3D Simulation for the ATLAS Education and Outreach Group. BRIAN
AMADIO (Rensselaer Polytechnic Institute, Troy, NY, 12180)
MICHAEL BARNETT (Lawrence Berkeley
National Laboratory, Berkley, CA, 94720)
ATLAS is a particle
detector under construction at the Large Hadron Collider facility
at the CERN Laboratory in Geneva, Switzerland. The project will
be the most expansive physics experiment ever attempted. The ATLAS
Education and Outreach Group was started to provide information
to students and the general public about the importance of this
project. A three-dimensional interactive simulation of ATLAS was
created, which allows users to explore the detector. This simulation,
named the ATLAS Multimedia Educational Laboratory for Interactive
Analysis (AMELIA), allows users to view detailed models of each
part of the detector, as well as view event data in 3D. A similar
project is called ATLANTIS, which allows users to examine events
in only two dimensions. Currently ATLANTIS allows more sophisticated
analysis of events. AMELIA will provide similar functionality,
but in a more intuitive way, which will be much friendlier to the
public.
A Comparison of DNA Damage Probes in Human Mammary Epithelial Cells with 150
kVp X-Rays. CHRISTY WISNEWSKI (University
of California, Davis, Davis, CA, 95616) ELEANOR BLAKELY AND KATHLEEN BJORNSTAD (Lawrence Berkeley National Laboratory, Berkley, CA, 94720)
In
this study we investigated 53BP1 and H2AX, DNA damage markers,
to look at genetic mechanisms underlying responses to radiation
insult. Two human mammary epithelial cell (HMEC) lines, one subtype
of HMEC 184 with a finite lifespan and S1 with an infinite lifespan
were investigated to research the role of immortalization in
DNA marker expression. Cells were irradiated with 50 cGy, fixed
after 1 hour with 4% paraformaldehyde, and processed through
immunofluorescence. Cells were imaged using an immunofluorescent
microscope and digitally captured using Image Pro Plus software.
8-bit images were analyzed using Image J and counted. The 184
cells showed more positive response within the irradiated samples
than the S1 samples. It was observed that the S1 had a previous
peak time of 30 minutes with an alternative DNA damage probe;
this could explain the decrease in signal for S1 for both probes
used in this research. We also noted that the H2AX response
was more punctate in the 184 cells, whereas the 53BP1 response
was punctate in both cell lines. We hope to expand the dose and
time course studied in the hope that this will broaden the knowledge
obtained from the preliminary data of this research. It is important
to understand whether the process of transformation to immortalization
compromises the DNA damage sensor and repair process.
A Miniature Quartz Crystal-based Device for Particulate Matter Monitoring with
Real-time Data Acquisition. ZHUO HUANG
(Sacramento State University, Sacramento, CA, 95819)
MICHAEL APTE (Lawrence Berkeley
National Laboratory, Berkley, CA, 94720)
Exposure to particulate
matter (PM) through inhalation has been associated with adverse
health problems. Accurately monitoring of the mass concentration
and chemical composition of PM are necessary for exposure assessment.
Many current instruments in use involve complex operation and labor-intensive
work to obtain necessary data for studies, or involve costly systems
to monitor a large population. One feasible solution to address
these drawbacks is to develop low-cost, compact, and miniaturized
real-time devices. The miniature system for particle exposure assessment
(MSPEA) developed at Lawrence Berkeley National Laboratory (LBNL)
is one approach available to the aerosol research community. MSPEA
PM mass detection uses a quartz crystal microbalance (QCM). All
the components including the quartz crystals for this system are
off-the-shelf items, and can be easily obtained. The particle deposition
mechanism used by this device is thermophoresis, while particles
are retained on the sensors using and van der Waals forces. The
QCM is constructed using an unexposed reference crystal oscillator
and a PM-exposed sensing crystal oscillator, and a mixing circuit
to that combines the oscillators’ outputs into a beat frequency
signal. A computer is used to incorporate the data acquisition
operation, but eventually a microprocessor can replace the computer
to miniaturize the device for personal monitoring at low-cost.
Another monitoring feature of the MSPEA system employing ultraviolet
and near-infrared optics is briefly discussed in this paper.
A New GUI for Global Orbit Correction at the ALS Using MATLAB. JACOB
PACHIKARA (University of Texas
at Arlington, Arlington, TX, 76019)
GREGORY J. PORTMANN (Lawrence Berkeley
National Laboratory, Berkley, CA, 94720)
Orbit correction
is a vital procedure at particle accelerators around the world.
It is very important to have a user friendly application. The orbit
correction routine currently used at the Advanced Light Source
(ALS) is a bit cumbersome and this paper describes a new Graphical
User Interface (GUI) developed for global orbit correction using
MATLAB. The correction algorithm uses a singular value decomposition
method for calculating the required corrector magnet changes for
correcting the orbit. The application has been successfully tested
at the ALS. The GUI display provided important information regarding
the orbit including the orbit errors before and after correction,
the amount of corrector magnet strength change and the standard
deviation of the orbit error with respect to the number of singular
values used. The use of more singular values resulted in better
correction of the orbit error but at the expense of enormous corrector
magnet strength changes. The results showed an inverse relationship
between the peak-to-peak values of the orbit error and the number
of singular values used. The plots on the GUI help the ALS physicists
and operators in understanding specific behavior of the orbit.
It is a convenient application to use and is a substantial improvement
over the previous orbit correction routine.
A Novel Approach to Estimating Thermal Conductivity. GORDON
WU (University of California, Berkeley, Berkeley, CA, 94720)
TIM KNEAFSEY (Lawrence Berkeley
National Laboratory, Berkley, CA, 94720)
Scientists at
Lawrence Berkeley National Laboratory (LBNL) are currently researching
natural gas recovery from gas hydrates in hopes that this will
one day become a viable source of energy. Natural gas hydrates
are water crystals located below permafrost and submarine environments
that contain methane gas. Knowledge of heat flow through the hydrate-bearing
reservoir must be understood and thermal conductivity is a fundamental
property of a material that indicates its ability to conduct heat.
The technique for estimating thermal conductivity calls for applying
a temperature changes and using thermocouples to accurately measure
the rate of temperature change. The thermal data were analyzed
using Microsoft Excel and iTOUGH2. The program iTOUGH2 computes
a best-fit to our measured data by optimizing the thermal conductivity
through automatic model calibration. ITOUGH2 estimates the thermal
conductivity based on previous output values and given parameters.
The four materials used were dry sand, polyvinyl chloride (PVC),
high density polyethylene (HDPE) and Pyrex borosilicate glass,
and were chosen because they have thermal conductivities close
to that of hydrate bearing sand (2.7 W/m K). Good matches were
obtained between the simulations and the measured data showing
the validity of the technique. It is important to realize that
the substances that we were using can vary in thermal conductivity
depending on the temperature, the porosity of the particular substance,
and the composition of the sample. Now that the technique is validated,
it can be used in other experiments to measure thermal conductivities.
A Search for Cerium Doped Lanthanum Oxide Scintillators. LATORIA
WIGGINS (North Carolina A&T State University, Greensboro, NC, 27411) DR. YETTA PORTER-CHAPMAN (Lawrence Berkeley
National Laboratory, Berkley, CA, 94720)
The need for
new and improved radiation detectors, scintillators, is at an all
time high due a progression in detection knowledge. Commonly used
scintillators such as BGO and LSO have undesirable properties such
as low luminosity, and slow decay times. Discovering new scintillators
required literature searches, synthesizing and the characterization
of compounds. The research at hand concentrated on cerium (III)
doped lanthanum oxides. Compounds were synthesized using solid-state
chemistry techniques such as ceramic and hydrothermal methods.
Characterization consisted of x-ray diffraction, fluorescence spectroscopy
and pulsed x-ray measurements. Several new inorganic scintillators
were founded, however, findings concerning lanthanum oxide synthesis
warrant further investigation of the compound.
A Statistical-Based Analysis of Cloud Properties at Various Locations Across
the Globe. PARMINDER SINGH (State University
of New York at Buffalo, Buffalo, NY, 14214) SURABI MENON (Lawrence Berkeley
National Laboratory, Berkley, CA, 94720)
The impact of
anthropogenic activities (fossil-fuel combustion, biomass burning,
and transportation) on climate includes contributions from both
greenhouse gases (GHG) and aerosol particles. The warming associated
with GHGs is well known but the negative forcing associated with
aerosol-cloud interactions, also referred to as the aerosol indirect
effect (AIE), is more difficult to evaluate. This forcing includes
changes to cloud droplet number and cloud optical depth from an
increase in aerosols that reduce droplet sizes and increase cloud
reflectivity; and the impact on cloud water and lifetime that again
increase cloud reflectivity. To understand these effects we use
data from Moderate Resolution Imaging Spectroradiometer to analyze
signatures of aerosol-cloud interactions over several regions across
the globe for July 2000. The specific products we examined were:
aerosol optical depth, cloud droplet effective radii, cloud optical
depth, cloud top pressure, cloud top temperature and liquid water
path (derived from cloud droplet effective radii and cloud optical
depth). We choose 20 different ocean regions based on proximity
to continental areas. Regions closer to the continent have higher
aerosols in general (more polluted) than those farther away from
the source (cleaner regions). We use cluster analysis, log-linear
regressions, correlation coefficients, probability density functions
and means to understand cloud response to aerosols at different
locations. While features of both indirect effects were observed
at most locations, for cleaner regions cloud property changes were
more susceptible to aerosol effects. In more polluted regions,
presence of dust or aerosols not conducive to cloud formation and
liquid water variability may mask the signal we expect. The meteorological
analysis of air mass origin and an independent measure of liquid
water path can better constrain our analysis for future studies
that would use this data to evaluate model representations of the
AIE.
