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RECENT TEST RESULTS OF THE FAST-PULSED 4 T COS DIPOLE GSI 001. (open access)

RECENT TEST RESULTS OF THE FAST-PULSED 4 T COS DIPOLE GSI 001.

For the FAIR-project at GSI a model dipole was built at BNL with the nominal field of 4 T and a nominal ramp rate of 1 T/S. The magnet design was similar to the RHIC dipole, with some changes for loss reduction and better cooling. The magnet was already successfully tested in a vertical cryostat, with good training behavior. Cryogenic losses were measured and first results of field harmonics were published. However, for a better understanding of the cooling process, quench currents at several ramp rates were investigated. Detailed measurements of the field harmonics at 2 T/S between 0 and 4 T were performed.
Date: May 26, 2005
Creator: Moritz, G.; Kaugerts, J.; Escallier, J.; Ganetis, G.; Jain, A.; Marone, A. et al.
System: The UNT Digital Library
THE BNL SUPER NEUTRINO BEAM PROJECT. (open access)

THE BNL SUPER NEUTRINO BEAM PROJECT.

BNL plans to create a very long base line super neutrino beam facility by upgrading the AGS from the current 0.14 MW to 1.0 MW and beyond. The proposed facility consists of three major components. First is a 1.5 GeV superconducting linac to replace the booster as injector for the AGS, second is the performance upgrade of the AGS itself for higher intensity and repetition rate, and finally is the target and horn system for the neutrino production. The major contribution for the higher power is from the increase of the repetition rate of the AGS from 0.3 Hz to 2.5 Hz, with moderate increase from the intensity. The accelerator design considerations to achieve high intensity and low losses for the new linac and the AGS will be presented. The target and horn design for high power operation and easy maintenance will also be covered.
Date: January 26, 2005
Creator: Raparia, D.
System: The UNT Digital Library
Detecting and Attributing External Influences on the Climate System: A Review of Recent Advances (open access)

Detecting and Attributing External Influences on the Climate System: A Review of Recent Advances

We review recent research that assesses evidence for the detection of anthropogenic and natural external influences on the climate. Externally driven climate change has been detected by a number of investigators in independent data covering many parts of the climate system, including surface temperature on global and large regional scales, ocean-heat content, atmospheric circulation, and variables of the free atmosphere, such as atmospheric temperature and tropopause height. The influence of external forcing is also clearly discernible in reconstructions of hemispheric scale temperature of the last millennium. These observed climate changes are very unlikely to be due only to natural internal climate variability, and they are consistent with the responses to anthropogenic and natural external forcing of the climate system that are simulated with climate models. The evidence indicates that natural drivers such as solar variability and volcanic activity are at most partially responsible for the large-scale temperature changes observed over the past century, and that a large fraction of the warming over the last 50 years can be attributed to greenhouse gas increases. Thus the recent research supports and strengthens the IPCC Third Assessment Report conclusion that ''most of the global warming over the past 50 years is likely due …
Date: January 26, 2005
Creator: Barnett, T.; Zwiers, F.; Hegerl, G.; Allen, M.; Crowley, T.; Gillett, N. et al.
System: The UNT Digital Library
Cylinder Lens Alignment in the LTP (open access)

Cylinder Lens Alignment in the LTP

The Long Trace Profiler (LTP), is well-suited for the measurement of the axial figure of cylindrical mirrors that usually have a long radius of curvature in the axial direction but have a short radius of curvature in the sagittal direction. The sagittal curvature causes the probe beam to diverge in the transverse direction without coming to a focus on the detector, resulting in a very weak signal. It is useful to place a cylinder lens into the optical system above the mirror under test to refocus the sagittal divergence and increase the signal level. A positive cylinder lens can be placed at two positions above the surface: the Cat's Eye reflection position and the Wavefront-Matching position. The Cat's Eye position, is very tolerant to mirror misalignment, which is not good if absolute axial radius of curvature is to be measured. Lateral positioning and rotational misalignments of lens and the mirror combine to produce unusual profile results. This paper looks at various alignment issues with measurements and by raytrace simulations to determine the best strategy to minimize radius of curvature errors in the measurement of cylindrical aspheres.
Date: July 26, 2005
Creator: Takacs, P. Z.
System: The UNT Digital Library
Effect of Stress Mitigation on Precipitation Kinetics of Alloy 22 Welds (open access)

