3D Animation of Pancreatic Molecules. BRITTANY
PETERS (Rochester Institute
of Technology, Rochester, NY, 14623)
DR. PAUL CRAIG (Brookhaven National Laboratory, Upton, NY, 11973)
The pancreas
is the supplier of a variety of digestive enzymes and hormones,
most notably insulin. In the past a virtual animation of the pancreas
has been created, showing a tour of its internal structure. To
continue this animation the goal is to introduce molecular detail
into this virtual model of the pancreas. We are using Maya’s 3D
modeling and animation capabilities to address the challenging
task of providing a greater understanding of the pancreas for students,
teachers and doctors. Pancreatic proteins contain hundreds or thousands
of atoms; the Protein Data Bank (www.rcsb.org) contains many pancreatic
proteins structures with x,y,z coordinates of each of its atoms
to form a molecule that can be visualized in 3D. The challenge
for molecular artists who use Maya is to model these molecules
accurately because their structure is too complex to create. One
easy was to provide these molecules is to download the PDB files
from the Protein Data Bank and visualize them in Maya, but Maya
is unable to recognize them. However, the files can be manipulated
and changed to achieve the objective. The PDB file first needs
to be converted to a simple text document so that the 3D program
can read its written information, then it can be drawn through
a Maya tool called a mel script. This script is a code that allows
Maya to read the PDB file, import it, and model it. From this point
the molecular structure can be rendered and animated. This procedure
will help to show an up close view of a pancreatic molecule in
action. We are developing techniques to display these proteins
in a surface format which highlights the overall shape of each
molecule, as well as a ball-and-stick format, which emphasizes
the individual atoms. One of the advantages of this approach is
the molecular artist can import any protein structure that is available
in the PDB file format, which will enable viewers to better visualize
the physiology of the human pancreas at the molecular level.
3D Stereoscopic Fantastic Voyage of the Heart. NATHANIEL SKINNER (Jamestown Community
College, Jamestown, NY, 14702) LEN SLATEST (Brookhaven National Laboratory, Upton, NY, 11973)
For first year
Anatomy/Physiology students, the visualization of various organs
and body systems can be a bit daunting. This project was designed
to combat that problem. Being the first in a long string of organs
this model of the heart was designed to give students a working
visual knowledge of the heart. The movie starts outside the heart
and shows all of the major parts of the heart in their relative
positions. The movie then takes the viewer inside the heart. The
inside is the part that will be the most helpful for the students,
because the best they will ever see if they are lucky are cadavers
and drawings. By the end of the movie those viewing this movie
will have seen not only the major parts of the movie, but they
will also have had a first hand experience with watching the heart
beat with the proper timing of the valves. This movie was also
put into a stereo version, which will a greatly enhance the viewing
experience. The movie was created in the 3D design and rendering
program, Maya. Each part of the heart was created as a separate
object, which allowed easy manipulation of the parts to get them
into the right proportions to each other. The overall movie is
actually composed of several smaller movies that were combine with
video editing software to give the impression of one voyage through
the heart. As stated above the next step is to use some of the
same techniques to create various other body parts and organs.
The overall long-term goal is to have a flythrough video of every
system in the human body.
3-Dimensional Visualization of Molecular Reactions. ANGELICA CORBY (Alfred State
College, Alfred, NY, 14802) ROBERT BENNET (Brookhaven National Laboratory, Upton, NY, 11973)
To the undergraduate
student certain chemical reactions such as the SN1 and SN2 reactions
can be difficult to visualize. By displaying these reactions through
a 3-dimensional stereoscopic viewer they become much easier for
the student to see. One way to display chemical reactions in 3-D
is to take the chemical markup language (CML) file, created from
the initial z-matrix used by MOPAC to compute the reactions’ Cartesian
coordinates, and convert this file into an extensible 3-Dimensional
(X3D) file which can be viewed through a 3-D stereoscopic viewer.
After researching the format of the CML and X3D files it is possible
to write a Visual BASIC program to rearrange the text of the CML
file to the format of the X3D file. The program called “CML-X3D
Convert” can take a CML file and convert it into an animated X3D
file. This program is intended for educational use. With these
X3D files an instructor can more accurately show the 3-dimensional
structure of a chemical reaction to a student.
A Comparative Study of the Age Class Structures of Quercus alba, Quercus coccinea,
Quercus velutina and Pinus rigida as an Indicator of Forest
Health within the Long Island Pine Barrens Core Area. KATHRYN GUTLEBER (Connecticut College, New London,
CT, 6320) TIM GREEN (Brookhaven National Laboratory, Upton,
NY, 11973)
Investigation
of the age class structure of Quercus species and Pinus rigida
within the Long Island Pine Barrens core area is an important
aspect of monitoring the health of the Pine Barrens. The age
class structures of Quercus alba, Quercus coccinea, Quercus velutina,
and Pinus rigida are primary indicators of successful reproduction
and the possibility of the successional change between community
types. By comparing the numbers of seedlings, saplings and mature
trees, the success of reproduction for these three Quercus species
and Pinus rigida was analyzed. The numbers of seedlings and saplings
were recorded through the use of four two-meter wide belt transects
within 16 by 25 meter plots. These plots were located within
the Pine Barrens subtargets of Pitch Pine, Pine-Oak, Oak-Pine,
Coastal Oak, Scrub Oak and Dwarf Pine forests. This study found
the success of reproduction for all the study tree species within
the six community types to be varied. Q. alba, Q. coccinea and
Q. velutina all displayed a low number of saplings in all community
types surveyed, indicating that current reproduction is not very
successful. In Coastal Oak and Oak-Pine communities, Q. alba
was the most successful in reproduction. The reproduction of
P. rigida was dominant within Pine-Oak, Pitch Pine and Pitch
Pine-Scrub Oak Woodland communities. However, the low average
number of P. rigida saplings found could possibly indicate the
succession from pine-dominated forest to oak dominated forest.
There are several factors that may influence these trends in
reproduction, including exposure to light, levels of litter and
duff, and deer browse. Although the current levels of reproduction
for Quercus species and P. rigida are varied and range across
the different community types, they are still an important indicator
of forest succession within the Long Island Pine Barrens core
area. Forest succession is an important factor in this ten-year
longitudinal study of the Long Island Pine Barrens core area,
as forest succession and species competition are primary indicators
of forest health.
A Comparison of Litter Densities in Six Community
Types of the Long Island Central Pine
Barrens. DANA TIEVSKY (University of Rochester, Rochester, NY, 14627) TIM GREEN (Brookhaven National Laboratory, Upton, NY, 11973)
The vulnerability
of major dams subjected to large transient loads is unknown since
these loads were not considered during the design process of
the dams. Due to the proprietary nature of the data in relation
to dams, exact results cannot be shared. The complexity of these
loads, in addition to the unique geometric and material properties
of a dam, make it extremely difficult to assess a dam’s vulnerability.
To overcome this obstacle, state of the art computational techniques
such as finite element analysis must be utilized to assess the
vulnerability of dams to these large transient loads. Use of
a general finite element analysis program, ANSYS, allows the
modeling of complex structures and loads. In order to construct
these models, information is gathered from various sources such
as structural plans and research papers about related engineering
problems. Basic analyses of simplified models are run to determine
which dams are more vulnerable and require further detailed study.
The results from the detailed studies will reveal possible weaknesses
and allowed corrective measures to be taken to secure the structure
against this type of loading.
A Comparison of the Chemistry of Soil Surrounding Natural and Anthropogenic
Ponds at Brookhaven National Laboratory. SHURRITA S. DAVIS, ROY COOMANS (North Carolina A&T State University, Greensboro, NC 27411), TIMOTHY GREEN (Brookhaven National Laboratory,. SHURRITA DAVIS (North Carolina A & T State University, Greensboro, OR, 27411) TIM GREEN (Brookhaven National Laboratory, Upton, NY, 11973)
Brookhaven
National Laboratory (BNL) is located in the Long Island Pine
Barrens, an area formed through decomposition and reworking of
glacial materials. BNL has many wetland structures including
costal plain ponds, vernal ponds, recharge basins, and streams.
