Nuclear Effects in Neutrino Induced Coherent Pion Production at K2K and MiniBooNE Neutrino Energies

The coherent pion production induced by neutrinos in nuclei is studied using a delta hole model in local density approximation taking into account the renormalization of $\Delta$ properties in a nuclear medium. The pion absorption effects have been included in an eikonal approximation. These effects give a large reduction in the total cross section. The numerical results for the total cross section are found to be consistent with recent experimental results from K2K and MiniBooNE collaborations and other older experiments in the intermediate energy region.Comment: 4pages, 5figure

Magnetic flux pumping in 3D nonlinear magnetohydrodynamic simulations

A self-regulating magnetic flux pumping mechanism in tokamaks that maintains the core safety factor at $q\approx 1$, thus preventing sawteeth, is analyzed in nonlinear 3D magnetohydrodynamic simulations using the M3D-C$^1$ code. In these simulations, the most important mechanism responsible for the flux pumping is that a saturated $(m=1,n=1)$ quasi-interchange instability generates an effective negative loop voltage in the plasma center via a dynamo effect. It is shown that sawtoothing is prevented in the simulations if $\beta$ is sufficiently high to provide the necessary drive for the $(m=1,n=1)$ instability that generates the dynamo loop voltage. The necessary amount of dynamo loop voltage is determined by the tendency of the current density profile to centrally peak which, in our simulations, is controlled by the peakedness of the applied heat source profile.Comment: submitted to Physics of Plasmas (23 pages, 15 Figures

Compensation of atmospheric CO2 buildup through engineered chemical shrinkage

Retrieval of background carbon dioxide into regional chemical extractors would counter anthropogenic inputs in a manner friendly to established industries. We demonstrate via atmospheric transport/scaling calculations that for idealized flat removal units, global coverage could be less than two hundred thousand square kilometers. The disrupted area drops to a small fraction of this with engineering into the vertical to bypass laminarity. Fence structures and artificial roughness elements can both be conceived. Sink thermodynamics are analyzed by taking calcium hydroxide as a sample reactant. Energy costs could be minimized at near the endothermicity of binding reversal. In the calcium case the value is 25 kcal mole-1, as against a fuel carbon content of 150 in the same units. Aqueous kinetics are less than favorable for the hydroxide, but misting could counteract slow liquid phase transfer. Properties of superior scrubbers are outlined

Chemical transport modeling of potential atmospheric CO2 sinks

The potential for carbon dioxide (CO2) sequestration via engineered chemical sinks is investigated using a three dimensional chemical transport model (CTM). Meteorological and chemical constraints for flat or vertical systems that would absorb CO2 from the atmosphere, as well as an example chemical system of calcium hydroxide (Ca(OH)2) proposed by Elliott et al. [Compensation of atmospheric CO2 buildup through engineered chemical sinkage, Geophys. Res. Lett. 28 (2001) 1235] are reviewed. The CTM examines land based deposition sinks, with 4° × 5° latitude/longitude resolution at various locations, and deposition velocities (v). A maximum uptake of ∼20 Gton (1015 g) Cyr-1 is attainable with v ≥ 5 cms-1 at a mid-latitude site. The atmospheric increase of CO2 (3 Gtonyr-1) can be balanced by an engineered sink with an area of no more than 75, 000 km2 at v of 1 cms-1. By building the sink upwards or splitting this area into narrow elements can reduce the active area by more than an order of magnitude as discussed in Dubey et al. © 2002 Elsevier Science Ltd. All rights reserved

Comparative Analysis of Protein Structure Alignments

Background: Several methods are currently available for the comparison of protein structures. These methods have been analysed regarding the performance in the identification of structurally/evolutionary related proteins, but so far there has been less focus on the objective comparison between the alignments produced by different methods. Results: We analysed and compared the structural alignments obtained by different methods using three sets of pairs of structurally related proteins. The first set corresponds to 355 pairs of remote homologous proteins according to the SCOP database (ASTRAL40 set). The second set was derived from the SISYPHUS database and includes 69 protein pairs (SISY set). The third set consists of 40 pairs that are challenging to align (RIPC set). The alignment of pairs of this set requires indels of considerable number and size and some of the proteins are related by circular permutations, show extensive conformational variability or include repetitions. Two standard methods (CE and DALI) were applied to align the proteins in the ASTRAL40 set. The extent of structural similarity identified by both methods is highly correlated and the alignments from the two methods agree on average in more than half of the aligned positions. CE, DALI, as well as four additional methods (FATCAT, MATRAS, C -match and SHEBA) were then compared using the SISY and RIPC sets. The accuracy of the alignments was assessed by comparison to reference alignments. The alignments generated by the different methods on average match more than half of the reference alignments in the SISY set. The alignments obtained in the more challenging RIPC set tend to differ considerably and match reference alignments less successfully than the SISY set alignments. Conclusion: The alignments produced by different methods tend to agree to a considerable extent, but the agreement is lower for the more challenging pairs. The results for the comparison to reference alignments are encouraging, but also indicate that there is still room for improvement.(VLID)221254