States

300 Area D4 Project Fiscal Year 2009 Building Completion Report (open access)

300 Area D4 Project Fiscal Year 2009 Building Completion Report

This report summarizes the deactivation, decontamination, decommissioning, and demolition activities of seven facilities in the 300 Area of the Hanford Site in fiscal year 2009. The D4 of these facilities included characterization; engineering; removal of hazardous and radiologically contaminated materials; equipment removal; utility disconnection; deactivation, decontamination, demolition of the structure; and stabilization or removal of slabs and foundations. This report also summarizes the nine below-grade slabs/foundations removed in FY09 of buildings demolished in previous fiscal years.
Date: January 27, 2010
Creator: Skwarek, B. J.
Object Type: Report
System: The UNT Digital Library
Building the RHIC tracking lattice model (open access)

Building the RHIC tracking lattice model

In this note we outline the procedure to build a realistic lattice model for the RHIC beam-beam tracking simulation. We will install multipole field errors in the arc main dipoles, arc main quadrupols and interaction region magnets (DX, D0, and triplets) and introduce a residual closed orbit, tune ripples, and physical apertures in the tracking lattice model. Nonlinearities such as local IR multipoles, second order chromaticies and third order resonance driving terms are also corrected before tracking.
Date: January 27, 2010
Creator: Luo, Y.; Fischer, W. & Tepikian, S.
Object Type: Report
System: The UNT Digital Library
Creep and Creep-Fatigue Crack Growth at Structural Discontinuities and Welds (open access)

Creep and Creep-Fatigue Crack Growth at Structural Discontinuities and Welds

The subsection ASME NH high temperature design procedure does not admit crack-like defects into the structural components. The US NRC identified the lack of treatment of crack growth within NH as a limitation of the code and thus this effort was undertaken. This effort is broken into two parts. Part 1, summarized here, involved examining all high temperature creep-fatigue crack growth codes being used today and from these, the task objective was to choose a methodology that is appropriate for possible implementation within NH. The second part of this task, which has just started, is to develop design rules for possible implementation within NH. This second part is a challenge since all codes require step-by-step analysis procedures to be undertaken in order to assess the crack growth and life of the component. Simple rules for design do not exist in any code at present. The codes examined in this effort included R5, RCC-MR (A16), BS 7910, API 579, and ATK (and some lesser known codes). There are several reasons that the capability for assessing cracks in high temperature nuclear components is desirable. These include: (1) Some components that are part of GEN IV reactors may have geometries that have sharp …
Date: January 27, 2010
Creator: Brust, F. W.; Wilkowski, G. M.; Krishnaswamy, P. & Wichman, Keith
Object Type: Report
System: The UNT Digital Library
Environmental Monitoring Plan, Revision 5 (open access)

Environmental Monitoring Plan, Revision 5

The purpose of environmental monitoring is to promote the early identification of, and response to, potential adverse environmental impacts associated with Lawrence Livermore National Laboratory (LLNL) operations. Environmental monitoring supports the Integrated Safety Management System (ISMS), International Organization for Standardization (ISO) 14001 Environmental Management Systems standard, and U. S. Department of Energy (DOE) Order 450.1A, Environmental Protection Program. Specifically, in conformance with DOE Order 450.1A, Attachment 1, paragraph 1(b)(5), environmental monitoring enables LLNL to detect, characterize, and respond to releases from LLNL activities; assess impacts; estimate dispersal patterns in the environment; characterize the pathways of exposure to members of the public; characterize the exposures and doses to individuals and to the population; and to evaluate the potential impacts to the biota in the vicinity of LLNL. Environmental monitoring also serves to demonstrate compliance with permits and other regulatory requirements. The Environmental Monitoring Plan (EMP) addresses the sample collection and analytical work supporting environmental monitoring to ensure the following: (1) A consistent system for collecting, assessing, and documenting environmental data of known and documented quality. (2) A validated and consistent approach for sampling and analysis of samples to ensure laboratory data meets program-specific needs and requirements within the framework of a …
Date: January 27, 2010
Creator: Gallegos, G M; Blake, R G; Bertoldo, N A; Campbell, C G; Coty, J; Folks, K et al.
Object Type: Report
System: The UNT Digital Library
Integration of the Mini-Sulfide Sulfite Anthraquinone (MSS-AQ) Pulping Process and Black Liquor Gasification in a Pulp Mill (open access)