Some of these serve as breeding grounds for tiger salamanders
(Ambystoma tigrinum), a species listed as endangered by the New
York Natural Heritage Program. Anthropogenic habitats need to
possess suitable characteristics with respect to soil and water
chemistry in order to serve as successful breeding habitat for
tiger salamanders. Soil is an important factor in controlling
vegetation and water chemistry. In this study five ponds were
selected for a study of soil chemistry: two natural and three
anthropogenic. Nine soil samples were collected from each pond,
eight around the perimeter and one from the pond bottom. Global
Positioning System (GPS) was used to locate the sample points
and ArcGIS was used to map the ponds and sample points. Soil
samples were tested for pH, nitrate nitrogen, phosphorus, potassium,
aluminum, ferric iron, magnesium, sulfate, calcium, and chloride
using LaMotte Combination Soil and LaMotte Soil Micronutrient
Kits. Soil moisture content was also determined. Soil color,
texture, structure, consistency, and mottling were also observed
and recorded. Five of the nine soil samples from each pond were
digested using EPA method 3050B for Acid Digestion of sediment,
sludge, and soil and then tested for copper, iron, molybdenum,
magnesium, cadmium, aluminum, chromium, manganese, potassium
and lead using an Inductively Coupled Plasma - Atomic Emission
Spectroscope (ICP-AES). The natural ponds were more acidic then
the anthropogenic ponds. The soil temperature is higher around
the anthropogenic ponds (BP7, BP13, MM) than the natural ponds
(BP9, BP6). Nutrient levels were low and consistent across pond
types. Though these differences exist, both types of ponds accomplish
the goal of providing suitable breeding sites for tiger salamanders
(Ambystoma tigrinum). This information will serve as baseline
data for BNL’s natural resource manager and enable BNL to optimize
the management of amphibian and reptile habitats
A Comparison of Water Chemistry between Natural, Modified, and Manmade Ponds
within Brookhaven National Laboratory. PRISCILLA RANDOLPH (North Carolina A&T State University, Greensboro, NC, 27411) TIM GREEN (Brookhaven National Laboratory, Upton, NY, 11973)
Brookhaven
National Laboratory (BNL) is located in the center of the Long
Island Pine Barrens. Within BNL’s 5,265-acre site there are 26
wetlands. Included are coastal plain ponds, vernal ponds, recharge
basins, and streams, making it an ideal ecological site to study
water chemistry. We tested water samples from seven coastal plain
ponds on BNL: four natural (BP1, BP2, BP6, BP9), one man-modified
(BP7), and two manmade (BP13a, Meadow Marsh). Five water samples
were collected from each pond. An eTrex Vista Cx Global Positioning
System (GPS) was used to mark each water sample point. An YSI
659 MDS meter fitted with a multiprobe was utilized to determine
temperature, pH, dissolved oxygen, conductivity, and turbidity
at each sample point. Water samples were analyzed for sulfate,
nitrate, iron, phosphorus, chlorine, calcium, magnesium, copper,
tannin-lignin, chromium, molybdenum, aluminum, and suspended
solids using Hach DREL/2000 and CEL/890 water test kits. Water
samples were also analyzed for eleven different elements using
an ICP-AES. The pH in the anthropogenic ponds was found to be
more basic than that of natural ponds. Phosphorous, tannin-lignin,
and hardness were elevated in the natural ponds when compared
to manmade and modified ponds, but only the difference in tannin-lignin
content proved statistically significant. The natural ponds were
shaded by the canopy of the surrounding forest while the manmade
and modified ponds where located directly in the sun. This had
a affect on water temperature. The results of this research will
give environmental scientists an insight into water chemistry
and interrelationships between abiotic and biotic factors and
will enable BNL to optimize the management of amphibian and reptile
habitats.
A Matlab® Simulation of the Energy Recovery Linac
RF Superconducting Cavity. RANDALL PLATE (Cedarville University, Cedarville, OH, 45314) CARL SCHULTHEISS (Brookhaven National Laboratory, Upton, NY, 11973)
Linear particle
accelerators (linacs) accelerate ions to near the speed of light
in order to conduct experiments on particle collisions. Energy
recovery linacs (ERLs) consist of both a linac radio frequency
(RF) superconducting cavity and an electron ring which can be used
for electron cooling. It is crucial to operate as close to the
resonant frequency of this RF cavity as possible in order to maintain
a proper accelerating field, but factors such as Lorentz forces
and microphonics can detune the cavity. A Matlab simulation of
the cavity provides the ability to analyze these affects and develop
a digital control system to counteract them and retain the desired
electric field gradient. A simulation of the cavities employed
in Tesla, Spallation Neutron Source (SNS), and the Rare Isotope
Accelerator (RIA) was analyzed and modified to be consistent with
the cavity at Brookhaven’s linac by changing the quality factors,
resonant frequencies, and time constants of the various operating
modes. This simulation and control system will be the foundation
for the development of another, real-time, simulator which will
be applied to the physical cavity. This paper presents the development
and implementation of this simulation and discusses the implications
of the results obtained.
A Molten Salt Synthesis of Single Crystalline YBCO
Nanorods. DARYL WONG (University of California, Berkeley, Berkeley, CA, 94720)
STANISLAUS S. WONG (Brookhaven National Laboratory, Upton, NY, 11973)
YBa2Cu3O7 (YBCO) is a high Tc superconductor that has potential applications in both high
field magnets and superconductive circuitry. Although its utility
as a high field magnet has been realized, bulk YBCO loses its high
temperature superconducting ability due to low critical current
densities deriving from the bulk’s polycrystalline nature which
lacks directionality. One potential remedy, aligning monocrystalline
subunits through material texturing techniques, can be achieved
with the production of uniform, monocrystalline one-dimensional
YBCO nanorod structures. The molten salt synthesis method has been
shown to be a procedurally simple technique to create metal oxide
nanorods. Using a molten salt method, attempts to make YBCO have
been conducted with a number of yttrium, barium, and copper containing
precursors which are combined with a salt, usually sodium chloride
and/or potassium chloride, in varying precursor and salt ratios.
These precursors were finely ground with a mortar and pestle and
baked in a furnace to temperatures above the melting point of the
salt. Powder x-ray diffraction (XRD) analysis was conducted to
determine whether the molten salt samples contained the orthorhombic
crystal structure indicative of high temperature superconducting
YBCO, while scanning electron microscopy (SEM) and atomic force
microscopy (AFM) images were taken to determine if a rod morphology
had been formed. XRD analysis of the numerous molten salt products
has shown that the desired orthorhombic YBCO nanorods cannot readily
be formed, while SEM and AFM images show aggregates of nanorods
and nanoparticles which vary in size. Other analytical techniques,
including SQUID (Superconducting Quantum Interference Device) measurements,
will be useful to further ascertain and characterize the properties
of as-prepared YBCO nanorods. Because the mechanism of molten salt
nanorod formation is not fully understood, creation of these desired
nanorods involves a lot of experimentation with variable parameters.
A more comprehensive analysis of precursors, precursor ratios,
and baking temperatures should be performed before concluding the
inefficacy of the use of the molten salt technique in the generation
of nanoscale motifs of these superconducting materials.
A Noninvasive Method to Assess Left and Right Ventricular Fractional Area Change
in Genetically Altered Mice. MEAGAN
GREEN (La Salle University, Philadelphia, PA, 19141) HELENE BENVENISTE (Brookhaven National Laboratory, Upton, NY, 11973)
The techniques
which allow a comprehensive assessment of cardiovascular performance
in small animals are still limited. The development of a noninvasive
cardiac MRI- based method to facilitate the analysis of both right
and left ventricular function in a mouse heart is essential in
a cardiac study. The use of animals with genetic modifications,
which lacks the ability to produce vasointestinal peptide (VIP),
and important cardiovascular regulatory factor. The use of these
animals with genetic modifications allows for a more precise assessment
of cardiovascular failure development. Changes in myocardial VIP
concentration or with alteration of physiological responsiveness
of VIP receptors have been links to the development of severe cardiovascular
disorders, such as myocardial fibrosis, heart failure, cardiomyopathy
and pulmonary hypertension. The goal of this study was to compare
the left and right ventricle to see if they are both equally involved
in the development of cardiomyopathy in VIP-deficient mice. The
cardiac imagine was performed in five anesthetized animals using
several different Flash_movie sequences in a 9.4T MicroMRI system.
Once the images were obtained Amira Imaging software was utilized
to make outlines of the left and right ventricular cavities and
areas for each ventricle were obtained during different phase of
the cardiac cycle. A transactional view through the midpapillary
level was used for analysis. Functional ventricular assessment
was performed by calculating the fractional area change (FRAC)
during systole. Data showed that there was not a significant difference
between the left ventricle (53.87 +/- 13.66%) and the right ventricle
(52.90 +/- 15.01%) FRAC. Both sides developed significant hypertrophy
of the myocardial wall. In summary, the VIP- deficient mouse, the
development of cariomyopathy was shown to similarly affect both
the left and right ventricular function. We were able to develop
a noninvasive method for advanced characterization of cardiac function
in the murine model. This will help to facilitate longitudinal
study of the heart disease process. The long term goal of this
study is to map the development of heart disease.
A Numerical Model of the Critical Charge Density Surface of Ultra High Energy
Cosmic Ray Induced Extensive Air Showers Using the SCILAB Programming
Language. ALLEN SHARPER (Florida A&M University, Tallahassee, FL, 32301)
HELIO TAKAI (Brookhaven National Laboratory, Upton, NY, 11973)
A numerical model
of the critical charge density surface of ultra high-energy cosmic
ray (UHECR) induced extensive air showers (EAS) has been computed.
The critical charge density surface defines the surface for specula
reflection of radio waves with frequency less than the natural
oscillation frequency (plasma frequency) of the EAS charges. Using
a numerical model to understand how radio waves reflect from the
air shower will help improve the design of devices (antennas, arrays)
used to detect the reflected waves. The numerical model will allow
the power and direction of the reflected waves to be calculated
which will provide a map of the spatial distribution of reflected
wave power and polarization incident to the surface of the earth.
The program of the numerical model, written in the SCILAB language,
calculates the density of ionization electrons as a function of
radial distance from the shower axis and location along the axis.
The cosmic ray tracing model is part of the Mixed Apparatus for
Radar investigation of Cosmic-rays of High Ionization (MARIACHI)
project. The MARIACHI project, consist of research that investigates
an unconventional way of detecting UHECR. Based upon a method successfully
used to detect meteors entering the upper atmosphere. Mariachi
seeks to listen to television signals reflected off the ionization
trail of an UHECR.