Effect of Stress Mitigation on Precipitation Kinetics of Alloy 22 Welds

Understanding the phase stability of Alloy 22 (N06022) is important since the precipitation of tetrahedrally close-packed (TCP) phases over time has been known to adversely affect corrosion and mechanical properties. Prior observations have shown that these phases precipitate during the welding process. After welding, residual stresses due to the solidification and cooling from temperature remain. When the weld cannot be stress-relieved by solution annealing, the application of commercially available stress-mitigation processes such as low plasticity burnishing (LPB) and laser shock peening (LSP) may be used to produce near-surface compressive stresses. This study involved examination of cross-sectional samples of aged 1.25 inch thick welds of Alloy 22 plates using electron backscatter diffraction (EBSD) for TCP identification and micrograph analysis for TCP quantification. Precipitation in both the as-welded and LSP weld was observed primarily in inter-dendritic regions whilst precipitation in the LPB weld was in both inter- and intra-dendritic regions.
Date: January 26, 2005
Creator: El-Dasher, B S & Torres, S G
System: The UNT Digital Library
Low-Temperature Agining Behavior of U-6 wt% Nb (open access)

Low-Temperature Agining Behavior of U-6 wt% Nb

Phase stability and aging mechanisms in a water-quenched (WQ) U-6wt% Nb (U-14at% Nb) alloy artificially aged at 200 C and naturally aged at ambient temperature for 15 years have been investigated and studied using Vickers-hardness measurement, X-ray diffraction (XRD) analysis, and transmission electron microscopy (TEM) techniques. Age hardening/softening phenomenon is recorded from the artificially aged samples based upon the microhardness measurement. The age hardening can be readily rationalized by the occurrence of fine-scaled Nb segregation, or spinodal decomposition, within the {alpha}'' domains, which results in the formation of a modulated structure containing nano-scaled Nb-rich and Nb-lean domains. Prolonged aging leads to age softening of the alloy by coarsening of the modulated structure. Chemical ordering, or disorder-order phase transformation, is found within the naturally aged alloy according to TEM observations of antiphase domain boundaries (APBs) and superlattice diffraction patterns. A possible superlattice structure for the ordered {alpha}'' phase observed in the naturally aged sample and underlying low-temperature aging mechanisms are proposed.
Date: January 26, 2005
Creator: Hsiung, L L
System: The UNT Digital Library
Implementation of a New Nonnuclear Standard at LLNL (open access)

Implementation of a New Nonnuclear Standard at LLNL

The objective of this paper is to introduce the process and philosophies used to implement the new Work Smart Standard (WSS), ''Safety Basis Requirements for Nonnuclear Facilities at Lawrence Livermore National Laboratory Site Specific Standard'' (UCRL-ID-150214), approved in 2003 and revised January, 2004. This work relates directly to the following workshop theme: ''Improvements in Chemical, Biological, and Non-nuclear Safety Analysis.'' This paper will describe the approach used to implement the new nonnuclear standard at LLNL and corresponding guidance manual: ES&H Manual, Document 3.1. The varied activities can be broken down into three main parts: (1) Implementation Plan Schedule. The Implementation Plan includes the due dates for revising nonnuclear facility safety analysis documentation to meet the new standard. Implementation of the new methodology is being phased over a 4-year period. Each directorate was tasked to schedule the revision date for each of their nonnuclear facilities, using agreed upon priority-ranking criteria. (2) Program Infrastructure. This includes the development of training courses, procedures, a website and tools required to perform the work (i.e. Q List, de minimus list) or tools helpful to perform the work; such as a program to automate the classification of chemical inventories and establish maximum facility inventory limits (MFILs). …
Date: April 26, 2005
Creator: van Warmerdam, C
System: The UNT Digital Library
Helium Pot System for Maintaining Sample Temperature after Cryocooler Deactivation (open access)

