Physical Sciences and Mathematics Commons^™

A Cultured Greigite-Producing Magnetotactic Bacterium In A Novel Group Of Sulfate-Reducing Bacteria, Christopher T. Lefèvre, Nicholas Menguy, Fernanda Abreu, Ulysses Lins, Mihály Pósfai, Tanya Prozorov, David Pignol, Richard B. Frankel, Dennis A. Bazylinski

Physics

Magnetotactic bacteria contain magnetosomes—intracellular, membrane-bounded, magnetic nanocrystals of magnetite (Fe₃O₄) or greigite (Fe₃S₄)—that cause the bacteria to swim along geomagnetic field lines. We isolated a greigite-producing magnetotactic bacterium from a brackish spring in Death Valley National Park, California, USA, strain BW-1, that is able to biomineralize greigite and magnetite depending on culture conditions. A phylogenetic comparison of BW-1 and similar uncultured greigite- and/or magnetite-producing magnetotactic bacteria from freshwater to hypersaline habitats shows that these organisms represent a previously unknown group of sulfate-reducing bacteria in the Deltaproteobacteria. Genomic analysis of BW-1 reveals …

Veritas Observations Of Gamma-Ray Bursts Detected By Swift, V. A. Acciari, E. Aliu, T. Arlen, T. Aune, M. Beilicke, W. Benbow, S. M. Bradbury, J. H. Buckley, V. Bugaev, K. Byrum, A. Cannon, A. Cesarini, J. L. Christiansen, L. Ciupik, E. Collins-Hughes, M. P. Connolly, W. Cui, C. Duke, M. Errando, A. Falcone, J. P. Finley, G. Finnegan, L. Fortson, A. Furniss, N. Galante, D. Gall, S. Godambe, S. Griffin, J. Grube, R. Guenette, G. Gyuk, D. Hanna, J. Holder, G. Hughes, C. M. Hui, T. B. Humensky, D. J. Jackson, P. Kaaret, N. Karlsson, M. Kertzman, D. Kieda, H. Krawczynski, F. Krennrich, M. J. Lang, A. S. Madhavan, G. Maier, S. Mcarthur, A. Mccann, P. Moriarty, M. D. Newbold, R. A. Ong, M. Orr, A. N. Otte, N. Park, J. S. Perkins, M. Pohl, H. Prokoph, J. Quinn, K. Ragan, L. C. Reyes, P. T. Reynolds, E. Roache, H. J. Rose, J. Ruppel, D. B. Saxon, M. Schroedter, G. H. Sembroski, G. D. Şentürk, A. W. Smith, D. Staszak, S. P. Swordy, G. Tešić, M. Theiling, S. Thibadeau, K. Tsurusaki, A. Varlotta, V. V. Vassiliev, S. Vincent, M. Vivier, S. P. Wakely, J. E. Ward, T. C. Weekes, A. Weinstein, T. Weisgarber, D. A. Williams, M. Wood

Physics

We present the results of 16 Swift-triggered Gamma-ray burst (GRB) follow-up observations taken with the Very Energetic Radiation Imaging Telescope Array System (VERITAS) telescope array from 2007 January to 2009 June. The median energy threshold and response time of these observations were 260 GeV and 320 s, respectively. Observations had an average duration of 90 minutes. Each burst is analyzed independently in two modes: over the whole duration of the observations and again over a shorter timescale determined by the maximum VERITAS sensitivity to a burst with a t^−1.5 time profile. This temporal model is characteristic of GRB …

The Lick Agn Monitoring Project 2011: Reverberation Mapping Of Markarian 50, Aaron J. Barth, Anna Pancoast, Shawn J. Thorman, Vardha N. Bennert, David J. Sand, Weidong Li, Gabriela Canalizo, Alexei V. Filippenko, Elinor L. Gates, Jenny E. Greene, Matthew A. Malkan, Daniel Stern, Tommaso Treu, Jong-Hak Woo, Roberto J. Assef, Hyun-Jin Bae, Brendon J. Brewer, Tabitha Buehler, S. Bradley Cenko, Kelsey I. Clubb, Michael C. Cooper, Aleksandar M. Diamond-Stanic, Kyle D. Hiner, Sebastian F. Hönig, Michael D. Joner, Michael T. Kandrashoff, C. David Laney, Mariana S. Lazarova, A. M. Nierenberg, Dawoo Park, Jeffrey M. Silverman, Donghoon Son, Alessandro Sonnenfeld, Erik J. Tollerud, Jonelle L. Walsh, Richard Walters, Robert L. Da Silva, Michele Fumagalli, Michael D. Gregg, Chelsea E. Harris, Eric Y. Hsiao, Jeffrey Lee, Liliana Lopez, Jacob Rex, Nao Suzuki, Jonathan R. Trump, David Tytler, Gábor Worseck, Hassan M. Yesuf

