Student Abstracts at LBNL:

1-D Simulations of Metallic Foams Heated by Ion Beam Energy Deposition. ALEX ZYLSTRA (Pomona College, Claremont, CA, 91711) JOHN BARNARD (Lawrence Berkeley National Laboratory, Berkley, CA, 94720)

One dimensional simulations of various initial average density aluminum foams (modeled as slabs of solid metal separated by low density regions) heated by volumetric energy deposition have been conducted with a Lagrangian hydrodynamics code, DISH (Deeply Simplified Hydrodynamics by R. More), using a van der Waals equation of state (EOS). The resulting behavior has been described to facilitate the design of future warm dense matter (WDM) experiments. Deposition in the simulations ranges from 15 to 30 kJ/g total energy and from 0.075 to 0.9 ns total pulse length, resulting in temperatures from 1 to 4 eV. The peak temperature reached in the foam was found to be greater than linearly dependent on the energy deposition, increasing with increasing density to a peak at approximately 75% solid initial average density and decreasing rapidly with increasing density beyond that peak, and essentially independent of the pulse length for pulse lengths shorter than the macro hydro time, approximately 1 ns. The peak pressure increases rapidly with increasing density, increases with increasing energy, and is roughly independent of the pulse length for lengths on the order of the macro hydro time. For pulse lengths of approximately the hydro time for one slab of the foam (~0.1 ns) an increase in the maximum pressure is observed. The expansion velocity is proportional to the density for pulses on the order of the hydro time of one slab of the foam; for longer pulses a dramatic increase in the expansion velocity is observed at approximately 75% solid density initial. We find that the homogenization time of the foam increases with increasing pulse length, and the remaining inhomogeneities in the homogenized foam decrease with increasing density. These results will help future experiments examine the equation of state in the WDM regime.

²³⁸UFission Ion Chamber for Neutron Dosimetry at the 88-Inch Cyclotron. BRENT WILSON (University of California, Davis, Davis, CA, 95616) PEGGY MCMAHAN (Lawrence Berkeley National Laboratory, Berkley, CA, 94720)

Neutrons are difficult to detect directly due to a neutral charge; however, there are several different ways to measure neutron flux density indirectly. This paper investigates testing a commercial ²³⁸U fission ion chamber to measure neutron flux density, as well as conducting efficiency measurements using two sets of three activation foils (²⁷Al, ⁵⁸Ni, and ⁵⁹Co) at different locations to sample beam uniformity at the 88-Inch Cyclotron at Lawrence Berkeley National Laboratory. Fast, monoenergetic neutrons in the energy range of 5 to 30 MeV are under development at the facility through deuteron break-up, for radiation effects testing and cross-section measurements for a variety of applications. Through comparisons with absolute fluxes obtained using activation foils, and energy spectra obtained using the time-of-flight method, efficiency for both monoenergetic and white spectrum neutrons can be calculated. Preliminary neutron flux density measurements indicate 1.44x10⁷ neutrons per second per cm² per steradian were collected by the fission ion chamber for 30 minutes using a 38 MeV deuteron beam with 50 nanoamps of current. Preliminary activation foil data results indicate the center activation foils received roughly 20% more beam than the side foils, separated by a distance of 1.2 cm.

A Biochemical and Computational Confirmation of ncRNAs in Ecoli. REBECCA ROHA (Gettysburg College, Gettyburg, PA, 17325) STEPHEN R. HOLBROOK (Lawrence Berkeley National Laboratory, Berkley, CA, 94720)

Non-coding RNAs (ncRNAs) are transcripts that do not code for a protein, but rather functional RNA molecules in that have roles in protein manufacturing, DNA replication, cellular control and many other processes. However important, ncRNAs are difficult to study because their sequences lack clear start and stop signals, making them practically invisible on the genome scale. Bioinformatics techniques must be designed for the classification and discovery of ncRNAs. The Positive Sample only Learning Algorithm (PSoL) suggested a highly accurate machine learning algorithm to identify ncRNAs by using a support vector machine to combine many ncRNA detection signals in order to distinguish ncRNA sequences from intergenic sequences. This method identified to predict 420 ncRNA sequences in the E. coli genome. The PSoL predicted sequences were then clustered using LocARNA, folded using RNAalifold, and interpreted. Several trials were completed to test LocARNA’s ability to cluster large amounts of sequences, correctly cluster identical sequences and to determine the effect of inaccurate sequences on the accurate clusters. Clusters were identified and a representative ncRNA from each was selected. For each chosen ncRNA, a Northern Analysis was completed; total E.coli RNA was extracted, the RNA was electrophoresed and transferred to a positively charged membrane, the membrane was then probed with non-isotopically labeled DNA complementary to the predicted ncRNA, hybridized, detected and developed. LocARNA successfully grouped the sequences into 9 clusters. ncRNA expression verification by Northern analysis is ongoing yet advancements have been made; DNA oligomers were successfully labeled and control RNA sequences were detected. A potential ncRNA has been identified, while further validation is necessary, a predicted sequence appears to be expressed. This work demonstrated that LocARNA is adequate clustering software for grouping predicted sequences into families. These findings are significant because they contribute to the search for a technique to identify and classify ncRNAs. Future research includes identifying more predicted ncRNAs as well as assigning the identified LocARNA clusters to known ncRNA families.

A Search for Scintillators: Ce3+ doping of alkali gadolinium halides and Eu2+ doping of barium zinc oxides. LATORIA WIGGINS (North Carolina Agricultural and Technical State University, Greensboro, NC, 27411) STEPHEN DERENZO (Lawrence Berkeley National Laboratory, Berkley, CA, 94720)

The need for new and improved gamma ray and X-ray detectors, scintillators, is at an all time high due a progression in detection knowledge. Commonly used scintillators such as BGO and YAP have undesirable properties such as low luminosity, and slow decay times. The mission of the High Throughput Characterization and Synthesis Facility(HTCSF)is to develop scintillators with rapid decay times, high luminosities and crystal production at low costs. Discovering new scintillators required literature searches, synthesizing and the characterization of compounds. The research at hand concentrated on cerium (III) doped alkali halides and europium (II) doped barium zinc oxides. Compounds were synthesized using the ceramic method mostly performed in a nitrogen filled glove box because of the hygroscopic nature of the halides. Characterization consisted of X-ray diffraction, X-ray luminescence and pulsed X-ray measurements. Several new inorganic scintillators were founded, however, findings concerning barium zinc oxide synthesis warrant further investigation of the compound.

Accuracy of sequence-based identifications of filamentous fungal species using ITS2 and LSU rDNA sequences. IVY MCDANIEL (Scripps College, Claremont, CA, 91711) TAMAS TOROK (Lawrence Berkeley National Laboratory, Berkley, CA, 94720)

As fungi are becoming increasingly relevant to human society, the number of scientists qualified to identify fungal species using traditional methods is dwindling. There is therefore a need to develop tools that use standard molecular methods to accurately identify filamentous fungi at the species level. Our laboratory examined the effectiveness of making DNA sequence-based identifications of a collection of filamentous fungi by comparing the sequences of different variable regions of the ribosomal DNA to those in the NCBI Genbank database. By examining a conserved gene such as the ribosomal DNA, we hypothesized that there would be low variability among the sequence of conspecific organisms, but enough variability in the sequence of different species to clearly separate the organisms. We analyzed sequences from the D1/D2 domains of the large-subunit rDNA of 159 organisms from 85 species and 44 genera, and the ITS2 sequences of 28 organisms from 23 species and 13 genera. In both regions, the sequences by themselves did not appear to be variable across all genera and divisions of fungi to the point that the sequences could be used as an accurate identifier of a single species.

Air Quality Impacts of Gas Appliance Usage. TRANG HUYNH (DePaul University, Chicago, Illinois, 60647) BRETT SINGER (Lawrence Berkeley National Laboratory, Berkley, CA, 94720)

Liquefied natural gas (LNG) from the Pacific Rim is being considered for use in Californian homes to supplement domestic natural gas supplies. Because the composition of natural gas varies depending on the origin of the gas supplies and the process of purification used by gas companies, studies are being performed to determine if this new source of natural gas can be introduced safely and efficiently into Californian homes. To determine the health and environmental impacts of LNG, NOx, CO2, and CO and fine particle concentrations (below 1 x107 particles/cm3) were collected through an exhaust hood and measured using gas and particle analyzers during gas appliance usage. Before LNG fuel sources can be tested, it is necessary to develop a method for determining conditions for optimal appliance performance and minimal particle emissions during appliance usage using current natural gas supplies to compare with future experiments with LNG. Currently, studies are being performed to determine the effect of cleaning ovens on the amount of particles that form during oven usage. The concentration of particles measured during oven usage varied (approximately 1x107 to 1 x104 particles/cm3) by oven temperature setting and by oven model. Following cleaning, oven particle concentrations decreased by an order of magnitude. These results will be used to develop a standardized method of conditioning appliances and to study gas appliance performance in a range of conditions to compare with future experimental studies using LNG.