Helium Pot System for Maintaining Sample Temperature after Cryocooler Deactivation

A system for maintaining a sample at a constant temperature below 10K after deactivating the cooling source is demonstrated. In this system, the cooling source is a GM cryocooler that is joined with the sample through an adaptor that consists of a helium pot and a resistive medium. Upon deactivating the cryocooler, the power applied to a heater located on the sample side of the resistive medium is decreased gradually to maintain an appropriate temperature rise across the resistive medium as the helium pot warms. The temperature is held constant in this manner without the use of solid or liquid cryogens and without mechanically disconnecting the sample from the cooler. Shutting off the cryocooler significantly reduces sample motion that results from vibration and expansion/contraction of the cold head housing. The reduction in motion permits certain processes that are very sensitive to sample position stability, but are not performed throughout the duration that the sample is at low-temperature. An apparatus was constructed to demonstrate this technique using a 4K GM cryocooler. Experimental and theoretical predictions indicate that when the helium pot is pressurized to the working pressure of the cryocooler's helium supply, a sample with continuous heat dissipation of several-hundred milliwatts …
Date: January 26, 2005
Creator: Haid, B J
System: The UNT Digital Library
Systems Analysis for Modular Versus Multi-Beam HIF Drivers (open access)

Systems Analysis for Modular Versus Multi-Beam HIF Drivers

Previous modeling for HIF drivers concentrated on designs in which 100 or more beams are grouped in an array and accelerated through a common set of induction cores. The total beam energy required by the target is achieved by the combination of final ion energy, current per beam and number of beams. Economic scaling favors a large number of small ({approx}1 cm dia.) beams. An alternative architecture has now been investigated, which we refer to as a modular driver. In this case, the driver is subdivided into many (>10) independent accelerators with one or many beams each. A key objective of the modular driver approach is to be able to demonstrate all aspects of the driver (source-to-target) by building a single, lower cost module compared to a full-scale, multi-beam driver. We consider and compare several design options for the modular driver including single-beam designs with solenoid instead of quadrupole magnets in order to transport the required current per module in a single beam, solenoid/quad combinations, and multi-beam, all-quad designs. The drivers are designed to meet the requirements of the hybrid target, which can accommodate a larger spot size than the distributed radiator target that was used for the Robust Point …
Date: January 26, 2005
Creator: Meier, W. R. & Logan, B. G.
System: The UNT Digital Library
Experimental characterization of initial conditions and spatio-temporal evolution of a small Atwood number Rayleigh-Taylor mixing layer (open access)

Experimental characterization of initial conditions and spatio-temporal evolution of a small Atwood number Rayleigh-Taylor mixing layer

The initial multi-mode interfacial velocity and density perturbations present at the onset of a small Atwood number, incompressible, miscible, Rayleigh-Taylor instability-driven mixing layer have been quantified using a combination of experimental techniques. The streamwise interfacial and spanwise interfacial perturbations were measured using high-resolution thermocouples and planar laser-induced fluorescence (PLIF), respectively. The initial multi-mode streamwise velocity perturbations at the two-fluid density interface were measured using particle-image velocimetry (PIV). It was found that the measured initial conditions describe an initially anisotropic state, in which the perturbations in the streamwise and spanwise directions are independent of one another. The evolution of various fluctuating velocity and density statistics, together with velocity and density variance spectra, were measured using PIV and high-resolution thermocouple data. The evolution of the velocity and density statistics is used to investigate the early-time evolution and the onset of strongly-nonlinear, transitional dynamics within the mixing layer. The early-time evolution of the density and vertical velocity variance spectra indicate that velocity fluctuations are the dominant mechanism driving the instability development. The implications of the present experimental measurements on the initialization of Reynolds-averaged turbulent transport and mixing models and of direct and large-eddy simulations of Rayleigh-Taylor instability-induced turbulence are discussed.
Date: September 26, 2005
Creator: Mueschke, N J; Andrews, M J & Schilling, O
System: The UNT Digital Library
Melting of Xenon to 80 GPa, p-d hybridization, and an ISRO liquid (open access)