A Simplified Approach to Stereoscopic Imaging of Tomographic
Reconstructions in Transmission Electron Microscopy. LAURA DEPOULI, MICHAEL LAMB, SALIM RAHIMI, ROMAN ZRAZHEVSKIY(Nassau Community College, Garden City,
NY, 11530) ROBERT BENNETT (Brookhaven National Laboratory,
Upton, NY, 11973)
In biological
applications, transmission electron microscopy (TEM) enables an
investigator to view a specimen at the molecular level, offering
a resolving power of ~0.2nm. The two-dimensional (2-D) micrographs
captured using the TEM are grayscale images in which contrast is
typically achieved using heavy metal stains that limit electron
transmission with respect to specimen density. In order to ascertain
an adequate understanding of the structure and function of biological
systems, it is important to view these structures in three dimensions
(3-D), as they appear in life. Currently, there is a myriad of
protocols that use various software applications for creating tomographic
volumes. Moreover, the lack of a uniform approach often makes the
process difficult to replicate for those with limited resources.
A simple, consistent method for generating tomographic volumes
of TEM micrographs to be viewed stereoscopically was investigated.
Sections ranging from ~60-100nm in thickness were collected on
formvar-coated copper grids. Samples were viewed using a Philips
EM300 TEM with a side-mounted goniometer stage, and images were
captured with an integrated Gatan ES500W CCD camera. Common to
many laboratories working with limited budgets, various challenges
are faced during data acquisition and processing. Physical limitations
of the goniometer have restricted datasets to a 45 degree maximum
rotation in either direction about the horizontal axis. A tilt
image series was digitally captured from -45 to +45 degrees in
1 or 2 degree increments and reconstructed into tomograms and rendered
using Stanford University’s EM3D software. Finally, stereoscopic
visualizations of the rendered three-dimensional volumes were generated
through the creation of movies that were viewed using the software
application StereoMovie Maker.
A Stereoscopic Model of a Theoretical Einstein-Rosen Bridge, i.e. Wormhole,
as part of an Expedition to a Black Hole at the Center of a Supernova
Remnant. TAISIA CARDO (Suffolk County Community College, Selden,
NY, 11794) DAVE STAMPF (Brookhaven National Laboratory, Upton,
NY, 11973)
A representation
of an Einstein-Rosen bridge in three dimensional space has the
potential to provide the scientific community with a new educational
learning tool. Maya™, a computer program designed to create three
dimensional (3-D) renderings, was used to design Non-Uniform Rational
B-Spline (NURBS) objects to construct a scaled version of a wormhole.
Steady research shows that wormholes are created from two connected
singularities, points with infinite densities, from within black
holes. The tunnel is theoretically smaller than an atom and stays
open for merely a fraction of a second. Kip Thorne suggested that
it would be possible to travel through time if one could complete
the course through a wormhole intact. Considering such theories,
a scaled tunnel-like wormhole was constructed. Using the capabilities
of Maya™ all breaks, tears, and/or misalignments throughout the
structure were disencumbered. The resulting wormhole has arched
curves with no visible attached pieces. This 3-D representation
has the potential to aid the inquisitive mind of students and scientists
alike in uncovering the mysteries the universe has to offer.
A Study of Gas Electron Multiplier (GEM) Foils. MATTHEW RUMORE (Worcester Polytechnic
Insitute, Worcester, MA,
1609) CRAIG WOODY (Brookhaven National Laboratory, Upton, NY, 11973)
Advances have
been made in the field of high-energy nuclear physics due to the
increased usage of Gas Electron Multiplier (GEM) foils, which are
known for their versatility and their ability to detect and amplify
charge. For instance, GEM foils will be implemented in the Pioneering
High Energy Nuclear Interaction eXperiment (PHENIX) and Solenoidal
Tracker At RHIC (STAR) experiments at the Relativistic Heavy Ion
Collider (RHIC) for the detection of signals from high-energy particle
interactions. The reliable production of GEM foils depends on a
study of their properties and operating conditions. Two of the
most important properties are the absolute gain and the gain stability
over time. To test the gain, each foil is placed in an Argon/Carbon
Dioxide environment in the ratio of 70:30. An alpha particle emitted
above the foil by an Americium-241 source ionizes the gas and produces
a cluster of electrons. This primary charge is then collected and
amplified by the GEM foil. The amplified signals are read out through
a conductive pad on the bottom of the GEM detector using a digital
oscilloscope. Because the amount of primary charge is known, the
absolute gain will be calculated for each GEM foil as a function
of voltage. The gain stability measurements entail taking successive
gain measurements over time for a constant voltage. The manufacturing
process strongly influences the performance of each GEM foil. As
a result, a number of foils produced under different manufacturing
conditions were studied in terms of their overall gain and gain
stability. This study, which will mostly likely continue until
August 2006, will allow the scientific community to understand
the properties of the GEM foils and improve the ability to manufacture
better foils in the future.
A Study of Seedling Numbers in Relation to Canopy
Cover in Six Long Island Pine Barren Community
Types. EMILY EFSTRATION (University
of Delaware, Newark, DE, 19717) TIM GREEN (Brookhaven National Laboratory, Upton, NY, 11973)
Seedlings and
saplings are important to forest health because they provide insight
as to how the forest will develop and survive in the years to come.
The canopy cover’s density has much to do with how these seedlings
and saplings will develop and survive. Canopy cover, density and
the amount of seedlings were studied in different forest communities
to help predict the future of these forests. Using a Geographic
Information System (GIS) and Global Positioning System (GPS), points
were selected at random and twenty five by sixteen meter plots
were analyzed. By using a densitometer, the canopy cover was determined
in each plot along ten transects at randomly determined intervals.
Seedlings and saplings were counted in four belt transects as well
as noted in the entire plot. The different communities that were
compared include Pine Oak, Oak Pine, Pitch Pine, Coastal Oak areas,
Dwarf Pine and Pitch Pine-Scrub Oak Woodland/Shrubland. In the
Coastal Oak community, where the cover was found to be 96% hardwood
cover and no pine cover, no seedlings or saplings found. On the
other hand, in a Pitch Pine plot, with 72% pine cover and 1.5%
hardwood cover, approximately 86 seedlings and 85 saplings were
found. When this study is redone in ten years to determine the
progress of the forest, the investigators will determine if human
intervention is needed to aid in forest growth. If adolescent trees
were found healthy and growing, this would show the progression
of the Pine Barrens and would also prove that the forest is capable
of recuperating without human aid.
A Study of Variations in Soil and Water Chemistry
of Selected Ponds at Brookhaven National Laboratory. JAMIE S. BRUNGARD, ROY COOMANS, NINA KEAN, & GEORGIA SAWYER (North
Carolina A&T State University, Greensboro, NC, 27411) DR. TIM GREEN (Brookhaven National Laboratory, Upton, NY, 11973)
Brookhaven National
Laboratory (BNL), a 5,265 acre site, contains a variety of wetlands;
included are coastal plain ponds, vernal ponds, recharge basins,
and streams. Wetland habitats in Pine Barrens communities serve
important ecosystem functions including providing critical habitat
for the state endangered tiger salamander (Ambystoma tigrinum)
and a number of other rare species. Survey techniques were used
to gather information on soil and water chemistry of seven coastal
plain ponds at BNL: four natural ponds, one man-modified pond,
and two man-made ponds. Each pond was tracked using Global Positioning
System (GPS) technology and mapped using ArcGIS. Five water samples
were collected at each pond; nine soil samples were collected at
five of the seven ponds. Water samples were analyzed for iron,
sulfate, total chlorine, copper, aluminum, nitrate, phosphorus,
tannin-lignin, suspended solids, hardness, total chromium, and
molybdenum using HACH DREL/2000 and HACH CEL/890 water test kits.
Soil samples were analyzed for pH, nitrate nitrogen, phosphorus,
potassium, aluminum, ferric iron, magnesium, sulfate, calcium,
and chloride using LaMotte soil test kits. Soil temperature, color,
texture, structure, and consistency were also determined. A YSI
650 MDS meter with multi-probe was used to field-test water temperature,
pH, dissolved oxygen, turbidity, and conductivity at each sample
point. Water samples and soil extracts were also analyzed using
an ICP-AES. The pH and temperature of the soil around the natural
ponds was significantly lower than that of the anthropogenic ponds.
The pH of the water from the natural ponds was significantly more
acidic and the tannin-lignin content significantly higher than
that of the anthropogenic ponds. We propose that these differences
in the soil and water chemistry of the ponds can be explained by
the nature of the surrounding vegetation. The presence of a tree
canopy and dense shrub layer around the natural ponds reduces their
exposure to solar radiation and increases the amount of leaf litter
being added to the soil and water. This results in lower soil and
water temperatures, lower soil and water pH, and a higher tannin-lignin
content in the water of the natural ponds versus the anthropogenic
ponds. The results of this study provide baseline data for monitoring
pond health in the future and for assessing the suitability of
ponds as breeding sites for tiger salamanders.
A Survey for the Southern Leopard Frog (Rana sphenocephala)
on Long Island. CHRIS
CAMACHO (Wesleyan University, Middletown, CT,
6459) JEREMY FEINBERG (Brookhaven National Laboratory, Upton, NY, 11973)
The southern
leopard frog (Rana sphenocephala) was once one of the most common
frog species on Long Island. However, over the last thirty years,
populations have declined rapidly and the southern leopard frog
may be extirpated from Long Island. In order to assess the status
of R. sphenocephala on Long Island, all wetlands on the island
with suitable habitat were surveyed. Historic leopard frog sites
and areas within the previous range of the species were thoroughly
surveyed by foot in an attempt to document any remaining populations.