Adsorbent-Coated Polyurethane Foam as a Denuder and Size-Selective Inlet for
Ambient Air Samplers. JEFF DUARTE
(University of California, Davis, Davis, CA, 95616)
LARA GUNDEL (Lawrence Berkeley
National Laboratory, Berkley, CA, 94720)
For practical
use, ambient air samplers for assessing human exposure to airborne
particles must decrease in size and cost. One major step toward
this change is replacement of large, adsorbent-coated glass denuders
with small, cheaper adsorbent-coated PUF (polyurethane foam) denuders
for capturing SVOC (semi-volatile organic compounds). The purpose
of a denuder is to capture SVOC from the sampled air on its extractable
adsorbent coat while allowing particles to pass through for collection
on a filter. The purpose of this project was to determine if PUF
could meet the latter requirement. It was hypothesized that PUF
denuders could pass PM2.5 (particles with an aerodynamic diameter
of 2.5 microns or less) and match or even exceed conventional glass
denuders in SVOC capture because they have more surface area and
are more compact. A bifurcated particle sampler that excluded particles
larger than 2.5um was used on multiple 24-hour sampling runs in
several configurations. Data were initially collected without any
denuders, then in another configuration containing glass denuders
on both sides to determine the variability of particle capture
between the two columns, and then lastly with glass denuders on
both sides as well as a PUF denuder on one side. The PUF denuder
was placed downstream of the glass denuder so as to have normal
SVOC capture. This allowed the focus to be solely on whether or
not the PUF was allowing PM2.5 through. In earlier work with PUF
denuders by M. T. Minjares, it was found that the filter downstream
of the PUF had one third less mass then the filter with no PUF.
Minjares had no upstream glass denuders, so her result was thought
to be caused by either PM2.5 collection by the PUF or SVOC adsorption
by the Teflon filter. In this follow-up experiment, upstream SVOC
was collected by the glass denuders. The average PM2.5 concentration
difference between the filters in the two columns in a non-denuded
configuration was 8.6%. The average PM2.5 concentration difference
between the two filters in the configuration with glass denuders
on both sides and the PUF denuder on one side was 10.2%. With a
mass measurement uncertainty of 3.6%, the difference between these
two results is insignificant. The conclusions from this project
are 1) the PUF does pass PM2.5 well and 2) the Teflon filter adsorbed
SVOC. This is contrary to the prevailing belief that Teflon does
not measurably adsorb SVOC, and it was causing the artifact that
Minjares observed.
Adsorbent-Coated Polyurethane Foam as a Denuder for Particle Samplers. JEFF DUARTE (University
of California, Davis, Davis, CA, 95616)
LARA GUNDEL (Lawrence Berkeley
National Laboratory, Berkley, CA, 94720)
For practical
use, ambient air samplers for assessing human exposure to airborne
particles must decrease in size and cost. One major step toward
this change is replacement of large, adsorbent-coated glass denuders
with small, cheaper adsorbent-coated PUF (polyurethane foam) denuders
for capturing SVOC (semi-volatile organic compounds). The purpose
of a denuder is to capture SVOC from the sampled air on its extractable
adsorbent coat while allowing particles to pass through for collection
on a filter. The purpose of this project was to determine if PUF
could meet the latter requirement. It was hypothesized that PUF
denuders could pass PM2.5 (particles with an aerodynamic diameter
of 2.5 microns or less) and match or even exceed conventional glass
denuders in SVOC capture because they have more surface area and
are more compact. A bifurcated particle sampler that excluded particles
larger than 2.5um was used on multiple 24-hour sampling runs in
several configurations. Data were initially collected without any
denuders, then in another configuration containing glass denuders
on both sides to determine the variability of particle capture
between the two columns, and then lastly with glass denuders on
both sides as well as a PUF denuder on one side. The PUF denuder
was placed downstream of the glass denuder so as to have normal
SVOC capture. This allowed the focus to be solely on whether or
not the PUF was allowing PM2.5 through. In earlier work with PUF
denuders by M. T. Minjares, it was found that the filter downstream
of the PUF had one third less mass then the filter with no PUF.
Minjares had no upstream glass denuders, so her result was thought
to be caused by either PM2.5 collection by the PUF or SVOC adsorption
by the Teflon filter. In this follow-up experiment, upstream SVOC
was collected by the glass denuders. The average PM2.5 concentration
difference between the filters in the two columns in a non-denuded
configuration was 8.6%. The average PM2.5 concentration difference
between the two filters in the configuration with glass denuders
on both sides and the PUF denuder on one side was 10.2%. With a
mass measurement uncertainty of 3.6%, the difference between these
two results is insignificant. The conclusions from this project
are 1) the PUF does pass PM2.5 well and 2) the Teflon filter adsorbed
SVOC. This is contrary to the prevailing belief that Teflon does
not measurably adsorb SVOC, and it was causing the artifact that
Minjares observed.
AMELIA: ATLAS Multimedia Educational Lab for Interactive Analysis. DAVID MEDOVOY (Columbia University, New
York, NY, 10027)
MICHAEL BARNETT (Lawrence Berkeley
National Laboratory, Berkley, CA, 94720)
AMELIA is an
educational software program designed to allow the public to view,
on a home computer, a 3D model of ATLAS detector at CERN, as well
as visualization of recorded particle tracks. Models of the detector’s
geometry, created in ‘3ds Max,’ are loaded by the software, which
is written using the C++ language and the ‘Irrlicht’ visualization
engine. Particle track data in the JiveXML file format is loaded
and displayed simultaneously. The use of the standard JiveXML format
allows for file-type compatibility with other software, such as
the 2D visualization tool ATLANTIS. The ‘camera’ is fully movable
by the user, and custom cutaway views can be created based on the
camera’s position, to facilitate viewing the interior parts of
the detector, as well the particle tracks within. Tracks are color-coded
based on particle type, and will soon be individually selectable.
Programs exist to visualize particle track data in 3D, and to simplify
scientific data for outreach purposes, but only AMELIA is designed
for both. Further, AMELIA is the only project of its kind designed
to take advantage of technology developed for video games. An early
2007 public release is anticipated.
Amplification and Tagging of Sulfolobus solfataricus Genes for Recombinant
Expression. STEPHANIE PETERSON (Del Mar College, Corpus
Christi, TX, 78404)
STEVEN M. YANNONE (Lawrence Berkeley
National Laboratory, Berkley, CA, 94720)
In organisms
that thrive at moderate temperatures, many biological processes
such as DNA repair occur through transient protein interactions.
Understanding these interactions and the temporary protein complexes
that they form is vital to understanding how cells function especially
in how they repair damaged DNA. Protein interactions within hyperthermophiles
like Sulfolobus solfataricus may be stabilized at moderate temperatures.
The work presented in this study provides the initial steps towards
thermally trapping otherwise short-lived protein complexes. Genes
associated with DNA repair were selected from the S. solfataricus
P2 genome and were modified with a directional tag on the N-terminus
and a six-histidine tag (6x-hist) on the C-terminus using gene
specific primers. Genes were amplified, cloned into entry vectors,
and transformed into E. coli cells. Colonies were then selected
and grown in liquid culture. Plasmid DNA was isolated using alkaline-lysis
extraction method and constructs were confirmed with restriction
digestion. Sixteen out of twenty-nine constructs were successfully
confirmed by restriction digestion and fragment pattern on 1% agarose
gels. These constructs will be further studied through two different
expression systems: E. coli expression and S. solfataricus expression.
E. coli expression should provide insight into independent protein
structure and function. Native expression will not only provide
information about the structure and function but will also identify
obligate protein partners in their native organism. In addition,
this approach will identify the root causes of difficulties that
arise from recombinant expression.