An Ergonomics Guide to Pipette Selection and Use. MONICA LICHTY (University of Michigan, Ann Arbor, MI, 48109) IRA JANOWITZ (Lawrence Berkeley National Laboratory, Berkley, CA, 94720)

The ergonomics of laboratory environments has not been developed as thoroughly as that of computer workstations and there is not much current guidance on ergonomics attributes of common lab equipment for the scientific community. This means that scientists and technicians are in great danger of developing upper extremity cumulative trauma disorders (CTDs) such as tendonitis and carpal tunnel syndrome from their regular activities. The focus of this project was on providing a usable guide to pipette and pipet controller selection for the employees at the Lawrence Berkeley National Laboratory (LBNL) to facilitate purchasing decisions and reduce the rate and severity of injuries associated with manual pipetting. The first step in the development was to become familiar with the pipette models that are commercially available. Interviews were conducted to learn which qualities of a pipette are important to users. Insight was also gained into the ways in which pipettes are held and operated through observation. Once a final list of attributes was determined, meetings were held with pipette manufacturer representatives to obtain demonstration products for assessment and to learn about the different product lines. The main quantitative measurements were: weight, plunger force, tip ejection force, blowout force, maximum thumb displacement, girth, and overall length from the thumb support to the end of the tip ejector sleeve. Other qualities were recorded such as autoclavability, electronic program options, and charging method of the pipettes. A section of comments was developed based on user input and ergonomics factors including handle comfort, display legibility, and ease of volume adjustment. The guide will be available in two versions. The quick reference guide is comprised of product ratings in a variety of categories including weight/balance, grip comfort, and control forces. The extended user guide includes all of the quantitative information obtained as well as free-form comments about the products. Both versions of the guide will be available online to all employees of LBNL. The guides also come with a set of tips on posture, workstation layout, and task design to address the task as a system of interacting factors rather than solely a tool design issue. Although the guides provide an increased level of assistance to consumers, they will only remain relevant if they are updated on a regular basis to include new products and improvements.

Analysis of X-Ray Spectra Emitted from the VENUS ECR Ion Source. JANILEE BENITEZ (California State University, East Bay, Hayward, CA, 94542) DANIELA LEITNER (Lawrence Berkeley National Laboratory, Berkley, CA, 94720)

The Versatile Electron Cyclotron resonance ion source for NUclear Science, VENUS, produces its record breaking ion beam currents and high charge state distributions because it uses strong magnetic fields to confine the plasma and high microwave frequencies to heat it. The magnetic fields are produced using liquid helium cooled superconducting coils. While in operation, VENUS produces significant quantities of bremsstrahlung, in the form of x-rays, through two processes: 1) electron-ion collisions within the plasma, and 2) electrons are lost from the plasma and collide with the plasma chamber wall and release energy. The energy lost by electron collisions with the chamber wall presents a significant heat load on the cryostat needed to keep the coils superconducting. In order for VENUS to reach its maximum operating potential at 10kW of 28GHz microwave heating frequency, the heat load posed by the emitted bremsstrahlung must be understood. A code has been written, using the Python programming language, to analyze the recorded bremsstrahlung spectra. The code outputs a spectral temperature and total integrated count number corresponding to each spectra. Bremsstrahlung spectra are analyzed and compared by varying two parameters: 1) the heating frequency, 18 and 28GHz, and 2) the magnetic field gradient, 44% and 70%, at the electron resonant zone.

Bystander Analyses of X-ray Microbeam Induced gamma-H2AX Punctate Signals in the Human Mammary Epithelial Cell Line 184V. MICHELLE SALCEDO (Diablo Valley College, Pleasant Hill, CA, 94523) ELEANOR BLAKELY (Lawrence Berkeley National Laboratory, Berkley, CA, 94720)

Damage to DNA can be caused by direct and indirect effects of ionizing radiation absorbed by irradiated cells. Radiation damage to DNA can trigger a sequential cascade of responding DNA-repair molecules that can be visualized microscopically with the use of specific fluorescently-labelled antibodies and immunohistochemistry. The focus of my research has been to use a 12.5 keV X-ray microbeam produced at the LBNL Advanced Light Source beamline 10.3.1 to target a dose stripe of 100 microns wide on a population of 184V Human Mammary Epithelial Cells (HMEC) and to process the cell samples for DNA damage response markers as a function of time and distance from the dose stripes. This allows me to study both targeted and untargeted cells. The response of untargeted cells not in the radiation field is called a “bystander effect”. Comparisons have been made after doses of either a relatively high dose stripe of 100 cGy or a relatively low dose stripe of 10 cGy. Gamma-H2AX and 53BP1 are the two DNA damage response markers I have studied. Some differences were noted in the phosphorylation response of each of these markers in the nuclei of irradiated HMEC. Gamma-H2AX and 53BP1 appear to co-localize, but with a different time course. I developed a scoring system to compare the morphological differences noted in these two DNA damage response markers in large montages of HMEC irradiated with the X-ray microbeam. Comparisons were made with unirradiated control cultures. The results indicated that a significant diversity of gamma-H2AX fluorescent signals exist in the unirradiated control possibly due to asynchronous cells varying in different stages of the cell cycle or culturing conditions. Irradiated areas expressing a high response of gamma-H2AX were an efficient indicator of the location and width of the stripe of dose, especially within the 100 cGy 10 minute montage image. Physical measurements of the stripe confirmed widths of 100 to 110 microns verifying the accuracy of the microbeam used. Histograms of different levels of intensities of gamma-H2AX expression were created using the data collected by using the devised scoring system. The data analyzed in the histograms demonstrated potentially novel fingerprints of the background fluorescent signal, the direct radiation damage effect, and the bystander effect. Future replication of this experiment is needed to validate significance of these results.

Characterization of Neutron Spectra from Coulombic Deuteron Breakup. BRAD BARQUEST (University of California at Berkeley, Berkeley, CA, 94704) PEGGY MCMAHAN (Lawrence Berkeley National Laboratory, Berkley, CA, 94720)

A source of tunable, quasi-monoenergetic neutrons is under development at the 88-Inch Cyclotron at Lawrence Berkeley National Laboratory (LBNL). The neutrons are produced through breakup of deuterons in a nuclear coulombic field. As neutrons from both direct nuclear reactions and coulomb-induced breakup contribute to the outgoing flux, characterization of the neutron spectra as a function of deuteron energy, target material and angle are needed to determine the relative contributions from the two channels. 29 MeV deuterons impinged upon a Ta foil, and the residual beam was dumped in an adjacent room. Measurements were taken at 25, 35, and 45 degrees with respect to the target in the lab frame, and time-of-flight (TOF) techniques were used to determine the neutron energies. Results demonstrate a decreasing flux with increasing lab angle for neutrons with energy greater than or equal to 10 MeV, which is consistent with coulombic breakup. Further comparison with theory is necessary to determine the extent of direct reaction contributions.

CMOS Monolithic Pixel Sensors with in-pixel CDS and fast readout for the ILC Vertex Tracker. TERRI SCOTT (New York University, New York City, NY, 10003) MARCO BATTAGLIA (Lawrence Berkeley National Laboratory, Berkley, CA, 94720)

The International Linear Collider (ILC) Vertex Tracker requires detectors of new design in order to meet its physics requirements in terms of material, accuracy and readout speed. The detectors must be sufficiently thin, in order that incident particles may pass through several layers of sensors without substantial scattering. Readout should be fast enough that occupancy caused by machine-induced background does not spoil the track pattern recognition. Monolithic silicon pixel sensors provide a solution to these constraints due to their high resolution and ability to be thinned to several tens of micrometers. One detector currently under testing is the LDRD2 chip, designed and developed at the Lawrence Berkeley National Laboratory. The detector features 20 x 20 µm pixels with in-pixel charge storage for correlated double sampling, a technique by which the difference is taken between a reference and the pixel signal voltage. Half of the chip utilizes 5 x 5 µm diodes, and 3 x 3 µm diodes in the second half. To characterize its performance, lab tests were conducted using a pulsed laser and a Fe55 x-ray source. In particular, the chip was readout at several frequencies to determine the effect of the readout speed and the charge integration time on efficiency and noise. It was found that the LDRD2 chip responds to both laser pulses and incident x-rays at readout frequencies up to the highest design frequency of 25MHz. This work is part of an ongoing R&D program at LBNL which will continue to investigate the LDRD2 and further generations of pixel sensors.