The southern leopard frog was not seen at any of the sites that
were evaluated. However, this still does not confirm that this
species no longer exists on Long Island. There may still be small,
very localized populations which could only be identified during
the calling season from Late March to early May, when the species
is most easily found.
Acetyltransferase activity of the 11-amino acid peptide
cofactor of the adenovirus proteinase. YUE
LIANG (University of California, Berkeley, Berkeley, CA, 94704)
WALTER F. MANGEL (Brookhaven National Laboratory, Upton, NY, 11973)
The 11-amino
acid peptide pVIc (GVQSLKRRRCF) from the C-terminus of the precursor
to adenovirus protein VI has a transacetylase activity. Acetylation
is an important physiological process in eukaryotic cells. For
example, it is involved in DNA replication, transcription and repair.
pVIc was incubated with acetyl coenzyme-A (Ac-CoA) at pH 7.0 for
15 minutes and the reaction was fractionated by high performance
liquid chromatography (HPLC). A new peak appeared whose mass corresponded
to mono-acetylated pVIc as determined by Matrix-Assisted Laser
Desorption Ionization (MALDI) Mass Spectrometry. The kinetics of
acetylation were linear for at least 21 minutes. The equilibrium
dissociation constant (Kd) for the interaction of Ac-CoA with pVIc
was 1.1 mM. When purified mono-acetylated pVIc obtained at pH 7.7
was incubated at pH 10.3 for 15 minutes, multiple peaks were observed
upon HPLC. MALDI analysis of each peak indicated one peak contained
pVIc, another the original mono-acetylated pVIc, two other peaks
contained mono-acetylated pVIc, three peaks contained di-acetylated
pVIc and one peak contained tri-acetylated pVIc. The reaction at
pH 10.3 was repeated but in the presence of the C-to-A mutant of
pVIc. The mutant pVIc did not become acetylated. Thus, the new
acetylations at pH 10.3 occurred in cis, except for the trans-acetylation
between cysteine residues on different pVIc. A long-term goal is
to find out the effects of acetylation on pVIc and, therefore,
on viron assembly, and further discover anti-viral agents that
can interfere with viral assembly.
Addition of Wet Turbine Pod and its related heat Exchangers
nto Realativistic Heavy Ion Collider Cryogenic System. CLARENCE
DZUBEY, JR. (CUNY - Bronx Community College, Bronx, NY, 10453)
TOM TALLERICO (Brookhaven National Laboratory, Upton, NY, 11973)
The Relativistic
Heavy Ion Collider (RHIC) consists of two rings of super-conducting
magnets to help guide and focus beams of ions during various scientific
experiments. All magnets must be maintained at a temperature of
4.5 degrees Kelvin (K). The basic function of the RHIC Cryogenic
System is to maintain the super-conducting magnets in the two rings
of the collider at 4.5 K or below. The Cryogenics Group (CG) cycles
liquid helium throughout the rings in varying amounts to keep these
magnets cold at 4.5 K by removing the heat generated locally due
to currents and heat leakage from its surroundings. The Cryogenic
System (CS) was originally designed for the Isabelle project, another
collider, which required a larger heat load (~25 kW at 3.8 K) however,
it was never completed. The RHIC inherited this CS but only needs
at most approximately 13 kW at 4.5 K of refrigeration power. The
CG has been implementing upgrades over the last three years to
achieve greater system efficiency by reducing the power usage.
This year’s main upgrade consisted of adding a load turbine and
its associated heat exchangers that are enclosed in a cold box
(CB). A turbine is an enclosed rotary engine that extracts energy
from a fluid flow while a CB can be described as a low pressure
vessel providing vacuum insulation for cryogenic heat exchangers,
which are devices built for efficient heat transfer from one fluid
to another. This upgrade would result in a 1 MW power decrease
from 6 MW to 5 MW of compressor power. We worked on the planning
and implementation that went into incorporating additional control
and monitoring instrumentation into the existing CS for the new
turbine and CB. The planning stage included engineering and design
of digital and analog input and output wiring diagrams, programmable
logic card diagrams, and the construction of an additional human
machine interface computer screen. The implementation stage involved
installation of computer racks and wiring along with analog valves,
gauges and sensors.
An Alternative Nonvolatile Solvent to Dissolve Metals: The Mixture of Choline
Chloride and Urea. DORRA KRIDIS (The Cooper
Union for the Advancement of Sciences and Art, New
York, NY, 10003)
MARK FUHRMANN (Brookhaven National Laboratory, Upton, NY, 11973)
The mixture of
urea and choline chloride, two inexpensive, non-toxic, but high
melting point organic solids in a specific ratio, produces an easy
to make, colorless, and nonvolatile ionic liquid at 60°C. The prepared
nonvolatile liquid is stable at room temperature. The goal of this
experiment is to assess a comprehensive, environmentally friendly
and efficient utilization of an ionic liquid (choline chloride
and urea) and to determine the percentage of dissolved metal elements
in the liquid; for example, aluminum, copper, iron, silica and
zinc. In the present study, the Inductively Coupled Plasma-Atomic
Emission Spectroscopy (ICP-ASE) instrument is used to determine
the concentration of dissolved metal in a diluted ionic liquid.
The collected data is compared to the solubility of each metal
in water at 25°C, 50°C and 70°C. The inexpensive ionic liquid is
easily prepared where the number of moles of urea is half of the
choline chloride. The reactants are the urea, and the choline chloride.
The products present are an ionic liquid in the form of a salt
and water. The novel ionic liquid chemical name is determined to
be 3,5,5-triamino-4,6-dihydroxy-1,2,2-trimethylhexahydropyrimidin-1-ium
chloride. The density of this salt is determined to be 1.14 g/ml.
The solubility of metal oxides at 25°C, 50°C and 70 °C such as
copper oxide, zinc oxide, aluminum oxide and quartz are greater
in ionic liquid compared to water. Solubility of elemental zinc,
iron and copper also show a greater percentage over those in water.
Aluminosilicate minerals also show a greater solubility in an ionic
liquid compared to water. The potential structures of the formed
ionic liquid suggest that it may be useful in catalysis when metals
are added. The solubility results also suggest that this ionic
liquid could be applied to use as metal polishing and to remove
metals from soil and other contaminated material.
An Examination of Perseveration in Cocaine Abusers. TANYA LUKASIK (Stony Brook University,
Stony Brook, NY, 11794)
RITA GOLDSTEIN, PH.D. & PATRICIA WOICIK, PH.D. (Brookhaven
National Laboratory, Upton, NY, 11973)
Drug addiction
is associated with executive deficits that are typically attributed
to dysfunction in prefrontal brain regions (e.g., the ventromedial
region of the orbitofrontal cortex and dorsolateral prefrontal
cortex). Cocaine-addicted individuals exhibit mild performance
deficits on neuropsychological tasks that require set shifting,
instead, perseverating on previously rewarded behavior. However,
the research reported is inconclusive possibly due to the heterogeneity
among cocaine-abusing populations. In the current study, cocaine
abusers were compared to healthy control subjects on the Wisconsin
Card Sorting Task, (WCST); a classical neuropsychological task
that assesses concept formation, cognitive flexibility and set
shifting. Cocaine abusers were grouped according to their ability
to complete all categories on the WCST (high functioning versus
low functioning). Compared to higher functioning cocaine subjects,
lower functioning cocaine abusers were associated with more positive
urine screens. Lower functioning cocaine subjects also scored lower
on indices of general intelligence and traditional indices (total
scores) of the WCST as compared to higher functioning cocaine subjects
and controls. In contrast, higher functioning cocaine abusers scored
similarly to controls on total scores of the WCST, however, an
examination of performances at the category level suggests a different
pattern of learning, specifically a tendency to perseverate in
the first sequence of the task. Results suggest two patterns of
executive dysfunction in cocaine abusers; one associated with lower
functioning cocaine abusers that is more severe and possibly related
to acute withdrawal (recent cocaine use) and another associated
with higher functioning cocaine abusers characterized by mild perseverative
deficits.
Analysis of a Proposed Very Long Baseline Neutrino
Oscillation Experiment. CHRISTINE LEWIS (Columbia
University, New York, NY, 10027)
MILIND DIWAN (Brookhaven National Laboratory, Upton, NY, 11973)
The Very Long
Baseline Neutrino Oscillation (VLBNO) study aims to determine how
to best design a second generation experiment to measure the neutrino
oscillation parameters and possible violation of charge/parity
(CP) invariance. Using the General Long Baseline Experiment Simulation
(GLoBES) software and considering a 500kT water Cherenkov detector
at 1300km, corresponding to a baseline from Fermilab to the Homestake
mine, we calculate the sensitivity to 13 and the CP phase. We find that with 2500kT*MW*107s
of neutrino running and 5000kT*MW*107s of antineutrino running the experiment could measure sin2213 to
9-14% and dCP to
~15° at 1s. Moreover, the experiment is sensitive to non-zero sin2213 as
low as 4x10-3 at
99% confidence.
