Trumpet Initial Data for Boosted Black Holes

We describe a procedure for constructing initial data for boosted black holes in the moving-punctures approach to numerical relativity that endows the initial time slice from the outset with trumpet geometry within the black hole interiors. We then demonstrate the procedure in numerical simulations using an evolution code from the Einstein Toolkit that employs 1+log slicing. The Lorentz boost of a single black hole can be precisely specified and multiple, widely separated black holes can be treated approximately by superposition of single hole data. There is room within the scheme for later improvement to re-solve (iterate) the constraint equations in the multiple black hole case. The approach is shown to yield an initial trumpet slice for one black hole that is close to, and rapidly settles to, a stationary trumpet geometry. Initial data in this new approach is shown to contain initial transient (or "junk") radiation that is suppressed by as much as two orders of magnitude relative to that in comparable Bowen-York initial data.Comment: 18 pages, 18 figure

POD

This thesis explores the themes which motivate the creation of abstract sculpture, searching for common forms and universal shapes throughout the pieces examined in the thesis. The examples presented were created by other artists and by the author, which include ceramic sculpture and earthenware oxides and glazes

Multiplexed DNA-Modified Electrodes

We report the use of silicon chips with 16 DNA-modified electrodes (DME chips) utilizing DNA-mediated charge transport for multiplexed detection of DNA and DNA-binding protein targets. Four DNA sequences were simultaneously distinguished on a single DME chip with 4-fold redundancy, including one incorporating a single base mismatch. These chips also enabled investigation of the sequence-specific activity of the restriction enzyme Alu1. DME chips supported dense DNA monolayer formation with high reproducibility, as confirmed by statistical comparison to commercially available rod electrodes. The working electrode areas on the chips were reduced to 10 μm in diameter, revealing microelectrode behavior that is beneficial for high sensitivity and rapid kinetic analysis. These results illustrate how DME chips facilitate sensitive and selective detection of DNA and DNA-binding protein targets in a robust and internally standardized multiplexed format

Trumpet Initial Data for Highly Boosted Black Holes and High Energy Binaries

Initial data for a single boosted black hole is constructed that analytically contains no initial transient (junk) gravitational radiation and is adapted to the moving punctures gauge conditions. The properties of this data are investigated in detail. It is found to be generally superior to canonical Bowen-York data and, when implemented numerically in simulations, yields orders of magnitude less junk gravitational radiation content and more accurate black hole velocities. This allows for modeling of black holes that are boosted faster than previously possible. An approximate superposition of the data is used to demonstrate how a binary black hole system can be constructed to retain the advantages found for the single black hole. Extensions to black holes with spin are considered.Doctor of Philosoph

DNA charge transport over 34 nm

Molecular wires show promise in nanoscale electronics but the synthesis of uniform, long conductive molecules is a significant challenge. DNA of precise length, by contrast, is easily synthesized, but its conductivity has not been explored over the distances required for nanoscale devices. Here we demonstrate DNA charge transport (CT) over 34 nm in 100-mer monolayers on gold. Multiplexed gold electrodes modified with 100-mer DNA yield sizable electrochemical signals from a distal, covalent Nile Blue redox probe. Significant signal attenuation upon incorporation of a single base pair mismatch demonstrates that CT is DNA-mediated. Efficient cleavage of these 100-mers by a restriction enzyme indicates that the DNA adopts a native conformation that is accessible to protein binding. Similar electron transfer rates are measured through 100-mer and 17-mer monolayers, consistent with rate-limiting electron tunneling through the saturated carbon linker. This DNA-mediated CT distance of 34 nm surpasses most reports of molecular wires

Studies of Immunogenetic Variation in Cattle

Genetic selection for animal health and disease resistance has been limited, likely due to the challenges of performing controlled studies with an industry relevant phenotype. Studies in large populations of animals of unknown relationship pose challenges for genome wide association studies of disease resistance. The aims of this project were to characterize variation in the bovine major histocompatibility complex (BoLA), a specific region of the bovine genome known be critical for development of immune response, and then investigate individual variation in host immunity to a specific viral pathogen of cattle, bovine viral diarrhea virus (BVDV). Cattle “homozygous” for BoLA were identified from approximately 2,000 head of Holstein calves in large genome wide association studies. Cattle were genotyped on the Illumina BovineHD SNP chip and PHASED for the characterization of BoLA haplotypes. Among 160 “homozygous” animals, we identified 38 different haplotype groups. The 38 haplotype groups maintained the structure predicted by earlier studies that identified 50K SNP haplotypes, but demonstrated that more diversity is present among these 38 BoLA haplotype groups than was indicated by the 50K haplotypes. Among the 1,221 SNPs genotyped on the HD chip were 230 SNPs with no calls in at least one of the 160 homozygous animals. The no call SNPs are located predominately in regions predicted to contain copy number variation, and no call SNPs appear to likely mark regions of polymorphic structural variation otherwise undetected in the SNP defined haplotypes. This structural variation may be important for future genome association studies. Cattle diseases are often difficult to diagnose due to presentation with different disease phenotypes, ranging from subclinical to lethal. Likewise, immune response to vaccination is also variable and may be related to individual differences in disease susceptibilities. To evaluate individualized response to BVDV vaccination, we evaluated protection afforded by commercial vaccines against a BVDV challenge. The results from the BVDV challenge study indicate that measuring antibody titer as a response to BVDV vaccination may not be predictive of a protective immune response. Rectal temperature alone for health classification missed up to 50% of animals with subclinical disease. Variation in host immunity appears to underlie the response to pathogens and likely to vaccination as well. Host differences in immunity between Bos indicus and Bos taurus cattle were evaluated subsequent to BVDV vaccination. Differences in baseline immune cell counts were observed. Indicine cattle had higher white blood cell counts primarily influenced by the 2-fold higher neutrophil levels. Response to vaccination was primarily observed as an innate immune response with an increase in neutrophils. The largest change was in neutrophil response observed in the taurine calves. Immunosuppression from the modified live vaccination was greater in the indicine calves compared to taurine calves. However, a combination of vaccination protocols appear to mitigate the immunosuppression observed in the indicine cattle