a fixed mutation in the coding region, in contrast to GIF1 that was selected in the promoter region. GIF1 and OsCIN1 have evolved into different expression patterns and probable different kinetics parameters of enzymatic activity with the latter displaying less enzymatic activity. Overexpression of GIF1 and OsCIN1 also resulted in different phenotypes, suggesting that OsCIN1 might regulate other unrecognized biological process. Conclusion: How gene duplication and divergence contribute to genetic novelty and morphological adaptation has been an interesting issue to geneticists and biologists. Our discovery that the duplicated pair of GIF1 and OsCIN1 has experiencedsub-functionalization implies that selection could act independently on each duplicate towards different functional specificity, which provides a vivid example for evolution of genetic novelties in a model crop. Our results also further support the established hypothesis that gene duplication with sub-functionalization could be one solution for genetic adaptive conflict.

Domain wall resistance in perpendicular (Ga,Mn) As: Dependence on pinning

We have investigated the domain wall resistance for two types of domain walls in a (Ga,Mn)As Hall bar with perpendicular magnetization. A sizeable positive intrinsic DWR is inferred for domain walls that are pinned at an etching step, which is quite consistent with earlier observations. However, much lower intrinsic domain wall resistance is obtained when domain walls are formed by pinning lines in unetched material. This indicates that the spin transport across a domain wall is strongly influenced by the nature of the pinning.

Aharonov-Bohm oscillation and chirality effect in optical activity of single-wall carbon nanotubes

We study the Aharonov-Bohm effect in the optical phenomena of single-wall carbon nanotubes (SWCN) and also their chirality dependence. Especially, we consider the natural optical activity as a proper observable and derive its general expression based on a comprehensive symmetry analysis, which reveals the interplay between the enclosed magnetic flux and the tubule chirality for arbitrary chiral SWCN. A quantitative result for this optical property is given by a gauge invariant tight-binding approximation calculation to stimulate experimental measurements.

Pressure-induced Raman-active radial breathing mode transition in single-wall carbon nanotubes

Using classical constant-pressure molecular dynamics simulations and the force constants model, radial breathing mode (RBM) transition of single-wall carbon nanotubes under hydrostatic pressure is reported. With the pressure increased, the RBM shifts linearly toward higher frequency, and the RBM transition occurs at the same critical pressure as the structural transition. The group theory indicates that the RBMs are all Raman-active; however, due to the effect of the frequency transition and the electronic structure change for tube radial deformation, the Raman intensity of the modes becomes so weak as not to be experimentally detected, which is in agreement with a recent experiment by S. Lebedkin [Phys. Rev. B 73, 094109 (2006)]. Furthermore, the calculated RBM transition pressure is well fitted to the cube of diameter (similar to 1/d(3)).

Chiral symmetry analysis and rigid rotational invariance for the lattice dynamics of single-wall carbon nanotubes

We provide a detailed expression of the vibrational potential for the lattice dynamics of single-wall carbon nanotubes (SWCNT's) satisfying the requirements of the exact rigid translational as well as rotational symmetries, which is a nontrivial generalization of the valence force model for the planar graphene sheet. With the model, the low-frequency behavior of the dispersion of the acoustic modes as well as the flexure mode can be precisely calculated. Based upon a comprehensive chiral symmetry analysis, the calculated mode frequencies (including all the Raman- and infrared-active modes), velocities of acoustic modes, and the polarization vectors are systematically fitted in terms of the chiral angle and radius, where the restrictions of various symmetry operations of SWCNT's are fulfilled.

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.

Correlation effects for semiconducting single-wall carbon nanotubes: A density matrix renormalization group study

In this paper we report the applicability of the density matrix renormalization group (DMRG) approach to the cylindrical single wall carbon nanotube (SWCN) for the purpose of its correlation effect. By applying the DMRG approach to the t+U+V model, with t and V being the hopping and Coulomb energies between the nearest neighboring sites, respectively, and U the on-site Coulomb energy, we calculate the phase diagram for the SWCN with chiral numbers (n(1)=3, n(2)=2), which reflects the competition between the correlation energy U and V. Within reasonable parameter ranges, we investigate possible correlated ground states, the lowest excitations, and the corresponding correlation functions in which the connection with the excitonic insulator is particularly addressed.

TEM study of dislocations in ZnTe/GaAs heterostructure grown by hot-wall epitaxy

A ZnTe layer grown on GaAs substrate by hot-wall epitaxy (HWE) was studied using transmission electron microscopy (TEM). For a (110) cross-sectional specimen, its (001) ZnTe/GaAs interface was analysed by large angle stereo-projection (LASP) and high resolution electron microscopy (HREM). In the LASP, a double diffraction occurred and moire fringes were formed, meanwhile misfit dislocations were revealled clearly by weak beam technique. In HREM, not only Lomer and 60 degrees types of misfit dislocations were observed, but also two types of stacking faults were analysed. The residual strain was estimated by both methods.