Integration of the Mini-Sulfide Sulfite Anthraquinone (MSS-AQ) Pulping Process and Black Liquor Gasification in a Pulp Mill

As many of the recovery boilers and other pieces of large capital equipment of U.S. pulp mills are nearing the end of their useful life, the pulp and paper industry will soon need to make long-term investments in new technologies. The ability to install integrated, complete systems that are highly efficient will impact the industry’s energy use for decades to come. Developing a process for these new systems is key to the adoption of state-of-the-art technologies in the Forest Products industry. This project defined an integrated process model that combines mini-sulfide sulfite anthraquinone (MSS-AQ) pulping and black liquor gasification with a proprietary desulfurization process developed by the Research Triangle Institute. Black liquor gasification is an emerging technology that enables the use of MSS-AQ pulping, which results in higher yield, lower bleaching cost, lower sulfur emissions, and the elimination of causticization requirements. The recently developed gas cleanup/absorber technology can clean the product gas to a state suitable for use in a gas turbine and also regenerate the pulping chemicals needed to for the MSS-AQ pulping process. The combination of three advanced technologies into an integrated design will enable the pulping industry to achieve a new level of efficiency, environmental performance, and …
Date: January 27, 2010
Creator: Hasan Jameel, North Carolina State University; Adrianna Kirkman, North Carolina State University; Ravi Chandran,Thermochem Recovery International Brian Turk Research Triangle Institute & Brian Green, Research Triangle Institute
Object Type: Report
System: The UNT Digital Library
MEASUREMENTS TAKEN IN SUPPORT OF QUALIFICATION OF PROCESSING SAVANNAH RIVER SITE LOW-LEVEL LIQUID WASTE INTO SALTSTONE (open access)

MEASUREMENTS TAKEN IN SUPPORT OF QUALIFICATION OF PROCESSING SAVANNAH RIVER SITE LOW-LEVEL LIQUID WASTE INTO SALTSTONE

The Saltstone Facility at the Savannah River Site (SRS) immobilizes low-level liquid waste into Saltstone to be disposed of in the Z-Area Saltstone Disposal Facility, Class Three Landfill. In order to meet the permit conditions and regulatory limits set by the South Carolina Department of Health and Environmental Control (SCDHEC), the Resource Conservation and Recovery Act (RCRA) and the Environmental Protection Agency (EPA), both the low-level salt solution and Saltstone samples are analyzed quarterly. Waste acceptance criteria (WAC) are designed to confirm the salt solution sample from the Tank Farm meets specific radioactive and chemical limits. The toxic characteristic leaching procedure (TCLP) is used to confirm that the treatment has immobilized the hazardous constituents of the salt solution. This paper discusses the methods used to characterize the salt solution and final Saltstone samples from 2007-2009.
Date: January 27, 2010
Creator: Reigel, M.; Bibler, N.; Diprete, C.; Cozzi, A.; Staub, A. & Ray, J.
Object Type: Article
System: The UNT Digital Library
Optimizing of the higher order mode dampers in the 56MHz SRF cavity (open access)

Optimizing of the higher order mode dampers in the 56MHz SRF cavity

Earlier, we reported that a 56 MHz cavity was designed for a luminosity upgrade of the RHIC, and presented the requirements for Higher Order Mode (HOM) damping, the design of the HOM dampers, along with measurements and simulations of the HOM dampers. In this report, we describe our optimization of the dampers performance, and the modifications we made to their original design. We also optimized the number of the HOM dampers, and tested different configurations of locations for them.
Date: January 27, 2010
Creator: Wu, Q. & Ben-Zvi, Ilan
Object Type: Report
System: The UNT Digital Library
The Porcelain Crab Transcriptome and PCAD, the Porcelain Crab Microarray and Sequence Database (open access)

