We have developed a mixed Vector Finite Element Method (VFEM) for Maxwell's equations with a nonlinear polarization term. The method allows for discretization of complicated geometries with arbitrary order representations of the B and E fields. In this paper we will describe the method and a series of optimizations that significantly reduce the computational cost. Additionally, a series of test simulations will be presented to validate the method. Finally, a nonlinear waveguide mode mixing example is presented and discussed.

This work is motivated by the growing interest in injectingcarbon dioxide into deep geological formations as a means of avoidingatmospheric emissions of carbon dioxide and consequent global warming.One of the key questions regarding the feasibility of this technology isthe potential rate of leakage out of the primary storage formation. Weseek exact solutions in a model of gas flow driven by a combination ofbuoyancy, viscous and capillary forces. Different combinations of theseforces and characteristic length scales of the processes lead todifferent time scaling and different types of solutions. In the case of athin, tight seal, where the impact of gravity is negligible relative tocapillary and viscous forces, a Ryzhik-type solution implies square-rootof time scaling of plume propagation velocity. In the general case, a gasplume has two stable zones, which can be described by travelling-wavesolutions. The theoretical maximum of the velocity of plume migrationprovides a conservative estimate for the time of vertical migration.Although the top of the plume has low gas saturation, it propagates witha velocity close to the theoretical maximum. The bottom of the plumeflows significantly more slowly at a higher gas saturation. Due to localheterogeneities, the plume can break into parts. Individual plumes alsocan coalesce and from larger plumes. The …

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Shock initiation experiments were performed on the plastic bonded explosive (PBX) LX-04 (85% HMX, 15% Viton binder) using single and multiple low amplitude shocks to obtain pressure history data for use in Ignition and Growth reactive flow modeling parameterization. A 100 mm diameter propellant driven gas gun was utilized to initiate the LX-04 explosive charges containing manganin piezoresistive pressure gauge packages placed between explosive discs. In the single shock experiments, the run distances to detonation at three shock pressures showed agreement with previously published data above 3 GPa. Even longer run distances to detonation were measured using 80 mm long by 145 mm diameter LX-04 charges impacted by low velocity projectiles from a 155 mm diameter gun. The minimum shock pressure required to cause low levels of exothermic reaction were determined for these large LX-04 charge dimensions. Multiple shocks were generated as double shocks by using a flyer plate with two materials and as reflected shocks by placing a high impedance material at the rear of the explosive charge. In both cases, the first shock pressure was not high enough to cause detonation of LX-04, and the second shock pressure, which would have been sufficient to cause detonation if generated …

Initiation of insensitive high explosives is affected by porosity in the 100 nm to micron size range. It is also recognized that as-pressed plastic bonded explosives (PBX) are heterogeneous in composition and density at much coarser length scale (10 microns-100 microns). However, variations in density and composition of these explosives have been poorly characterized. Here, we characterize the natural variations in composition and density of TATB-based PBX LX-17 with synchrotron radiation tomography and ultra small angle x-ray scattering. Large scale variations in composition occur as a result of binder enrichment at the prill particle boundaries. The pore fraction is twice as high in the prill particle as in the boundary. The pore distribution is bimodal, with small pores of 50-100 nm in radius and a broader distribution of pores in the 0.5-1.5 micron size range. The higher pore density within the prill particle is attributed to contact asperities between the crystallites that might inhibit complete consolidation and binder infiltration.

Protein microarrays in which proteins are immobilized to a solid surface are ideal reagents for high-throughput experiments that require very small amounts of analyte. Such protein microarrays (''protein chips'') can be used very efficiently to analyze all kind of protein interactions en masse. Although a variety of methods are available for attaching proteins on solid surfaces. Most of them rely on non-specific adsorption methods or on the reaction of chemical groups within proteins (mainly, amino and carboxylic acid groups) with complementary reactive groups. In both cases the protein is attached to the surface in random orientations. The use of recombinant affinity tags addresses the orientation issue, however in most of the cases the interaction of the tags are reversible (e.g., glutathione S-transferase, maltose binding protein and poly-His) and, hence, are not stable over the course of subsequent assays or require large mediator proteins (e.g., biotin-avidin and antigen antibody). The key for the covalent attachment of a protein to a solid support with a total control over the orientation is to introduce two unique and mutually reactive groups on both the protein and the surface. The reaction between these two groups should be highly selective thus behaving like a molecular ''velcro''.