In-Situ Boron and Aluminum Doping and Their Memory Effects in 4H-SiC Homoepitaxial Layers Grown by Hot-Wall LPCVD

The in-situ p-type doping of 4H-SiC grown on off-oriented (0001) 4H-SiC substrates was performed with trimethylaluminum (TMA) and/or diborane (B2H6) as the dopants. The incorporations of Al and B atoms and their memory effects and the electrical properties of p-type 4H-SiC epilayers were characterized by secondary ion mass spectroscopy (SIMS) and Hall effect measurements, respectively. Both Al- and B-doped 4H-SiC epilayers were p-type conduction. It was shown that the profiles of the incorporated boron and aluminum concentration were in agreement with the designed TMA and B2H6 flow rate diagrams. The maximum hole concentration for the Al doped 4H-SiC was 3.52x10(20) cm(-3) with Hall mobility of about 1 cm(2)/Vs and resistivity of 1.6 similar to 2.2x10(-2) Omega cm. The heavily boron-doped 4H-SiC samples were also obtained with B2H6 gas flow rate of 5 sccm, yielding values of 0.328 Omega cm for resistivity, 5.3x10(18) cm(-3) for hole carrier concentration, and 7 cm(2)/VS for hole mobility. The doping efficiency of Al in SiC is larger than that of B. The memory effects of Al and B were investigated in undoped 4H-SiC by using SIMS measurement after a few run of doped 4H-SiC growth. It was clearly shown that the memory effect of Al is stronger than that of B. It is suggested that p-type 4H-SiC growth should be carried out in a separate reactor, especially for Al doping, in order to avoid the join contamination on the subsequent n-type growth. 4H-SiC PiN diodes were fabricated by using heavily B doped epilayers. Preliminary results of PiN diodes with blocking voltage of 300 V and forward voltage drop of 3.0 V were obtained.

Homoepitaxial growth and characterization of 4H-SiC epilayers by low-pressure hot-wall chemical vapor deposition

Horizontal air-cooled low-pressure hot-wall CVD (LP-HWCVD) system is developed to get high quality 4H-SiC epilayers. Homoepitaxial growth of 4H-SiC on off-oriented Si-face (0001) 4H-SiC substrates purchased from Cree is performed at a typical temperature of 1500 degrees C with a pressure of 40 Torr by using SiH4+C2H4+H-2 gas system. The surface morphologies and structural and optical properties of 4H-SiC epilayers are characterized with Nomarski optical microscope, atomic force microscopy (AFM), x-ray diffraction, Raman scattering, and low temperature photoluminescence (LTPL). The background doping of 32 pm-thick sample has been reduced to 2-5 x 10(15) cm(-3). The FWHM of the rocking curve is 9-16 arcsec. Intentional N-doped and B-doped 4H-SiC epilayers are obtained by in-situ doping of NH3 and B2H6, respectively. Schottky barrier diodes with reverse blocking voltage of over 1000 V are achieved preliminarily.

Growth and characterization of 4H-SiC by horizontal hot-wall CVD

4H-SiC layers have been homoepitaxially grown at 1500 degrees C with the use of a horizontal hot-wall chemical vapor deposition (CVD) system, which was built in the author's group. The typical growth rate was 2 mu m/h at a pressure of 40 Torr. The background donor concentration has been reduced to 2.3 x 10(15) cm(-3) during a prolonged growth run. It confirmed the idea that the high background concentration of thin films was caused by the impurities inside the susceptor and thermal insulator The FWHM of x-ray co-rocking curves show 9 similar to 15 aresecs in five different areas of a 32-mu m-thick 4H-SiC epilayer The free exciton peaks dominated in the near-band-edge low-temperature photoluminescence spectrum (LTPL), indicating high crystal quality.

Scattering of linear water waves by a fixed and infinitely long rectangular structure parallel to a vertical wall in oblique seas

The scattering of linear water waves by an infinitely long rectangular structure parallel to a vertical wall in oblique seas is investigated. Analytical expressions for the diffracted potentials are derived using the method of separation of variables. The unknown coefficients in the expressions are determined through the application of the eigenfunction expansion matching method. The expressions for wave forces on the structure are given. The calculated results are compared with those obtained by the boundary element method. In addition, the influences of the wall, the angle of wave incidence, the width of the structure, and the distance between the structure and the wall on wave forces are discussed. The method presented here can be easily extended to the study of the diffraction of obliquely incident waves by multiple rectangular structures.

Luminescence properties of ZnSe films grown by hot wall epitaxy

The photoluminescence (PL) properties of ZnSe films grown by hot wall epitaxy are reported. The PL spectra show clear neutral donor-bound exciton peak; donor acceptor pair (DAP) peak, conduction band to acceptor (CA) peak, and their phonon replicas until fourth order. The conduction band to acceptor peak and it's phonon replicas exist until room temperature. From the ratio of PL intensities of DAP and CA peaks and their replicas, we obtain the Huang-Rhys factor S = 0.58, in agreement with other experiments for acceptor-bound exciton transitions. From the temperature dependence of PL intensities we derive the activation energy of thermal quenching process for the DAP transitions as about 7 meV.