Optical matrix elements in tight-binding models with overlap

We investigate the effect of orbital overlap on optical matrix elements in empirical tight-binding models. Empirical tight-binding models assume an orthogonal basis of (atomiclike) states and a diagonal coordinate operator which neglects the intra-atomic part. It is shown that, starting with an atomic basis which is not orthogonal, the orthogonalization process induces intra-atomic matrix elements of the coordinate operator and extends the range of the effective Hamiltonian. We analyze simple tight-binding models and show that non-orthogonality plays an important role in optical matrix elements. In addition, the procedure gives formal justification to the nearest-neighbor spin-orbit interaction introduced by Boykin [Phys. Rev \textbf{B} 57, 1620 (1998)] in order to describe the Dresselahaus term which is neglected in empirical tight-binding models.Comment: 16 pages 6 figures, to appear in Phys. Rev.

GC Preps: Fast and Easy Extraction of Stable Yeast Genomic DNA

Existing yeast genomic DNA extraction methods are not ideally suited to extensive screening of colonies by PCR, due to being too lengthy, too laborious or yielding poor quality DNA and inconsistent results. We developed the GC prep method as a solution to this problem. Yeast cells from colonies or liquid cultures are lysed by vortex mixing with glass beads and then boiled in the presence of a metal chelating resin. In around 12 minutes, multiple samples can be processed to extract high yields of genomic DNA. These preparations perform as effectively in PCR screening as DNA purified by organic solvent methods, are stable for up to 1 year at room temperature and can be used as the template for PCR amplification of fragments of at least 8 kb

Development of a Bahiagrass \u3cem\u3ePaspalum Notatum\u3c/em\u3e Flugge With Increased Short-Day Biomass

Low herbage productivity of subtropical grasses during the short-day winter months of October through to March can place a severe burden on livestock producers in Southeastern U.S. Researchers at the University of Florida (Sinclair et al., 2001) hypothesised that the decrease in forage production might result from physiological dormancy induced by short day length. A study using artificial lights to extend the day length demonstrated that maintaining the day length at 15 hr during the short-day length period increased \u27Pensacola\u27 bahiagrass P. notatum Flugge saure Parodi forage yield 122% when compared with normal photoperiod (Mislevy et al., 2001). A Pensacola-derived bahiagrass population was selected for increased vegetative growth under short-day length using restricted recurrent phenotypic selection for three cycles (UF Cycle 3) to increase forage yield. Plants that comprise this population were less sensitive to short photoperiod and produced increased forage mass during the short days. The objective of this clipping study was to evaluate forage production and forage nutritive value of UF Cycle 3 compared with selected standard entries during short and long day length periods

LIDAR DERIVED SALT MARSH TOPOGRAPHY AND BIOMASS: DEFINING ACCURACY AND SPATIAL PATTERNS OF UNCERTAINTY

As valuable and vulnerable blue carbon ecosystems, salt marshes require adaptable and robust monitoring methods that span a range of spatiotemporal scales. The application of unmanned aerial vehicle (UAV) based remote sensing is a key tool in achieving this goal. Due to the particular characteristics of tidal wetlands, however, there are challenges in obtaining research and management relevant data with the requisite level of accuracy. In this study, the spatial patterns in uncertainty stemming from scan angle, binning method, vegetation structure and platform surface morphology are examined in the context of UAV light detection and ranging (LiDAR) derived digital elevation models (DEM). The results demonstrate that overlapping the UAV flight paths sufficiently to avoid sole reliance on LIDAR data with scan angles exceeding 15 degrees is advisable. Furthermore, the spatial arrangement of halophyte species and marsh morphology has a clear influence on DEM accuracy. The largest errors were associated with sudden structural transitions at the marsh channel boundaries. The DEMmean was found to be the most accurate for bare ground, while the DEMmin was the most accurate for channels and the middle to high marsh vegetation (MAEs = −0.01m). For the low to middle vegetation, all the trialled DEMs returned a similar magnitude of mean error (MAE = ± 0.03m). The accuracy difference between the two vegetation associations examined appears to be connected to variations in coverage, height and biomass. Overall, these findings reinforce the link between salt marsh biogeomorphic complexity and the spatial distribution and magnitude of LiDAR DEM erro

Small Leaf Mid-Rib Xylem Related to Leaf Freeze Tolerance Trait in Bahia (\u3cem\u3ePaspalum Notatum\u3c/em\u3e Flugge) Grass Lines