Coil Configurations Study for Bi-2212 Subscale Magnets. CHRISTOPHER ENGLISH (Texas A&M University, College Station, TX, 77841) HELENE FELICE (Lawrence Berkeley National Laboratory, Berkley, CA, 94720)

The Superconducting Magnet Group at Lawrence Berkeley National Laboratory is developing subscale magnets consisting of Bi-2212 (Bi₂-St₂-Ca-Cu₂O_x) racetrack coils as part of its subscale program. Several configurations are being considered: the stand-alone racetrack, subscale common coil, subscale dipole, and subscale hybrid dipole. In order to prepare for the assembly and testing of these magnets, a study has been carried out to determine the short sample current (I_ss) and the Lorentz forces for each configuration. OPERA 3D has been used to determine the field distributions on the coils. The maximum field on the conductor determined the load line of each subscale magnet. The intersection of these load lines with the engineering critical current density versus magnetic field curve (J_EC(B)) for Bi-2212 round wire subsequently determined the Iss. The results show little variation in the Iss of each configuration due to the small slope of the J_CE(B) in the field range of 5-10 T. The Lorentz forces, also determined with OPERA 3D, have been analyzed by defining the magnetic pressure on the coils. Results from the analysis show that a possible testing sequence for the subscale program could be the stand-alone racetrack, subscale common coil, subscale dipole, and finally the subscale hybrid dipole, in order of increasing magnetic pressure. Future simulations for hybrid dipoles based on varying the current in the Nb3Sn from the current in the Bi-2212 coil are recommended.

Construction of a Circularly Polarized Far Off Resonance Trap to Measure Beta Decay Correlation Coefficients in 21Na. DYLAN GORMAN (Contra Costa College, San Pablo, CA, 94806) PAUL VETTER (Lawrence Berkeley National Laboratory, Berkley, CA, 94720)

We report the partial construction of a circularly polarized optical dipole trap, also known as a far off resonance trap. We create a trap with the ability to choose either of two opposite senses of circular polarization in order to spin polarize the trapped atoms, and measure β decay correlation coefficients.

Development of a Vacuum Monte Carlo Code. REYNALDO LOPEZ (University of California, Los Angeles, Los Angeles, CA, 90095) MATTHAEUS LEITNER (Lawrence Berkeley National Laboratory, Berkley, CA, 94720)

This paper presents the initial development of a three-dimensional Monte Carlo computer code that calculates the vacuum pressure of a sample cylindrical pipe vacuum vessel. The implementation of a basic Monte Carlo molecule-tracing algorithm is discussed. The pressure distribution is determined by tracing particles through the vessel structure; converting the trajectory lengths to molecular residency time by using the average molecular velocity. Simulations with various molecule sample sizes are implemented and compared to conventional analytical vacuum formulas. First code results calculate a correct parabolic pressure profile. Future work will include the development of a new geometry module for 3D CAD data, and the implementation of different surface conditions.

Diffractive Optics at Soft X-Ray Wavelengths. TERENCE HOLLOWAY (Norfolk State University, Norfolk, VA, 23504) YANWEI LIU & DAVID ATWOOD (Lawrence Berkeley National Laboratory, Berkley, CA, 94720)

The Center for X-Ray Optics (CXRO) at Lawrence Berkeley National Laboratory works to advance the science and technology of short-wave optical systems through applications using extreme ultraviolet light (EUV) and Soft X-Ray wavelengths that range from 1 nm - 50 nm. The short wavelength radiation is generated by a machine known as a synchrotron. The synchrotron used in our experiment, operated by Lawrence Berkeley National Labs, is the Advance Light Source (ALS). At these wavelengths there are a large number of atomic resonances which cause the absorption of radiation over short distances (in nanometers or micrometers) in most materials. As a result, conventional devices which operate in the optical region of the electromagnetic spectrum are no longer applicable at these short wavelengths. CXRO specializes in two classes of optics that operate at EUV/Soft X-ray wavelengths, reflective multilayer coatings and diffractive optics. This SULI research project places emphasis on nanometer scale diffractive optics. It begins by creating programs for the optical devices using Matlab. A Graphical User Interface (GUI) was created to generate desired patterns for the optics chosen by the user. The GUI runs a simulation of diffractive soft x-ray optics based on electromagnetic wave propagation. The simulation will give us a good idea of how the experiments performed in the ALS will result. After running the simulation, we performed actual synchrotron experiments using those specialized optics at ALS beamline 12.0.2.

Dynamic Behavior of Nicotine and Its Impact on Assessment of Human Exposure to Secondhand Smoke. EMMA SMITH (Yale University, Albany, CA, 94706) LARA GUNDEL (Lawrence Berkeley National Laboratory, Berkley, CA, 94720)

Secondhand tobacco smoke (SHS) is a common toxic contaminant in indoor air. Exposure to SHS has been linked to increased risk of lung cancer, asthma and acute respiratory illness. LBNL is currently measuring concentrations of SHS in bars and restaurants in Minneapolis-St. Paul, MN, in collaboration with colleagues at the Center for Energy and Environment. The goals are to correlate exposure data with health profiles of employees and assess the effects of prolonged indoor exposure to SHS. Measured concentrations of nicotine, 3-ethenyl pyridine and pyridine are being used as tracers of exposure. Nicotine is the most common tracer due to its uniqueness to tobacco, and its metabolite, cotinine, is a useful biomarker. However, earlier work at LBNL has shown that sampling nicotine in real environments is strongly influenced by changes between emission and collection, due to its affinity for surfaces (i.e., walls, clothes, hardware) and its reactivity (i.e., oxidation, acid-base reactions). This project measured the stability of gas-phase nicotine in humid air and pure nitrogen, and dry air and nitrogen. High purity nicotine was injected into inert Tedlar bags and heated to vaporize it. Samples were collected after one, six and twenty-four hours, and analyzed using the same methods as the MN study (active sampling onto sorbent tubes, followed by gas chromatography with nitrogen-specific detection). After accounting for sorption of nicotine to the walls of the gas bags, the results showed that gaseous nicotine in dry N2 remained stable, but samples of nicotine in humid air produced chromatograms with the same unusual features seen in field samples from MN, as well as peaks corresponding to the oxidation products nicotinaldehyde, N-methyl formamide, myosmine and cotinine. These data strongly suggest that nicotine oxidation is expedited over time in the presence of humid air. Thus, the degradation of nicotine either in the environment or inside sampling equipment may contribute to inaccurate concentration and exposure calculations. Future experiments are needed to monitor the behavior of nicotine for longer time periods, with varying amounts of nicotine and at different temperatures.

Effects of Climate Change on the Leaf Gene Expression of Avena barbata in a California Grassland Ecosystem. LALEH ESMAILI (Gavilan College, Gilroy, CA, 95020) GARY L. ANDERSEN (Lawrence Berkeley National Laboratory, Berkley, CA, 94720)

Global climate changes are impacting the environmental conditions of many ecosystems. In order to develop an informed understanding of the effects of climatic changes on a grassland ecosystem, a study was conducted to examine plant response to altered rainfall pattern and increase nitrogen availability. Avena barbata, an abundant species in many Californian annual grasslands, was grown on natural soil in a climate-controlled greenhouse and submitted to three precipitation treatments (low, ambient and high rainfall) and two levels of nitrogen (ambient and addition of NH₄NO₃). The transcript abundance of three genes of interest (RbcS, GS1 and GS2) was studied in leaf samples collected from A. barbata plants at peak physiology. The changes in rainfall patterns did not have a significant effect on the total RNA content from A. barbata leaves or leaf gene expression except for GS1.Fertilization of the ambient soil conditions with NH₄NO₃ significantly increased the leaf RNA content and also lead to increased transcript levels for RbcS and GS2. The results suggest that A. barbata plants grown under high nitrogen availability respond by changing their gene expression possibly to increase the rate of photosynthesis and growth. This data will be used together with biochemistry and physiology data in a model to predict ecosystem response to climate change.

Effects of Naturally Occurring Ions on Arsenic Remediation in Bangladesh. EMILY DESLEY-BLOOM (Contra Costa COllege, San Pablo, CA, 94806) ASHOK GADGIL (Lawrence Berkeley National Laboratory, Berkley, CA, 94720)

Bangladeshis have been drinking arsenic contaminated water for over 20 years. Methods involving electrochemistry are being developed to improve the drinking water in Bangladesh. Few comprehensive studies have been performed on the naturally occurring ions found in Bangladesh, but a review of the available literature is essential to understand the potential effect such ions could have on remediation strategies employed in Bangladesh. In the following review, it was determined that phosphate had the greatest potential for interference, but it will not be a problem since the average concentration of phosphate in Bangladesh is less than was in the studies. However, in regions with high concentrations of these ions, an increased amount of iron hydroxides may be required to effectively remove arsenic from groundwater. The following report details the effects of various ions on arsenic removal via complexation with iron hydroxides.

