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Characterizing the Properties of Clusters of Galaxies As a Function of Luminosity and Redshift (open access)

Characterizing the Properties of Clusters of Galaxies As a Function of Luminosity and Redshift

Abstract: We report the application of the new Monte Carlo method, Smoothed Particle Inference (SPI, described in a pair of companion papers), towards analysis and interpretation of X-ray observations of clusters of galaxies with the XMM-Newton satellite. Our sample consists of publicly available well-exposed observations of clusters at redshifts z > 0.069, totaling 101 objects. We determine the luminosity and temperature structure of the X-ray emitting gas, with the goal to quantify the scatter and the evolution of the L{sub X} - T relation, as well as to investigate the dependence on cluster substructure with redshift. This work is important for the establishment of the potential robustness of mass estimates from X-ray data which in turn is essential towards the use of clusters for measurements of cosmological parameters. We use the luminosity and temperature maps derived via the SPI technique to determine the presence of cooling cores, via measurements of luminosity and temperature contrast. The L{sub X}-T relation is investigated, and we confirm that L{sub X} {proportional_to} T{sup 3}. We find a weak redshift dependence ({proportional_to} (1 + z){sup {beta}{sub LT}}, {beta}{sub LT} = 0.50 {+-} 0.34), in contrast to some Chandra results. The level of dynamical activity is established …
Date: February 24, 2009
Creator: Andersson, K.; Peterson, J. R.; Madejski, G. & Goobar, A.
System: The UNT Digital Library
First Step Towards a Non-Adiabatic Description of the Fission Process Based on the Generator Coordinate Method (open access)

First Step Towards a Non-Adiabatic Description of the Fission Process Based on the Generator Coordinate Method

Among the different theoretical approaches able to describe fission, microscopic ones can help us in the understanding of this process, as they have the advantage of describing the nuclear structure and the dynamics in a consistent manner. The sole input of the calculations is the nucleon-nucleon interaction. Such a microscopic time-dependent and quantum mechanical formalism has already been used, based on the Gaussian Overlap Approximation of the Generator Coordinate Method with the adiabatic approximation, to analyze the collective dynamics of low-energy fission in {sup 238}U. However, at higher energies, a few MeV above the barrier, the adiabatic approximation doesn't seem valid anymore. Indeed, manifestations of proton pair breaking have been observed in {sup 238}U and {sup 239}U for an excitation energy of 2.3 MeV above the barrier. Taking the intrinsic excitations into account during the fission process will enable us to determine the coupling between collective and intrinsic degrees of freedom, in particular from saddle to scission. Guidelines of the new formalism under development are presented and some preliminary results on overlaps between non excited and excited states are discussed.
Date: November 24, 2009
Creator: Bernard, R; Goutte, H; Gogny, D; Dubray, N & Lacroix, D
System: The UNT Digital Library
First Direct Observation of a Nearly Ideal Graphene Band Structure (open access)

First Direct Observation of a Nearly Ideal Graphene Band Structure

None
Date: November 24, 2009
Creator: Sprinkle, M; Siegel, D; Hu, Y; Hicks, J; Tejeda, A; Taleb-Ibrahimi, A et al.
System: The UNT Digital Library
STEAM REFORMING TECHNOLOGY DEMONSTRATION FOR THE DESTRUCTION OF ORGANICS ON ACTUAL DOE SAVANNAH RIVER SITE TANK 48H WASTE 9138 (open access)

STEAM REFORMING TECHNOLOGY DEMONSTRATION FOR THE DESTRUCTION OF ORGANICS ON ACTUAL DOE SAVANNAH RIVER SITE TANK 48H WASTE 9138

This paper describes the design of the Bench-scale Steam Reformer (BSR); a processing unit for demonstrating steam reforming technology on actual radioactive waste [1]. It describes the operating conditions of the unit used for processing a sample of Savannah River Site (SRS) Tank 48H waste. Finally, it compares the results from processing the actual waste in the BSR to processing simulant waste in the BSR to processing simulant waste in a large pilot scale unit, the Fluidized Bed Steam Reformer (FBSR), operated at Hazen Research Inc. in Golden, CO. The purpose of this work was to prove that the actual waste reacted in the same manner as the simulant waste in order to validate the work performed in the pilot scale unit which could only use simulant waste.
Date: February 24, 2009
Creator: Burket, P
System: The UNT Digital Library
Analysis of systematic errors in lateral shearing interferometry for EUV optical testing (open access)

Analysis of systematic errors in lateral shearing interferometry for EUV optical testing