Physics

The Lick AGN Monitoring Project 2011 observing campaign was carried out over the course of 11 weeks in spring 2011. Here we present the first results from this program, a measurement of the broad-line reverberation lag in the Seyfert 1 galaxy Mrk 50. Combining our data with supplemental observations obtained prior to the start of the main observing campaign, our data set covers a total duration of 4.5 months. During this time, Mrk 50 was highly variable, exhibiting a maximum variability amplitude of a factor of ~4 in the U-band continuum and a factor of ~2 in the Hβ …

Synthesis Of An Antimicrobial Textile Coating, William M. Morris

Chemistry and Biochemistry

A titania nanosol was synthesized and coated onto nylon/cotton blended textile substrates. The substrates were characterized via SEM for adhesion and nanoparticle formation, then subjected to antimicrobial efficacy tests. The titania nanosol was successfully coated on to textiles samples. Particles were observed to be around 2 by 3 micrometers and formed between the interstitial space of textile fibers. Although larger than typical nanoparticles, the coatings exhibited what seemed to be antimicrobial activity. Titania nanosol coated textile samples were subjected to Kirby Bauer Assay in the presence of S. aureus. The coated textile sample exhibited an inhibition of growth around its …

An Analysis Of Breast Cancer Metastasis, Jennifer Lee Gildner

Statistics

The main objective of this paper is to evaluate possible socio-economic status, clinical, and treatment associations with the occurrence of distant metastasis in Stage I – III breast cancer patients. After analysis in a logistic regression model, four variables were found to be significant with occurrence of distant metastases. These variables were: education, disease group (Triple-negative, Her2Neu-positive and Luminal A), stage at diagnosis, and concordance to chemotherapy based on the NCCN guidelines. Patients without a college degree were found to be more likely to develop distant metastasis than those with a college degree (OR = 2.46 95% CI 1.44 – …

The Relation Between Black Hole Mass And Host Spheroid Stellar Mass Out To Z~2, Vardha N. Bennert, Matthew A. Auger, Tommaso Treu, Jong-Hak Woo, Matthew A. Malkan

Physics

We combine Hubble Space Telescope images from the Great Observatories Origins Deep Survey with archival Very Large Telescope and Keck spectra of a sample of 11 X-ray-selected broad-line active galactic nuclei in the redshift range 1 < z < 2 to study the black-hole-mass-stellar-mass relation out to a look-back time of 10 Gyr. Stellar masses of the spheroidal component (M _sph, ) are derived from multi-filter surface photometry. Black hole masses (M _BH) are estimated from the width of the broad Mg II emission line and the 3000 Å nuclear luminosity. Comparing with a uniformly measured local sample and taking into account selection effects, we find evolution in the form M _BH/M _sph, (1 + z)^{1.96 …}

Morphological Features Of Elongated-Anisotropic Magnetosome Crystals In Magnetotactic Bacteria Of The Nitrospirae Phylum And The Deltaproteobacteria Class, Christopher T. Lefèvre, Mihály Pósfai, Fernanda Abreu, Ulysses Lins, Richard B. Frankel, Dennis A. Bazlinski

Physics

High resolution transmission electron microscopy was used to study the crystallographic habits of the elongated magnetite crystals, variously described as bullet-, tooth- or arrowhead-shaped, in two recently described, uncultured, magnetotactic bacteria belonging to the Nitrospirae phylum designated Candidatus Magnetoovum mohavensis strain LO-1, and Candidatus Thermomagnetovibrio paiutensis strain HSMV-1; and a cultured sulfate-reducing magnetotactic bacterium of the Deltaproteobacteria class of the Proteobacteria phylum designated strain AV-1. The elongation axes of the magnetosomes do not coincide with the easy magnetization axis (which is [111]) but they are parallel to [100] in LO-1 and AV-1 and parallel to [110] in HSMV-1. In all …