An Evaluation of Vista Performance on Current Windows
Computer Systems. JAMES
ARRIAGA (BigBend Community
College, Moses Lake, WA, 98823) CHARLIE VERBOOM (Lawrence Berkeley
National Laboratory, Berkley, CA, 94720)
With the impending
release of Windows Vista in January 2007, the Information Technology
Division at Lawrence Berkeley Laboratory is faced with a decision
involving the future transition of computers from the Windows XP
operating system to the Windows Vista operating system. Research
involved a review of benchmarking tools, the selection of a standard
set of tests, and the application of those tests to workstation
hardware in use at Berkeley Laboratory. To evaluate the impact
of installing the new operating system, performance benchmarks
were run on 3 desktop systems with both a standard configuration
and with selected hardware upgrades. This provided a comparative
analysis to determine the effects of Vista with the Authentic,
Energetic, Reflective, and Open (AERO) graphical user interface
and how it will react on hardware specifications as determined
by Microsoft on systems commonly used at Berkeley Laboratory. The
new enhanced user interface built into Vista requires more powerful
hardware resources than current computers running XP can handle.
The comparison of the minimum and recommended requirements for
computer hardware with the Vista operating system installed indicated
that legacy systems were more likely to be replaced than upgraded.
Computers manufactured within the last 2 years that meet the published
guidelines should run Vista with or without the AERO interface.
Arsenic Removal from Ground Waters: An Investigation of the Effects of Temperature. MARIA MELISSA QUEMADA (University
of California, Berkeley, Berkeley, CA, 94720)
ASHOK J. GADGIL (Lawrence Berkeley
National Laboratory, Berkley, CA, 94720)
Arsenic, a naturally
occurring element is a major contaminant in ground waters. Approximately
40 million people in Bangladesh and tens of millions more in neighboring
countries are being poisoned by arsenic in their drinking water.
The World Health Organization has set a standard of 10-µg/L arsenic
in drinking water, while Bangladesh standard remains 50-µg/L. In
California, approximately 600,000 households use water with arsenic
concentrations higher than the required standard. Lawrence Berkeley
National Laboratory has developed a technology for arsenic removal
using coal ash coated with ferric hydroxide (media). This process
enables the arsenic bind to the iron oxide complex that is coated
around the ash particles, and thus lowers the arsenic concentration
in drinking water. This technology has high efficacy and very cost
effective. My goal in this project is to test the performance of
this technology on U.S. waters over a range of temperature values
and to test the arsenic removal capacity of the media using coal
fly ash that are commonly found in the US. The temperature values
I investigated were 4 and 35 degree Celsius. This was accomplished
through a series of experiments that allowed me to find the time
the process reaches equilibrium in the two temperature values I
investigated. Once the equilibrium time was established, the process
was repeated to obtain adsorption isotherm curves for the two different
temperature values. The equilibrium times that were found were
4 and 16 hours for 4°C and 35°C respectively. The arsenic removal
capacity was analyzed using an arsenic field kit test (Quick Test©)
and the results were confirmed by Inductively Coupled Plasma Mass
Spectroscopy analysis.
Arsenic Removal Using Ferric Hydroxide Coated Coal Ash. CLETE
READER (MiraCosta College, Oceanside, CA, 92056) ASHOK GADGIL (Lawrence Berkeley
National Laboratory, Berkley, CA, 94720)
Chronic ingestion
of arsenic (As), usually through contaminated drinking water, leads
to serious health problems, including cancers, neural disorders,
or failure of the kidneys and liver. The present project aims to
address the crises in Bangladesh where an estimated 40 million
people are consuming water with arsenic levels greater than the
World Health Organization’s recommended maximum 10 µg As per liter
of water (or 10 ppb). The technology is also being extended for
applications in the U.S. regions of low population density where
the small municipal water systems makes conventional approaches
of arsenic removal impractical. The technology relies on the documented
ability of Fe (III) to immobilize arsenic. A coating of the iron
complex onto coal ash, which has a surface area of 600m2/g, provides abundant active sites for the adsorption to occur.
This study investigates the effect of pH on the arsenic removal
capacity of the coated coal ash media with the goal of providing
an accurate prediction of the media’s performance at a range of
pH levels and arsenic concentrations. It was first necessary to
determine the time-to-equilibrium for the reaction, at different
pH levels. This was achieved by mixing the media with synthetic
ground water spiked with 50 ppb As (V) and analyzing the As concentrations
in the water at times ranging from 0.5 – 15 hours using Inductively
Coupled Plasma Mass Spectrometry. Data on adsorption for various
starting concentrations of As was generated in a similar manner,
with time-to-equilibrium determined by above experiments. In the
range of pH levels tested equilibrium occurred within 4 hours.
Adsorption data were obtained for starting As concentrations of
50 and 150 ppb. Further experiments at additional concentrations
will be conducted to develop an adsorption curve that will allow
accurate prediction of performance. Preliminary results suggest
that the removal capacity of the media is highest at mildly acidic
(5.5) pH levels. The low cost, low input, nature of the technology
makes it a viable alternative to other removal technologies; characterizing
the effect of pH will allow for optimization across a range of
pH levels and arsenic concentrations.
Automatic Detection of CRISPR elements. KYNDALL
BROWN & MICHAEL LOWE (Jackson State University, Jackson, MS, 39217) NIKOS KIRPEDES (Lawrence Berkeley
National Laboratory, Berkley, CA, 94720)
Due to the growing
interest and importance of CRISPR elements in the scientific community,
there was a desire for devices that would speedily and efficiently
detect CRISPRs. Initially their detection relied on tandem repeat
finding tools such as PatScan, Piler, and Reputer. Unfortunately,
this process required hours of manual post processing due to the
software being inaccurate in distinguishing CRIPSR elements. To
solve this problem, the research team at the Lawrence Berkeley
National Laboratory (LBNL) created a CRISPR Recognition Tool (CRT),
to fast and efficiently detect CRISPR loci. CRT was implemented
in Java, an object-oriented programming language. This algorithm
used Boyer-Moore searching and skips techniques in locating CRISPRs.
The program starts by scanning for a small region of bases that
appear within the searchwindow. Assuming that the pattern is part
of a CRISPR, it will appear within a range that is relative to
the size of the spacer and repeat. Once the range is determined,
the program searches for the pattern using Boyer-Moore and the
skip method. Once the match is found, and the full repeat length
is determined, it is deemed a CRISPR candidate. The program then
passes the candidate through three filters with the user specified
parameters. Once the candidate passes all requirements it is confirmed
as a CRISPR, and the program repeats the process until all CRISPR
elements are found. To determine the effectiveness of CRT, its
speed and accuracy was tested against PatScan and PilerCR. As a
result, the tests proved CRT to be the fastest and most accurate
of the three tools. In conclusion, the algorithm efficiently detected
CRISPR elements and will be a useful tool in the scientific community.
Bacterial Diversity in Soil and Sediments From a Former Bombing Range
(Vieques, PR). ERNIE
PEREZ (University of Puerto
Rico at Mayaguez, Mayaguez,
PR, 680) TERRY C. HAZEN (Lawrence Berkeley
National Laboratory, Berkley, CA, 94720)
Bombing sites
used for military training activities can have considerable amounts
of contaminants and pose significant risks for people and the environment.
Until 2003, the eastern part of Vieques, Puerto Rico, was used
as a bombing range by the US Navy. Since then, leaching of explosive
compounds from unexploded ordnance represents a serious threat
to the marine ecosystem. The contribution of microbial populations
to natural attenuation of explosives, including sulfate-reducing
bacteria (SRB) has been demonstrated in soils but little is known
about their contribution in marine environments. Characterization
assays were employed to assess the effects of explosive compounds
(TNT, RDX, HMX) on Desulfovibrio vulgaris Hildenborough
and five novel SRB isolates from marine sediments in costal waters
adjacent to the former military facilities. Pure cultures were
combined with media in a covered 96-well micro plate and the opacity
was monitored in real time as the bacteria grew in a temperature-controlled
plate reader. A dose-response curve was used to estimate minimum
inhibitory concentrations (MICs) for TNT, RDX and HMX in 0, 1.5
and 3.0% (w/v) NaCl. Some of the bacterial isolates grew better
in explosive-containing environments than in regular media. The
chemotactic response to nitrocompounds was evaluated for D.
vulgaris using
a Palleroni chamber. D.
vulgaris responded positively towards TNT, but not to RDX or HMX. Elucidating
the diversity and behavior of SRBs to explosives in tropical sediments
could help us understand the role of these microbial populations
in explosive-contaminated marine environments.
Bombing sites used for military training activities can have considerable amounts
of contaminants and pose significant risks for people and the
environment. Until 2003, the eastern part of Vieques, Puerto
Rico, was used as a bombing range by the US Navy. NATALIA RAMOS (University
of Puerto Rico, Mayaguez,
PR, 727) TERRY C. HAZEN (Lawrence Berkeley
National Laboratory, Berkley, CA, 94720)
Bombing sites
used for military training activities can have considerable amounts
of contaminants and pose significant risks for people and the environment.