Melting of Xenon to 80 GPa, p-d hybridization, and an ISRO liquid

Measurements made in a laser heated diamond-anvil cell are reported that extend the melting curve of Xe to 80 GPa and 3350 K. The steep lowering of the melting slope (dT/dP) that occurs near 17 GPa and 2750 K results from the hybridization of the p-like valence and d-like conduction states with the formation of clusters in the liquid having Icosahedral Short-Range Order (ISRO).
Date: July 26, 2005
Creator: Ross, M; Boehler, R & Soderlind, P
System: The UNT Digital Library
Visualization of Force Fields in Protein StructurePrediction (open access)

Visualization of Force Fields in Protein StructurePrediction

The force fields used in molecular computational biology are not mathematically defined in such a way that their mathematical representation would facilitate the straightforward application of volume visualization techniques. To visualize energy, it is necessary to define a spatial mapping for these fields. Equipped with such a mapping, we can generate volume renderings of the internal energy states in a molecule. We describe our force field, the spatial mapping that we used for energy, and the visualizations that we produced from this mapping. We provide images and animations that offer insight into the computational behavior of the energy optimization algorithms that we employ.
Date: April 26, 2005
Creator: Crawford, Clark; Kreylos, Oliver; Hamann, Bernd & Crivelli, Silvia
System: The UNT Digital Library
An Approach Towards a Long-life, Microwave-assisted H- Ion Soucrefor Proton Drivers (open access)

An Approach Towards a Long-life, Microwave-assisted H- Ion Soucrefor Proton Drivers

This paper reports on experiments aimed at developing a new high-intensity H{sup -} ion source with long lifetime whose concept had recently been introduced. Starting from the motivation for this effort, several steps of the earlier development work are recapitulated, and the performance of the latest design variant is discussed in detail. The basic concept consists in coupling an ECR ion source to a standard SNS multi-cusp H{sup -} ion source that is driven by pulsed dc, rather than rf, power. As a key result, an electron beam of 1.5 A current has been extracted from the ECR discharge operating at 1.9 kW c. w. power, and a maximum discharge current of 17.5 A was achieved in the H{sup -} ion source. Production of H{sup -} ions, however could not yet been demonstrated in the one, preliminary, experiment conducted so far. The paper concludes by outlining further envisaged development steps for the plasma generator and an expansion towards a novel extraction system.
Date: October 26, 2005
Creator: Keller, R.; Regis, M.; Wallig, J.; Hahto, S.; Monroy, M.; Ratti, A. et al.
System: The UNT Digital Library
Threshold Studies on TNT, Composition B, and C-4 Explosives Using the Steven Impact Test (open access)

Threshold Studies on TNT, Composition B, and C-4 Explosives Using the Steven Impact Test

Steven Impact Tests were performed at low velocity on the explosives TNT, Comp B, and C-4 in attempts to obtain a threshold for reaction. A 76 mm helium driven gas gun was used to accelerate the Steven Test projectiles up to approximately 200 m/s in attempts to react (ignite) the explosive samples. Blast overpressure gauges, acoustic microphones, standard video and high-speed photography were used to characterize the level of any high explosive reaction violence. No bulk reactions were observed in the TNT, Composition B, or C-4 explosive samples impacted up to velocities in the range of 190-200 m/s. This work will outline the experimental details and discuss the lack of reaction when compared to the reaction thresholds of other common explosives.
Date: September 26, 2005
Creator: Vandersall, K S; Switzer, L L & Garcia, F
System: The UNT Digital Library
Extended embedded-atom method for platinum nanoparticles (open access)