Lateral shearing interferometry (LSI) provides a simple means for characterizing the aberrations in optical systems at EUV wavelengths. In LSI, the test wavefront is incident on a low-frequency grating which causes the resulting diffracted orders to interfere on the CCD. Due to its simple experimental setup and high photon efficiency, LSI is an attractive alternative to point diffraction interferometry and other methods that require spatially filtering the wavefront through small pinholes which notoriously suffer from low contrast fringes and improper alignment. In order to demonstrate that LSI can be accurate and robust enough to meet industry standards, analytic models are presented to study the effects of unwanted grating and detector tilt on the system aberrations, and a method for identifying and correcting for these errors in alignment is proposed. The models are subsequently verified by numerical simulation. Finally, an analysis is performed of how errors in the identification and correction of grating and detector misalignment propagate to errors in fringe analysis.
Date: February 24, 2009
Creator: Miyakawa, Ryan; Naulleau, Patrick & Goldberg, Kenneth A.
System: The UNT Digital Library
An Overview Of The ITER In-Vessel Coil Systems (open access)

An Overview Of The ITER In-Vessel Coil Systems

ELM mitigation is of particular importance in ITER in order to prevent rapid erosion or melting of the divertor surface, with the consequent risk of water leaks, increased plasma impurity content and disruptivity. Exploitable "natural" small or no ELM regimes might yet be found which extrapolate to ITER but this cannot be depended upon. Resonant Magnetic Perturbation has been added to pellet pacing as a tool for ITER to mitigate ELMs. Both are required, since neither method is fully developed and much work remains to be done. In addition, in-vessel coils enable vertical stabilization and RWM control. For these reasons, in-vessel coils (IVCs) are being designed for ITER to provide control of Edge Localized Modes (ELMs) in addition to providing control of moderately unstable resistive wall modes (RWMs) and the vertical stability (VS) of the plasma.
Date: September 24, 2009
Creator: Heitzenroeder, P. J.; Chrzanowski, J. H.; Dahlgren, F.; Hawryluk, R. J.; Loesser, G. D.; Neumeyer, C. et al.
System: The UNT Digital Library
RAPID MEASUREMENTS OF NEPTUNIUM OXIDATION STATES USING CHROMATOGRAPHIC RESINS (open access)

RAPID MEASUREMENTS OF NEPTUNIUM OXIDATION STATES USING CHROMATOGRAPHIC RESINS

The Savannah River Site's (SRS) H-Canyon facility uses ceric ammonium nitrate (CAN) to separate impure neptunium (Np) from a high sulfate feed stream. The material is processed using a two-pass solvent extraction purification which relies on CAN to oxidize neptunium to Np(VI) during the first pass prior to extraction. Spectrophotometric oxidation-state analyses normally used to validate successful oxidation to Np(VI) prior to extraction were compromised by this feed stream matrix. Therefore, a rapid chromatographic method to validate successful Np oxidation was developed using Eichrom Industries TRU and TEVA{reg_sign} resins. The method was validated and subsequently transferred to existing operations in the process analytical laboratories.
Date: March 24, 2009
Creator: Diprete, D; C Diprete, C; Mira Malek, M & Eddie Kyser, E
System: The UNT Digital Library
Heterozygosity for a Bub1 mutation causes female-specific germ cell aneuploidy in mice (open access)

Heterozygosity for a Bub1 mutation causes female-specific germ cell aneuploidy in mice

Aneuploidy, the most common chromosomal abnormality at birth and the main ascertained cause of pregnancy loss in humans, originates primarily from chromosome segregation errors during oogenesis. Here we report that heterozygosity for a mutation in the mitotic checkpoint kinase gene, Bub1, induces aneuploidy in female germ cells of mice, and that the effect increases with advancing maternal age. Analysis of Bub1 heterozygous oocytes showed that aneuploidy occurred primarily during the first meiotic division and involved premature sister chromatid separation. Furthermore, aneuploidy was inherited in zygotes and resulted in the loss of embryos after implantation. The incidence of aneuploidy in zygotes was sufficient to explain the reduced litter size in matings with Bub1 heterozygous females. No effects were seen in germ cells from heterozygous males. These findings show that Bub1 dysfunction is linked to inherited aneuploidy in female germ cells and may contribute to the maternal age-related increase in aneuploidy and pregnancy loss.
Date: June 24, 2009
Creator: Leland, Shawn; Nagarajan, Prabakaran; Polyzos, Aris; Thomas, Sharon; Samaan, George; Donnell, Robert et al.
System: The UNT Digital Library
Probing Reaction Dynamics of Transition-Metal Complexes in Solution via Time-Resolved X-ray Spectroscopy (open access)

