In 2003, Bronx Community College received a grant of $481,000 through the United States Department of Energy for the purpose of conducting research- related activities leading to the creation of the Center for Sustainable Energy at Bronx Community College. The award, which was administered on behalf of Bronx Community College by the Research Foundation of the City University of New York, was initially for one year, from October 2003 through September 30, 2004. It received a no-cost extension to June 30, 2005. This report presents a summary of the activities and accomplishments attributable to the award.

Phylogenetic relationships among species of the salamanderfamily Salamandridae are investigated using nearly 3000 nucleotide basesof newly reported mitochondrial DNA sequence data from the mtDNA genicregion spanning the genes tRNALeu-COI. This study uses nearlycomprehensive species-level sampling to provide the first completephylogeny for the Salamandridae. Deep phylogenetic relationships amongthe three most divergent lineages in the family Salamandrina terdigitata,a clade comprising the "True" salamanders, and a clade comprising allnewts except S. terdigitata are difficult to resolve. However, mostrelationships within the latter two lineages are resolved with robustlevels of branch support. The genera Euproctus and Triturus arestatistically shown to be nonmonophyletic, instead each contains adiverse set of lineages positioned within the large newt clade. The genusParamesotriton is also resolve as a nonmonophyletic group, with the newlydescribed species P. laoensis constituting a divergent lineage placed ina sister position to clade containing all Pachytriton species and allremaining Paramesotriton species. Sequence divergences between P.laoensis and other Paramesotriton species are as great as those comparingP. laoensis and species of the genera Cynops and Pachytriton. Analyses oflineage diversification across the Salamandridae indicate that, despiteits exceptional diversity, lineage accumulation appears to have beenconstant across time, indicating that it does not represent a truespecies radiation.

We performed ab initio quantum chemical studies for the development of intra and intermolecular interaction potentials for formic acid for use in molecular dynamics simulations of formic acid molecular crystal. The formic acid structures considered in the ab initio studies include both the cis and trans monomers which are the conformers that have been postulated as part of chains constituting liquid and crystal phases under extreme conditions. Although the cis to trans transformation is not energetically favored, the trans isomer was found as a component of stable gas-phase species. Our decomposition scheme for the interaction energy indicates that the hydrogen bonded complexes are dominated by the Hartree-Fock forces while parallel clusters are stabilized by the electron correlation energy. The calculated three-body and higher interactions are found to be negligible, thus rationalizing the development of an atom-atom pair potential for formic acid based on high-level ab initio calculations of small formic acid clusters. Here we present an atom-atom pair potential that includes both intra- and inter-molecular degrees of freedom for formic acid. The newly developed pair potential is used to examine formic acid in the condensed phase via molecular dynamics simulations. The isothermal compression under hydrostatic pressure obtained from molecular dynamics …

The authors present molecular dynamics simulations of aggregation kinetics in a colloidal suspension modeled as a highly asymmetric binary mixture. Starting from a configuration with largely uncorrelated colloidal particles the system relaxes by coagulation-fragmentation dynamics to a structured state of low-dimensionality clusters with an exponential size distribution. The results show that short range repulsive interactions alone can give rise to so-called cluster phases. For the present model and probably other, more common colloids, the observed clusters appear to be equilibrium phase fluctuations induced by the entropic inter-colloidal attractions.

Biofilms are surface-attached structured communities that are encased by an extra polymeric slime (EPS) matrix. Bacteria are also in close connection with these structures. They exchange certain materials like DNA and signaling molecules. These materials are linked to the biofilms and can be dangerous. The biofilm lifestyle can contribute to disease, and are beneficial to chemical productions processes. Biofilms on surfaces cost the nation billions of dollars last year with damage of equipment, energy loss, and medical infection. It also offers opportunities for positive effects, such as biofiltering industrial water to keep it clean, and forming biobarriers to protect soil and groundwater from contamination.

The broad goal of this research is to improve climate prediction through better representation of cirrus cloud microphysical and radiative properties in global climate models (GCMs). Clouds still represent the greatest source of uncertainty in climate prediction, and the representation of ice clouds is considerably more challenging than liquid water clouds. While about 40% of cloud condensate may be in the form of ice by some estimates, there have been no credible means of representing the ice particle size distribution and mass removal rates from ice clouds in GCMs. Both factors introduce large uncertainties regarding the global net flux, the latter factor alone producing a change of 10 W/m2 in the global net flux due to plausible changes in effective ice particle fallspeed. In addition, the radiative properties of ice crystals themselves are in question. This research provides GCMs with a credible means of representing the full (bimodal) ice particle size distribution (PSD) in ice clouds, including estimates of the small crystal (D < 65 microns) mode of the PSD. It also provides realistic estimates of mass sedimentation rates from ice clouds, which have a strong impact on their ice contents and radiative properties. This can be done through proper …