Extended embedded-atom method for platinum nanoparticles

We present a new technique to extend the embedded-atom method (EAM) for the simulations of non-bulk systems down to the atomic cluster level. To overcome the limitation of the traditional bulk-fit EAM interatomic potentials, bond characteristics from first-principles calculations are systematically included by introducing a local structure dependent prefactor with three additional parameters to the conventional EAM many-body term. The additional parameters improve the local potential landscape virtually for the entire range of atomic configuration space in a quantitative sense. The proposed scheme is applied to two different EAM function sets and validated for both bulk and non-bulk environments in elemental platinum. The obtained material properties, including the binding energies of Pt particles and the Pt adatom diffusion barrier on the Pt (111) surface, show a significant improvement over the conventional EAM formalism.
Date: September 26, 2005
Creator: Lee, B & Cho, K
System: The UNT Digital Library
TIME RESOLVED X-RAY SPOT DIAGNOSTIC (open access)

TIME RESOLVED X-RAY SPOT DIAGNOSTIC

A diagnostic was developed for the determination of temporal history of an X-ray spot. A pair of thin (0.5 mm) slits image the x-ray spot to a fast scintillator which is coupled to a fast detector, thus sampling a slice of the X-Ray spot. Two other scintillator/detectors are used to determine the position of the spot and total forward dose. The slit signal is normalized to the dose and the resulting signal is analyzed to get the spot size. The position information is used to compensate for small changes due to spot motion and misalignment. The time resolution of the diagnostic is about 1 ns and measures spots from 0.5 mm to over 3 mm. The theory and equations used to calculate spot size and position are presented, as well as data. The calculations assume a symmetric, Gaussian spot. The spot data is generated by the ETA II accelerator, a 2kA, 5.5 MeV, 60 ns electron beam focused on a Tantalum target. The spot generated is typically about 1 mm FWHM. Comparisons are made to an X-ray pinhole camera which images the X-Ray spot (in 2D) at four time slices.
Date: April 26, 2005
Creator: Richardson, R.; Guethlein, G.; Falabella, S.; Chambers, F.; Raymond, B. & Weir, J.
System: The UNT Digital Library
27Al and 1H Solid State NMR Studies Show Evidence of TiAl3 and TiH2 in Ti-doped NaAlH4 (open access)

27Al and 1H Solid State NMR Studies Show Evidence of TiAl3 and TiH2 in Ti-doped NaAlH4

Previous X-ray Diffraction (XRD) and Nuclear Magnetic Resonance (NMR) studies on Ti-doped NaAlH{sub 4} revealed the reaction products of two heavily doped (33.3 at.%) samples that were solvent-mixed and mechanically-milled. This investigation revealed that nano-crystalline or amorphous Al{sub 2}O{sub 3} forms from the possible coordination of aluminum with oxygen atom of the furan ring system from added tetrahydrofuran (THF) in the solvent-mixed sample, and that TiAl{sub 3} forms in mechanically-milled samples. The present paper provides a more sophisticated NMR investigation of the these materials. On heavily doped (33.3 at.%) solvent-mixed samples, {sup 27}Al Magic Angle Spinning (MAS) NMR {sup 27}Al multiple quantum MAS (MQMAS) indicates the presence of an oxide layer of Al{sub 2}O{sub 3} on the surfaces of potentially bulk nanocrystalline Ti, nanocrystalline TiAl{sub 3}, and/or metallic aluminum. The {sup 1}H MAS NMR data also indicate the possible coordination of aluminum with the oxygen atom in the THF. On heavily doped samples that were mechanically milled, {sup 27}Al MAS NMR and static NMR confirms the presence of TiAl{sub 3}. In addition, the {sup 1}H MAS NMR and {sup 1}H spin-lattice relaxation (T{sub 1}) measurements are consistent with the presence of TiH{sub 2}. These results are in agreement with recent …
Date: May 26, 2005
Creator: Herberg, J; Maxwell, R & Majzoub, E
System: The UNT Digital Library
The March 11, 2002 Masafi, United Arab Emirates Earthquake: Insights into the Seismotectonics of the Northern Oman Mountains (open access)

The March 11, 2002 Masafi, United Arab Emirates Earthquake: Insights into the Seismotectonics of the Northern Oman Mountains