Probing Reaction Dynamics of Transition-Metal Complexes in Solution via Time-Resolved X-ray Spectroscopy

We report measurements of the photo-induced Fe(II) spin crossover reaction dynamics in solution via time-resolved x-ray absorption spectroscopy. EXAFS measurements reveal that the iron?nitrogen bond lengthens by 0.21+-0.03 Angstrom in the high-spin transient excited state relative to the ground state. XANES measurements at the Fe L-edge show directly the influence of the structural change on the ligand-field splitting of the Fe(II) 3d orbitals associated with the spin transition.
Date: May 24, 2009
Creator: Huse, Nils; Khalil, Munira; Kim, Tae Kyu; Smeigh, Amanda L.; Jamula, Lindsey; McCusker, James K. et al.
System: The UNT Digital Library
CZT Virtual Frisch-grid Detector: Principles and Applications (open access)

CZT Virtual Frisch-grid Detector: Principles and Applications

Cadmium Zinc Telluride (CdZnTe or CZT) is a very attractive material for using as room-temperature semiconductor detectors, because it has a wide bandgap and a high atomic number. However, due to the material's poor hole mobility, several special techniques were developed to ensure its suitability for radiation detection. Among them, the virtual Frisch-grid CZT detector is an attractive option, having a simple configuration, yet delivering an outstanding spectral performance. The goal of our group in Brookhaven National Laboratory (BNL) is to improve the performance of Frisch-ring CZT detectors; most recently, that effort focused on the non-contacting Frisch-ring detector, allowing us to build an inexpensive, large-volume detector array with high energy-resolution and a large effective area. In this paper, the principles of virtual Frisch-grid detectors are described, especially BNL's innovative improvements. The potential applications of virtual Frisch-grid detectors are discussed, and as an example, a hand-held gamma-ray spectrometer using a CZT virtual Frischgrid detector array is introduced, which is a self-contained device with a radiation detector, readout circuit, communication circuit, and high-voltage supply. It has good energy resolution of 1.4% (FWHM of 662-keV peak) with a total detection volume of {approx}20 cm{sup 3}. Such a portable inexpensive device can be used …
Date: March 24, 2009
Creator: Cui,Y.; Bolotnikov, A.; Camarda, G.; Hossain, A. & James, R. B.
System: The UNT Digital Library
A dedicated superbend x-ray microdiffraction beamline for materials, geo-, and environmental sciences at the advanced light source (open access)

A dedicated superbend x-ray microdiffraction beamline for materials, geo-, and environmental sciences at the advanced light source

A new facility for microdiffraction strain measurements and microfluorescence mapping has been built on beamline 12.3.2 at the advanced light source of the Lawrence Berkeley National Laboratory. This beamline benefits from the hard x-radiation generated by a 6 T superconducting bending magnet (superbend) This provides a hard x-ray spectrum from 5 to 22 keV and a flux within a 1 mu m spot of ~;;5x109 photons/ s (0.1percent bandwidth at 8 keV). The radiation is relayed from the superbend source to a focus in the experimental hutch by a toroidal mirror. The focus spot is tailored bytwo pairs of adjustable slits, which serve as secondary source point. Inside the lead hutch, a pair of Kirkpatrick-Baez (KB) mirrors placed in a vacuum tank refocuses the secondary slit source onto the sample position. A new KB-bending mechanism with active temperature stabilization allows for more reproducible and stable mirror bending and thus mirror focusing. Focus spots around 1 um are routinely achieved and allow a variety of experiments, which have in common the need of spatial resolution. The effective spatial resolution (~;;0.2 mu m) is limited by a convolution of beam size, scan-stage resolution, and stage stability. A four-bounce monochromator consisting of two …
Date: March 24, 2009
Creator: Lawrence Berkeley National Laboratory. Advanced Light Source.
System: The UNT Digital Library
Probing the hydrogen-bond network of water via time-resolved soft x-ray spectroscopy (open access)

Probing the hydrogen-bond network of water via time-resolved soft x-ray spectroscopy