Effects on soils after burning prairie ecosystem. PALOMA MARTINA CUARTERO (Contra Costa College, San Pablo, CA, 94806) MARGARET TORN (Lawrence Berkeley National Laboratory, Berkley, CA, 94720)

Soil respiration is one of the many ways C is released in the atmosphere in form of CO2. And since soils are the largest reservoir of carbon on land, where it accumulates roughly three times compared to that of the aboveground biomass and just about twice that of the atmosphere (Eswaran et al. 1993), the smallest change in soil carbon cycling worldwide can lead to major global climate change. Although fire is used to manage prairie ecosystem, wildfire is also a common event with effects on C balance that are not well understood. This study explains how burning affects C balance in the terrestrial ecosystem by comparing the C properties of burned and unburned soils. As expected, the C content of soil is much higher in the top surface soil where decomposition of organic matters occurs. Our data for the unburned soils shows C accumulates over time. However, burning prairie ecosystem allows C to escape from soils (in form of CO2) causing a change of flux between the soil and the atmosphere. The total C lost is approximately 0.50 kg/m2.

Electrochemical Arsenic Remediation of Drinking Water in Rural Bangladesh. YOLA BAYRAM (University of Michigan-Dearborn, Dearborn, MI, 48128) ASHOK GADGIL (Lawrence Berkeley National Laboratory, Berkley, CA, 94720)

According to the World Health Organization, in Bangladesh over 60 million people drink arsenic-laden water making it the largest case of mass poisoning in human history. Available methods of treating arsenic are too expensive, ineffective, or commonly difficult to implement, making them unsuitable for a poor or undeveloped country such as Bangladesh. Electrochemistry may provide an innovative, effective, and inexpensive method for arsenic remediation of drinking water. The method is an improvement upon a known method of using Fe(III) to remove arsenic. The Fe(III) combines with As(V), forming an insoluble complex which then can be easily filtered out. The innovative step of electrochemistry allows control over the amount of Fe(III) produced as well as electrochemical oxidation of the As(III) into reactive As(V) anion, making the method far more effective. Experiments were performed with water samples with 600ppb of total arsenic that received currents of 70mA and 110mA for varying durations of time. The objective is to determine the appropriate current and time necessary for an arsenic removal above 99% in order to meet WHO standards. Experimental results showed that using a current of 110mA for 11 minutes showed a removal rate from 98-100%. This same current and length of time also oxidized 96-100% of As(III) to As(V). Once the process is well understood and the electrochemical variables are optimized, the method will be applied to a practical water filter. The hope is that this filter will be applied in Bangladesh and other areas affected by arsenic poisoning to provide millions of people with safe drinking water and an improved standard of living.

Electrochemical Remediation of Arsenic Contaminated Groundwater. KRISTIN KOWOLIK (University of California, Berkeley, Berkeley, CA, 94704) ASHOK GADGIL (Lawrence Berkeley National Laboratory, Berkley, CA, 94720)

Millions of people worldwide do not have access to clean water. This problem is especially severe in Bangladesh where water is severely contaminated with arsenic. Chronic arsenic exposure has devastating health effects: cardiovascular diseases, cancers, and eventually death. Many methods of arsenic removal have been studied but most of these are too expensive and impractical to be implemented in poor countries such as Bangladesh. This project investigates electrochemistry as an affordable means of removing arsenic. Experiments are performed using a whisk like device made out of iron as the cathode and copper as the anode. Both electrodes are immersed in simulated groundwater spiked with an arsenic concentration of 600 ppb. During voltage application, currents of 70 mA and 110 mA are passed through the system. The water is stirred gently to ensure uniform electron distribution. While the electrochemical process is progressing, iron metal is oxidized to Fe(III). As an ionic species, iron will bind free arsenic in solution. After the desired amount of charge is passed, the treated water is allowed to precipitate for 24 hours and is then filtered by means of vacuum filtration. One of the significant major tasks of the project was to develop an experimental protocol (methods, measurement techniques, experimental conditions) to obtain proof of concept, so this process can be investigated further. We showed that if certain conditions are met such as (1) optimal charge per volume, (2) optimal current density and (3) precipitation time of 24 hours, promising results are obtained. An initial arsenic concentration of 600 ppb can be reduced to a final concentration of 50 ppb in 2.5 L water by application of 70.08 C/L at 70 mA and 107.5 C/L at 110 mA. These results are very encouraging and provide great promise that electrochemistry is a powerful, and most importantly, an affordable tool in the remediation of arsenic from contaminated groundwater.

Electrodymanics Simulation of the Pulse Line Ion Accelerator. ROXANNE MARTINEZ (Stanford University, Stanford, CA, 94305) ENRIQUE HENESTROZA (Lawrence Berkeley National Laboratory, Berkley, CA, 94720)

The Heavy Ion Fusion Science Virtual National Laboratory is currently studying the Pulse Line Ion Accelerator (PLIA), a slow-wave accelerator that would substantially reduce the cost of experiments for studies of high energy density matter and fusion ignition conditions. The PLIA uses a high voltage pulse at the input end of a helical pulse line structure as a means to accelerate charged particles. The high voltage pulse generates an electric field that travels across the span of the accelerator. This wave pulse can be used to accelerate the ions to energies far greater than the peak voltage which was applied to the input end of the structure. Moreover, the PLIA can axially confine the heavy ion beam bunch, making it an excellent candidate for a high intensity, short bunch injector. The electrodynamics of the system will be presented. This analysis was performed using MAFIA (MAxwell’s equations by the Finite Integration Algorithm), an electromagnetic and particle dynamics code.

Electron Cloud Modeling for the Positron Damping Ring Wigglers in the International Linear Collider. JENNIFER YU (Cornell University, Ithaca, NY, 14853) C.M. CELATA (Lawrence Berkeley National Laboratory, Berkley, CA, 94720)

The positron-electron collisions in the ILC must be simple, clean, and precise. However, the presence of an electron cloud in the positron damping ring would lead to a positron beam with unfavorable behavior and position. The research conducted for the Center of Beam Physics looked at the formation of the electron clouds using computer simulations, specifically in the wiggler section of the ring. The wiggler section is two hundred meters of magnetic dipoles that produce vertical fields of alternating sign. In the wigglers, the accelerated beam emits intense synchrotron radiation. When it hits the chamber walls, the radiation initiates the build-up of electrons. These primary electrons, trapped in the wigglers, also hit the vacuum walls and make even more electrons, called secondary electrons. The secondary electrons also produce electrons as the positron beam attracts the electron cloud and swings it to the opposite wall. The electron cloud can send the beam off track so the beam misses its collision or worse, hits the chamber walls. The electrons can also give the positron beam energy, which can make it harder to focus the beam. The research conducted tracked the formation of the electron clouds using Posinst, a benchmarked 2D code, and Warp, a code with both 2D and 3D capabilities. A 3D code is needed to follow the electrons in the changing magnetic fields of the ILC wiggler. However, as a first step, the research aimed to match the results of 2D Posinst-like Warp with Posinst, which has been checked with numerous electron cloud experiments and against other benchmarked codes. The agreement of 2D-Warp and Posinst shows the accuracy and precision of Warp and will lead to electron cloud modeling with 3D Warp. The computer simulations in 3D Warp will track the electron cloud in the ILC wiggler and will help find limiting parameters for the cloud.The computer simulations in 3D Warp will track the electron cloud in the ILC wiggler and will help find limiting parameters for the cloud.

Electronic Characterization of Rare-Earth Doped Telluride Semiconductors. ANDREW OLSON and ERIK TOPP (Diablo Valley College, Pleasant Hill, CA, 94523) DALE L. PERRY (Lawrence Berkeley National Laboratory, Berkley, CA, 94720)

Zinc telluride and telluride-containing compounds have been extensively analyzed by X-ray photoelectron spectroscopy (XPS) and Auger electron spectroscopy (AES) in order to determine the chemical states and shifts in electronic energy levels of the elements present in the materials. To a lesser extent, chemical shifts of gadolinium lines in various compounds have also been studied. However, the characterization of ZnTe:Gd by XPS and AES is practically non-existent. Use of this material as a semiconductor in various applications requires that electrical contact be maintained between the material’s surface and other electrical components. Buildup of oxides and other species on the surface can cause insulating effects, hampering the material’s intended performance. It is, therefore, of interest to study surface reactions of the compound with air in order to identify surface product films that may adversely affect the utility of ZnTe:Gd as a multipurpose semiconductor. The current study was an initial characterization of these materials using XPS and AES. Observed spectra for the initial, "as received" surface yielded data consistent with the presence of Gd₂O₃, ZnO, and TeO₂. Spectral parameters including binding energies, spin-orbit splitting, satellite structure, and kinetic energy Auger lines of elements compared favorably to analogous features in spectra of other Zn-Te-Gd compounds. Surface charging of the material was observed and studied in conjunction with argon ion sputtering. The results indicated that insulating surface films do indeed form on these materials in air, films that can act as interfacial layers between the semiconductor material and other materials such as electrical contacts attached to the surface of the semiconductor. A future examination of this material by other characterizing methods and types of instrumentation will provide further insight into the chemistry, structure, and electronic properties of this material and shed more light on the formation of the surface layers under ambient air exposure.