Simulated Effects Of Varied Landscape-Scale Fuel Treatments On Carbon Dynamics And Fire Behavior In The Klamath Mountains Of California, Kevin J. Osborne

Master's Theses

I utilized forest growth model (FVS-FFE) and fire simulation software (FlamMap, Randig), integrated through GIS software (ArcMap9.3), to quantify the impacts varied landscape-scale fuel treatments have on short-term onsite carbon loss, long-term onsite carbon storage, burn probability, conditional flame length, and mean fire size. Thirteen fuel treatment scenarios were simulated on a 42,000 hectare landscape in northern California: one untreated, three proposed by the US Forest Service, and nine that were spatially-optimized and developed with the Treatment Optimization Model in FlamMap. The nine scenarios developed in FlamMap varied by treatment intensity (10%, 20%, and 30% of the landscape treated) and …

Astronomical Spectroscopy At The Cal Poly Observatory, Christopher James Almich

Physics

Embarking on the first ever astronomical spectroscopy project at the Cal Poly Observatory, I have tested the capabilities of our equipment. Our spectrograph, in conjunction with a telescope and CCD camera, is capable of making fairly precise measurements of absorption and emission lines with sub-nanometer precision. In my research I obtained a spectrum of Jupiter and was able to confidently identify a number of Fraunhofer solar absorption lines.

Achieving Laser Wavelength Stability For Use In Neutral Atom Quantum Computing, Jennifer H. Rushing

Physics

Quantum computing may still be decades away from realization but the pieces necessary for the construction of the first quantum chip are beginning to come together. One piece still eluding researchers is the ability to address individual atoms within a scalable quantum chip structure. The resolution to this issue may be found in any one of several promising implementations, including the use of neutral atoms trapped in 2D optical lattices. One method of constructing such lattices, which has been shown to be computationally viable, employs the diffraction pattern just behind a circular aperture. Laser wavelength stability plays a crucial role …

Adhesion And Durability Of Coatings On Polypropylene Exterior Sidings, Logan Riekio Stark

Master's Theses

Plastics have become a universal material for use in a myriad of commercial and consumer products. One such product, exterior siding, is the focus of this project. Although siding products were originally made from wood, vinyl siding, which offered superior performance, was introduced in the 1950’s. More recently, polypropylene (PP) siding has been introduced; PP provides a stronger product, which allows for deeper patterns and better edge detailing. PP siding, compared to traditional wood siding, doesn’t warp, crack, or degrade as easily with extended exposure to the elements, and is cheaper to maintain. However, even plastic siding must be coated. …

Hubble Space Telescope Imaging Of Post-Starburst Quasars, S. L. Cales, M. S. Brotherton, Zhaohui Shang, Vardha N. Bennert, G. Canalizo, R. Stoll, R. Ganguly, D. Vanden Berk, C. Paul, A. Diamond-Stanic

Physics

We present images of 29 post-starburst quasars (PSQs) from a Hubble Space Telescope (HST) Advanced Camera for Surveys (ACS) Wide Field Channel Snapshot program. These broadlined active galactic nuclei (AGNs) possess the spectral signatures of massive (M _burst ~ 10¹⁰ M _☉), moderate-aged stellar populations (hundreds of Myr). Thus, their composite nature provides insight into the AGN-starburst connection. We measure quasar-to-host galaxy light contributions via semi-automated two-dimensional light profile fits of point-spread-function-subtracted images. We examine the host morphologies and model the separate bulge and disk components. The HST/ACS-F606W images reveal an equal number …

Calibration Systems And Methods For Infrared Cameras, Russell Granneman, Nuwan Nagahawatte, Richard M. Goeden, Ted Takagi, Robert Ernst, Gary B. Hughes, Joseph Kostrzewa, John Graff, George Speake, Michael Kent, Neela Nalam, Stephen Lyon, Barbara Sharp, Pierre Boulanger, Neil Cutcliffe, Tim Martin, Ted Hoelter

Statistics

Systems and methods directed to calibration techniques for infrared cameras are disclosed. For example, a method of obtaining calibration information for an infrared device includes providing a calibration target adapted to provide a low-emissivity scene; performing a calibration operation on the infrared device to obtain the calibration information; and storing the calibration information.