We report time-resolved studies of hydrogen bonding in liquid H2O, in response to direct excitation of the O-H stretch mode at 3 mu m, probed via soft x-ray absorption spectroscopy at the oxygen K-edge. This approach employs a newly developed nanofluidic cell for transient soft x-ray spectroscopy in liquid phase. Distinct changes in the near-edge spectral region (XANES) are observed, and are indicative of a transient temperature rise of 10K following transient laser excitation and rapid thermalization of vibrational energy. The rapid heating occurs at constant volume and the associated increase in internal pressure, estimated to be 8MPa, is manifest by distinct spectral changes that differ from those induced by temperature alone. We conclude that the near-edge spectral shape of the oxygen K-edge is a sensitive probe of internal pressure, opening new possibilities for testing the validity of water models and providing new insight into the nature of hydrogen bonding in water.
Date: April 24, 2009
Creator: Huse, Nils; Wen, Haidan; Nordlund, Dennis; Szilagyi, Erzsi; Daranciang, Dan; Miller, Timothy A. et al.
System: The UNT Digital Library
DEVELOPMENT OF GLASS COMPOSITIONS TO IMMOBILIZE ALKALI, ALKALINE EARTH, LANTHANIDE AND TRANSITION METAL FISSION PRODUCTS FROM NUCLEAR FUEL REPROCESSING (open access)

DEVELOPMENT OF GLASS COMPOSITIONS TO IMMOBILIZE ALKALI, ALKALINE EARTH, LANTHANIDE AND TRANSITION METAL FISSION PRODUCTS FROM NUCLEAR FUEL REPROCESSING

The Advanced Fuel Cycle Initiative (AFCI) waste management strategy revolves around specific treatment of individual or groups of separated waste streams. A goal for the separations processes is to efficiently manage the waste to be dispositioned as high level radioactive waste. The Advanced Fuel Cycle Initiative (AFCI) baseline technology for immobilization of the lanthanide (Ln) and transition metal fission product (TM) wastes is vitrification into a borosilicate glass. A current interest is to evaluate the feasibility of vitrifying combined waste streams to most cost effectively immobilize the wastes resulting from aqueous fuel reprocessing. Studies showed that high waste loadings are achievable for the Ln only (Option 1) stream. Waste loadings in excess of 60 wt % (on a calcined oxide basis) were demonstrated via a lanthanide borosilicate (LaBS) glass. The resulting glasses had excellent relative durability as determined by the Product Consistency Test (PCT). For a combined Ln and TM waste stream glass (Option 2), noble metal solubility was found to limit waste loading. However, the measured PCT normalized elemental releases for this glass were at least an order of magnitude below that of Environmental Assessment (EA) glass. Current efforts to evaluate the feasibility of vitrifying combined Ln, TM, alkali …
Date: June 24, 2009
Creator: Marra, J. & Billings, A.
System: The UNT Digital Library
Fast Pulsing Neutron Generators for Security Application (open access)

Fast Pulsing Neutron Generators for Security Application

Active neutron interrogation has been demonstrated to be an effective method of detecting shielded fissile material. A fast fall-time/fast pulsing neutron generator is needed primarily for differential die-away technique (DDA) interrogation systems. A compact neutron generator, currently being developed in Lawrence Berkeley National Laboratory, employs an array of 0.6-mm-dia apertures (instead of one 6-mm-dia aperture) such that gating the beamlets can be done with low voltage and a small gap to achieve sub-microsecond ion beam fall time and low background neutrons. Arrays of 16 apertures (4x4) and 100 apertures (10x10) have been designed and fabricated for a beam extraction experiment. The preliminary results showed that, using a gating voltage of 1200 V and a gap distance of 1 mm, the fall time of extracted ion beam pulses is approximately 0.15 mu s at beam energies of 1000 eV.
Date: April 24, 2009
Creator: Ji, Q.; Regis, M. & Kwan, J. W.
System: The UNT Digital Library
NSTX Protection And Interlock Systems For Coil And Powers Supply Systems (open access)

NSTX Protection And Interlock Systems For Coil And Powers Supply Systems

NSTX at Princeton Plasma Physics Laboratory (PPPL) requires sophisticated plasma positioning control system for stable plasma operation. TF magnetic coils and PF magnetic coils provide electromagnetic fields to position and shape the plasma vertically and horizontally respectively. NSTX utilizes twenty six coil power supplies to establish and initiate electromagnetic fields through the coil system for plasma control. A power protection and interlock system is utilized to detect power system faults and protect the TF coils and PF coils against excessive electromechanical forces, overheating, and over current. Upon detecting any fault condition the power system is restricted, and it is either prevented from initializing or suppressed to de-energize coil power during pulsing. Power fault status is immediately reported to the computer system. This paper describes the design and operation of NSTX's protection and interlocking system and possible future expansion.
Date: September 24, 2009
Creator: X. Zhao, S. Ramakrishnan, J. Lawson, C.Neumeyer, R. Marsala, H. Schneider, Engineering Operations
System: The UNT Digital Library
A Decade of NSTX Operations Using Collaborative Software (open access)