The Porcelain Crab Transcriptome and PCAD, the Porcelain Crab Microarray and Sequence Database

Background: With the emergence of a completed genome sequence of the freshwater crustacean Daphnia pulex, construction of genomic-scale sequence databases for additional crustacean sequences are important for comparative genomics and annotation. Porcelain crabs, genus Petrolisthes, have been powerful crustacean models for environmental and evolutionary physiology with respect to thermal adaptation and understanding responses of marine organisms to climate change. Here, we present a large-scale EST sequencing and cDNA microarray database project for the porcelain crab Petrolisthes cinctipes. Methodology/Principal Findings: A set of ~;;30K unique sequences (UniSeqs) representing ~;;19K clusters were generated from ~;;98K high quality ESTs from a set of tissue specific non-normalized and mixed-tissue normalized cDNA libraries from the porcelain crab Petrolisthes cinctipes. Homology for each UniSeq was assessed using BLAST, InterProScan, GO and KEGG database searches. Approximately 66percent of the UniSeqs had homology in at least one of the databases. All EST and UniSeq sequences along with annotation results and coordinated cDNA microarray datasets have been made publicly accessible at the Porcelain Crab Array Database (PCAD), a feature-enriched version of the Stanford and Longhorn Array Databases.Conclusions/Significance: The EST project presented here represents the third largest sequencing effort for any crustacean, and the largest effort for any crab species. …
Date: January 27, 2010
Creator: Tagmount, Abderrahmane; Wang, Mei; Lindquist, Erika; Tanaka, Yoshihiro; Teranishi, Kristen S.; Sunagawa, Shinichi et al.
Object Type: Article
System: The UNT Digital Library
Reply to Comment on"Coherent rho0 photoproduction in bulk matter at high energies" (open access)

Reply to Comment on"Coherent rho0 photoproduction in bulk matter at high energies"

In their interesting comment on 'Coherent {rho}0 photoproduction in bulk matter at high energies', Rogers and Strikman point out that, at high energies, q{bar q} dipoles with small separations (d) become more important, and that most of the growth of the cross-section is 'driven by the increasingly large contributions from small size (high mass) configurations'; at photon energies of 10{sup 20} eV, over half of the total cross-section is due to dipoles smaller than 0.25 fm. They state that charm production will increase, and may be as much as 30% of the cross-section. The coherent photoproduction of heavier states requires higher energies than coherent {rho} photoproduction, because the formation length scales as 1/M{sup 2}. For the J/{psi}, the required photon energy is 14 times higher than for the {rho}. We agree that higher-mass states become important at higher energies. However, at this point, additional factors come into play; as we note after Eq. (7), our calculation is only properly normalized when the conversion probability is relatively small. At the energies where coherent production of high mass states is possible, the coherent {rho} production probability is large, and it is necessary to consider reverse reactions such as vector meson 'back-propagation' into …
Date: January 27, 2010
Creator: Couderc, E. & Klein, S.
Object Type: Article
System: The UNT Digital Library
Sim Track User's Manual (v 1.0) (open access)

Sim Track User's Manual (v 1.0)

SimTrack is a simple c++ library designed for the numeric particle tracking in the high energy accelerators. It adopts the 4th order symplectic integrator for the optical transport in the magnetic elements. The 4-D and 6-D weak-strong beam-beam treatments are integrated in it for the beam-beam studies. SimTrack is written with c++ class and standard template library. It provides versatile functions to manage elements and lines. It supports a large range of types of elements. New type of element can be easily created in the library. SimTrack calculates Twiss, coupling and fits tunes, chromaticities and corrects closed orbits. AC dipole and AC multipole are available in this library. SimTrack allows change of element parameters during tracking.
Date: January 27, 2010
Creator: Luo, Y.
Object Type: Report
System: The UNT Digital Library
A Survey of Wireless Communications for the Electric Power System (open access)