Through horizontal and vertical excitations, we have been able to make a precision measurement of linear geometric optics parameters with a Model-Independent Analysis (MIA). We have also been able to build up a computer model that matches the real accelerator in linear geometric optics with an SVD-enhanced Least-square fitting process. Recently, with the addition of longitudinal excitation, we are able to build up a computer virtual machine that matches the real accelerators in linear optics including dispersion without additional fitting variables. With this optics-matched virtual machine, we are able to find solutions that make changes of selected normal and skew quadrupoles for machine optics improvement. It has made major contributions to improve PEP-II optics and luminosity. Examples from application to PEP-II machines will be presented.

Isopiestic vapor pressure measurements were made for (xZnCl{sub 2} + (1 - x)ZnSO{sub 4})(aq) solutions with ZnCl{sub 2} molality fractions of x = (0, 0.3062, 0.5730, 0.7969, and 1) at the temperature 298.15 K, using KCl(aq) as the reference standard. These measurements cover the water activity range 0.901-0.919 {le} a{sub w} {le} 0.978. The experimental osmotic coefficients were used to evaluate the parameters of an extended ion-interaction (Pitzer) model for these mixed electrolyte solutions. A similar analysis was made of the available activity data for ZnCl{sub 2}(aq) at 298.15 K, while assuming the presence of equilibrium amounts of ZnCl{sup +}(aq) ion-pairs, to derive the ion-interaction parameters for the hypothetical pure binary electrolytes (Zn{sup 2+}, 2Cl{sup -}) and (ZnCl{sup +},Cl{sup -}). These parameters are required for the analysis of the mixture results. Although significant concentrations of higher-order zinc chloride complexes may also be present in these solutions, it was possible to represent the osmotic coefficients accurately by explicitly including only the predominant complex ZnCl{sup +}(aq) and the completely dissociated ions. The ionic activity coefficients and osmotic coefficients were calculated over the investigated molality range using the evaluated extended Pitzer model parameters.

This article performs a comparative analysis of the predicted proteomes derived from 10 different sequenced genomes, including budding and fission yeast, worm, fly, mosquito, Arabidopsis, rice, mouse, rat, and human.

Future high-energy accelerators such as the Next Linear Collider (NLC) will accelerate multi-bunch beams of high current and low emittance to obtain high luminosity, which put stringent requirements on the accelerating structures for efficiency and beam stability. While numerical modeling has been quite standard in accelerator R&D, designing the NLC accelerating structure required a new simulation capability because of the geometric complexity and level of accuracy involved. Under the US DOE Advanced Computing initiatives (first the Grand Challenge and now SciDAC), SLAC has developed a suite of electromagnetic codes based on unstructured grids and utilizing high performance computing to provide an advanced tool for modeling structures at accuracies and scales previously not possible. This paper will discuss the code development and computational science research (e.g. domain decomposition, scalable eigensolvers, adaptive mesh refinement) that have enabled the large-scale simulations needed for meeting the computational challenges posed by the NLC as well as projects such as the PEP-II and RIA. Numerical results will be presented to show how high performance computing has made a qualitative improvement in accelerator structure modeling for these accelerators, either at the component level (single cell optimization), or on the scale of an entire structure (beam heating and …

Reflectivity measurements in the far infrared, performed on aluminum and copper samples, are presented and analyzed. Over a frequency range of interest for the LCLS bunch, the data is fit to the free-electron model, and to one including the anomalous skin effect. The models fit well, yielding parameters dc conductivity and relaxation times that are within 30-40% of expected values. We show that the induced energy in the LCLS undulator region is relatively insensitive to variations on this order, and thus we can have confidence that the wake effect will be close to what is expected.

A Super Flavor Factory, an asymmetric energy e{sup +}e{sup -} collider with a luminosity of order 10{sup 36} cm{sup -2} s{sup -1}, can provide a sensitive probe of new physics in the flavor sector of the Standard Model. The success of the PEP-II and KEKB asymmetric colliders in producing unprecedented luminosity above 10{sup 34} cm{sup -2} s{sup -1} has taught us about the accelerator physics of asymmetric e{sup +}e{sup -} collider in a new parameter regime. Furthermore, the success of the SLAC Linear Collider and the subsequent work on the International Linear Collider allow a new Super-Flavor collider to also incorporate linear collider techniques. This note describes the parameters of an asymmetric Flavor-Factory collider at a luminosity of order 10{sup 36} cm{sup -2} s{sup -1} at the Y(4S) resonance and about 10{sup 35} cm{sup -2} s{sup -1} at the {tau} production threshold. Such a collider would produce an integrated luminosity of about 10,000 fb{sup -1} (10 ab{sup -1}) in a running year (10{sup 7} sec) at the Y(4S) resonance. In the following note only the parameters relative to the Y(4S) resonance will be shown, the ones relative to the lower energy operations are still under study.