A moderate (M{approx}5) earthquake struck the northeastern United Arab Emirates (UAE) and northern Oman on March 11, 2002. The event was felt over a wide area of the northern Emirates and was accompanied by smaller (felt) events before and after the March 11 main shock. The event was large enough to be detected and located by global networks at teleseismic distances. We estimated focal mechanism and depth from broadband complete regional waveform modeling. We report a normal mechanism with a slight right-lateral strike-slip component consistent with the large-scale tectonics. The normal component suggests relaxation of obducted crust of the Semail Ophilite (specifically, the Khor Fakkan Block) while the right-lateral strike-slip component of the mechanism is consistent with shear across the Oman Line. Felt earthquakes are rare in the region, however no regional seismic network exists in the UAE to determine local seismicity. This event offers a unique opportunity to study the active tectonics of the region as well as inform future studies of seismic hazard in the UAE and northern Oman.
Date: April 26, 2005
Creator: Rodgers, A.; Fowler, A.; Al-Amri, A. & Al-Enezi, A.
System: The UNT Digital Library
An embedded boundary method for the wave equation with discontinuous coefficients (open access)

An embedded boundary method for the wave equation with discontinuous coefficients

A second order accurate embedded boundary method for the two-dimensional wave equation with discontinuous wave propagation speed is described. The wave equation is discretized on a Cartesian grid with constant grid size and the interface (across which the wave speed is discontinuous) is allowed to intersect the mesh in an arbitrary fashion. By using ghost points on either side of the interface, previous embedded boundary techniques for the Neumann and Dirichlet problems are generalized to satisfy the jump conditions across the interface to second order accuracy. The resulting discretization of the jump conditions has the desirable property that each ghost point can be updated independently of all other ghost points, resulting in a fully explicit time-integration method. Numerical examples are given where the method is used to study electro-magnetic scattering of a plane wave by a dielectric cylinder. The numerical solutions are evaluated against the analytical solution due to Mie, and point-wise second order accuracy is confirmed.
Date: September 26, 2005
Creator: Kreiss, H O & Petersson, N A
System: The UNT Digital Library
Weather-based forecasts of California crop yields (open access)

Weather-based forecasts of California crop yields

Crop yield forecasts provide useful information to a range of users. Yields for several crops in California are currently forecast based on field surveys and farmer interviews, while for many crops official forecasts do not exist. As broad-scale crop yields are largely dependent on weather, measurements from existing meteorological stations have the potential to provide a reliable, timely, and cost-effective means to anticipate crop yields. We developed weather-based models of state-wide yields for 12 major California crops (wine grapes, lettuce, almonds, strawberries, table grapes, hay, oranges, cotton, tomatoes, walnuts, avocados, and pistachios), and tested their accuracy using cross-validation over the 1980-2003 period. Many crops were forecast with high accuracy, as judged by the percent of yield variation explained by the forecast, the number of yields with correctly predicted direction of yield change, or the number of yields with correctly predicted extreme yields. The most successfully modeled crop was almonds, with 81% of yield variance captured by the forecast. Predictions for most crops relied on weather measurements well before harvest time, allowing for lead times that were longer than existing procedures in many cases.
Date: September 26, 2005
Creator: Lobell, D B; Cahill, K N & Field, C B
System: The UNT Digital Library
A Constrained Optimization Algorithm for Total Energy Minimizationin Electronic Structure Calculation (open access)

A Constrained Optimization Algorithm for Total Energy Minimizationin Electronic Structure Calculation

A new direct constrained optimization algorithm forminimizing the Kohn-Sham (KS) total energy functional is presented inthis paper. The key ingredients of this algorithm involve projecting thetotal energy functional into a sequences of subspaces of small dimensionsand seeking the minimizer of total energy functional within eachsubspace. The minimizer of a subspace energy functional not only providesa search direction along which the KS total energy functional decreasesbut also gives an optimal "step-length" to move along this searchdirection. A numerical example is provided to demonstrate that this newdirect constrained optimization algorithm can be more efficient than theself-consistent field (SCF) iteration.
Date: July 26, 2005
Creator: Yang, Chao; Meza, Juan C. & Wang, Lin-Wang
System: The UNT Digital Library
Parallel Clustering Algorithms for Structured AMR (open access)