A Survey of Wireless Communications for the Electric Power System

A key mission of the U.S. Department of Energy (DOE) Office of Electricity Delivery and Energy Reliability (OE) is to enhance the security and reliability of the nation’s energy infrastructure. Improving the security of control systems, which enable the automated control of our energy production and distribution, is critical for protecting the energy infrastructure and the integral function that it serves in our lives. The DOE-OE Control Systems Security Program provides research and development to help the energy industry actively pursue advanced security solutions for control systems. The focus of this report is analyzing how, where, and what type of wireless communications are suitable for deployment in the electric power system and to inform implementers of their options in wireless technologies. The discussions in this report are applicable to enhancing both the communications infrastructure of the current electric power system and new smart system deployments. The work described in this report includes a survey of the following wireless technologies: • IEEE 802.16 d and e (WiMAX) • IEEE 802.11 (Wi-Fi) family of a, b, g, n, and s • Wireless sensor protocols that use parts of the IEEE 802.15.4 specification: WirelessHART, International Society of Automation (ISA) 100.11a, and Zigbee • …
Date: January 27, 2010
Creator: Akyol, Bora A.; Kirkham, Harold; Clements, Samuel L. & Hadley, Mark D.
Object Type: Report
System: The UNT Digital Library
Analysis of the Younger Dryas Impact Layer (open access)

Analysis of the Younger Dryas Impact Layer

We have uncovered a thin layer of magnetic grains and microspherules, carbon spherules, and glass-like carbon at nine sites across North America, a site in Belgium, and throughout the rims of 16 Carolina Bays. It is consistent with the ejecta layer from an impact event and has been dated to 12.9 ka BP coinciding with the onset of Younger Dryas (YD) cooling and widespread megafaunal extinctions in North America. At many locations the impact layer is directly below a black mat marking the sudden disappearance of the megafauna and Clovis people. The distribution pattern of the Younger Dryas boundary (YDB) ejecta layer is consistent with an impact near the Great Lakes that deposited terrestrial-like ejecta near the impact site and unusual, titanium-rich projectile-like ejecta further away. High water content associated with the ejecta, up to 28 at. percent hydrogen (H), suggests the impact occurred over the Laurentide Ice Sheet. YDB microspherules and magnetic grains are highly enriched in TiO{sub 2}. Magnetic grains from several sites are enriched in iridium (Ir), up to 117 ppb. The TiO{sub 2}/FeO, K/Th, TiO{sub 2}/Zr, Al{sub 2}O{sub 3}/FeO+MgO, CaO/Al{sub 2}O{sub 3}, REE/ chondrite, FeO/MnO ratios and SiO{sub 2}, Na{sub 2}O, K{sub 2}O, Cr{sub 2}O{sub 3}, …
Date: February 27, 2010
Creator: Firestone, Richard B.; West, Allen; Revay, Zsolt; Hagstrum, Jonathon T,; Belgya, Thomas; Hee, Shane S. Que et al.
Object Type: Article
System: The UNT Digital Library
Final Report on CRADA ORNL05-0703 (open access)

Final Report on CRADA ORNL05-0703

The work of this CRADA has been focused on the development of Rolling-Assisted Biaxially Textured Substrate (RABiTS)-based high-temperature superconducting (HTS) coated conductor technology that is in the pre-commercial development stage. Metal-Oxide Technologies, Inc. (MetOx) is a Houston-based small business that is developing and manufacturing second-generation (2G) HTS wire using an all-Metallo-Organic Chemical Vapor Deposition (MOCVD) process, including the buffer layers and HTS coating. Advances toward commercialization were enabled by coordinated interactions that facilitated the synthesis, characterization, and iterative optimization of prototype 2G wire segments.
Date: April 27, 2010
Creator: Christen, D.K.
Object Type: Report
System: The UNT Digital Library
HEP Science Network Requirements (open access)