Analysis of Beam Deviation Due to Quadrupole Misalignment
Caused by Ambient Ground Motion in the Relativistic Heavy Ion
Collider. BRANDON BELEW (Rensselaer Polytechnic Institute, Troy, NY, 12180) CHRISTOPH MONTAG (Brookhaven National Laboratory, Upton, NY, 11973)
Within the Relativistic
Heavy Ion Collider (RHIC) and particle accelerators in general,
proper alignment of the focusing and defocusing quadrupole magnets
is essential to maintaining a stable beam orbit. However, it is
also a fact that there will always be some misalignment due to
ambient ground motion. The extent of this displacement is given
by a simple linear formula of time, distance and a site-specific
constant (the ‘ATL Rule’). Using known values of the beta function,
phase advance, and focusing strength at the RHIC quadrupoles, code
was written to simulate expected beam deviation at specific monitor
points according to the ATL rule, for arbitrary values of the constant
A. This expected deviation was then compared with actual logged
beam data over the course of several months to arrive at the site-specific
value of A. The end result, the constant of ambient ground motion
specific to the RHIC location, was calculated to be around 3e-11
mm^2/m*s. Knowing this value will allow for more accurate predictions
of future beam deviation, and facilitate the proper application
of correcting dipole magnets to counteract these effects.
Analytical Data Acquisition via Radar of Ionization
Electrons in Cosmic-ray Extensive Air Showers. JEREMY
MARTIN (FAMU-FSU College of Engineering, Tallahassee, FL, 32310)
HELIO TAKAI (Brookhaven National Laboratory, Upton, NY, 11973)
Ultrahigh-energy
cosmic-rays initiate cosmic showers of high-energy, electrically
charged particles upon interaction with the atmosphere of the earth.
Evidence of radio wave reflection is collected from ultrahigh-energy
comic-ray (UHECR)-induced extensive air showers (EAS) of high energy
electrically charged particles when entering the stratosphere.
Optimal detection of UHECR entails facilitating a more pertinent
understanding of the high-energy particle and its celestial origin.
The challenge is using a type of radar detection to separate the
radio signals reflected by EAS from radio waves reflected from
other sources (i.e., clouds, meteor trails, air crafts, emissions
from lightening). This requires an approach involving Fourier transform,
power spectrum analysis, as well as other series evaluation techniques
to discriminate between the EAS reflected waves which contain data
from high ionization particle interaction and oscillations that
are irrelevant to this research. To distinguish EAS radio waves
from other atmospheric sources of radio waves, a set of software
tools were developed. Using this uniquely developed data acquisition
software, randomly reflected radio waves about the atmosphere can
be manipulated from their intrinsic state to isolate the power
spectrum of the EAS waveforms in an attempt to efficiently identify
these particular signatures of undulation in greater proportion.
By analyzing the frequencies of these signals the intention is
to later demonstrate a correlation between the radio waves occurring
in specific VHF radio frequencies and cosmic-ray events detected
by other means. This research is a portion of a process in which
the goal is to develop a basis for further study of UHECR within
the Mixed Apparatus for Radar Investigation of Cosmic-rays of High
Ionizations (MARIACHI) project, which seeks to develop radar detection
techniques for related studies of high energy physics.
Arc Flash. YEVHEN
RUTOVYTSKYY (Three Rivers Community College, Norwich, CT, 6360)
SWAPNA MUKHERJI (Brookhaven National Laboratory, Upton, NY, 11973)
Analyzing BNL
electrical distribution system. Determine the incident energy,
boundary requirements, and the personal protective equipment necessary
tin order to minimize the possibility of electric shock to personal.
All the calculations are done by using PTW (Power Tools for Windows)
software and based on measured data or information, obtained from
the manufactures labels (such as: operating voltage, breaker size,
size of the wire etc.) After completing this project we expect
to come up with a universal label that will be posted on all electrical
equipment that exists at BNL. New label will contain the name of
the panel, warning statement "Arc Flash Hazard!!!" and
category PPE (Personnel Protective Equipment)
Assessment of Biometrics System. KWOK
WING LEE (Stony Brook University, Stony Brook, NY, 11794) UPENDRA S. ROHATGI (Brookhaven National Laboratory, Upton, NY, 11973)
Biometric systems
are used to authenticate users based on their biological characteristics
such as face, voice, fingerprint, and hand geometry. This kind
of identification system provides the user with logon convenience
and extra protection against theft. The Russian Academy of Sciences
Institute of Applied Physics is involved with the project and they
are developing a software development kit (SDK), where others can
use this product and create their own biometric identification
system. To evaluate the quality of their product, a Biologin program
was created using C++ programming and other technologies such as
Microsoft Graphical Identification and Authentication Dynamic Link
Library (MSGINA DLL). Communication with the Russian institute
was established daily via internet, to provide them with feedback
on their SDK and documentation. The goal of creating a Biologin
was to determine if the SDK is useable and if the product can be
sold to consumers. Product documentation is very important for
a SDK but was lacking in the product and constant communication
was required. Testing of the recognition system was very accurate
and accounted for only a 3% error rate. It is difficult to work
with another country because of language barriers and the time
difference. This was a learning experience for the Russian Institute
because they must develop software products that can compete with
existing ones in the market.
Baseline pH and the Variability of pH within Plots and Community Types of the Central
Pine Barrens. NEAL JACK (Pennsylvania State University, University
Park, PA, 16801) TIM GREEN (Brookhaven National Laboratory, Upton,
NY, 11973)
The Long Island
Central Pine Barrens (CPB) is a valuable natural resource for its
beauty, natural water aquifer and for being the habitat of many
endangered and threatened species of plants animals and insects.
The Foundation for Ecological Research in the Northeast (FERN)
is an organization committed to the preservation of the Pine Barrens
ecosystem by maintaining or improving the health of the forests
located in the CPB. FERN, in conjunction with other organizations,
implemented a ten-year longitudinal study on the health of the
CPB. Data collected on the pH of the soil will provide a piece
of the baseline health record for this ten-year longitudinal study.
To establish a baseline health record for each forest type, several
16 x 25m plots were set up, according to established protocols,
within each forest community type. Using a Kelway HB-2 Soil pH
meter / moisture tester the pH of the soil was taken at eight points
within each plot. The average pH of the forest types were 6.3 for
Coastal Oak, Pitch Pine 5.9, Pine-Oak 6.0, Oak-Pine 5.9, Pitch
Pine Scrub Oak 6.1, and 6.1 for Dwarf Pine. Analyzing this data
and data collected at the end of the ten-year study will be valuable
in determine the long-term health of the forest as well as the
effect of human intervention such as acid rain pollution.
Calibration for Methane Hydrate Research Unit. XIAE SHI (State University of New
York at Stony Brook, Stony Brook, NY, 11790) DEVINDER MAHAJAN (Brookhaven
National Laboratory, Upton, NY, 11973)
Methane hydrate,
one of the most common gas hydrates, forms at low temperature and
high pressure; conditions typically found below the seafloor and
permafrost. Although the amount of methane hydrate trapped under
the seafloor on Earth has been estimated to be enough to meet human
needs for the next several hundred years, due to their dispersed
nature it is very difficult to extract the hydrates1. A customized
unit, named Flexible Integrated Study of Hydrates (FISH) that BNL
is using for methane hydrate research, mimics seafloor conditions.
In a typical process, methane gas is charged to the vessel, which
initially contains a water/sediment mixture under high pressure,
cooled down to 4 degrees Celsius. The hydrate formation can be
visualized in the vessel through a 12-inch glass window. The kinetics
of methane hydrate formation and decomposition could be studied
through temperature, pressure and flow/mass meters for the duration
of the experiment. The goal of my project is to test the operation
and dynamics of the system, such as calibration of all flow/mass
meters and BPR (Back Pressure Regulator), as well as testing the
system’s cooling rate. Preliminary results show that the system
is well suited for hydrate formation. Volumetric balances at the
inlet and outlet reveal a discrepancy of approximately 4 ml, which
is well within tolerances for experimental error. Heat transfer
analyses revealed a maximum cooling rate of 0.293 ºC/hr using a
tube-like heat exchanger with forced convection in conjunction
with a thermally controlled water-ethylene glycol bath.
Calibration of Small Pb-Glass Photomultiplier Cells in the FPD++ (Forward Pion
Detector). SHAWN PEREZ (State University of New
York at Stony Brook, Stony Brook, NY, 11790) LESLIE BLAND (Brookhaven
National Laboratory, Upton, NY, 11973)
The FPD++ (Forward
Pion Detector) at Brookhaven National Lab, consists of two matrices
of Pb-glass bars viewed by photomultiplier tubes that are positioned
left and right of the colliding beam axis. These detectors are
used to explore transverse single spin asymmetries through analysis
of forward pion production and its corresponding jet shape. In
order to extract information from polarized proton - proton collisions,
the FPD++ had to be calibrated cell by cell. Reconstructed di-photon
invariant mass is associated with the highest energy cell in the
inner matrix. Distributions of high tower invariant mass are fit
by a Gamma function to describe background in the detectors and
a Gaussian to describe the Pi0 peak. The absolute gain of each
tower is then varied until the Pi0 peak is centered at its known
position of .135 GeV/c^2. Once the relative gain correction factors
of each iteration performed have converged, the cells have been
calibrated. Currently the Small cells of the FPD++ are calibrated
within an accuracy of 2%, while the large cells still need to be
calibrated. Comparing the summed energy spectra of polarized up
and down proton collisions in the west-north and west-south modules
of the FPD++, will reveal more information about transverse single
spin asymmetries and possibly the relative contributions from the
Collins and Sivers effect toward these asymmetries observed in
forward pion production. The Collins and Sivers effect are theoretical
models developed to explain transverse single spin asymmetries,
dependent on spin and transverse momentum distribution functions
or fragmentation functions. Analyzing the pseudorapidity (-ln(tan(/2))
dependence on particle production will explore parton distributions
within the proton.