Until 2003, the eastern part of Vieques, Puerto Rico, was used
as a bombing range by the US Navy. Since then, leaching of explosive
compounds from unexploded ordnance represents a serious threat
to the marine ecosystem. The contribution of microbial populations
to natural attenuation of explosives, including sulfate-reducing
bacteria (SRB) has been demonstrated in soils but little is known
about their contribution in marine environments. Characterization
assays were employed to assess the effects of explosive compounds
(TNT, RDX, HMX) on Desulfovibrio vulgaris Hildenborough
and five novel SRB isolates from marine sediments in costal waters
adjacent to the former military facilities. Pure cultures were
combined with media in a covered 96-well micro plate and the opacity
was monitored in real time as the bacteria grew in a temperature-controlled
plate reader. A dose-response curve was used to estimate minimum
inhibitory concentrations (MICs) for TNT, RDX and HMX in 0, 1.5
and 3.0% (w/v) NaCl. Some of the bacterial isolates grew better
in explosive-containing environments than in regular media. The
chemotactic response to nitrocompounds was evaluated for D.
vulgaris using
a Palleroni chamber. D.
vulgaris responded positively towards TNT, but not to RDX or HMX. Elucidating
the diversity and behavior of SRBs to explosives in tropical sediments
could help us understand the role of these microbial populations
in explosive-contaminated marine environments.
Characterization of Long Cosmic Ray Muon Tracks in IceCube detector at South
Pole. DANIEL HART (Southern University, Baton
Rouge, LA, 70813)
AZRIEL GOLDSCHMIDT (Lawrence Berkeley
National Laboratory, Berkley, CA, 94720)
Ice Cube is studying
high-energy neutrino astronomy. IceCube uses an array of optical
modules to detect faint Cerenkov light produced by muons. These
muons are the result of nuetrino interactions with matter. Using
the information received from data acquisition systems at the South
Pole, software was developed using the C language to read this
data and use it to produce possible muon paths. Events were filtered
through by placing cuts on the calculated paths that passed through
the full geometry of IceCube, had velocity within 5% the speed
of light, and were of low multiplicity. This resulted in path distance
distributions that showed exponential decay of modules to receive
light as a function of distance. The probability curves produced,
followed along the same traits. However, the distance distributions
were not exactly smooth as would be expected, and the selection
of paths that were to be considered as neutrino candidates behaved
similarly. These impurities are interpreted as the integration
of multiple muons in a single event. In further studies, the plan
is not only to add in more data from additional days, but also
to employ more sophisticated methods for separating true events
from those produced by multiple muons.
Cloning of DNA Repair Genes from a Hydrothermal Vent Worm. ANABEY
CORNEJO (Contra Costa College, San
Pablo, CA, 94806) JILL O. FUSS (Lawrence Berkeley
National Laboratory, Berkley, CA, 94720)
The primary structure
of DNA is highly reactive with molecular by-products of metabolism
as well as UV radiation from the sun, and these reactions alter
and damage the human genome. Alterations to the DNA structure and
chemistry result not only from natural physical agents but also
from man made chemicals, although to a lesser extent. If these
alterations are not detected and either corrected or removed, a
mutation can be fixed in the genome potentially leading to cancer
and aging. Through evolutionary adaptation, cells have developed
a series of mechanisms which allow them to remove the damage and
restore the normal nucleotide sequence and DNA structure. One such
mechanism is Nucleotide Excision Repair (NER) which removes oligonucleotides,
which are short nucleotide segments that contain damaged bases.
NER is further categorized based on the location of the repair.
GG-NER or global genome repair refers to NER taking place in DNA
not undergoing transcription. TC-NER or transcription-coupled repair
refers to NER occurring in the transcribed strand of active genes.
If the NER pathway is compromised, a number of human genetic diseases
such as Xeroderma pigmentosum (XP), Cockayne syndrome (CS) and
Trichothiodystrophy (TTD) may result. These diseases are characterized
by causing premature aging or a predisposition for cancer. To investigate
the human DNA mechanisms of repair, we are studying an organism
highly genetically homologous to humans, in this case Alvinella
pompejana or Pompeii worm. The effectiveness behind using the Pompeii
worm as a model for studying the process of DNA repair is due to
the fact that most of its protein activity occurs at temperatures
as high as 80C. The Pompeii worm inhabits geysers found along
underwater volcanic mountain ranges known as hydrothermal vents.
These underwater formations release jets of water reaching temperatures
as high as 300C. Not only does it serve as a great organism for
comparative studies due to its genetic similarity to the human
genome but also because of its extreme heat tolerance. This would
imply that its proteins will be fairly stable at room temperature
which will allow for extensive in vitro study. More specifically
to investigate DNA repair genes involved in NER, through the cloning
of these genes from Alvinella pompejana as well as constructing
plasmid vectors for recombinant protein expression, protein purification,
protein to protein interaction studies, transfection of cultured
human cells with expression vectors followed by assays for reporter
gene expression, and analyzing particular proteins as a function
of the cell cycle in mammalian cells.
Compact Nanosecond High Current Pulser Design. MICHAEL
MALLO (University of Oklahoma, Norman, OK, 73019) SOREN PRESTEMON (Lawrence Berkeley
National Laboratory, Berkley, CA, 94720)
A pulser is an
electronic circuit which generates a high voltage or current pulse
with a very short pulse-width. Pulsers can be implemented using
various topologies, such as Marx Generators, capacitor banks, coaxial
transmission lines, helical lines, striplines, and Blumleins. The
goal of this project was to review basic pulser theory and to design,
test, and compare several pulsers using various topologies. The
final design should deliver a repeatable pulse greater than 1 kA
with 10 ns or less pulse-width to a 1 Ohm inductive load (high
field microcoil) and be small enough to allow for insertion into
an ultra high vacuum accelerator environment. The pulser topologies
tested were capacitor bank, coaxial transmission line, stripline,
and parallel plate Blumlein. The capacitor bank produced an output
voltage of 289 V with a ringing frequency of 17.9 MHz, corresponding
to a positive voltage pulse-width of 28 ns. The load impedance
of this circuit is unknown. The coaxial transmission line was expected
to produce an output voltage pulse of 500 V with a pulse-width
of 13.2 ns; the actual output was 500 V, but with a pulse-width
of 11.8 ns. The stripline was expected to produce a 1 kV 4 ns voltage
pulse through a 1 O inductive load. The parallel plate Blumlein
was expected to produce a 1 kV 1.2 ns voltage pulse through a 1
O inductive load. However, the stripline and Blumlein both produced
far less voltage than anticipated and voltage pulse-widths of just
over 10 ns. Three factors may have lead to this inconsistency in
predicted versus measured pulse-widths. First, the diagnostic tool
used to measure the stripline and Blumlein voltage pulses was a
Tektronix P5102 1 kVRMS 100
MHz 10x high voltage probe. The 100 MHz bandwidth prevents the
probe from accurately measuring pulse-widths shorter than 10 ns.
Second, the short lengths of these lines may have lead to a greater
prominence of end effects, or variations in the electric and magnetic
fields at the ends of the transmission lines, in the output pulses.
Third, the low 1 O load impedances combined with the stray inductances
may have caused longer than expected pulse rise times. The latter
two factors warrant further investigation to better understand
what electrical and geometric properties lead to end effects and
long rise times, and to what extent they affect the output pulse.
Comparison of Intrabeam Scattering High Energy Approximations, and Equilibrium. ROBERT OWENS (North Carolina A&T State University, Greensboro, NC, 27411) MIGUEL FURAN (Lawrence Berkeley
National Laboratory, Berkley, CA, 94720)
The International
Linear Collider (ILC) is a particle accelerator being designed
with the hopes of exploring higher energy particles in the universe
that have never previously been accessible. Two of the major components
of the ILC are the electron and positron damping rings, which serve
the purpose of shrinking the emittances of the beams. There are
several competing processes that affect the beam emittances. Synchrotron
radiation damping serves to decrease the emittances. A major contributor
to emittance growth is a phenomenon called Intrabeam Scattering
(IBS), wherein particles within a single bunch Coulomb scatter
off one another, thereby causing the beam emittance to increase.
The IBS emittance growth rates are calculated using computer codes,
and often it is too time consuming to use the full theory of IBS.
In order to calculate IBS growth rates in the most efficient manner,
several high-energy approximations to the full theory have been
developed for the energy regime of the ILC. It is important to
find the most accurate approximation. We analyzed three approximations
of IBS using the software package, Mathematica; Bane’s approximation,
a new Diagonal Matrices approximation, and a recent CIMP one-log
approximation, while attempting to develop a better two-log approximation
to the CIMP formulas. We also analyzed the equilibrium emittances
of the beams at different charges to determine if the transverse
emittances, bunch length, and energy spread would meet the necessary
requirements for the ILC. After comparing the various approximations,
the Diagonal Matrices approximation proved to be the closest approximation
to the full theory of IBS.