HEP Science Network Requirements

The Energy Sciences Network (ESnet) is the primary provider of network connectivity for the US Department of Energy Office of Science, the single largest supporter of basic research in the physical sciences in the United States. In support of the Office of Science programs, ESnet regularly updates and refreshes its understanding of the networking requirements of the instruments, facilities, scientists, and science programs that it serves. This focus has helped ESnet to be a highly successful enabler of scientific discovery for over 20 years. In August 2009 ESnet and the Office of High Energy Physics (HEP), of the DOE Office of Science, organized a workshop to characterize the networking requirements of the programs funded by HEP. The International HEP community has been a leader in data intensive science from the beginning. HEP data sets have historically been the largest of all scientific data sets, and the communty of interest the most distributed. The HEP community was also the first to embrace Grid technologies. The requirements identified at the workshop are summarized below, and described in more detail in the case studies and the Findings section: (1) There will be more LHC Tier-3 sites than orginally thought, and likely more Tier-2 …
Date: April 27, 2010
Creator: Bakken, Jon; Barczyk, Artur; Blatecky, Alan; Boehnlein, Amber; Carlson, Rich; Chekanov, Sergei et al.
Object Type: Report
System: The UNT Digital Library
MODEL 9975 LIFE EXTENSION PACKAGE 2 FINAL REPORT (open access)

MODEL 9975 LIFE EXTENSION PACKAGE 2 FINAL REPORT

Life extension package LE2 (9975-04162) was instrumented and subjected to an extreme temperature environment for 81 weeks. During this time, the maximum fiberboard temperature was {approx}240 - 250 degrees F, and was established by a combination of internal heat (19 watts) and external heat. This temperature matches the fiberboard continuous service rating, although such extremes are not expected for normal operation in KAMS. Several tests and parameters were used to characterize the package components. Results from these tests generally indicate agreement between this full-scale shipping package and small-scale laboratory tests on fiberboard and O-ring samples. These areas of agreement include the rate of fiberboard weight loss, change in fiberboard thermal conductivity, fiberboard compression strength, and O-ring compression set. In addition, this package provides an example of the extent to which moisture within the fiberboard can redistribute in the presence of a temperature gradient such as might be created by a 19 watt internal heat load. Moisture re distribution in this package was further exaggerated by a majority of the fiberboard being heated to above the boiling point of water. The majority of water within the fiberboard migrated to the bottom layers of fiberboard, where it contributed to accelerated degradation beyond …
Date: April 27, 2010
Creator: Daugherty, W.
Object Type: Report
System: The UNT Digital Library
Multi-keV X-Ray Source Development Experiments on the National Ignition Facility (open access)

Multi-keV X-Ray Source Development Experiments on the National Ignition Facility

None
Date: April 27, 2010
Creator: Fournier, K B; May, M J; Colvin, J D; Kane, J O; Schneider, M; Dewald, E et al.
Object Type: Article
System: The UNT Digital Library
A Pilot Study of the Effectiveness of Indoor Plants for Removal of Volatile Organic Compounds in Indoor Air in a Seven-Story Office Building (open access)

A Pilot Study of the Effectiveness of Indoor Plants for Removal of Volatile Organic Compounds in Indoor Air in a Seven-Story Office Building

The Paharpur Business Centre and Software Technology Incubator Park (PBC) is a 7 story, 50,400 ft{sup 2} office building located near Nehru Place in New Delhi India. The occupancy of the building at full normal operations is about 500 people. The building management philosophy embodies innovation in energy efficiency while providing full service and a comfortable, safe, healthy environment to the occupants. Provision of excellent Indoor Air Quality (IAQ) is an expressed goal of the facility, and the management has gone to great lengths to achieve it. This is particularly challenging in New Delhi, where ambient urban pollution levels rank among the worst on the planet. The approach to provide good IAQ in the building includes a range of technical elements: air washing and filtration of ventilation intake air from rooftop air handler, the use of an enclosed rooftop greenhouse with a high density of potted plants as a bio-filtration system, dedicated secondary HVAC/air handling units on each floor with re-circulating high efficiency filtration and UVC treatment of the heat exchanger coils, additional potted plants for bio-filtration on each floor, and a final exhaust via the restrooms located at each floor. The conditioned building exhaust air is passed through an …
Date: April 27, 2010
Creator: Apte, Michael G. & Apte, Joshua S.
Object Type: Report
System: The UNT Digital Library
Semi-annual monitoring report for Barnes, Kansas, for July-December 2009. (open access)

Semi-annual monitoring report for Barnes, Kansas, for July-December 2009.