CCD Quantum Efficiency Characterization for LSST. XIAOQIAN ZHANG (Cornell University, Ithaca, NY, 14853) JAMES S. FRANK (Brookhaven National Laboratory, Upton, NY, 11973)
The optical performance
of charge coupled devices (CCDs), the fundamental units used for
digital cameras, can be characterized by their quantum efficiency.
The Large Synoptic Survey Telescope (LSST) project, an ongoing
project aiming for completion in 2013, needs a high-efficiency
digital camera with 3.2 Giga-pixels of CCDs for its acquisition
of astronomical images. The CCDs used in this camera need to attain
nearly 50 % quantum efficiency in the near-infrared (1000nm) while
operating in a vacuum Dewar at a temperature of 173K. To test this
requirement, instrumentation of a device that measures quantum
efficiency of manufactured CCDs is under development at Brookhaven
National Laboratory (BNL) and is based partially on the similar
instrumentation developed in 2004 and 2005 in the Lawrence Berkeley
National Laboratory (LBNL). This device consists of multiple light
sources, a shutter, several filters, a coupled monochromator, a
12-inch diameter integrating sphere, a black box, and a dewar where
the cooled CCD is to be placed. The equipment is assembled in the
order listed above so that the monochromator first selects the
desired wavelength of light emitted from the light source. This
beam is then monitored in the integrating sphere, and made uniform
through the black box before it reaches the CCD in the dewar. Picoammeters
and photodiodes are placed in several locations for light intensity
measurements. After examining the light leakage of the integrating
sphere, calibration of the coupled monochromator was performed
using a Hg light source. Properties of gratings, filters, and slits
were studied by comparing measured spectral lines of Hg and Xe
light source. A LabView program was developed and used to operate
the assembled devices and take readings from the photodiodes. These
programs, devices, and data will be used to measure the quantum
efficiency as a function of wavelength in CCDs currently under
development for LSST.
Centrality Determination in Heavy Ion Collisions for the Pioneering High Energy
Nuclear Interaction eXperiment (PHENIX) at the Relativistic Heavy
Ion Collider (RHIC). ELI LANSEY (Yeshiva University, New
York, NY, 10033) ALEXANDER MILOV (Brookhaven National Laboratory, Upton, NY, 11973)
In the physics
of Relativistic Heavy Ions (RHI), the centrality related parameters
(such as the number of participating nucleons or number of binary
collisions between nucleons) are the essential characteristics
of the collisions. The majority of publications from all four RHIC
experiments related to RHI physics present their results as functions
of one or more centrality-related parameters. Centrality's precise
determination is therefore critical to understand most of the RHI
results. The distribution of the number of participating nucleons
can be obtained with the commonly used Glauber model. In the PHENIX
experiment, this distribution is related to the number of particle
hits in the Beam-Beam Counters via statistics of the Negative Binomial
Distribution (NBD). These properties allow us to achieve two principle
goals: to validate the commonly used theoretical model and to establish
an accurate relationship between the observable quantity (number
of hits) and the number of participating nucleons. Using the data
collected during full energy (200 GeV) Au+Au Run4 of the PHENIX
experiment we studied the parameters of the NBD, their systematic
dependencies and accuracy to which they can be determined. The
work is done by using the MINUIT minimization tool in the ROOT
environment. This work will contribute to future analysis by many
members of the PHENIX collaboration, yielding better measurements
of the centrality-related parameters.
Characteristic colonization of poplar trees with gfp expressing bacterial endophytes. ERIKA
FREIMUTH (Cornell University, Ithaca, NY, 14850) DANIEL VAN DER
LELIE (Brookhaven National Laboratory, Upton, NY, 11973)
Endophytic bacteria
that colonize the internal systems and spaces of plants contribute
valuable functions and services to the plant both individually
and as a community. The enhancement of plant growth and metabolic
processes by endophytic bacteria offers the opportunity to mediate
both increased production of plant material and the sequestration
of toxins within its tissues. Cuttings of poplar trees were inoculated
with selected strains of endophytic bacteria (Pseudomonas putida W619
and Enterobacter sp.
638) genetically modified to stably express a green fluorescent
protein and resistance to kanamycin. The colonization behavior
and effects of these bacteria on the plant were monitored biweekly
using fluorescent microscopy as well as by grinding and plating
different sections of plant tissue (including sections of the rhizosphere,
roots, shoots, and leaves). By thus tracking select endophytic
bacterial strains marked with gfp through the plant’s development, the colonization efficiency
and patterns of these endophytes in poplar can be utilized in various
applications. Poplar biomass production and chemical sequestration
efficiency can be maximized via endophytic bacteria for use in
biofuels, carbon management and recycling, and the phytoremediation
of environmental pollutants.
Chytrid Fungus and Ranavirus on Long Island. KATIE HEISER (University of Maryland, College Park,
MD, 20740) TIM GREEN (Brookhaven National Laboratory, Upton, NY,
11973)
Amphibian populations
worldwide have been devastated by Chytridiomycosis, a disease caused
by Chytrid fungus (Bactrachytrium dendrobatidis). Having
likely originated in Africa, it has been found on nearly every
continent and can be spread by a number of hosts. Many amphibian
species do not have any tolerance to the fungus and populations can quickly
disappear following its introduction to the area. However, some
can survive the disease and will act as carriers to spread it.
Iridovirus is also a threat to local populations and was found
at the Brookhaven National Lab last year. As such, this project
was conducted to investigate the potential link that these diseases
may have with a recent island wide decline and possible extirpation
of the southern leopard frog (Rana sphenocephala). In their
absence, several common and related potential vector frog
species were sampled from various Long Island wetlands.
Frogs were swabbed and the swabs were tested for Chytrid and
Iridovirus. PCR and gel electrophoresis will be used to confirm
the presence or absence of the diseases. The presence of chytrid
or iridovirus in local populations would serve as a possible lead
in the decline of Southern Leopard Frogs on Long Island. This was
a data collection study and will not include the final results.
Cold Flow Properties of Biodiesel. KAITLIN
THOMASSEN (State University
of New York at Geneseo, Geneseo, NY, 14454)
DR. C. R. KRISHNA (Brookhaven National Laboratory, Upton, NY, 11973)
Biodiesel has
become one of the most promising alternative fuels; however, its
relatively high cloud point (CP) temperature is one of the reasons
limiting it from replacing the widespread use of fossil fuels in
today’s society. Reducing the CP of biodiesel is one the last major
obstacles scientists need to overcome before the fuel can be marketed
for consumers. Unfortunately, not much is known about the cold
flow properties of biodiesel, their dependence on the source material
from which biodiesel is made, and about methods to reduce the CP
temperature. Previously, scientists have theorized that the higher
the percent of saturated fatty acids in the source material from
which the biodiesel is made, the higher the CP temperature. As
part of this research project, samples of biodiesel made from soy,
tallow, canola, and yellow grease were blended in different percent
ratios to test this theory. Tallow and soy were blended together
at 20%, 50%, and 80% ratios. Separately, yellow grease was blended
with soy and canola was blended with tallow at these same ratios.
These biodiesel samples were chosen due to the large contrast in
the percent saturation. Soy and canola contain a low percent saturation,
while tallow and yellow grease have a high percent saturation.
The test results showed that CP temperature increased linearly
as the percent of saturated components increased in the biodiesel
samples. In addition, the CP temperature was found for No.2 oil
and biodiesel blends. B5, B20, B50, and B80 blends were made with
yellow grease, canola, soy, and tallow-based biodiesel. The results
showed that as the percent of No.2 oil increases in each sample
the CP temperature decreases. The tests also concluded that making
blends of No. 2 oil and biodiesel from different sources can yield
a very different CP temperature. Furthermore, in the effort to
reduce the CP temperature of biodiesel, a proprietary additive
was blended with several types of neat and blended biodiesel samples.
What was concluded from this proprietary additive is that CP was
not effectively changed however, observation indicated that the
pour point (PP) temperature seemed to have been lowered. In future
research, the CP of different biodiesel types will be correlated
with their chemical structure.
Comparing the physical properties of ionic liquids
bearing chiral and achiral hydroxyl units. JASMINE
HATCHER (Queensborough Comunity college, Bayside, NY, 11364)
JAMES WISHART (Brookhaven National Laboratory, Upton, NY, 11973)
Ionic liquids
have generated much interest due to their potential green chemistry
applications. They are considered to be environmentally friendlier
solvent alternatives to traditional volatile (and hazardous) organic
solvents because of their lack of vapor pressure. We report here
on the synthesis and preliminary characterization of achiral and
chiral ionic liquids. The chiral species were synthesized by taking
a chiral auxiliary, 3-chloro-1,2-propanediol, and adding it to
a tertiary amine. The achiral ionic liquids were synthesized by
adding our achiral auxiliary 3-chloro-1-propanol, to a tertiary
amine. Some of the tertiary amines used were DMAP (4-dimethylaminopyridine)
N,N,N’,N’ tetramethyl hexadiamine. The halide salts were converted
into potential ionic liquids by anion exchange. Anions studied
include phosphate and bis(trifyl)imide. A large problem with many
ionic liquids is that they are very viscous. Theoretically, the
induction of a chiral center would reduce viscosity, however this
has not been the case with the materials synthesized using 3-chloro-1,2-propanediol.