Construction of the La-Bi-O Phase Equilibria: The Search for Inorganic Scintillators. STEVEN VILAYVONG (North Carolina A&T State University, Greensboro, NC, 27411) YETTA PORTER-CHAPMAN (Lawrence Berkeley
National Laboratory, Berkley, CA, 94720)
Scintillators
have been around forever, however the demand for scintillators
has risen exponentially since World War II. This need for viable
scintillators to be used in the detection of ionizing radiation
has spurred research around the world. The New Detector Group of
the Department of Functional Imaging in the Life Sciences Division
of Lawrence Berkeley National Laboratory conducts systematic searches
of various compounds to find the most effective scintillator. Much
of their work focuses on compounds that contain Bismuth (III) and
Lanthanum (III) ions. Bismuth (III) ions have the capability to
be luminescent sometimes providing intrinsic scintillation as seen
in the commonly used scintillator, Bi4Ge3O12, (BGO). Phases containing lanthanum (III) ions are also investigated
to utilize their sites for cerium (III) (another luminescent ion)
doping. In this work, various molar ratios of La2O3 and
Bi2O3 were
reacted by solid state chemistry techniques to find phases that
may exhibit scintillation. To be classified as a good scintillator,
one must characterize these phases by x-ray diffraction (XRD),
fluorescence spectroscopy, and pulsed x-ray measurements. Four
La-Bi-O phases, La0.176Bi0.824O1.5, La0.12Bi1.88O3, La4Bi2O9, and an unknown phase were found however, none are good scintillators.
Creating Code for Automed Demand Response. ARRAN
BLATTEL (Stanford University, Stanford, CA, 94305) MARY ANN PIETTE (Lawrence Berkeley
National Laboratory, Berkley, CA, 94720)
Energy efficiency,
conservation, and peak load management are important approaches
to protecting the power grid, saving consumers money, and reducing
impact on the environment. Demand Response (DR) is an attempt to
curtail energy demand during the handful of days each year when
the grid is strained. The local electric company, Pacific Gas & Electric
(PG&E), created a voluntary program called Critical Peak Pricing
(CPP), in which participants are asked to curb energy use for 12
independent summer days that PG&E deems are most likely to
strain the grid. Participants receive lower electric rates on non-CPP
days, but much higher rates during peak hours on CPP days, creating
an incentive to reduce demand. Automated Demand Response (Auto-DR)
is a novel approach focused on fully automating buildings participating
in the CPP program, so during a CPP event their buildings will
reduce its energy demands without any human interaction. The system
works by using a computer program to continuously monitor CPP status
posted on PG&E’s server. When the program detects a CPP event
in progress, it triggers pre-programmed energy saving strategies
to take affect in the building such as dimming lights and reducing
AC use. For buildings that are currently automated, post-event
surveys are conducted to measure occupants’ response to the changed
environment from load reduction. This research also gives feedback
to participants as soon as possible so they can see the correlation
between their buildings’ energy saving actions and their electrical
shed. The main focus of this research is on studying the electrical
demand of participating buildings evaluating how much they reduced
their energy consumption. Over the past three years, this research
has come to show that Auto-DR is a viable form of dynamic energy
conservation, by consistently providing load sheds during CPP days.
Due to the inherent lack of manual labor required to operate in
this program and no reliance upon present personnel, Auto-DR may
prove to be more efficient and cost-effective than DR for certain
buildings.
CRISPR Recognition Tool (CRT): A Tool for Automatic Recognition of CRISPR Elements. CHARLES BLAND (Jackson State University, Jackson, MS, 0)
CHARLES BLAND (Lawrence Berkeley National Laboratory, Berkley, CA, 94720)
Repetitive sequences
make up a significant portion of the genomes of both prokaryotes
and eukaryotes. The human genome, for example, is known to be composed
of as much as 50% repeating patterns. These repeats come in various
forms/sizes and may be found dispersed throughout a genome, clustered
near each other or occurring contiguously. The identification of
repeats has proven to be of great consequence as they have been
connected to a number of human diseases, including fragile-X mental
retardation, Huntington’s disease, myotonic dystrophy and muscular
atrophy. Repetitive sequences also have various functional roles
such as gene regulation and immune system development. Furthermore,
they are a useful tool to scientists for DNA fingerprinting and
genome alignment. This research focuses on a recently recognized
family of repeats that has attracted a lot of interest recently.
Clustered Regular Interspaced Repeat (CRISPR) are composed of short
direct repeats ranging in size from 21 – 51 base pairs. CRISPR
are unique in that their repeats are interspaced by non-repeating
sequences of similar size and are found only in the genome on prokaryotes.
Because of the importance of repetitive sequences, it is essential
to develop fast and accurate methods for their detection. Several
tools are available for identifying various forms of repeats, however,
because the focus on CRISPR elements is only recent, no published
tools are yet available for their automatic discovery. Their detection
currently uses a generic repeat searching tools (Patscan) and requires
considerable manual post-processing. In this study, we present
a tool for reliable, fast, and automatic detection of CRISPR elements.
This software program, CRISPR Recognition Tool (CRT), uses a fast
linear search method for their detection. Accuracy and speed of
CRT is determined by analyzing its performance on finished microbial
genomes available in the IMG version 1.5 database. Additionally,
CRT is compared to Patscan and a recently discovered and unpublished
CRISPR detection program, PilerCR, an offshoot of the Piler program.
We found CRT to be superior to both Patscan and PilerCR in terms
of both accuracy and speed.
Data Encryption for Windows PC's. BRICE
LUCERO (Big Bend community college, Moses Lake, WA, 98837) CHARLIE
VERBOOM (Lawrence Berkeley National Laboratory, Berkley, CA, 94720)
In today’s society
the use of mobile technology is becoming increasingly popular.
The demand for the ability to secure sensitive data in a safe and
easy manner on Windows operating systems is growing with the use
of mobile technology. This project involved an analysis of present
and future methods for data encryption for Windows operating systems:
XP and the soon to be released Vista operating system. The project
scope included Encryption File System (EFS) in Vista and XP along
with Bitlocker, a new feature that will be included in Vista. In
addition two third party programs, Safe Disk and True Crypt, were
reviewed. Tests were run in order to measure the time each method
took to encrypt as well as the impact they had on data transfer
performance. Ease of use, data recovery methods and known vulnerabilities
were also taken into consideration during the review. It was determined
that Windows EFS and Bitlocker were effective, easy to use methods
for data encryption and have reliable recovery methods when managed
though a domain. Safe Disk is protected by one centralized password
and has an interface that was easy to learn but offered no recovery
method. It is not a recommended method. True Crypt had limited
options available for data recovery and a choice of password or
key files for authentication. The interface was slightly more complicated
then Safe Disk and the native Windows encryption methods. True
Crypt is still a recommended method for data encryption.
Design, Fabrication and Measurement of Nb/Si Multilayers and Niobium Transmission
Filters. SUNEIDY LEMOS FIGUEREO (University
of Puerto Rico, Rio Piedras, Rio Piedras,
PR, 931) DAVID ATTWOOD & ERIK GULLIKSON (Lawrence Berkeley
National Laboratory, Berkley, CA, 94720)
The extreme ultraviolet
(EUV) region of the electromagnetic spectrum is being used in multilayer
optical systems to design technology projected for use in the fabrication
of nano-electronics. Multilayer optical systems with high reflectivity
have been produced in the soft x-ray and EUV regions of the spectrum.
Due to the limited understanding of the Nb/Si optical systems,
our research group fabricated and measured Nb/Si multilayers and
Nb transmission filters for the soft x-ray and EUV regions. Multilayer
optical systems are used in applications ranging from EUV lithography
to synchrotron radiation. The films were deposited using dc magnetron
sputtering in the Center for X-Ray Optics at the Lawrence Berkeley
National Laboratory. Reflectivity and transmission measurements
were performed at the Advanced Light Source beamline 6.3.2. The
Nb/Si multilayer mirrors fabricated have a reflectivity of approximately
65% in the extreme ultraviolet region, which makes these systems
practical for applications where a high reflectivity is required,
such as Astronomy and instrumentation development. Transmission
measurements of up to 90% were observed in the soft x-ray and EUV
regions as well. Future work in the research group includes the
design and fabrication of an Nb/Si multilayer with a B4C interface.
The Nb/B4C/Si optical systems are expected to have a higher reflectivity
than Nb/Si systems.
Detection of Ionizing Radiation Based on Metastable States of Polymer Dispersed
Liquid Crystals. TIMOTHY PHUNG (University
of California, Berkeley, Berkeley, CA, 94720)
CARL HABER (Lawrence Berkeley
National Laboratory, Berkley, CA, 94720)
Polymer dispersed
liquid crystals (PDLCs) may be a suitable medium for future tracking
detectors used in particle physics. Such a detector will work in
analogy with the bubble chamber by using the metastable states
in LC materials. A PDLC cell is fabricated and the optical transmission
of the cell is measured as a function of the voltage applied across
the cell and the temperature. The optical transmission of the PDLC
is found to be temperature dependent below the nematic-isotropic
phase transition temperature when a field is applied across the
cell as is reported in the literature. When no field is applied,
the PDLC cell is strongly temperature dependent near the nematic-isotropic
phase transition temperature, which also agrees with previous results.