Energy Efficiency of Desktop and Laptop Computers. MAT DOIRON (Big Bend Community College, Moses Lake, Wa, 98823) CHARLIE VERBOOM (Lawrence Berkeley National Laboratory, Berkley, CA, 94720)

As the number of computers in use worldwide increases, so does the demand for electricity to power them. This research focused on measuring computers typically used at Lawrence Berkeley National Laboratory in order to determine their power consumption. This included the Optiplex 745 series from Dell, ClientPro series from MPC and a custom made computer designed to run Computer-Aided Design (CAD) software. Three Dell Latitude Laptops( D600, D610, D630) were included. Measurements were taken during five different “states”; off, booting, idle, active and sleep, with a Kill-A-Watt meter. Two Operating systems, Microsoft Windows XP Professional and Windows Vista Business were also compared to determine their impact on power use. PassMark Performance Test V 6.1, a benchmarking program, was used to evaluate the performance of the computers. It was also used to simulate the computer in an active state. It was discovered that the computer uses less energy while sitting idle than while active and significantly less while in sleep mode. Putting the computer to sleep during non-working hours would be ideal but several factors currently prevent this from taking place, including scheduled backups and remote access. New desktop computers being implemented at the lab use less energy than those currently in use despite their superior performance. The new computers are the Dell Optiplex 745 series, which were tested in three different configurations: Minitower, Small Form Factor and Ultra Small Form Factor. The three were compared to see if size or component differences affected power consumption and performance. There was very little difference between the Minitower and Small Form Factor. In contrast, the Ultra Small Form Factor used less power with reduced performance. This could be because of the external power brick and lack of dedicated graphics card. The laptops in this study consumed significantly less power than did the desktops: 22W while idle compared to 68W. This is significant because it includes the monitor. An LCD monitor uses 30W and a CRT up to 130W, which is more than the entire laptop. Windows Vista and Windows XP were also compared using identical computers. Vista performed worse and consumed more power despite the fact that it is the successor to XP. It is recommended that customers wait for the first service pack to switch to Vista if performance or power management is a major concern.

Engineering novel gene-regulatory RNA aptamers. YUVRAAJ KAPOOR and LESLEY LARA (University of California, Berkeley, Berkeley, CA, 94609) JAY KEASLING (Lawrence Berkeley National Laboratory, Berkley, CA, 94720)

Aptamers are RNA sequences that bind to target molecules and consequently regulate gene expression in a ligand-dependent fashion. They are frequently employed in nature to couple fluctuations in the concentration of a metabolite with changes in gene expression. Upon binding a small molecule, aptamers sequester the ribosome binding site [RBS] of a cis mRNA and repress translation. Synthetic aptamers eliminate the need to rely upon pre-existing biological molecules as the source of binding structure. Generation of synthetic aptamers occurs through in vitro selection, iterative rounds of enrichment and amplification which eventually select for an RNA molecule with high binding affinity [~100uM] and specificity. Through a combination of directed evolution and rational design we generated functional, ligand-binding RNA structures that control the cis-expression of mRNA transcripts in response to tetramethylrhodamine [TMR], a small fluorescent dye that is cell permeable. Iterative rounds of reselections and binding assays in in vivo like conditions have generated 3 isolates of TMR-binding aptamers. When incorporated into constructs with self-cleaving hammerhead ribozymes, such molecules will provide general tools for simultaneously varying the expression levels of toxic intermediates in engineered pathways such as that of the anti-malarial drug, Artemisinin.

Estimating Evaporative Transpiration in Wetlands of the San Joaquin Valley. ADAM HALL (Bowdoin College, Brunswick, ME, 4011) NIGEL QUINN (Lawrence Berkeley National Laboratory, Berkley, CA, 94720)

Since the water resources of Central California are intensively used in agricultural and municipal contexts water resources available for managed wetlands are very limited and must be carefully managed. Modeling patterns of evaporation and transpiration, collectively referred to as ET, is an important step in managing irrigation regimes with the goals of limiting evapo-concentration of salts and maintaining high levels of water quality with the greatest possible water use efficiency. In agricultural systems water needs are often estimated by reference to potential ET (ETo) values, the ET of a well watered pasture plot. ETo data is readily available from weather stations reporting to the California Irrigation Management Information System from locations throughout the state. The relationship between ET and ETo in agricultural systems is well understood. This relationship is less well understood for wetlands because of the complex vegetation and moisture dynamics within these systems. A Bowen Ratio Energy Balance Station was deployed to a wetland near Los Banos to estimate ET using a Bowen Ratio Energy Balance Equation. Micro-meteorological sensors measure incoming and outgoing energy fluxes through air and soil and estimate the latent heat flux of the system, which is proportional to ET. Our estimates of ET are compared to ETo values reported to the CIMIS network. Wetland ET and ETo values do not correlate well. The dynamic nature of wetland plant communities and water resources create more complex patterns of ET than those observed at ETo plots where water resources and plant communities are intentionally held constant. Modeling of wetland ET based on ETo data will must account for seasonal changes in soil moisture and plant community composition and distribution. This research contributes to a larger project of understanding the relationships between irrigation timing, water use, water quality, and plant communities. A variety of methods, including soil salinity surveys and remote sensing estimates of plant community distributions will be integrated to model wetland moisture and plant community dynamics with the aim of improving wetland best management practices and water use efficiency while sustaining valuable wetland habitat.

Evaluating the efficacy of mustard (Sinapis alba) seed meal as an organic control method for invasive Harding grass. GREGORY RYBKA (The Pennsylvania State University, University Park, PA, 16802) ROBERT VAN BUSKIRK (Lawrence Berkeley National Laboratory, Berkley, CA, 94720)

Biodiesel is widely viewed as an alternative to fossil-based fuels. The production of oil for biodiesel by pressing mustard seed has been studied and found to be feasible though the process has shown to be uneconomical. White mustard meal (Sinapis alba) contains glucosinolates (GLS) which when hydrolyzed break down into toxins to various plants, such as ionic isothyocianate and thyociante. The research reported in this study considers using the remaining mustard seed meal as an organic bioherbicide to control Harding grass, an invasive plant in California. A randomized complete block experimental design was employed in field trials, involving four treatments of mustard meal applied at varying rates of 0.5 t/acre, 1 t/acre, 4 t/acre and 0 t/acre (the control). The treatments were applied to two plots each with 16 subplots, where one plot had above ground (AG) biomass removed prior to application and on the other no removal took place. The subplots were initially characterized by the quantity of Harding grass per unit area, at 20%, 40%, 60% and 80% coverage. On all subplots water was applied exclusively by rainfall and totaled 1.5 inches. After six weeks, the Harding grass was removed and weighed; the water content of the removed grass was measured in order to determine the AG biomass for each subplot. The average AG biomass of all treated plots and that at each application rate were larger than that for their respective control subplots, though using an analysis of variance the data sets were not found to be statistically different. The initial and final measurements of Harding grass were also found to have discrepancies as they were negatively correlated for the control plots, indicating an issue with the use of both area and mass measurements. Due to the lack of statistically significant evidence it is not possible to draw conclusions on the potential of mustard meal as economically supporting mustard seed as a source for alternative fuel.

