Tracing magnetic separators and their dependence on IMF clock angle in global magnetospheric simulations

A new, efficient, and highly accurate method for tracing magnetic separators in global magnetospheric simulations with arbitrary clock angle is presented. The technique is to begin at a magnetic null and iteratively march along the separator by finding where four magnetic topologies meet on a spherical surface. The technique is verified using exact solutions for separators resulting from an analytic magnetic field model that superposes dipolar and uniform magnetic fields. Global resistive magnetohydrodynamic simulations are performed using the three-dimensional BATS-R-US code with a uniform resistivity, in eight distinct simulations with interplanetary magnetic field (IMF) clock angles ranging from 0 (parallel) to 180 degrees (anti-parallel). Magnetic nulls and separators are found in the simulations, and it is shown that separators traced here are accurate for any clock angle, unlike the last closed field line on the Sun-Earth line that fails for southward IMF. Trends in magnetic null locations and the structure of magnetic separators as a function of clock angle are presented and compared with those from the analytic field model. There are many qualitative similarities between the two models, but quantitative differences are also noted. Dependence on solar wind density is briefly investigated.Comment: 10 pages, 10 figures, Presented at 2012 AGU Fall Meeting and 2013 Geospace Environment Modeling (GEM) Worksho

Asymmetric magnetic reconnection with a flow shear and applications to the magnetopause

We perform a theoretical and numerical study of anti-parallel 2D magnetic reconnection with asymmetries in the density and reconnecting magnetic field strength in addition to a bulk flow shear across the reconnection site in the plane of the reconnecting fields, which commonly occurs at planetary magnetospheres. We predict the speed at which an isolated X-line is convected by the flow, the reconnection rate, and the critical flow speed at which reconnection no longer takes place for arbitrary reconnecting magnetic field strengths, densities, and upstream flow speeds, and confirm the results with two-fluid numerical simulations. The predictions and simulation results counter the prevailing model of reconnection at Earth's dayside magnetopause which says reconnection occurs with a stationary X-line for sub-Alfvenic magnetosheath flow, reconnection occurs but the X-line convects for magnetosheath flows between the Alfven speed and double the Alfven speed, and reconnection does not occur for magnetosheath flows greater than double the Alfven speed. We find that X-line motion is governed by momentum conservation from the upstream flows, which are weighted differently in asymmetric systems, so the X-line convects for generic conditions including sub-Alfvenic upstream speeds. For the reconnection rate, while the cutoff condition for symmetric reconnection is that the difference in flows on the two sides of the reconnection site is twice the Alfven speed, we find asymmetries cause the cutoff speed for asymmetric reconnection to be higher than twice the asymmetric form of the Alfven speed. The results compare favorably with an observation of reconnection at Earth's polar cusps during a period of northward interplanetary magnetic field, where reconnection occurs despite the magnetosheath flow speed being more than twice the magnetosheath Alfven speed, the previously proposed suppression condition.Comment: 46 pages, 7 figures, abstract abridged here, accepted to Journal of Geophysical Research - Space Physic

The local dayside reconnection rate for oblique interplanetary magnetic fields

We present an analysis of local properties of magnetic reconnection at the dayside magnetopause for various interplanetary magnetic field (IMF) orientations in global magnetospheric simulations. This has heretofore not been practical because it is difficult to locate where reconnection occurs for oblique IMF, but new techniques make this possible. The approach is to identify magnetic separators, the curves separating four regions of differing magnetic topology, which map the reconnection X-line. The electric field parallel to the X-line is the local reconnection rate. We compare results to a simple model of local two-dimensional asymmetric reconnection. To do so, we find the plasma parameters that locally drive reconnection in the magnetosheath and magnetosphere in planes perpendicular to the X-line at a large number of points along the X-line. The global magnetohydrodynamic simulations are from the three-dimensional Block-Adaptive, Tree Solarwind Roe-type Upwind Scheme (BATS-R-US) code with a uniform resistivity, although the techniques described here are extensible to any global magnetospheric simulation model. We find that the predicted local reconnection rates scale well with the measured values for all simulations, being nearly exact for due southward IMF. However, the absolute predictions differ by an undetermined constant of proportionality, whose magnitude increases as the IMF clock angle changes from southward to northward. We also show similar scaling agreement in a simulation with oblique southward IMF and a dipole tilt. The present results will be an important component of a full understanding of the local and global properties of dayside reconnection

Electromagnetic Energy for a Charged Kerr Black Hole in a Uniform Magnetic Field

With the Komar mass formula we calculate the electromagnetic energy for a charged Kerr black hole in a uniform magnetic field. We find that the total electromagnetic energy takes the minimum when the Kerr black hole possesses a non-zero net charge $Q = 2\xi B_0 J_H$ where $B_0$ is the strength of the magnetic field, $J_H$ is the angular momentum of the black hole, $\xi$ is a dimensionless parameter determined by the spin of the black hole.Comment: 9 pages, 1 figur

Rapid West Nile Virus Antigen Detection

We compared the VecTest WNV antigen assay with standard methods of West Nile virus (WNV) detection in swabs from American Crows (Corvus brachyrhynchos) and House Sparrows (Passer domesticus). The VecTest detected WNV more frequently than the plaque assay and was comparable to a TaqMan reverse transcription–polymerase chain reaction

Consequences of a covariant Description of Heavy Ion Reactions at intermediate Energies