Parallel Clustering Algorithms for Structured AMR

We compare several different parallel implementation approaches for the clustering operations performed during adaptive gridding operations in patch-based structured adaptive mesh refinement (SAMR) applications. Specifically, we target the clustering algorithm of Berger and Rigoutsos (BR91), which is commonly used in many SAMR applications. The baseline for comparison is a simplistic parallel extension of the original algorithm that works well for up to O(10{sup 2}) processors. Our goal is a clustering algorithm for machines of up to O(10{sup 5}) processors, such as the 64K-processor IBM BlueGene/Light system. We first present an algorithm that avoids the unneeded communications of the simplistic approach to improve the clustering speed by up to an order of magnitude. We then present a new task-parallel implementation to further reduce communication wait time, adding another order of magnitude of improvement. The new algorithms also exhibit more favorable scaling behavior for our test problems. Performance is evaluated on a number of large scale parallel computer systems, including a 16K-processor BlueGene/Light system.
Date: October 26, 2005
Creator: Gunney, B T; Wissink, A M & Hysom, D A
System: The UNT Digital Library
Heterogeneity, growing lenght scales, and universality in thedynamicsof kinetically constrained lattice gases in two dimensions (open access)

Heterogeneity, growing lenght scales, and universality in thedynamicsof kinetically constrained lattice gases in two dimensions

We study dynamical heterogeneity and growing dynamical length scales in two kinetically constrained models, namely, the one- and two-vacancy assisted triangular lattice gases. One of the models is a strong glassformer and the other is a fragile glassformer. Both exhibit heterogeneous dynamics with broadly distributed timescales as seen in the distribution of persistence times. We show that the Stokes-Einstein relation is violated, to a greater degree in the fragile glassformer, and show how this violation is related to dynamic heterogeneity. Finally, we extract dynamical length scales from structure factors of mobile particles and show, quantitatively, the growth of this lengthscale as density increases. Our results indicate that the one-vacancy assisted lattice gas is in the same universality class as the one-spin facilitated Fredrickson-Andersen model, while the two-vacancy assisted model is in a different universality class. Our findings support the idea that the dynamics of supercooled liquids can be understood from the existence of a zero temperature dynamic critical point.
Date: June 26, 2005
Creator: Pan, Albert P.; Garrahan, Juan P. & Chandler, David
System: The UNT Digital Library
Using Partial Genomic Fosmid Libraries for Sequencing CompleteOrganellar Genomes (open access)

Using Partial Genomic Fosmid Libraries for Sequencing CompleteOrganellar Genomes

Organellar genome sequences provide numerous phylogenetic markers and yield insight into organellar function and molecular evolution. These genomes are much smaller in size than their nuclear counterparts; thus, their complete sequencing is much less expensive than total nuclear genome sequencing, making broader phylogenetic sampling feasible. However, for some organisms it is challenging to isolate plastid DNA for sequencing using standard methods. To overcome these difficulties, we constructed partial genomic libraries from total DNA preparations of two heterotrophic and two autotrophic angiosperm species using fosmid vectors. We then used macroarray screening to isolate clones containing large fragments of plastid DNA. A minimum tiling path of clones comprising the entire genome sequence of each plastid was selected, and these clones were shotgun-sequenced and assembled into complete genomes. Although this method worked well for both heterotrophic and autotrophic plants, nuclear genome size had a dramatic effect on the proportion of screened clones containing plastid DNA and, consequently, the overall number of clones that must be screened to ensure full plastid genome coverage. This technique makes it possible to determine complete plastid genome sequences for organisms that defy other available organellar genome sequencing methods, especially those for which limited amounts of tissue are available.
Date: August 26, 2005
Creator: McNeal, Joel R.; Leebens-Mack, James H.; Arumuganathan, K.; Kuehl, Jennifer V.; Boore, Jeffrey L. & dePamphilis, Claude W.
System: The UNT Digital Library