Examining the Relationship between Soil Carbon Stability and Mineral Surface Reactivity in an Ultisol from the Tennessee Valley. RACHEL PORRAS (California State University, East Bay, Hayward, CA, 94543) MARGARET S. TORN (Lawrence Berkeley National Laboratory, Berkley, CA, 94720)

Soil Organic Matter (SOM) represents a major reservoir of biosphere carbon which may be chemically or biologically transformed to atmospheric CO2 as well as other greenhouse gases. Despite its importance in maintenance of ecosystem integrity and critical role in regulation of climate system stability, the actual physicochemical and biotic factors that govern the partitioning and long-term stabilization of organic matter within the soil environment remain poorly understood. SOM stability derives principally from physical protection within aggregates and association with reactive mineral surfaces. Mineral associated C is believed to be irreversibly bound. However, evidence from recent 14C studies of mineral stabilized OM appears to indicate that the mineral fraction contains a more labile carbon component that is capable of actively exchanging over time. In this this preliminary experiment radiocarbon measurements were utilized to assess the size and relative stability of two operationally defined SOM pools within the dense mineral fraction of a carbonaceous soil (Ultisol) in an effort to gain insight into the capacity of the mineral fraction of these soils to actively adsorb and stabilize organic inputs. AMS results obtained for the 0-15 cm depth class were contrary to initial predictions. The dense fraction (rho> 2.4 g cm-3) contained a greater concentration of pulse-derived 14C than the lower density fraction. The trend observed for the 0-15 cm depth is reversed in the 15-30 cm depth for all treatments with the 1.7-2.4 g cm-3 fraction exhibiting a greater concentration of pulse-derived14C. Measured soil delta 14C indicates greater retention of rhizospheric inputs by both fractions. The ???C measured for the litter treated plots was similar in magnitude to that of the control. The effect of depth and treatment were found to be highly significant on measured delta 14C (P<0.001). The effect of density on delta 14C was also found to be significant across treatments. Although additional analyses are necessary to quantify labile C in the two density fractions, characterize mineralogic composition, and assess mineral surface reactivity, these results indicate that the method utilized successfully isolated two SOM pools from the dense fraction with differing chemical properties and C stabilization efficiencies.

Expression and Purification of a Vaccinia Virus Nudix Family Decapping Enzyme. BRANDI WENGER (Diablo Valley College, Pleasant Hill, CA, 94523) STEPHEN R. HOLBROOK (Lawrence Berkeley National Laboratory, Berkley, CA, 94720)

The Nudix (nucleoside diphosphates linked to another moiety x) hydrolase superfamily of proteins is characterized by its conserved 23 amino acid signature sequence. The motif is found among eukaryotes, bacteria, archaea and viruses. Proteins of the Nudix hydrolase superfamily perform a wide variety of functions using diverse substrates. The Nudix proteins have very low sequence conservation outside the signature and have a large amount of structural variation around a conserved structural core. Protein D10 contains this motif and is conserved in all poxviruses. In recent research, it was revealed that without the Nudix motif expressed in protein D10 of the laboratory prototype of poxviruses, vaccinia virus (VACV), the virus was unable to successfully target a host. Altering the motif in protein D10 caused VACV to lose its ability for mRNA decapping. With this ability lost, VACV no longer had the ability to suppress synthesis of cellular proteins and regulate its own gene expression. Solving the structure of protein D10 would allow an inhibitor to be designed to prevent poxviruses from successfully targeting a host. VACV D10 was cloned and expressed in Escherichia coli bacterial cells as a maltose binding protein (MBP) fusion (pMalD10) and a His-tagged protein (pETD10). Although expression is low for both the fusion and tagged versions of protein D10, preliminary results indicate that purification by affinity chromatography is feasible. Further experiments are underway to improve expression and purification of protein D10 with the goal of obtaining sufficient homogeneous material to perform crystallization experiments.

Expression, Purification, and Small Angle X-Ray Scattering of DNA Replication and Repair Proteins from the Hyperthermophile Sulfolobus solfataricus. STEPHANIE PATTERSON (Del Mar College, Corpus Christi, TX, 78404) STEVEN M. YANNONE (Lawrence Berkeley National Laboratory, Berkley, CA, 94720)

Vital molecular processes such as DNA replication, transcription, translation, and maintenance occur through transient protein interactions. Elucidating the mechanisms by which these protein complexes and interactions function could lead to treatments for diseases related to DNA damage and cell division control. In the recent decades since its introduction as a third domain, Archaea have shown to be simpler models for complicated eukaryotic processes such as DNA replication, repair, transcription, and translation. Sulfolobus solfataricus (S. so) is one such model organism. A hyperthermophile with an optimal growth temperature of 80°C, S. so protein complexes and transient interactions should be more stable at moderate temperatures, providing a means to isolate and study their structure and function. Here we provide the initial steps towards characterizing DNA-related S. so proteins with small angle X-ray scattering (SAXS). We focused on three S. so proteins: Sso0257, a cell division control/ origin recognition complex homolog, Sso0768, the small subunit of the replication factor C, and Sso3167, a Mut-T like protein. E. coli cells transformed with the pet21a expression vector containing the S. so gene of interest were grown to logarithmic phase. Protein expression was induced with 1mM Isopropyl ß-D-1-thiogalactopyranoside (IPTG). Cells were harvested by centrifugation. Proteins were extracted by sonication, then the extracts heated to denature any contaminating E. coli proteins. Soluble protein was purified by Ni-affinity column chromatography in a Fast Protein Liquid Chromatography (FPLC) system. S. so proteins were eluted with an imidazole gradient and collected as fractions, then concentrated to a range of 1-10mg/ml. S. so proteins were analyzed with SAXS at multiple concentrations for both short and long exposure times. The Sso0257 sample was determined to be a 1:1 combination of monomer and dimer states. Sso0768 was found to be a complex mixture of multimeric states. Molecular envelope reconstruction from SAXS data for Sso3167 revealed a novel structural component which may function as a disordered to ordered region in the presence of its substrates and/or protein partners.

Fast Vertexing Studies for the STAR Experiment at RHIC. MICHAEL ERICKSTAD (University of Minnesota, Minneapolis, MN, 55414) HOWARD MATIS (Lawrence Berkeley National Laboratory, Berkley, CA, 94720)

On-line or fast vertexing (the real-time determination of the position of a collision) can be used as a trigger in data acquisition. Triggers are used in experiments to select specific classes of events and to reduce the storage of uninteresting events. Fast vertexing, when combined with fast secondary vertexing, also enables a detector to focus on certain physics topics (i.e. B-tagging, a method of determining the presence of a bottom quark based on decay length, the distance of travel before decay). The goal of this project was to test the effectiveness of a few potential fast vertexing algorithms for use with the proposed Heavy Flavor Tracker (HFT) detector at the Solenoidal Tracker at RHIC (Relativistic Heavy Ion Collider) (STAR) experiment. Simulations, which use simulated event data to predict the efficiency of these algorithms, were created. This code was written in the c++ programming language. The layers of the HFT have a cylindrical geometry and coordinate system with the beam-line as the Z-axis. The collisions take place along the beam-line. The most effective algorithm, which was tested, separates the hits (on two detector layers) into groups in Φ and then uses all combinations of two hits (one on each layer) to fill and fit a histogram of the Z intercept values for a line through the two points. It was determined that this method of using linear approximation can measure the collision vertex to a s of 430 ± 20 µm for central Au + Au events, 950 ± 20 µm for minimum-bias Au+Au collisions and 6,100 ± 200 µm for p + p events, when used with the Silicone Strip Detector and the Intermediate Silicone Tracker. It was also found that using this method with the two layers of the Pixel detector can approximate a vertex to 113 ± 7 µm for central Au + Au events, 507 ± 30 µm for minimum-bias Au+Au collisions and 1310 ± 90 µm for p + p events. Each simulation had incident particles at 200 GeV/A. A Pixel detector can achieve these results with this algorithm, if it detects particles with a suitable technology possessing no significant pile-up. These results indicate that this algorithm has a potential for implementation in the STAR experiment, for quick identification of the vertex, as well as for use in B-tagging and other decay length based particle identification methods.

Finding Variable Stars. DANIEL WONG (University of California, Berkeley, Berkeley, CA, 94709) CECILIA ARAGON (Lawrence Berkeley National Laboratory, Berkley, CA, 94720)

The the Nearby Supernova Factory (SNF) seeks to observe several hundred type Ia supernovae, but their search is partially impeded by the presence of variable stars in the images they collect. To aid in their search, we tried to develop a catalog of known variable stars using their archival data, consisting of over 1 million images with 1.5 billion photometric measurements. By comparing magnitudes measured on different dates, variability could be detected and a classification could be assigned to each star. Early versions of our selection algorithm were able to detect variability in a subset of stars that we gave as input. Upon closer inspection, we found that the apparent variability in the candidates was most likely due to calibration errors, rather than intrinsic variability. To calibrate the data we supplied to our algorithm, we used the United States Naval Observatory catalog as a reference. We supposed that the difference between our instrument magnitudes (a quantity known as magi) and those listed in the catalog (known as magc to differentiate from magi) would be about constant with respect to each image. Upon reexamination, we found that a non-constant relationship existed between the difference in magnitude and magc. To describe this relationship, we developed an iterative fitting technique to be carried out separately for each image. We did not attempt to develop a physical model to describe this relationship, as an empirical understanding would have been sufficient for our variability study. To evaluate our new calibration technique, we reexamined the candidates previously selected by our algorithm. We found that many of the oddities of the original light curves were removed as a result of our new calibration technique. To see if our new technique provided consistent improvement, we compared the standard deviation in magnitude for each star caused by the original calibration technique with that of the new technique which we had developed. The reason to do this is that most stars are not variable; hence, the best calibration technique should minimize the standard deviation through all magnitude ranges. We would have considered our new technique to be a success if we could improve (i.e. decrease) the spread in all magnitude ranges. Although there was a marked improvement in the one case we examined closely, the overall improvement was not as significant. Further investigations on why this occurred should be conducted in the future.