Heavy ion collisions at intermediate energies are studied by using a new RQMD code, which is a covariant generalization of the QMD approach. We show that this new implementation is able to produce the same results in the nonrelativistic limit (i.e. 50MeV/nucl.) as the non-covariant QMD. Such a comparison is not available in the literature. At higher energies (i.e. 1.5 GeV/nucl. and 2 GeV/nucl.) RQMD and QMD give different results in respect to the time evolution of the phase space, for example for the directed transverse flow. These differences show that consequences of a covariant description of heavy ion reactions within the framework of RQMD are existing even at intermediate energies.Comment: LaTex-file, 28 pages, 8 figures (available upon request), accepted for publication in Physical Review

Dirac-Schr\"odinger equation for quark-antiquark bound states and derivation of its interaction kerne

The four-dimensional Dirac-Schr\"odinger equation satisfied by quark-antiquark bound states is derived from Quantum Chromodynamics. Different from the Bethe-Salpeter equation, the equation derived is a kind of first-order differential equations of Schr\"odinger-type in the position space. Especially, the interaction kernel in the equation is given by two different closed expressions. One expression which contains only a few types of Green's functions is derived with the aid of the equations of motion satisfied by some kinds of Green's functions. Another expression which is represented in terms of the quark, antiquark and gluon propagators and some kinds of proper vertices is derived by means of the technique of irreducible decomposition of Green's functions. The kernel derived not only can easily be calculated by the perturbation method, but also provides a suitable basis for nonperturbative investigations. Furthermore, it is shown that the four-dimensinal Dirac-Schr\"odinger equation and its kernel can directly be reduced to rigorous three-dimensional forms in the equal-time Lorentz frame and the Dirac-Schr\"odinger equation can be reduced to an equivalent Pauli-Schr\"odinger equation which is represented in the Pauli spinor space. To show the applicability of the closed expressions derived and to demonstrate the equivalence between the two different expressions of the kernel, the t-channel and s-channel one gluon exchange kernels are chosen as an example to show how they are derived from the closed expressions. In addition, the connection of the Dirac-Schr\"odinger equation with the Bethe-Salpeter equation is discussed

A Climate Index Optimized for Longshore Sediment Transport Reveals Interannual and Multidecadal Littoral Cell Rotations

A recent 35-year endpoint shoreline change analysis revealed significant counterclockwiserotations occurring in north-central Oregon, USA, littoral cells that extend 10s of kilometers in length.While the potential for severe El Niños to contribute to littoral cell rotations at seasonal to interannual scalewas previously recognized, the dynamics resulting in persistent (multidecadal) rotation were unknown,largely due to a lack of historical wave conditions extending back multiple decades and the difficulty ofseparating the timescales of shoreline variability in a high energy region. This study addresses this questionby (1) developing a statistical downscaling framework to characterize wave conditions relevant for longshoresediment transport during data-poor decades and (2) applying a one-line shoreline change model toquantitatively assess the potential for such large embayed beaches to rotate. A climateINdex was optimizedto capture variability in longshore wave power as a proxy for potentialLOngshore Sediment Transport(LOST_IN), and a procedure was developed to simulate many realizations of potential wave conditions fromthe index. Waves were transformed dynamically with Simulating Waves Nearshore to the nearshore asinputs to a one-line model that revealed shoreline rotations of embayed beaches at multiple time and spatialscales not previously discernible from infrequent observations. Model results indicate that littoral cellsrespond to both interannual and multidecadal oscillations, producing comparable shoreline excursions toextreme El Niño winters. The technique quantitatively relates morphodynamic forcing to specific climatepatterns and has the potential to better identify and quantify coastal variability on timescales relevant to achanging climate.This work would not have been possible without funding from the NSF Graduate Research Fellowship Program (GRFP) through NSF grant DGE-1314109, the Coastal and Ocean Climate Applications (COCA) program through NOAA grant NA15OAR4310243, NOAA’s Regional Integrated Sciences and Assessments Program (RISA), under NOAA grant NA15OAR4310145, and the Spanish Ministerio de Educación Cultura y Deporte FPU (Formación del Profesorado Universitario) studentship BOE-A-2013-12235. Beach survey data collection undertaken on the Oregon coast was made possible by the Northwest Association of Networked Ocean Observing Systems (NANOOS) through NOAA grant NA16NOS0120019

Correlation between nucleotide composition and folding energy of coding sequences with special attention to wobble bases

Background: The secondary structure and complexity of mRNA influences its accessibility to regulatory molecules (proteins, micro-RNAs), its stability and its level of expression. The mobile elements of the RNA sequence, the wobble bases, are expected to regulate the formation of structures encompassing coding sequences. Results: The sequence/folding energy (FE) relationship was studied by statistical, bioinformatic methods in 90 CDS containing 26,370 codons. I found that the FE (dG) associated with coding sequences is significant and negative (407 kcal/1000 bases, mean +/- S.E.M.) indicating that these sequences are able to form structures. However, the FE has only a small free component, less than 10% of the total. The contribution of the 1st and 3rd codon bases to the FE is larger than the contribution of the 2nd (central) bases. It is possible to achieve a ~ 4-fold change in FE by altering the wobble bases in synonymous codons. The sequence/FE relationship can be described with a simple algorithm, and the total FE can be predicted solely from the sequence composition of the nucleic acid. The contributions of different synonymous codons to the FE are additive and one codon cannot replace another. The accumulated contributions of synonymous codons of an amino acid to the total folding energy of an mRNA is strongly correlated to the relative amount of that amino acid in the translated protein. Conclusion: Synonymous codons are not interchangable with regard to their role in determining the mRNA FE and the relative amounts of amino acids in the translated protein, even if they are indistinguishable in respect of amino acid coding.Comment: 14 pages including 6 figures and 1 tabl