Future research in this area will focus on finding the metastable
phenomena that exist near phase transitions of LC materials and
on the use of electric fields to shift the transition temperature.
Determination of a Role for Cellular XPG in Repair of Oxidative Damage to DNA. EMILY FOX (City College of San Francisco, San Francisco, CA, 94112)
HELEN BUDWORTH (Lawrence Berkeley
National Laboratory, Berkley, CA, 94720)
Mutation of XPG
can cause the debilitating diseases Xeroderma Pigmentosum (XP)
and Cockayne’s Syndrome (CS), which result from a deficiency in
DNA repair. XPG cuts 3’ to DNA lesions during nucleotide excision
repair (NER), as well performing the non-catalytic roles of recognizing
stalled RNA polymerase II and binding transcription-sized bubbles
in transcription coupled repair. Through in vitro tests
with purified proteins, XPG has been found to stimulate hNth1,
which removes oxidized pyrimidines in the base excision repair
(BER) pathway. In this study, whole cell extracts from XPG-deficient
cells obtained from patients with XP-G/CS were found to be defective
in incision of 5,6-dihydrouracil (DHU). This defect was corrected
by the addition of purified XPG, suggesting that the mutated XPG
in XP-G/CS cells is unable to stimulate hNth1. In addition, cells
from XP-G/CS patients were found to be slightly sensitive to X-rays
and hydrogen peroxide, as determined by colony formation survival
assays. shRNA against XPG was used to knockdown XPG in normal cells
in order to provide another model for XPG deficiency in which the
only variation from control cells is reduced levels of XPG.
Determining the Effect of Aerosol Composition on the Accuracy of Aethalometer
Real-Time Measurements of Black Carbon. SRYAN
RANGANATH (University of California, Berkeley, Berkeley, CA, 94709)
THOMAS W. KIRCHSTETTER (Lawrence Berkeley
National Laboratory, Berkley, CA, 94720)
Black carbon
(BC), a main component of soot, is studied for its associated climatic
and health effects. Filter-based light-transmission instruments
are commonly used for measuring properties of black carbon. The
aethalometer performs real-time measurements of black carbon concentration.
Previous studies indicate that measurements produced by light transmission
instruments, and the aethalometer specifically, are affected by
the enhancement in particle light absorption due to the light scattering
within the filters used to collect the particles. While the extent
of this enhancement varies with particle loading and particle composition,
the aethalometer algorithm does not consider these effects. This
result could jeopardize the quality of measurements of BC concentration
made with the aethalometer. This behavior was studied in the laboratory
using controlled generation of BC and light scattering aerosols.
An inverted diffusion flame produced BC aerosols with steady physical
characteristics. A nebulizer produced salt particles which were
mixed with BC from the flame. These particles were diluted with
filtered air prior to sampling. The aethalometer sampled pure BC
aerosols and BC + NaCl in individual experiments. In both cases,
the aethalometer reported a decreasing concentration despite sampling
a constant BC concentration. However, different decreasing trends
in concentration were observed, depending on the composition of
the aerosols sampled. This difference in instrument response means
that different empirical corrections are required, which is not
a practical solution to the problem. Continued investigation with
aerosols of different composition is the next expected step. These
results may be first steps in showing an empirical correction for
the aethalometer is not practical.
Development of a beam profile diagnostics device for the VENUS ECR ion source
beam line. CARY PINT (University
of Northern Iowa, Cedar
Falls, IA, 50614) DANIELA LEITNER (Lawrence Berkeley
National Laboratory, Berkley, CA, 94720)
This work describes
the design and development of the instrumentation for a beam profile
diagnostics unit for the low energy beam transport line of the
superconducting Electron Cyclotron Resonance (ECR) ion source VENUS
(Versatile ECR ion source for Nuclear Science). VENUS is currently
being commissioned at LBNL and serves as the prototype ECR injector
source for next generation heavy ion accelerators. In order to
enhance simulations of beam transport from extraction in VENUS,
a measurement device (called a harp) consisting of a grid of thin
conducting wires is placed into the beam line, directly downstream
from extraction, to measure the beam profile. Utilizing the diagnostics
unit developed and described in this work, the first measurements
of the beam profile for a simple helium beam are presented. By
changing the Glaser current to focus the ion beam onto the harp,
the helium beam profiles illustrate that the extracted beam has
the same symmetry as the plasma surface from which they are extracted,
and not the uniform circular symmetry that is assumed in most simulation
models. These results give quantitative insight into the enhancement
of initial conditions needed for using simulations to give a physically
accurate description of beam transport from extraction of an ECR
source.
Development of a Multi-Pollutant Personal Sampler (MPPS). MARIA
MINJARES (Our Lady of the Lake University, San
Antonio, TX, 78207) LARA GUNDEL (Lawrence Berkeley
National Laboratory, Berkley, CA, 94720)
The effects of
indoor and outdoor air pollutants on human health have long been
a concern to health care workers, environmental scientists, and
citizens alike. Previous work has consisted of developing methods
for separating and trapping particulate matter (PM) and gaseous
pollutants. Currently, the multi-pollutant personal sampler (MPPS)
consists of denuder with polyurethane foam coated with a ground
sorbent, XAD-4, followed by a filter to collect PM < 2.5 µm
diameters (PM2.5). Indoor and outdoor air sampling was conducted
at Lawrence Berkeley National Laboratory to determine how much
PM2.5 the polyurethane foam would retain. The results obtained
from sampling indoor ambient air proves our hypothesis that the
PM2.5 will pass through the 80 pores per linear inch (ppi) XAD-4
coated PUF. However, the 80 ppi XAD-coated PUF retained 30% of
PM2.5 in its structure during outdoor air sampling. Further experimentation
is needed to improve the MPPS geometry so that > 95% of PM2.5
passes through the XAD-coated PUF to the filter.
Development of Charged-Coupled Devices for Precision Cosmology and the Supernova
Acceleration Probe Satellite. JESSICA
WILLIAMSON (University of Alabama
in Huntsville, Huntsville, AL, 35899)
DR. NATALIE ROE (Lawrence Berkeley
National Laboratory, Berkley, CA, 94720)
Dark energy,
which is believed to be a cosmic energy density that is gravitationally
repulsive and does not appear to cluster in galaxies, has been
invoked to account for the recent measurement that the rate of
the universe’s expansion is accelerating. To better understand
these phenomena, scientists utilize type Ia supernovae as calibrated
candles. Lawrence Berkeley National Laboratory (LBNL) is developing
the Supernova Acceleration Probe (SNAP), a space-based telescope
that will be used to identify and measure supernovae. The SNAP
focal plane will consist of an innovative camera that integrates
two cutting-edge imaging sensor systems, one of which is the LBNL
high purity charged coupled device (CCD) for the visible light
range. We report on the development of a novel technique for extending
the spatial and photometric fidelity performance of the LBNL CCDs.
Presented are our results obtained from measurements using a 10.5 µm
pixel pitch, 1.4k×1.4k format, p channel CCD fabricated on high-resistivity
silicon at LBNL. The fully depleted device is 300 µm thick and
backside illuminated. Measurements of the device’s transverse diffusion
of charge carriers, pixel to pixel uniformity and intrapixel uniformity
will be reported. will be reported. Also presented are new, preliminary
results from the first implementation of CCD Phase Dithering, a
novel technique for achieving sub-pixel spatial resolution in undersampled,
pixelated image data as will be obtained by the SNAP satellite.
Development of Sixth Grade Decomposition Curriculum to Meet National Science
Education Standard: Science as Inquiry (Alternative Project).
AMY MORRIS (Vanderbilt University, Nashville, TN 37235)
MARGARET TORN (Lawrence Berkeley National Laboratory, Berkel. AMY MORRIS
(Vanderbilt University, Nashville, TN, 37235) MARGARET TORN (Lawrence Berkeley
National Laboratory, Berkley, CA, 94720)
A curriculum
on decomposition was developed to meet the National Science Education
Standard: Science as Inquiry by helping students acquire abilities
necessary to do scientific inquiry and understandings about scientific
inquiry. Additionally, the curriculum was developed to collect
data on changing decomposition rates across the nation for scientists
studying climate change. To meet the Science as Inquiry Standard,
the students will study the carbon cycle and feedback effects in
relation to climate change to identify questions that can be answered
through a scientific investigation of decomposition; conduct a
scientific investigation to determine the decomposition rates of
local leaf litter and a common substrate; use balances, ovens,
probes, and computers to gather, analyze, and interpret data; use
mathematics to make data tables, graphs, and equations to describe
their data; use evidence to develop explanations and predictions;
and present a final project to the class. To provide data on decomposition
rates for scientists studying climate change, sixth grade classrooms
across the nation to will follow a standard experimental protocol.