High-Throughput Protein Crystallography. TUYET NGUYEN (Contra Costa College, San Pablo, CA, 94803) MINMINYU (Lawrence Berkeley National Laboratory, Berkley, CA, 94720)

Proteins are the building blocks of living cells and control much of the biochemical processes that are important to all life. Different kinds of protein play different roles in the body. Because structure of proteins is essential to understand the natural function of cells, our goal is to identify the structures of the full complement of proteins, using x-ray crystallography. Using the computer system, the diffracted patterns of the protein crystal can be translated into a 3-D structure. The research group focuses mainly in producing protein crystals. Before setting plates to crystallize protein, the first step was to do cloning and purifying protein if necessary. In the process of protein purification, cells were added to lyses buffer sonicated to break the cells. The supernatant, which contained protein of interest, would be obtained after centrifuging the lysate. Later, the supernatant was run through Ni-NTA Chromatography to purify the protein and was done further purification using gel filtration column. After we got purified protein, a crystallization process was obtained using vapor diffusive method with sitting drop. Series of protein solutions were set up in droplet in a 96-well plate and let to crystallize for a certain time. During the time that protein was crystallizing, a close follow up viewing plate was taking place. Then the crystallization condition and crystal viewing results were entered into CLIMS database. We tried to find possible crystallization conditions from initial crystal hits. The initial hits of crystal formation leads to further optimization for obtaining high quality crystal that can give the best result in diffraction. The selective protein crystals were harvested and tested on the synchrotron beam line. Minmin Yu directly did the X-ray crystallography process. The crystals were mostly analyzed with the synchrotron at the Advance Light Source (ALS) of Lawrence Berkeley National Laboratory. Various proteins that are analyzed at this lab are for the Integrated Center Structure and Function Innovation, and TB Structural Genomic Consortium.

High-Throughput Protein Crystallography of Mycobacterium Tuberculosis Targets. ERIK WESTLING (City College of San Fransisco, San Fransisco, CA, 94112) MINMIN YU (Lawrence Berkeley National Laboratory, Berkley, CA, 94720)

High-throughput protein crystallography is an efficient method to manage researching the multitudes of proteins part of the Mycobacterium Tuberculosis bacterium. Since crystallization conditions are unpredictable, hundreds of different conditions must be arranged and observed for crystal growth. Each protein is screened through up to approximately 450 different chemical conditions. Conditions generally include a buffer of specific pH, a precipitant and salt. Experiments are created on 96 well plates. Each well corresponds to three droplets (0.2 micrometers in diameter). In each droplet, the chemical conditions are mixed with the protein. The droplets are observed routinely for crystal growth with an automated image-viewing device. In attempt to increase the quality and size of crystals, conditions in which crystals are observed to grow can be slightly altered. Changes are generally made to buffer pH and concentrations of precipitants and salts. Putting several proteins through this process at the same time will narrow down those that can crystallize in the available conditions. Of forty proteins received by our laboratory, thirty are crystallized. Eleven of those crystallized are verified to be protein crystals. Conformation of the remaining crystals is underway. This method allows research to progress for several proteins at once, rather than one at time.

How to Control a 7000 Ton Giant with Your Fingertips: An Interactive 3D Visualization of the ATLAS Experiment. EMILY GREENBERG (Dartmouth College, Hanover, NH, 3755) MICHAEL BARNETT, JOAO PEQUENAO (Lawrence Berkeley National Laboratory, Berkley, CA, 94720)

ATLAS, the particle detector currently under construction at CERN, Geneva, Switzerland, is scheduled to begin observing collisions between protons accelerated by the LHC (Large Hadron Collider) in 2008. In an effort to make the exciting events occurring at CERN accessible to students, interested members of the public, and fellow scientists, the ATLAS Collaboration is working to develop AMELIA (ATLAS Multimedia Educational Lab for Interactive Analysis), a real-time educational 3D visualization program featuring the ATLAS detector. Supported by the DOE, NSF, and CERN, AMELIA is expected to enter classrooms with the debut of the ATLAS detector next year. Before interacting with a 3D detector, AMELIA users will be able to learn basic concepts about particle physics and ATLAS through dynamic multimedia and written references. They will then enter a virtual environment where they can visualize an event and select tracks produced by the detected particles in order to analyze real and simulated collision data. After users have analyzed collision data and have found an interesting event, they will be invited to share their findings with the scientific community at a website that displays the analyses done by AMELIA users and provides links to related sites and web-based educational tools. AMELIA is being developed in C++ using wxWidgets, Mozilla, and the Irrlicht 3d Engine, a library typically used in the computer video game industry for real-time 3D graphics. Progress was made on the development of a streamlined interactive interface and menu, as well as the conceptualization of a pedagogical structure to ensure that the program will be comprehensible and engaging for users of differing interest levels and backgrounds.

Implicit Simulation for Beam Problems. KAM MAK (Contra Costa College, San Pablo, CA, 94806) ALEX FRIEDMAN (Lawrence Berkeley National Laboratory, Berkley, CA, 94720)

Experimental facilities that generate particle beams are expensive, while computers are getting more powerful. Computer simulation using the methods of computational plasma physics has become a reliable and effective approach to understanding beam behavior. Such simulation enables analysis of more realistic situations than are analytically tractable, so that researchers can explain the behavior of an existing machine, improve its performance, and predict the performance of a future machine. The research group in the Heavy Ion Fusion Science Virtual National Laboratory (HIFS-VNL) at Lawrence Berkeley National Laboratory (LBNL) develops and uses plasma and beam simulation programs. The most adaptable and reliable tools for the study of plasma behavior are Particle In Cell (PIC) simulations, in which a few thousand to many million particles are used to model the beam and/or plasma. These particles follow the Newton-Lorentz equations of motion in fields governed by Maxwell’s equation. However, traditional PIC codes require use of a time step shorter than the plasma period to maintain numerical stability. When plasma oscillations are not important and a larger time step is required, implicit methods can maintain the stability and model the macroscopic behavior. In such methods, the particle positions at the advanced time level depend on their accelerations due to the electric field at that time level. But that field itself depends on the density of particles at their new positions. A direct method for obtaining this field solves a modifed field equation which takes account of the effect of that field on itself through the particle motion. After the predicted field is known, the particles are advanced to the new time level. In this project we combined several old codes into a modern 1-D implicit test-bed, and made the new code user-steerable using the Python language, linked to Fortran by the Forthon system. We then studied the performance of various algorithms on a plasma expansion problem, and studied the behavior of a test electron in an electrostatic potential well that models the well caused by an ion beam. Regimes of reliable algorithmic performance were clarified.

Implications of Exhaust Stream Sampling Conditions for Measurement of Gas and Particle Emissions from Natural Gas Appliances. ADAM HALL (Bowdoin College, Brunswick, ME, 4011) BRETT SINGER (Lawrence Berkeley National Laboratory, Berkley, CA, 94720)

Accurate measurement of ultra-fine particle and gaseous emissions from natural gas fueled appliances are needed to quantify the potential health and environmental impacts of airborne emissions that may result from use of new gas supplies. In order to quantify differences in emissions between natural gas derived from liquefied natural gas versus conventional gas supplies a variety of used appliances will be accessed and operated. Concentrations of carbon dioxide, oxides of nitrogen, carbon monoxide, oxygen, and ultra-fine particles in the exhaust of these appliances are to be measured. Making such measurements requires that samples of the appliances’ exhaust be captured and delivered to a number of gas and particle analysis instruments. This sampling must not interfere with the normal operation of the appliance and must preserve the composition of the exhaust for measurement. Concern has been expressed that in drawing up these emissions the sampling system may change the airflow around the flame, possibly having effects on the levels of pollutants produced by the burner. Experiments were conducted to assess how the elevation of the exhaust hood relative to the stovetop burner impacts emissions formation. Hood elevation did not affect gaseous emissions appreciably. However, increased hood elevation lead to an increase in particle formation of roughly an order of magnitude. This suggests that even though the exhaust hood does not affect flame performance directly, it does impact characteristics of the exhaust stream, such as temperature, which have a measurable effect on particle formation. This finding illustrates the importance of designing our experimental system to reflect conditions in the consumer setting in all parameters relevant to pollutant formation.