A fast soft x-ray (SXR) pinhole camera has been implemented on the National Spherical Torus Experiment (NSTX). This paper presents observations and describes the Be foil Filter Knee Imaging (FKI) technique for reconstructions of a m/n=1/1 mode on NSTX. The SXR camera has a wide-angle (28{sup o}) field of view of the plasma. The camera images nearly the entire diameter of the plasma and a comparable region in the vertical direction. SXR photons pass through a beryllium foil and are imaged by a pinhole onto a P47 scintillator deposited on a fiber optic faceplate. An electrostatic image intensifier demagnifies the visible image by 6:1 to match it to the size of the charge-coupled device (CCD) chip. A pair of lenses couples the image to the CCD chip.

Solidification of Aluminum alloys is modeled on uneven surfaces characterized by sinusoidal curves. Wavelengths and amplitudes of these surfaces are varied to study the effect of changing surface topography on fluid flow, macrosegregation and inverse segregation in the solidifying alloy. Solidification is initiated by convective heat removal from the uneven surfaces and simulations are carried out in both vertical and horizontal configurations. Stabilized finite element methods, recently used for modeling solidification in the presence of shrinkage and buoyancy driven flows, are used to discretize and solve the governing transport equations derived by volume averaging. The effect of varying amplitudes and wavelengths is observed in heat transfer, fluid-flow, macrosegregation and inverse segregation processes. In vertical solidification, inverse segregation, that usually occurs at the bottom of the cavities, is studied for different sinusoidal topographies quantified by a particular wavelength and amplitude. The fluid flow here is driven by a combination of shrinkage and thermosolutal buoyancy. Shrinkage driven flow arises due to different densities of solid and liquid phases. During horizontal solidification of an Aluminum alloy from uneven surfaces, thermosolutal buoyancy plays a dominant role in fluid flow and the effect of shrinkage is neglected by assuming the individual phase densities to be …

This project supported seed money for the development of cDNA and genetic resources to support studies of the Drosophila melanogaster genome. Key publications supported by this work that provide additional detail: (1) ''The Drosophila gene collection: identification of putative full-length cDNAs for 70% of D. melanogaster genes''; and (2) ''The Berkeley Drosophila Genome Project gene disruption project: Single P-element insertions mutating 25% of vital Drosophila genes''.

The purpose of this project was to investigate the device properties of the quantum cascade laser (QCL), a type of laser invented at Bell Laboratories, Lucent Technologies in the device physics research lab of Dr. Federico Capasso and more specifically to determine the remote sensing capability of this device. The PI and Stevens Institute of Technology collaborated with Dr. Capasso and Bell Laboratories to carry out this research project. The QCL is a unique laser source capable of generating laser radiation in the middle-infrared spectral region that overlaps the most important molecular absorption bands. With appropriate modulation techniques it is possible to use the laser to measure the concentration of many molecules of interest to the remote sensing community. In addition, the mid-IR emission wavelength is well suited to atmospheric transmission as mid-IR experiences much less scattering due to dust and fog. At the onset of this project little was known about several key device performance parameters of this family of lasers and the NNSA supported research enabled them to determine values of several of these characteristics.

Tritium transport simulations were conducted to model the mechanisms associated with dilution, dispersion, and radioactive decay that attenuate the 618-11 tritium plume and limit the risk associated with exposure to the Columbia River and Energy Northwest water supply wells. A comparison of simulated and observed tritium concentrations at two downgradient monitoring wells indicated that the model was a reasonable representation of the tritium concentrations immediately downgradient of the site (699-13-3A) and near the leading edge of the plume (699-13-0A). This good match increased confidence in the conceptual model, its numeric implementation, and ultimately, the validity of predictive simulations of tritium fate and transport. Three release scenarios were investigated to measure the impact of the tritium plume at primary receptor locations under different conditions. The three cases were (1) a pulse release of tritium from the burial ground that was the best fit between observed and simulated tritium concentrations; (2) a continuing, decaying source beneath the burial ground through 2015, the milestone for source removal under the River Corridor Closure Contract; and (3) a pulse release as in the best fit case but at twice the concentration. For the best fit case, the model predicts that the maximum tritium concentration will …