Wavelength Dependence Of Transverse Mode Coupling With/Without E-Block Of Gan Laser Cavity, Krishneel Lal

Electrical Engineering

No abstract provided.

Similarity Scaling Of Turbulence Spectra And Cospectra In A Shallow Tidal Flow, Ryan K. Walter, Nicholas J. Nidzieko, Stephen G. Monismith

Physics

Measured turbulence power spectra, cospectra, and ogive curves from a shallow tidal flow were scaled using Monin‐Obukhov similarity theory to test the applicability to a generic tidal flow of universal curves found from a uniform, neutrally stable atmospheric boundary layer (ABL). While curves from individual 10 min data bursts deviate significantly from similarity theory, averages over large numbers of sufficiently energetic bursts follow the general shape. However, there are several differences: (1) Variance in the measured curves was shifted toward higher frequencies, (2) at low frequencies, velocity spectra were significantly more energetic than theory while cospectra were weaker, and (3) …

Road Runoff And Sediment Sampling For Determining Road Sediment Yield At The Watershed Scale, Christopher G. Surfleet, Arne E. Skaugset Iii, Matthew W. Meadows

Natural Resources Management and Environmental Sciences

In this study, we demonstrate that watershed-scale estimates of road sediment production are improved if field measurements of road runoff and sediment production are used in the analysis. We used several techniques to spatially extrapolate measurements of road runoff and sampled sediment: comprehensive road runoff measurements, runoff estimates derived from the Distributed Hydrology Soil Vegetation Model (DHSVM), and adjustment of the road erosion models WARSEM and SEDMODL2.The sediment yield for the Oak Creek, Oregon, road network based on measured road runoff and sediment was 6.5 tons/year. When DHSVM was used to simulate road runoff, the estimated sediment from roads was …

Post-Fire Near-Surface Runoff From Small-Scale Rainfall Simulations, Santa Cruz Mountains, Michael Founds

Natural Resources Management and Environmental Sciences

The influence of environmental variables on the runoff response to a fire is poorly understood. Small-scale rainfall simulation was used to study the factors impacting near-surface runoff following the Lockheed Fire, which occurred on August 12, 2009. A variable speed rainfall simulator was used to rain on 15 different test plots at an average rate of 50mmh^-1. Variables of burn severity, time following the fire, soil parent material, vegetation type, and presence of a duff layer were all analyzed using the ratio of runoff to rainfall. The difference in-between burned sites and similar control sites were 19±6%. Only …

Detection Of Pulsed Gamma Rays Above 100 Gev From The Crab Pulsar, E. Aliu, T. Arlen, T. Aune, M. Beilicke, W. Benbow, A. Bouvier, S. M. Bradbury, J. H. Buckley, V. Bugaev, K. Byrum, A. Cannon, A. Cesarini, J. L. Christiansen, L. Ciupik, E. Collins-Hughes, M. P. Connolly, W. Cui, R. Dickherber, C. Duke, M. Errando, A. Falcone, J. P. Finley, G. Finnegan, L. Fortson, A. Furniss, N. Galante, D. Gall, K. Gibbs, G. H. Gillanders, S. Godambe, S. Griffin, J. Grube, R. Guenette, G. Gyuk, D. Hanna, J. Holder, H. Huan, G. Hughes, C. M. Hui, T. B. Humensky, A. Imran, P. Kaaret, N. Karlsson, M. Kertzman, D. Kieda, H. Krawczynski, F. Krennrich, M. J. Lang, M. Lyutikov, A. S. Madhavan, G. Maier, P. Majumdar, S. Mcarthur, A. Mccann, M. Mccutcheon, P. Moriarty, R. Mukherjee, P. Nuñez, R. A. Ong, M. Orr, A. N. Otte, N. Park, J. S. Perkins, P. T. Reynolds, E. Roache, J. Rose, J. Ruppel, D. B. Saxon, M. Schroedter, G. H. Sembroski, G. D. Şentürk, A. W. Smith, D. Staszak, G. Tešić, M. Theiling, S. Thibadeau, K. Tsurusaki, J. Tyler, A. Varlotta, V. V. Vassiliev, S. Vincent, M. Vivier, S. P. Wakely, J. E. Ward, T. C. Weekes, A. Weinstein, T. Weisgarber, D. A. Williams, B. Zitzer