Improving Efficiency of Storage Gas Water Heaters. DEREK KING (Laney College, Oakland, CA, 94607) JIM LUTZ (Lawrence Berkeley National Laboratory, Berkley, CA, 94720)

The energy required for water heating accounts for approximately 25% of national residential natural gas consumption. In California that figure is closer to 40%. With water heating using such a substantial portion of valuable natural gas resources, water heating appliance efficiencies deserve some scrutiny. What is referred to as “standby losses” are addressed in this study. Typical storage gas water heaters have a flue for combustion exhaust located along the center of the storage tank. When the burner is inactive, ambient air flows through the flue. The cooler air absorbs heat from the storage tank and rises out of the exhaust vent. Fresh air is drawn in through openings at the base of the heater. This cycle continues until the stored water falls below the preset maintenance temperature and the burner is activated. Consequently, more fuel must be spent to maintain a store of hot water to keep up with the standby losses. Several alternative designs have been proposed to address this energy loss mechanism and remain competitively priced for consumers. The Department of Energy’s 24 hour efficiency test will be used to compare performance of an off-the-shelf storage gas water heater and the alternative prototypes. The prototypes that demonstrate an improvement in heating efficiency could then be further developed for the consumer market.

Large Hadron Collider. BOYAN TABAKOV (University of California, Berkeley, Berkeley, CA, 94720) DR. WEI-MING YAO (Lawrence Berkeley National Laboratory, Berkley, CA, 94720)

As the Large Hadron Collider is due to start operating in 2008, final performance tests are carried out to confirm the working parameters of its components. The alignment of the middle disk of Endcap A of the Pixel Detector of ATLAS is examined using data from test runs with cosmic muons. In the data, the x and y coordinates of the points of intersection of a particle trajectory with the disks were previously recorded. Based on records for the first and last disks, the position of an expected intersection point on the middle disk is calculated. The differences x and y between the coordinates of the expected and the actual intersection points are attributed to a hypothetical misalignment. With the help of geometrical arguments, a linear transformation that uses as parameters the offsets x₀,y  ₀, and z₀ and the displacements due to rotations alpha,beta, and gamma about the principal axes is developed to represent the misalignment. If the transformation is applied to the actual coordinates of an intersection point on the middle disk with the right parameter values, the actual point would be sent into the expected point. Hence, the values for the six parameters that provide the closest match between actual data and expected coordinates can be found from x and y by ² minimization. The preliminary conclusion is that the disk is perfectly aligned. The relatively high systematic uncertainties and ² values are subject to current research.

Model Based Illumination Optimization for a 003-Numerical Aperture Extreme Ultraviolet Lithography Tool. JONATHAN NATION (University of Arizona, Tucson, Tucson, AZ, 85701) PATRICK NAULLEAU (Lawrence Berkeley National Laboratory, Berkley, CA, 94720)

There have been many recent advances in high numerical aperture (NA) extreme ultraviolet (EUV) lithography systems. The 0.3-NA Micro Exposure Tool (MET) at the Advanced Light Source (ALS) currently utilizes a programmable coherence illuminator system with the capability of creating different pupil fills. It is well known that illumination settings can be tailored to optimize printing performance for particular features. The optimal illumination settings, however, depend not only on the feature type but also on the specifics of the pupil function, including phase (or aberrations) and amplitude (or pupil obscurations). In order to maximize the productivity of the MET, the best possible pupil fill should be chosen for the feature type being imaged in each experiment. In this research, aerial image modeling software is used to study the optimal illumination conditions for the SEMATECH Berkeley MET tool as a function of feature size and type taking into consideration the known pupil function of the optic. The metrics of maximum contrast over a 50 nm focus range and depth of focus with contrast greater than 0.5 are used to gauge the performance of each pupil fill tested. We will present the best annular, dipole, and monopole pupil fills for each feature type as well as for each individual feature size. Experiments relying on only one feature size will obtain the greatest improvement in contrast and depth of focus by using the presented pupil fills, at the possible expense of losing quality of other feature sizes. The results are also directly compared to the default annular 0.35-0.55 setting used in the commercial implementations of the MET tool. Initial results for annular pupil fills reveal that improvements of up to 12% in each metric can be obtained.

Modeling the Interactions among Microbial Communities under Environmental Conditions through High Density Phylogenetic Microarrays. CURTIS LUCE (New Mexico State University, Las Cruces, NM, 88001) TODD DESANTIS (Lawrence Berkeley National Laboratory, Berkley, CA, 94720)

The K-th order logical network modeling software determines significant interactions among microbes in a microbial community. Using inference of the K-th order the temporal information in the gene expression data sets provides a basis to examine interactions with a microbial community using the logical network model. In a logical network, a logical function, associated with each microbe population as a node, describes its behavior dictated by some other influential microbes. The optimal logics at each microbe node in the network will be searched so that they best explain the observed data. Determination of an optimal logic will involve parent node selection and truth-table generation. The maximum number of parents is set to a given number. If the current node shows consistent behavior during transition from one state to another given the parent nodes, then the parent nodes will be kept. The actual goodness of the transition will be calculated using the chi-square test.

Module Alignment and Resolution Studies for ATLAS Pixel Detector Endcap A. ANA OVCHAROVA (University of California, Berkeley, Berkeley, CA, 94720) WEI-MING YAO (Lawrence Berkeley National Laboratory, Berkley, CA, 94720)

Endcap A, a component of the ATLAS Pixel Detector, constitutes of 144 modules mounted onto three disks, whose centers lie on the Large Hadron Collider (LHC) beam pipe. Each module contains 47, 232 rectangular pixels, which are individually connected to a readout system. When in operation, the pixels containing sufficient charge deposited by particles are read out and the obtained information is used to reconstruct the paths of particles passing through the detector. Through offline analysis of data collected from cosmic muons passing through Endcap A, the current study investigates the relative alignment of the modules using the areas of overlap between adjacent modules. The method used is parallel to the one used in a previous study of the alignment, however, the current results incorporate masking of noise identified on Endcap A in order to determine more precisely the resolution of the detector. The analysis involves considering the module as a rigid body with 4 allowed degrees of freedom, including translation in x, y, z local coordinates of the module and rotation around z. The parameters (alignment constants) obtained in this manner indicate quantitatively the deviation of the position of each module, relative to an adjacent module, from the nominal detector geometry. The alignment constants are determined by examining the mean distance between the actual positions of clusters on one module and their expected positions as seen from an adjacent module. Comparing the values of the parameters to these obtained by surveying the geometry of Endcap A during assembly shows good agreement. Using the obtained alignment constants, the values of the mean distances are recalculated. The resolution obtained by plotting the recalculated values is 16.5 ± 0.2µm and 118 ± 1µm in short and long pixel dimension respectively. Resolution varies according to the number of pixels that are triggered by a passing particle. For two pixels triggered simultaneously, the resolution is 13.8 ± 0.3µm, compared to 14.7 ± 0.4µm for a single pixel. This method has proven itself efficient with the limited data available. When ATLAS is in operation in 2008, more data will provide sufficient statistics to increase the accuracy of the results.

Monte-Carlo Based Simulation of Double-Image Granvitational Lensing by Cosmic Strings. ERIC ALBIN (California Polytechnic State University, San Luis Obispo, CA, 93405) GEORGE SMOOT (Lawrence Berkeley National Laboratory, Berkley, CA, 94720)

Cosmic Strings have yet to be observed, but they are still experimentally sought after. The simulation of a Cosmic String lensing event signal is invaluable for testing detection criteria. Light sources from I-band survey flexible image transport system (FITS) images taken by the Advanced Camera for Surveys (ACS) aboard the Hubble Space Telescope (HST) are identified using the open-source astronomical software Source Extractor v2.2.2. All identified sources are then pseudo-randomly assigned redshift based on a parameterization of the measured redshift distribution as a function of source absolute magnitudes. Each identified source is also isolated from the FITS image file so that a particular Cosmic Strings can be simulated by re-integrating selected isolated sources back into the FITS image assuming a CDM cosmology with O_m = 0.3. Simulations are limited to perfectly straight Cosmic Strings which span across the entire FITS image used as well as to strongly-lensed events. Simulated Cosmic String lensing event signals are then applied towards calculating detection efficiencies in v1.0 data from the Great Observatories Origins Deep Survey (GOODS).

Noise Studies in ATLAS Pixel Detecto