The fabrication of precision laser targets requires a wide variety of specialized mesoscale manufacturing techniques. The diamond wire saw developed in this study provides the capability to precisely section meso-scale workpieces mounted on the assembly stations used by the Target Fabrication Group. This new capability greatly simplifies the fabrication of many types of targets and reduces the time and cost required to build the targets. A variety of materials are used to fabricate targets, including metals, plastics with custom designed chemical formulas, and aerogels of various densities. The materials are usually provided in the form of small pieces or cast rods that must be machined to the required shape. Many of these materials, such as metals and some plastics, can be trimmed using a parting tool on a diamond turning machine. However, other materials, such as aerogels and brittle materials, cannot be adequately cut with a parting tool. In addition, the geometry of the parts often requires that the workpieces be held in a special assembly station, which excludes the use of a parting tool. In the past, these materials were sectioned using a small, handheld coping saw that used a diamond-impregnated wire as a blade. This miniature coping saw …

SNAP is a candidate for the Joint Dark Energy Mission (JDEM) that seeks to place constraints on the dark energy using two distinct methods. The first, Type Ia SN, is discussed in a separate white paper. The second method is weak gravitational lensing, which relies on the coherent distortions in the shapes of background galaxies by foreground mass structures. The excellent spatial resolution and photometric accuracy afforded by a 2-meter space-based observatory are crucial for achieving the high surface density of resolved galaxies, the tight control of systematic errors in the telescope's Point Spread Function (PSF), and the exquisite redshift accuracy and depth required by this project. These are achieved by the elimination of atmospheric distortion and much of the thermal and gravity loads on the telescope. The SN and WL methods for probing dark energy are highly complementary and the error contours from the two methods are largely orthogonal. The nominal SNAP weak lensing survey covers 1000 square degrees per year of operation in six optical and three near infrared filters (NIR) spanning the range 350 nm to 1.7 {micro}m. This survey will reach a depth of 26.6 AB magnitude in each of the nine filters and allow for …

The AdS/CFT correspondence is a powerful tool to study the properties of conformal QCD at strong coupling in terms of a higher dimensional dual gravity theory. The power-law falloff of scattering amplitudes in the non-perturbative regime and calculable hadron spectra follow from holographic models dual to QCD with conformal behavior at short distances and confinement at large distances. String modes and fluctuations about the AdS background are identified with QCD degrees of freedom and orbital excitations at the AdS boundary limit. A description of form factors in space and time-like regions and the behavior of light-front wave functions can also be understood in terms of a dual gravity description in the interior of AdS.

The Supernova Acceleration Probe (SNAP) will use Type Ia supernovae (SNe Ia) as distance indicators to measure the effect of dark energy on the expansion history of the Universe. (SNAP's weak-lensing program is described in a separate White Paper.) The experiment exploits supernova distance measurements up to their fundamental systematic limit; strict requirements on the monitoring of each supernova's properties leads to the need for a space-based mission. Results from pre-SNAP experiments, which characterize fundamental SN Ia properties, will be used to optimize the SNAP observing strategy to yield data, which minimize both systematic and statistical uncertainties. With early R&D funding, we have achieved technological readiness and the collaboration is poised to begin construction. Pre-JDEM AO R&D support will further reduce technical and cost risk. Specific details on the SNAP mission can be found in Aldering et al. (2004, 2005). The primary goal of the SNAP supernova program is to provide a dataset which gives tight constraints on parameters which characterize the dark-energy, e.g. w{sub 0} and w{sub a} where w(a) = w{sub 0} + w{sub a}(1-a). SNAP data can also be used to directly test and discriminate among specific dark energy models. We will do so by building the …

A rather simple electronic bench experiment is proposed for obtaining a measure of the impulse energy loss of a stored particle bunch to an rf cavity or other vacuum-chamber structure--the so-called ''cavity radiation''. The proposed method is analyzed in some detail.

The authors have investigated the population of nuclei formed in binary reactions involving {sup 7}Li beams on targets of {sup 160}Gd and {sup 184}W. The {sup 7}Li + {sup 184}W data were taken in the first experiment using the LIBERACE Ge-array in combination with the STARS Si {Delta}E-E telescope system at the 88-Inch Cyclotron of the Lawrence Berkeley National Laboratory. By using the Wilczynski binary transfer model, in combination with a standard evaporation model, they are able to reproduce the experimental results. This is a useful method for predicting the population of neutron-rich heavy nuclei formed in binary reactions involving beams of weakly bound nuclei formed in binary reactions involving beams of weakly bound nuclei and will be of use in future spectroscopic studies.

A heavy ion driver for inertial fusion will accelerate an array of beams through common induction cores and then direct the beams onto the DT target. An array of quadrupole focusing magnets is used to prevent beam expansion from space charge forces. In the array, the magnet fields from the coils embracing the beams are coupled, which reduces the cost of superconductor and increases the focusing power. The challenges in designing such an array are meeting the strict requirements for the quadrupole field inside the beam pipes and preventing stray fields outside. We report our optimization effort on designing such an array and show that 3 x 3 or larger arrays are feasible and practical to build with flat racetrack coils.

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