Physics

We report the detection of pulsed gamma rays from the Crab pulsar at energies above 100 giga–electron volts (GeV) with the Very Energetic Radiation Imaging Telescope Array System (VERITAS) array of atmospheric Cherenkov telescopes. The detection cannot be explained on the basis of current pulsar models. The photon spectrum of pulsed emission between 100 mega–electron volts and 400 GeV is described by a broken power law that is statistically preferred over a power law with an exponential cutoff. It is unlikely that the observation can be explained by invoking curvature radiation as the origin of the observed gamma rays above …

Paleomagnetism And Investigation Of 40 Ma Lavas, Liverpool Range, New South Whales, Australia, Nathan M. Padilla

Physics

The main focus of this project is the continued study of a reversal of the earth’s magnetic field recorded from lavas in the Liverpool Range of New South Whales, Australia. This reverse-to-normal transition, recently dated at ~40 Ma, was first reported in Nature in 1986. [2] In March 2011 some 200+ cores were drilled from several sections about the volcanic range—Jemmy’s Creek, Bald Hill, Rock Creek, Yarraman, and Coolah Tops Road. Here we focus on paleomagnetic findings from samples drilled from the most extensive section, that being along the trail near Jemmy’s Creek. Results from alternating field demagnetization show the …

Quantification Of Nitrate Sources And Sinks Using A Water Quality Network In Morro Bay Estuary, California, Johanna Nadia Jean Weston

Master's Theses

Using an instrumented water quality network in Morro Bay Estuary, California from 2007 to 2010 (15 min sampling frequency), this study addressed the two objectives of constructing a nitrate budget and assessing the influence of sampling frequency on water quality parameters. These two objectives led to the submission of an original report of research (Appendix A) and a note (Appendix B) to peer-reviewed journals.

The first objective was to characterize the high spatial and temporal variation in physical parameters and nitrate concentrations and to construct a nitrate budget quantifying sources and sinks of nitrate from the ocean, streams, and groundwater, …

Radio Frequency Noise Effects On The Cern Large Hadron Collider Beam Diffusion, Themis Mastoridis, P. Baudrenghien, A. Butterworth, J. Molendijk, C. Rivetta, J.D. Fox

Physics

No abstract provided.

Numerical Ocean Modeling And Simulation With Cuda, Jason Mak, Paul Choboter, Chris Lupo

Computer Science and Software Engineering

ROMS is software that models and simulates an ocean region using a finite difference grid and time stepping. ROMS simulations can take from hours to days to complete due to the compute-intensive nature of the software. As a result, the size and resolution of simulations are constrained by the performance limitations of modern computing hardware. To address these issues, the existing ROMS code can be run in parallel with either OpenMP or MPI. In this work, we implement a new parallelization of ROMS on a graphics processing unit (GPU) using CUDA Fortran. We exploit the massive parallelism offered by modern …

Loss Of Landau Damping In The Lhc, E. Shaposhnikova, T. Argyropoulos, T. Bohl, C. Bhat, P. Baudrenghien, A. Butterworth, T. Mastoridis, J. Esteban Muller, G. Papotti, J. Tuckmantel, W. Venturini Delsolaro, U. Wehrle

Physics

Loss of Landau damping leading to a single bunch longitudinal instability has been observed in the LHC during the ramp and on the 3.5 TeV flat top for small injected longitudinal emittances. The first measurements are in reasonable agreement with the threshold calculated for the expected longitudinal reactive impedance budget of the LHC as well as with the threshold dependence on beam energy. The cure is a controlled longitudinal emittance blow-up during the ramp which for a constant threshold through the cycle should provide an emittance proportional to the square root of energy.