Preliminary results suggest that these chiral ionic liquids are
more viscous than the achiral ILS. This may be due to the presence
of an extra hydroxyl group, which increases hydrogen bonding. Future
work will focus on finding a new chiral auxiliary and comparing
the properties of racemic vs. enatiopure ionic liquids.
Completing phase iii of chipmunk electrical packaging upgrade. JULIAN DIAZ (Bronx Community College, Bronx, NY, 10453) VINCENT CASTILLO (Brookhaven National Laboratory, Upton, NY, 11973)
Chipmunks are
radiation monitoring devices used by the Collider Accelerator Department
(C-AD) at Brookhaven National Laboratory (BNL) that detect radiation
by means of an ionization chamber which generates a current that
is proportional to the radiation. The current is converted to a
frequency which is also proportional to the radiation. Different
levels of radiation are used to create interlocks on the C-A machines.
Chipmunks were developed at Fermi National Laboratory (FNAL) in
the early 1980s and for the past 26 years have been effective as
the detectors in the radiation monitoring system for the C-AD at
BNL. They were designed with 1980s technology which included extensive
hand-wiring and some of the components are actually obsolete. An
engineering upgrade was started three years ago with the help of
Community College students from the Community College Institutes
(CCI) summer student program at BNL. A backplane was designed to
replace hand-wiring and printed circuit boards (PCBs) were redesigned
with readily available components. This project is focused on the
design of circuits that will complete the upgrading process. Such
circuits include a PCB for the indicators lights; a PCB for the
front panel indicators; a PCB for the interlock circuits and completion
of the backplane wiring. With all this circuitry in place the upgraded
chipmunk will be ready for testing.
Computer Aided Engineering in the Development of the Electron Beam Ion Source
Electrostatic Components in the Low Energy Beam Transport Region. GAVIN MCINTYRE (Rensselaer Polytechnic Institute, Troy, NY, 12180) LOUIS SNYDSTRUP (Brookhaven National Laboratory, Upton, NY, 11973)
The Electron
Beam Ion Source (EBIS) is the new pre-injector system for the Relativistic
Heavy Ion Collider (RHIC) and will outperform the Tandem van de
Graff which is the current ion source for RHIC. The EBIS is more
versatile, with the ability to produce myriad stable ion species
from the noble gases to uranium. Deflectors (steering/minor focusing)
and quadrupoles (focusing/defocusing) ensure the beam quality and
are developed using computer aided drafting and engineering software.
The analysis is crucial to the success of the deflector and quadrupole
designs; thus simulations constructed in analytical software (Kobra)
are developed to ensure design integrity. The Adaptor Deflector
is the initial steering/focus device that is mounted concentrically
to the upstream ion lens. The deflector consists of electrode pairs
with equivalent potentials that are mounted either parallel or
alternating. Various designs were modeled using Pro/Engineer and
were comprised of two to eight electrode pairs. The investigated
designs included: the split cylinder, the dual dipole (two dipoles
offset from one another), and 8/16 congruent, electrode arrangements
in order to ascertain the design that produces the least aberrations
to the ion beam. The functionality of the deflector designs were
simulated with a theoretical beam in the electrostatic analysis
software, Kobra, and the 16 electrode deflector produced the most
desirable qualities. Three quadrupoles are located in the Low Energy
Beam Transport (LEBT) region of EBIS; the two simulated designs
were a basic quadrupole triple and a Helical Electrostatic Quadrupole
(HESQ). The triplet is composed of three inline quadrupoles, with
electrode pairs of equivalent electric potential which focuses/defocuses
the ion beam in two axial directions. The electrodes are oriented
by a stainless steel framework and ceramic standoffs that act as
insulators for the grounded vacuum vessel. The quadrupoles are
offset from the vacuum chamber using swivel bolts that aid in mounting.
The design incorporates two spring-loaded feedthroughs per quadrupole,
which supply the voltages to a divided contact pad that is directly
connected to the electrodes by solid wire. The HESQ has four helical
electrodes held concentric in a grounded vacuum vessel and offer
more locations for focusing/defocusing than the triplet while spanning
a shorter length. The electric fields the quadrupoles produced
were tested using the electrostatic capabilities of Kobra by applying
various potentials to the electrodes; both resultant fields were
adequate for focusing/defocusing the EBIS but the HESQ was superior
to the triplet.
Creating a new stereo viewing software platform. KYLE HUNT & SETH JACOBS (Alfred State College,
Alfred, NY, 14802) MIKE MIGUIGEN (Brookhaven National Laboratory,
Upton, NY, 11973)
Creating a new
stereo viewing software platform. SETH R. JACOBS (SUNY College
of Technology at Alfred, Alfred, NY 14802) MIKE MCGUIGAN(Brookhaven
National Lab, Upton, NY 14802) Living in a three dimensional world
poses a sizable problem when it comes to educating students and
the general public on topics that can not accurately be portrayed
in a two dimensional medium. Stereo projection systems and the
software used in conjunction with them provide a potentially intuitive
and useful tool in conveying ideas of this nature. At current,
however, there is no adequate software solution to act as a stable
base on which to develop and execute a successful lesson plan.
Software of this type that has been provided for public use lacks
a number of things that users need and appreciate. Some of these
issues include: presence of bugs, lack of support, lack of documentation,
lack of portability, lack of file compatibility and a lack of user-friendliness.
Due to this negligence on the behalf of software developers, these
types of learning tools are rarely used and are considered by many
to be a novelty. In order for stereo tools like these to be implemented
successfully in the educational environment, there must be at least
one single, intuitive and robust software solution. The objective
of this project is to create a software package that is full featured,
open in design, and addresses the shortcomings of current generation
stereo viewing programs. In order to accomplish this goal, the
Java programming language and the Java3D advanced programming interface
will be used, along with documentation provided by Sun Microsystems'
home page http://java.sun.com. The object oriented nature of Java
will allow for the program's functions to be split up into modular
classes which can be edited individually or completely replaced
as needed. The program will use a desktop-like graphical user interface
with tabbed windows to display models and views of those models.
There will be user interface objects to handle manipulation of
the models as well as activating and deactivating stereoscopic
viewing. The project will be posted to the public Internet along
with source code and documentation so that it can be improved upon
past the completion of the summer 2006 internship. Type: Environmental
Engineering/Other
Creating Information System of Oncological Methylated DNA data. REGINALD GABRIEL (Cheyney Unversity, Cheyney, PA, 19319)
DR. SEAN R. MC CORKLE (Brookhaven National Laboratory, Upton, NY, 11973)
DNA methylation
is the addition of a methyl group to the cytosine ring of the CpG
dinucleotide, forming methyl-cytosine and is catalysed by DNA methyltransferases.
An information system is needed for biologists to retrieve empirical
data and relate it to DNA methylation sequences experimentally
identified in human cancer cells. This project is intended to create
such information system available for biologists. Information was
collected from biomedical article reviews and existing Internet
database, such as RefSeq (NCBI), the UCSC Genome database. PostgreSQL
database server running on MAC OsX (DARWIN – BSD) system was established.
The tool NetBeans Integrated Development Environment (IDE) was
use to create the Graphical User Interface (GUI), the client application
with the Java programming language. The Java client can run virtually
on any computer because of the benefits of Java; “write once and
run anywhere”. Communication between the Java client and PostgreSQL
database server was established through the Java Data-Base Connectivity
(JDBC) package. Object Oriented Techniques (OOT) is ideal for connecting
various sub-components of the system: network connections and GUI
application. A class PostJDBC was implemented to connect to the
database, issue queries, and retrieve resultant data. UserGui,
the user interface, relies heavily on inheritance and polymorphism
techniques to achieve dynamic data manipulation and graphical display
of the output. The client application presents the user with a
list of gene symbols which are contained in the database, and allows
the user to browse for more detailed information by mouse selection.
This project can be easily expanded by including information about
different types of features in DNA sequences and their relation
to human cancer cells.
Creating Three Dimensional Stereoscopic Animations of Organic Chemical Reactions
through PYMOL for Enhanced Visualization of Reaction Mechanisms. MARIA MATEO (Bergen Community College, Paramus, NJ, 7652) ROB BENNETT (Brookhaven National Laboratory, Upton, NY, 11973)
Three dimensional
stereoscopic animation of organic chemical reactions is an effective
means for illustrating bond associations and conformational changes
that would otherwise be difficult to visualize if represented as
two dimensional images. Executing chemical reaction modeling requires
the use of various computer programs and programming languages.
The main foundation of this project is a chemical calculation program
called MOPAC (Molecular Orbital Package) which estimates both the
best structure and minimum energy of a molecule or a small reaction
given an initial presumption on the molecular structure or reaction
path. The information is input as a z-matrix which, after being
calculated by MOPAC, outputs an array of digital information that
is lengthy and complex. However, the Centre for Molecular and Biomolecular
Informatics (CMBI) at Radboud University Nijmegen in the Netherlands
created a website, called Mol4D, that presents the MOPAC data within
a friendlier, GUI-based (graphical user interface) environment.