The Commodity Credit Corporation of the U.S. Department of Agriculture (CCC/USDA) operated a grain storage facility at Barnes, Kansas, during most of the interval 1949-1974. Carbon tetrachloride contamination was initially detected in 1986 in the town's public water supply wells. In 2006-2007, the CCC/USDA conducted a comprehensive targeted investigation at and near its former property in Barnes to characterize this contamination. Those results were reported previously (Argonne 2008a). In November 2007, the CCC/USDA began quarterly groundwater monitoring at Barnes. The monitoring is being conducted on behalf of the CCC/USDA by Argonne National Laboratory, in accord with the recommendations made in the report for the 2006-2007 targeted investigation (Argonne 2008a). The objective is to monitor the carbon tetrachloride contamination identified in the groundwater at Barnes. The sampling is presently conducted in a network of 28 individual monitoring wells (at 19 distinct locations), 2 public water supply wells, and 1 private well (Figure 1.1). The results of the 2006-2007 targeted investigation and the subsequent monitoring events (Argonne 2008a-d, 2009a,b) demonstrated the presence of carbon tetrachloride contamination in groundwater at levels exceeding the Kansas Department of Health and Environment (KDHE) Tier 2 risk-based screening level (RBSL) of 5.0 {micro}g/L for this compound. The …
Date: April 27, 2010
Creator: LaFreniere, L. M. & Division, Environmental Science
Object Type: Report
System: The UNT Digital Library
TANK SPACE ALTERNATIVES ANALYSIS REPORT (open access)

TANK SPACE ALTERNATIVES ANALYSIS REPORT

This report addresses the projected shortfall of double-shell tank (DST) space starting in 2018. Using a multi-variant methodology, a total of eight new-term options and 17 long-term options for recovering DST space were evaluated. These include 11 options that were previously evaluated in RPP-7702, Tank Space Options Report (Rev. 1). Based on the results of this evaluation, two near-term and three long-term options have been identified as being sufficient to overcome the shortfall of DST space projected to occur between 2018 and 2025.
Date: April 27, 2010
Creator: DA, TURNER; NW, KIRCH; DJ, WASHENFELDER; PS, SCHAUS; DD, WODRICH & SA, WIEGMAN
Object Type: Report
System: The UNT Digital Library

Thermal Management of Power Semiconductor Packages - Matching Cooling Technologies with Packaging Technologies

Heat removal for power semiconductor devices is critical for robust operation. Because there are different packaging options, different thermal management technologies, and a range of applications, there is a need for a methodology to match cooling technologies and package configurations to target applications. To meet this need, a methodology was developed to compare the sensitivity of cooling technologies on the overall package thermal performance over a range of power semiconductor packaging configurations. The results provide insight into the trade-offs associated with cooling technologies and package configurations. The approach provides a method for comparing new developments in power semiconductor packages and identifying potential thermal control technologies for the package. The results can help users select the appropriate combination of packaging configuration and cooling technology for the desired application.
Date: April 27, 2010
Creator: Bennion, K. & Moreno, G.
Object Type: Presentation
System: The UNT Digital Library
Centroid Position as a Function of Total Counts in a Windowed CMOS Image of a Point Source (open access)

Centroid Position as a Function of Total Counts in a Windowed CMOS Image of a Point Source