Longitudinal Emittance Blow-Up In The Lhc, P. Baudrenghien, A. Butterworth, M. Jaussi, T. Mastoridis, G. Papotti, E. Shaposhnikova, J. Tuckmantel

Physics

The LHC relies on Landau damping for longitudinal stability. To avoid decreasing the stability margin at high energy, the longitudinal emittance must be continuously increased during the acceleration ramp. Longitudinal blow-up provides the required emittance growth. The method was implemented through the summer of 2010. We inject band-limited RF phase-noise in the main accelerating cavities during the whole ramp of about 11 minutes. Synchrotron frequencies change along the energy ramp, but the digitally created noise tracks the frequency change. The position of the noise-band, relative to the nominal synchrotron frequency, and the bandwidth of the spectrum are set by pre-defined …

An Axiomatic Approach To The Non-Linear Theory Of Generalized Functions And Consistency Of Laplace Transforms, Todor D. Todorov

Mathematics

We offer an axiomatic definition of a differential algebra of generalized functions over an algebraically closed non-Archimedean field. This algebra is of Colombeau type in the sense that it contains a copy of the space of Schwartz distributions. We study the uniqueness of the objects we define and the consistency of our axioms. Next, we identify an inconsistency in the conventional Laplace transform theory. As an application we offer a free of contradictions alternative in the framework of our algebra of generalized functions. The article is aimed at mathematicians, physicists and engineers who are interested in the non-linear theory of …

Projection Of Diffracted Optical Atom Traps, Jeremy Kruger

Physics

Theoretical calculations were performed for the projection of a diffraction pattern created by a pinhole through a single-lens system using vector diffraction theory and a combination of programs (MathCAD, Igor, etc.). The projected diffraction patterns were then experimentally created, recorded, and analyzed. This work is part of a larger collaboration with Dr. Kat Gillen, to trap and manipulate atoms in a Magneto Optical Trap (MOT) and to make further steps in the direction of Quantum Computing using trapped neutral atoms.

On Human Analyst Performance In Assisted Requirements Tracing: Statistical Analysis, A. Dekhtyar, O. Dekhtyar, J. Holden, D. Cuddeback, W. K. Kong

Computer Science and Software Engineering

Assisted requirements tracing is a process in which a human analyst validates candidate traces produced by an automated requirements tracing method or tool. The assisted requirements tracing process splits the difference between the commonly applied time-consuming, tedious, and error-prone manual tracing and the automated requirements tracing procedures that are a focal point of academic studies. In fact, in software assurance scenarios, assisted requirements tracing is the only way in which tracing can be at least partially automated. In this paper, we present the results of an extensive 12 month study of assisted tracing, conducted using three different tracing processes at …

A Sporadic Low‐Velocity Layer Atop The Western U.S. Mantle Transition Zone And Short‐Wavelength Variations In Transition Zone Discontinuities, B. Schmandt, K.G. Dueker, S.M. Hansen, John J. Jasbinsek, Z. Zhang

Physics

Teleseismic receiver function analysis of data from six dense arrays in the western U.S. is used to investigate mantle transition zone (MTZ) discontinuities and the prevalence of a low‐velocity layer atop the 410 km discontinuity (410‐LVL). Negative polarity Ps arrivals indicative of a low‐velocity layer with a top 25–60 km above the 410 are identified in 8–11 out of 18 stacks of receiver functions from highly sampled back azimuth corridors. The 410‐LVL is interpreted as partial melt resulting from upwelling of hydrated mantle across a water solubility contrast at the 410. The 669 km mean depth of the 660 km …

Automated Systems And Methods For Testing Infrared Cameras, Gary B. Hughes

Statistics

Systems and methods are disclosed herein to provide automated testing on infrared image data to detect image quality defects. For example, in accordance with an embodiment of the present invention, image processing algorithms are disclosed to generate an image quality metric that may be compared to one or more thresholds to perform an automated test for image quality defects. For example, the image quality metric may be compared to two thresholds to determine if the corresponding infrared sensor or infrared camera is defective or not due to image quality or requires further manual inspection by test personnel.

Polysat’S Next Generation Avionics Design, Greg Manyak, John M. Bellardo

Computer Science and Software Engineering

The CubeSat platform provides a unique challenge for flight software design due to the incredible size and power constraints. A number of tradeoffs must be made to balance effectiveness, fault tolerance, and cost. These basic requirements have been combined with the lessons learned from Cal Poly’s past 8-bit avionics system to design a significant revision based around a 32-bit microprocessor running Linux. This work analyzes both generations of avionics design, including a discussion of major design principles that are relevant to other CubeSat missions.