This website provides the output data that are needed to create
the stereoscopic version of the animation. PyMOL, a molecular modeling
program, is used to animate the chemical reaction in quad-buffered
stereo, which is the type of stereographic setting that is compatible
with the 3D projector being used for this project. Because PyMOL
functions mostly by command scripts, which can be very tedious
to learn, a combination of C++ and Python was used to program a
plug-in for PyMOL that, when prompted by the user, imports the
correct output file from the MOPAC calculations, separates that
file into distinct movie frames, creates the overall movie script
and runs it through the PyMOL viewer, and transmits the final animation
in quad-buffered stereo. The intention behind creating a more user-friendly
adaptation of PyMOL and using it in conjunction with the Mol4D
website is so that the final outcome can be used as a valuable
teaching tool for chemistry, specifically organic chemistry. The
3D stereoscopic projection of the desired reaction can help a student
vividly see the discrete conformational changes that occur within
an organic reaction, and thereby give the student a better understanding
of the mechanism of that reaction.
Creation of Computerized Datasheets for use in Calibrations. RACHEL KELLER (Hartwick College, Oneonta, NY, 13820) PAUL ZAHRA (Brookhaven National Laboratory, Upton, NY, 11973)
At Brookhaven
National Lab (BNL) the procedures used in the Radiological Control
Calibration and Instrumentation Group (Rad Con C&I Group) to
guide the calibration of radiological equipment cover an entire
class of instruments. These procedures provide the guidelines by
which an instrument is deemed fit for use; however, the usefulness
of these procedures is limited by the knowledge of the technician
concerning what needs to be done and what options provided are
not applicable for the unit. In addition, many paper data collection
forms are used throughout the course of a single instrument calibration,
making the procedure for data entry into the computer and managing
the hard copy collection of results difficult and cumbersome. Using
the upper level general procedures already in place as well as
information from the technical manuals for the instruments undergoing
revision, new, specific instructions and collections forms are
being formulated. Sources that were useful in the work so far to
create a computerized calibration included the manual for the Manual
Met/Cal program, and the upper level procedures already created
by the Rad Con C&I Group at BNL. The program Manual Met/Cal
aids in the creation of computerized datasheets with accompanying
instructions that match the data fields’ contents. These companion
pieces not only tell the technicians what to do, but also where
on the forms to enter the data they have collected. Since the datasheets
can be printed out to be used away from a computer terminal, the
data forms will now be in the same format as the computerized version,
thereby making the data entry process easier. When the data entry
is complete and the sheet is saved, a standardized report form
has now been created to be printed out, providing a hard copy detailing
the instrument specifics, the information collected, and the status
of the instrument. This is a small portion of a larger project
to bring the procedures and data collection systems for calibrations
up to date.
Crystal Structure of Mn2+ Bound Escherichia coli L-arabinose Isomerase Complex:
Its Implications in Protein Catalytic Mechanism and Thermo-Stability. WEISHA ZHU (Cornell University, Ithaca, NY, 14853) BABU MANJASETTY (Brookhaven National Laboratory, Upton, NY, 11973)
Escherichia coli L-arabinose isomerase (ECAI) is responsible for the initial
stage of L-arabinose catabolism, converting arabinose into ribulose in vivo.
This enzyme also plays a crucial role in catalyzing the conversion
of galactose into tagatose (low calorie natural sugar) in
vitro. The crystal structure of its native form has been recently
solved. This project aims to determine the crystal structure
of enzyme in complex with co-factor metal ions and candidate
substrates/inhibitors to further study structure-function relationships
important for the enzyme’s biological mechanism. High-throughput
techniques were adopted for protein structure analysis. Crystals
of different complexes were grown using hanging drop vapor diffusion
method. Diffraction datasets were collected at X4C, X6A and X29
beamlines, National Synchrotron Light Source, Brookhaven National
Laboratory. The method of molecular replacement was utilized
in structure solving using the native structure as the initial
model. A series of crystallographic software packages were used
to build and refine the structural model. The analysis of the
structure of Mn2+ bound
ECAI protein complex completed to 2.8 Å resolution with the R-factor
of 23% and the structure was deposited to Protein Data Bank (PDB
ID 2HXG). The overall fold and biological arrangement of the
complex are conserved. Active site of ECAI is located at the
subunit interface and forms deep cleft. Mn2+ ion
is identified at the active site surrounding with an octahedral
coordination. Comparison between apo and holo structures reveals
variations in the metal coordination sphere, conformational changes
associated with the active site residues and increased number
of interactions between subunits. The available biochemical and
structural data provides the structural basis for efficient protein
catalytic mechanism and increase in thermo-stability of the enzyme
induced by the presence of Mn2+. This study will benefit optimization of low-calorie sugar production.
The target of this project is one of the many selected under
investigation by New York Structural Genomics Research Consortium
(NYSGXRC ID T2031).
Decoherence Effects in Semi-Classical Trajectory Simulations of CH2 Mixed States. LAURA FREDRIKSEN (State University
of New York at Albany, Albany, NY, 12222) TREVOR SEARS (Brookhaven National Laboratory, Upton, NY, 11973)
The collision-induced
intersystem crossing between the singlet (ã 1A1)
and triplet (X 3B1) states of methylene (CH2) is crucial to the realistic modeling of combustion systems,
since these two forms of methylene have distinct reactivities and
product branching ratios. It is currently thought that this process
occurs through collisions involving a few special "gateway
states" occurring in pairs that are quantum mechanical mixtures
of singlet and triplet. Recent laser kinetic spectroscopy experiments
have identified a previously unrecognized collisional process that
evidently interconverts the two components of each mixed state
pair efficiently. A possible mechanism for this process is being
explored theoretically. A differential phase shift of the singlet
and triplet components of a single mixed state may be induced by
a rare gas collision, resulting in population transfer to the mixed-state
partner. A semiclassical trajectory study of this decoherence process
is being used to assess the consistency of this proposed model
with the experimental observations.
Design and Implementation of a High Availability Distribution
Layer In a Campus Environment. MANGAL
TYAGI JR. (Prairie State College, Chicago Heighs, IL, 60411)
AJ TEMPROSA (Brookhaven National Laboratory, Upton, NY, 11973)
The implementation
of a robust, scalable, and fault tolerant network is dependent
on logical and physical segmentation of workgroups to provide compartmentalization
in event of network failure. The Cisco hierarchical model simplifies
the task of building a reliable, scalable, and cost-efficient hierarchical
internetwork by introducing a modular approach to the design and
functionality of each network component. A distribution layer provides
policy-based connectivity for workgroup access without having to
route local data through the core or backbone of the network. By
determining the fastest or best path to transmit data, the distribution
layer will also send non-local requests to the high-end core, which
will then transport the request at high data transfer rates to
the correct service. Several policies provided at the distribution
layer include packet filtering, quality of service (QoS), virtual
LANs (VLAN), and manipulation of network traffic, which altogether
contribute to exerting control over network transmissions and what
goes in and out of the network. In order to improve Brookhaven
National Laboratory’s (BNL) network, a third distribution layer
(DL-3) will be configured and deployed which will be attached to
the core at high transfer rates and redistribute network data across
a portion of the BNL campus. DL-3 will have redundant chassis consisting
of the Cisco 6500 series, multi-layer switches, and dedicated power
distribution unit (PDU) feeds. In addition, port aggregation is
a technology that is implemented to provide higher bandwidth, and
will also serve as a backup if a link fails. Before the deployment
of DL-3, the components, such as the supervisor engines and multi-layer
switches, have to be properly configured. The configuration process
includes conversion of the Cisco supervisor engines from hybrid
to native mode, assigning VLANs and network addresses, and establishing
the spanning tree root. Once DL-3 is configured, it is connected
to the network to start servicing the BNL campus similar to the
other two distribution layers. The deployment of DL-3 will provide
more reliable connectivity at the BNL campus by reducing the amount
of hosts exposed to network failure. The work being performed is
part of an ongoing effort to BNL’s network reliability and performance.
Design of Plotting Utilities for the Collider-Accelerator Department. DAVID
KATZ (Alfred State College, Alfred, NY 14802)
SETH NEMESURE (Brookhaven National Laboratory, Upton, NY 11973). DAVID KATZ (Alfred State College, Alfred, NY, 14802) SETH NEMESURE (Brookhaven
National Laboratory, Upton, NY, 11973)
The Collider-Accelerator
Department at Brookhaven National Laboratory has developed a mature
set of C++ utilities for analyzing data. The purpose of this project
is to provide a set of similar tools written in Java that allows
both developers and users a similar set of functionality. The feature
set that has been provided to date includes a set of curve fitting
utilities, the ability to cut, paste, load, and save data sets
from plots, and a flexible way to add text to any plot. There are
two commercial packages being used for the development of the plotting
utilities. One is a math package created by Dr. Michael Thomas
Flanagan of University College London and the other is called JClass,
which is a plotting package created by Quest Software. The curve
fitting feature uses both of the packages to allow the user to
perform essential curve fits on raw data collected. Gaussian, Gaussian
with an offset, Exponential, Exponential with an offset, Polynomial,
and Double Exponential are among the fitting functions supported.
After the fits were coded there was extensive stress testing to
determine how well each fit performs on raw data. In addition to
curve fitting the Java package that has been developed provides
a means for the user to open saved plots created in the existing
C++ software. There is also a feature that allows the user to copy
and then paste a plot onto two independent y-axis setups with different
scales. Labels can also be added to the plots with a variety of
looks and styles which the user can customize to their preference.
The Java package has a similar graphical user interface setup as
the existing C++ utilities so essentially there is no learning
curve