We obtained 960,200 22-by-22-pixel windowed images of a pinhole spot using the Teledyne H2RG CMOS detector with un-cooled SIDECAR readout. We performed an analysis to determine the precision we might expect in the position error signals to a telescope's guider system. We find that, under non-optimized operating conditions, the error in the computed centroid is strongly dependent on the total counts in the point image only below a certain threshold, approximately 50,000 photo-electrons. The LSST guider camera specification currently requires a 0.04 arcsecond error at 10 Hertz. Given the performance measured here, this specification can be delivered with a single star at 14th to 18th magnitude, depending on the passband.
Date: May 27, 2010
Creator: Wurtz, R. E.; Olivier, S.; Riot, V.; Hanold, B. J. & Figer, D. F.
Object Type: Article
System: The UNT Digital Library
COMPACTION OF FIBERBOARD OVERPACK MATERIALS IN A 9975 SHIPPING PACKAGE (open access)

COMPACTION OF FIBERBOARD OVERPACK MATERIALS IN A 9975 SHIPPING PACKAGE

Compaction of lower layers in the 9975 fiberboard overpack has been observed in packages that contain excess moisture. Dynamic loading of the package during transportation may also contribute to compaction of the fiberboard. This condition is being tested and analyzed to better understand these compaction mechanisms and provide a basis from which to evaluate their impact to the safety basis for transportation (Safety Analysis Report for Packaging) and storage (facility Design Safety Analysis) at the Savannah River Site (SRS). A test program has been developed and is being implemented to identify the extent of the compaction as a function of fiberboard moisture and typical transport dynamic loadings. Test conditions will be compared to regulatory requirements for dynamic loading. Characterization of the recovery of short-term compaction following the application of dynamic loading is also being evaluated. Interim results from this test program will be summarized.
Date: May 27, 2010
Creator: Stefek, T.; Daugherty, W.; Estochen, E. & Murphy, J.
Object Type: Article
System: The UNT Digital Library
Gap Closing/Finishing by Targeted Genomic Region Enrichment and Sequencing (open access)

Gap Closing/Finishing by Targeted Genomic Region Enrichment and Sequencing

Gap Closing/Finishing of draft genome assemblies is a labor and cost intensive process where several rounds of repetitious amplification and sequencing are required. Here we demonstrate a high throughput procedure where custom primers flanking gaps in draft genomes are designed. Primer libraries containing up to 4,000 unique pairs in independent droplets are merged with a fragmented genomic template. From this millions of picoliter scale droplets are formed, each one being the functional equivalent of an individual PCR reaction. The PCR products are concatenated and sequenced by Illumina which is then assembled and used for gap closure. Here we present an overall experimental strategy, primer design algorithm and initial results.
Date: May 27, 2010
Creator: Singh, Kanwar; Froula, Jeff; Trice, Hope; Pennacchio, Len A. & Chen, Feng
Object Type: Report
System: The UNT Digital Library
Ion Mobility Mass Spectrometry Direct Isotope Abundance Analysis (open access)

Ion Mobility Mass Spectrometry Direct Isotope Abundance Analysis

The nuclear forensics community is currently engaged in the analysis of illicit nuclear or radioactive material for the purposes of non-proliferations and attribution. One technique commonly employed for gathering nuclear forensics information is isotope analysis. At present, the state-of-the-art methodology for obtaining isotopic distributions is thermal ionization mass spectrometry (TIMS). Although TIMS is highly accurate at determining isotope distributions, the technique requires an elementally pure sample to perform the measurement. The required radiochemical separations give rise to sample preparation times that can be in excess of one to two weeks. Clearly, the nuclear forensics community is in need of instrumentation and methods that can expedite their decision making process in the event of a radiological release or nuclear detonation. Accordingly, we are developing instrumentation that couples a high resolution IM drift cell to the front end of a MS. The IM cell provides a means of separating ions based upon their collision cross-section and mass-to-charge ratio (m/z). Two analytes with the same m/z, but with different collision cross-sections (shapes) would exit the cell at different times, essentially enabling the cell to function in a similar manner to a gas chromatography (GC) column. Thus, molecular and atomic isobaric interferences can be …
Date: May 27, 2010
Creator: Manuel J. Manard, Stephan Weeks, Kevin Kyle
Object Type: Article
System: The UNT Digital Library