Controlled freeze (-60o C) trials of 31 bahiagrass selections from a breeding program for cold tolerance by Blount et al. (2001) showed diverse genotype Leaf Tissue Cold Damage (LTCD). Breman et al. (2003) defined LTCD on a rating scale (1 = no damage to 9 = 100% leaf damage). Unique midrib damage was observed as part of LTCD in bahiagrass under transpiration stress after a freeze trial. Small xylem conduit diameter and area has been strongly correlated with reduced cavitation caused by freeze thaw cycles which maintain leaf tissue in evergreen temperate woody plants; further shown in twelve woody species by Davis et al. (1999). Air bubbles in vessel ice columns prevent normal refill and function upon thawing. The purpose of this study was to test whether genotype xylem diameter and area could be used to predict LTCD

A priori Wannier functions from modified Hartree-Fock and Kohn-Sham equations

The Hartree-Fock equations are modified to directly yield Wannier functions following a proposal of Shukla et al. [Chem. Phys. Lett. 262, 213-218 (1996)]. This approach circumvents the a posteriori application of the Wannier transformation to Bloch functions. I give a novel and rigorous derivation of the relevant equations by introducing an orthogonalizing potential to ensure the orthogonality among the resulting functions. The properties of these, so-called a priori Wannier functions, are analyzed and the relation of the modified Hartree-Fock equations to the conventional, Bloch-function-based equations is elucidated. It is pointed out that the modified equations offer a different route to maximally localized Wannier functions. Their computational solution is found to involve an effort that is comparable to the effort for the solution of the conventional equations. Above all, I show how a priori Wannier functions can be obtained by a modification of the Kohn-Sham equations of density-functional theory.Comment: 7 pages, RevTeX4, revise

Anomalous Hall effect in 2D Dirac band: link between Kubo-Streda formula and semiclassical Boltzmann equation approach

The anomalous Hall effect (AHE) is a consequence of spin-orbit coupling in a ferromagnetic metal and is related primarily to density-matrix response to an electric field that is off-diagonal in band index. For this reason disorder contributions to the AHE are difficult to treat systematically using a semi-classical Boltzmann equation approach, even when weak localization corrections are disregarded. In this article we explicitly demonstrate the equivalence of an appropriately modified semiclassical transport theory which includes anomalous velocity and side jump contributions and microscopic Kubo-Streda perturbation theory, with particular unconventional contributions in the semiclassical theory identified with particular Feynman diagrams when calculations are carried out in a band-eigenstate representation. The equivalence we establish is verified by explcit calculations for the case of the two-dimensional (2D) Dirac model Hamiltonian relevant to graphene.Comment: 17 pages, 13 figure

Measures of oxidative state are primarily driven by extrinsic factors in a long-distance migrant

This is the author accepted manuscript. The final version is available from the Royal Society via the DOI in this recordData accessibility: Data are available from the Dryad Digital Repository: https://doi.org/10.5061/dryad.j4k3t6f/1 [20].Oxidative stress is a likely consequence of hard physical exertion and thus a potential mediator of life-history trade-offs in migratory animals. However, little is known about the relative importance of intrinsic and extrinsic stressors on the oxidative state of individuals in wild populations. We quantified the relationships between air temperature, sex, body condition and three markers of oxidative state (malondialdehyde, superoxide dismutase and total antioxidant capacity) across hundreds of individuals of a long-distance migrant (the brent goose Branta bernicla hrota) during wintering and spring staging. We found that air temperature and migratory stage were the strongest predictors of oxidative state. This emphasizes the importance of extrinsic factors in regulating the oxidative state of migrating birds, with differential effects across the migration. The significance of abiotic effects demonstrates an additional mechanism by which changing climates may affect migratory costs.European Commissio

Electronic Structure of Three-Dimensional Superlattices Subject to Tilted Magnetic Fields

Full quantum-mechanical description of electrons moving in 3D structures with unidirectional periodic modulation subject to tilted magnetic fields requires an extensive numerical calculation. To understand magneto-oscillations in such systems it is in many cases sufficient to use the quasi-classical approach, in which the zero-magnetic-field Fermi surface is considered as a magnetic-field-independent rigid body in k-space and periods of oscillations are related to extremal cross-sections of the Fermi surface cut by planes perpendicular to the magnetic-field direction. We point out cases where the quasi-classical treatment fails and propose a simple tight-binding fully-quantum-mechanical model of the superlattice electronic structure.Comment: 8 pages, 7 figures, RevTex, submitted to Phys. Rev.

Tilting instability and other anomalies in the flux-lattice in some magnetic superconductors

The flux-line lattice in the compound $ErNi_2B_2C$, which has a tendency to ferromagnetic order in the a-b plane is studied with external magnetic field direction close to the c-axis. We show the existence of an instability where the direction of flux-lines spontaneously tilts away from that of the applied field near the onset of ferromagnetic order. The enhanced fluctuations in the flux lattice and the square flux lattice recently observed are explained and further experiments suggested.Comment: 12 pages, Latex file, no figur