The protocol will be repeated annually to provide data on how decomposition
rates are changing. This summer, the experimental protocol was
developed, as well as a timeline for executing the curriculum throughout
the school year, sample worksheets to supplement the protocol,
and a method for assessing students’ abilities to do scientific
inquiry and understandings about scientific inquiry. Further development
of activities to teach content and experimental skills to students
is needed. Students will benefit from a year-long project that
emphasizes the Science as Inquiry Standard and will be able to
help their world by collecting data for professional scientists
to use to study climate change.
Electrochemical Remediation of Arsenic Contaminated Groundwater. SCOTT MCLAUGHLIN (University
of California, Berkeley, Berkeley, CA, 94720)
ASHOK GADGIL (Lawrence Berkeley
National Laboratory, Berkley, CA, 94720)
Arsenic in drinking
water impacts 100 million people worldwide, 50 million of whom
are in danger of severe poisoning. The most dire situation is in
Bangladesh, where 45 million cases of arsenic related poisoning
makes it the largest case of mass poisoning in human history. Available
methods of treating arsenic are too expensive, not effective enough,
and often difficult to implement, making them inadequate for a
poor, largely undeveloped country such as Bangladesh. Electrochemistry
promises an innovative, effective, and inexpensive method for arsenic
remediation of drinking water. The method is an improvement upon
a known method of using Fe3+ to remove arsenic. The Fe3+ combines
with As(V), forming an insoluble complex which then can be easily
filtered out. The innovative step of electrochemistry allows for
control over the amount of Fe3+ produced as well as electrochemical
oxidation of the As(III) into reactive As(V) anion [H2AsO4]-, making
the method far more effective. Tests on a simple laboratory setup
show a drastic improvement in arsenic removal efficiency compared
to arsenic removal based on simple rusting of metallic iron. Application
of 70 mA current over 10 minutes in our electrochemical cell reduced
the arsenic concentration in 850 mL synthetic ground-water from
1000 ppb to less than 5 ppb, even without system optimization.
This is compared to a similar setup with a rusted iron coil without
application of electrochemistry which only removed down to 250
ppb in an entire hour. We completed a major goal for this summer
in understanding the effects of experimental conditions on the
system so that reproducible and consistent results can be obtained.
Currently, tests are being performed at various current densities
and durations to find the optimal electrochemical parameters for
efficient oxidation of Fe into Fe3+ and effective removal of arsenic.
Once the process is well understood, the method will be able to
be very efficiently applied to a water filter applicable to areas
with arsenic in the groundwater.
Enhancing the Target Chamber for the Second Phase of the Neutralized Drift
Compression Experiment. GUILLERMO GARCIA (University
of Southern California, Los Angeles, CA, 90089)
MATTHAEUS LEITNER (Lawrence Berkeley
National Laboratory, Berkley, CA, 94720)
The objective
of a controlled fusion power plant for worldwide energy production
has driven the Neutralized Drift Compression Experiment (NDCX)
to investigate characteristics of ion-beam manipulation. This report
focuses on enhancing the diagnostic target chamber for the second
phase of the NDCX project. A target capsule, loading dock, robotic
arm and target housing were developed to prepare the diagnostic
target chamber for integrated compression and focusing experiments
with energy transfer of 1 eV on target with a 500 MW, 1 ns ion
beam. Each component was developed to incorporate the design constraints
established by the diagnostic target chamber. A LabVIEW program
was created to monitor and control movement of the robotic arm.
The diagnostic target chamber was assembled and calibration of
the robotic arm showed that the system had successful interaction
between the LabVIEW program and the newly developed components.
Environmental Education Unit
Plan. AMY WEST (Lesley University, Cambridge, MA,
2138) MARY CONNELLY (Lawrence Berkeley
National Laboratory, Berkley, CA, 94720)
Research has
shown that incorporating environmental education into a schools
curriculum greatly affects student’s attitudes and motivation towards
education. Further research into different methodologies will help
conclude which techniques are most beneficial for students in the
elementary school classroom when teaching about the environment.
Studying several different types of environmental education camps
at the Lawrence Hall of Science and the UC Botanical Gardens, will
provide a strong background as to which methodologies work best
in an elementary school setting. As a result of observing and participating
in two environmental camps at Lawrence Hall of Science, one camp
at the UC Botanical gardens and one camp in the Sierra mountains,
the research has concluded that hands on, inquiry based learning
is the best methodology to use when teaching environmental science.
In conclusion, hands on, inquiry based environmental education
in elementary school curriculum would be the best, most beneficial
way to teach students about environmental science.
Evaluating Changes in Black Carbon Concentrations from California Diesel Emissions. JEFFERY AGUIAR (University of the Pacific, Stockton, CA, 95211) THOMAS KIRCHSTETTER (Lawrence Berkeley
National Laboratory, Berkley, CA, 94720)
In this paper
we show how changes in diesel fuel properties influenced black
carbon (BC) concentrations and emission factors during the past
37 years. In our analyses we use data from the San Francisco Bay
Area, where diesel traffic can be considered the primary source
of BC aerosol. We estimate BC concentrations from archived Coefficient
of Haze (COH) data, collected routinely since 1967 at a number
of Bay Area locations. COH values are a measure of the attenuation
of light by the collected filter deposit and are proportional to
BC concentrations measured by commonly used optical methods. Our
analyses of monthly and annual COH-derived BC concentrations show
that the Bay Area BC mass concentration is an order of magnitude
greater in winter than in summer. Our estimated diesel BC emission
factors changed from about 10 g kg-1 in the late 1960s to less than 1 g kg-1 in 2000. The seasonality is caused by unchanging monthly diesel
BC emissions modulated by synchronous area-wide changes in inversion
heights. Despite the continuous increase in diesel fuel consumption,
annual area-wide BC concentrations decreased from 3.5 µg m-3 in 1967 to about 0.9 µg m-3 in 2000. We attribute the BC concentration decrease to the changes
in diesel technology and fuel composition—particularly sulfur content
that occurred in the period. BC emission factors are possibly more
influenced by fuel property than engine technology. The intention
for the diesel sulfur reduction was to reduce the emissions of
sulfur oxides, which lower the effectiveness of exhaust particle
control devices. The observed BC reduction is, therefore, an unintended
benefit of the fuel sulfur reduction and steady improvements in
diesel technology.
Gene Cloning and Expression in the Hyperthermophile Sulfolobus solfataricus. MEGAN HOCH (Del Mar College, Corpus
Christi, TX, 78404)
STEVEN M. YANNONE (Lawrence Berkeley
National Laboratory, Berkley, CA, 94720)
Sulfolobus solfataricus is
a hyperthermophile Archaeon that lives in a very extreme environment,
and for this it is considered an extremophile. This organism
lives in acidic hot springs of Yellowstone National Park. S. solfataricus has
become a model system for studying human DNA repair. Protein
interactions that are needed to study DNA repair are sometimes
transient. Protein interactions that are transient in high temperatures
where Archaea live might be more stable at room temperature.
This would allow a better look at and understanding of the protein
complexes involved. Also, it is accepted that Archaea are more
closely related to humans than bacteria, and the DNA replication
and translation of the two is very similar. A group of genes
was selected for cloning, and primers were designed for each
gene. The genes were amplified using the polymerase chain reaction
(PCR) method. The PCR products for the gene of interest, were
cloned into a directional topoisomerase I (TOPO®)
cloning vector. These vectors were transformed into E.
coli cells from Invitrogen. The cells were then plated on Luria-Bertani
(LB) agar plates using sterile techniques. Clones were picked
from the plates and a culture was grown overnight. The plasmid
DNA was separated from the cells using alkaline lysis. Restriction
enzyme digests were set up to confirm that the correct gene was
inserted into the vector. The digest was visualized on a 1% agarose
gel. This study successfully cloned sixteen out of the original
twenty-nine genes selected. Some of the clones that grew on the
LB plates did not contain any gene at all; it was simply the
vector alone. After several restriction enzyme digests, there
were about eight genes whose digests were not clear enough to
confirm the prescense of the correct insert. These constructs
will need to be further digested with different restriction enzymes
to confirm the gene. Currently methods are being developed for
expressing these genes in E.
coli and S.
solfataricus.
In future studies, proteins expressed from S.
solfataricus will be studied and characterized to understand the protein-to-protein
interactions that are occurring.
High-Throughput X-ray Protein Crystallography. BINH NGUYEN
(Contra Costa College, San
Pablo, CA, 94806) DR. MINMIN YU (Lawrence Berkeley
National Laboratory, Berkley, CA, 94720)
Proteins play
an integral function in cells, hence understanding them is critical,
especially in medical research. Structural analysis of proteins
is particularly important to the field of Structural Genomics,
which aims to study protein molecules in nature to provide a fundamental
understanding in biology. Knowing the three dimensional structures
of proteins will enable the grouping of fold patterns and family
of proteins that can lead to clues of how the proteins work. High-throughput
protein crystallography allows structural determination of the
protein via x-ray diffraction. Proteins are crystallized and the
resulting crystals are analyzed with X-ray to create diffraction
patterns that can be determined into three dimensional structures.
The first important step in this process is we subject our proteins
to series of crystallization matrices to find the right crystallization
condition. We utilized various crystal screens from Hampton Research
and Emerald Biosystems. The initial crystal hits-crystal formation-leads
to further optimization of the crystallization solution so as to
obtain crystals that have reasonable diffraction quality. Our crystals
are analyzed mostly with the synchrotron at the Advance Light Source
(ALS) within the Lawrence Berkeley National Lab (LBNL). Through
protein 3-D structures, the folding topologies and local conformations
of the proteins can be analyzed. The Li-Wei Hung Lab is currently
analyzing various proteins for the Integrated Center for Structure
and Function Innovation (ISFI) and TB Structural Genomics Consortium
(TBSGC). These proteins are derived from interesting targeted DNA
sequences of various sources, mostly species causing human diseases.
Solved protein structures are deposited on our ISFI/TBSGC database
(www.tbgenomics.org, http://techcenter.mbi.ucla.edu) and the Protein
Data Bank (http://www.pdb.org).
Increasing the Durability and Reliability of Radiation Detectors used in Radiopharmaceutical
Chemistry. SIMARJIT
KAUR (Contra Costa College, San
Pablo, CA, 94806) JAMES P O'NEIL (Lawrence Berkeley
National Laboratory, Berkley, CA, 94720)
Radiation Detectors
are a necessary part of radiopharmaceutical synthesis in order
to determine the quantity of radioactivity throughout the synthesis.
They are used to track not only the progress of the chemical reactions
and the yield at each step but also to ensure the safety of the
personnel involved in this process. Radiation detectors are usually
installed in places where the potential of chemical exposure and
general physical abuse is quite high. To make the radiation detectors
more robust and reliable, a very easy and cost-effective method
of “epoxy potting” was devised. The radiation detector is placed
in a mold of appropriate dimensions and filled with epoxy (3M Scotch-Weld
DP270, black). After the epoxy cures, the radiation detector is
protected within a solid light resistant block. This particular
epoxy was chosen for this task because it is chemically inert and
provides both electrical and mechanical insulation of the detector
components from the harsh surroundings of the hot cell.
Inquiry-Based Learning at Its Best. SARAH
BAUM (Lesley University, Cambridge, MA, 2138) MARY CONNOLLY (Lawrence Berkeley
National Laboratory, Berkley, CA, 94720)
The Lawrence
Hall of Science (LHS) is one of the leading forces in the inquiry-driven,
direct experience approach to science and mathematics instruction
for grades K-12. LHS has developed several inquiry-based curriculum
projects that are used throughout the United States. This public
science center also provides educational exhibits and classes,
year-round outreach programs, as well as diverse summer camp programs
for children of the region. The investigative approach stems from
human beings’ natural curiosity to explore what is seen on a daily
basis. This strategy when applied to a classroom helps students
connect concrete ideas to their own experiences through open-ended
investigations and discussions. My goal throughout the summer was
to observe how instructors use guided inquiry techniques with a
variety of age groups to delve into life, physical, and earth science.
My research reflects an exploratory sample of age groups and content
areas. Working alongside LHS instructors has allowed me to study
inquiry-based education by observing, comparing, analyzing, and
applying themes and elements central to the process.
Investigating the Use of a Diffusion Flame to Produce Black Carbon Standards
for Thermal-Optical Analysis of Carbonaceous Aerosols. DIANA
ORTIZ MONTALVO (University of Puerto
Rico, San Juan, PR, 931) THOMAS W. KIRCHSTETTER
(Lawrence Berkeley National
Laboratory, Berkley, CA, 94720)
Combustion generated
particles impact climate and public health due to their ability
to scatter and absorb solar radiation and alter cloud properties,
and because they are small enough to be inhaled and deposit in
the lungs where they may cause respiratory and other health problems.
Specific concern is focused on particles that originate from the
combustion of diesel fuel. Diesels particles are composed mainly
of carbonaceous material, especially in locations where diesel
fuel sulfur is low. Diesel particles are black due to the strongly
light absorbing nature of the refractory carbon components, appropriately
called black carbon (BC). This research project focuses on the
uncertainty in the measurement of BC mass concentration, which
is typically determined by analysis of particles collected on a
filter using a thermal-optical analysis (TOA) method. Many studies
have been conducted to examine the accuracy of the commonly used
variations of the TOA method, which differ in their sample heating
protocol, carrier gas, and optical measurement. These studies show
that BC measurements are inaccurate due to the presence of organic
carbon (OC) in the aerosols. OC may co-evolve with BC or char to
form BC during analysis, both of which make it difficult to distinguish
between the OC and BC in the sample. The goal of this study is
to develop the capability of producing standard samples of known
amounts of BC, either alone or mixed with other aerosol constituents,
and then evaluate which TOA methods accurately determine the BC
amounts. An inverted diffusion flame of methane and air was used
to produce particle samples containing only BC as well as samples
of BC mixed with humic acid (HA). Our study found that HA particles
are light absorbing and catalyze the combustion of BC during TOA.
It is expected that both of these attributes will challenge the
ability of TOA methods in distinguishing between OC and BC, such
as the simple two step TOA method which relies solely on temperature
to distinguish between OC and BC. The samples prepared in this
study were analyzed using two TOA methods to compare the estimates
of BC concentration. Future work will focus on the preparation
of a variety of BC standards and comparing measurements of the
prepared samples using a range of TOA methods.
Investigation of a Rhodium Catalyst in the Reduction of Carbon Dioxide and
Pyruvate for Future Use in a Direct Electrochemical Methanol
Production Cell. LINDSAY DIERCKS (University of Iowa, Iowa
City, IA, 52242) JOHN KERR (Lawrence Berkeley
National Laboratory, Berkley, CA, 94720)
In a world with
dwindling oil reserves and increasing energy demands, reduction
of carbon dioxide to methanol using solar generated electricity
is a probable and environmentally conscious solution. The part
of the carbon dioxide to methanol process that this research is
specifically involved in is the reduction of carbon dioxide to
formate. The stereo-selectivity of Lactic Dehydrogenase (LDH) was
investigated in the reduction of pyruvate to lactic acid as was
the reduction of carbon dioxide to formate with only a Rhodium
catalyst. Reactions were run in a glass electrochemical cell, and
products of the reactions were analyzed on a Capillary Electrophoresis
(CE). The pyruvate reaction showed the presence of lactic acid,
however it was not certain if pyruvate was also present. The absence
of pyruvate on the CE analysis of the pyruvate reaction could mean
that there was a one hundred percent conversion of pyruvate to
lactic acid, but that result has yet to be reproduced. The carbon
dioxide reaction shows the presence of formate, but not oxalate-
also a product of carbon dioxide reduction. It has yet to be determined
if formate is the sole product of the reduction of carbon dioxide
with a Rhodium catalyst.
Isolation of Independent Spontaneous Thymidine Kinase-Deficient Mutants and
an Estimation of the Mutation Rate at the Thymidine Kinase Locus
in a Human B-Lymphoblast Clone. LAWRENCE CHYALL (University of California,
Berkeley, Berkeley, CA, 94720) AMY KRONENBERG (Lawrence Berkeley
National Laboratory, Berkley, CA, 94720)
Programmed cell
death, or apoptosis, is tightly regulated by signals originating
from both within the cell and its surroundings. The BCL-2 family
of proteins helps modulate the balance between the life and death
of cells. BCL-XL (a BCL-2-like protein) assists in limiting apoptosis by titrating
the concentration of pro-apoptotic proteins through the formation
of a heterodimer. TK6-Bcl-xL gly-159-ala #38 is a TK6 human B-lymphoblast cell line that
was engineered to express BCL-XL gly-159-ala, a mutated form of the BCL-XL protein
that does not have anti-apoptotic activity. A fluctuation experiment
was used to estimate the mutation rate of TK6-Bcl-xL gly-159-ala #38 cells. The mutation rate was found to be closer
to the historical results for TK6-neo #1 cells than cells expressing
the wild-type BCL-XL protein, TK6-Bcl-xL #4. The plating efficiency of TK6-Bcl-xL gly-159-ala
#38 cells was found to be the same as historical results for TK6-neo
#1 cells and TK6-Bcl-xL #4
cells. Thirty-four early-arising and sixty-three late-arising spontaneous
TK1-deficient mutants of the TK6-Bcl-xL gly-159-ala #38 cell line were isolated. DNA from each of these
mutants was extracted for future analysis.
Measurements of Gasoline and Diesel Vehicle Pollutant Emissions in the Caldecott
Tunnel. JOHN MCLAUGHLIN (University
of California, Berkeley, Berkeley, CA, 94720)
THOMAS KIRCHSTETTER (Lawrence Berkeley
National Laboratory, Berkley, CA, 94720)
Motor vehicles