A Decade of NSTX Operations Using Collaborative Software

Since the beginning of the National Spherical Torus Experiment's (NSTX) research activities in 1999, open-source and collaborative software have been used extensively for experimental operations. The software included Experimental Physics and Industrial Control System (EPICS) and the Model Data System plus (MDSplus). This paper will begin with a retrospective of ten years of integrated computing, control, and data analysis on NSTX. A variety of practical issues will be reviewed such as: system reliability, availability, and maintainability; using open source software with commercialoff- the-shelf (COTS) hardware; obsolescence and remaining current. Recent improvements, current status, and emerging issues will be presented. Numerous proposals for NSTX upgrades have been made that will extend the performance and operating lifetime of NSTX. In light of this, a collective strategy for improving NSTX's collaborative software model for a new decade of operations will be examined.
Date: September 24, 2009
Creator: P. Sichta, W. Davis, J. Dong, D. Mastrovito, G. Tchilinguirian, G. Zimmer
System: The UNT Digital Library
Restructuring of hex-Pt(100) under CO gas environments: formation of 2-D nanoclusters (open access)

Restructuring of hex-Pt(100) under CO gas environments: formation of 2-D nanoclusters

The atomic-scale restructuring of hex-Pt(100) induced by carbon monoxide with a wide pressure range was studied with a newly designed chamber-in-chamber high-pressure STM and theoretical calculations. Both experimental and DFT calculation results show that CO molecules are bound to Pt nanoclusters through a tilted on-top configuration with a separation of {approx}3.7-4.1 {angstrom}. The phenomenon of restructuring of metal catalyst surfaces induced by adsorption, and in particular the formation of small metallic clusters suggests the importance of studying structures of catalyst surfaces under high pressure conditions for understanding catalytic mechanisms.
Date: April 24, 2009
Creator: Tao, Feng; Dag, Sefa; Wang, Lin-Wang; Liu, Zhi; Butcher, Derek; Salmeron, Miquel et al.
System: The UNT Digital Library
Metrology Techniques for the Assembly of NCSX (open access)

Metrology Techniques for the Assembly of NCSX

In support of the National Compact Stellerator Experiment (NCSX), stellerator assembly activities continued this past year at the Princeton Plasma Physics Laboratory (PPPL) in partnership with the Oak Ridge National Laboratory (ORNL). The construction program saw the completion of the first two Half Field-Period Assemblies (HPA), each consisting of three modular coils. The full machine includes six such sub-assemblies. A single HPA consists of three of the NCSX modular coils wound and assembled at PPPL. These geometrically-complex threedimensional coils were wound using computer-aided metrology and CAD models to tolerances within +/- 0.5mm. The assembly of these coils required similar accuracy on a larger scale with the added complexity of more individual parts and fewer degrees of freedom for correction. Several new potential positioning issues developed for which measurement and control techniques were developed. To accomplish this, CAD coordinate-based computer metrology equipment and software similar to the solutions employed for winding the modular coils was used. Given the size of the assemblies, the primary tools were both interferometeraided and Absolute Distance Measurement (ADM)-only based laser trackers. In addition, portable Coordinate Measurement Machine (CMM) arms and some novel indirect measurement techniques were employed. This paper will detail both the use of CAD …
Date: September 24, 2009
Creator: C. Priniski, T. Dodson, M. Duco, S. Raftopoulos, R. Ellis, and A. Brooks
System: The UNT Digital Library
Point Defect Characterization in CdZnTe (open access)

Point Defect Characterization in CdZnTe

Measurements of the defect levels and performance testing of CdZnTe detectors were performed by means of Current Deep Level Transient Spectroscopy (I-DLTS), Transient Charge Technique (TCT), Current versus Voltage measurements (I-V), and gamma-ray spectroscopy. CdZnTe crystals were acquired from different commercial vendors and characterized for their point defects. I-DLTS studies included measurements of defect parameters such as energy levels in the band gap, carrier capture cross sections, and defect densities. The induced current due to laser-generated carriers was measured using TCT. The data were used to determine the transport properties of the detectors under study. A good correlation was found between the point defects in the detectors and their performance.
Date: March 24, 2009
Creator: Gul, R.; Li, Z.; Bolotnikov, A.; Keeter, K.; Rodriguez, R. & James, R.
System: The UNT Digital Library
Harnessing microbial subsurface metal reduction activities to synthesise nanoscale cobalt ferrite with enhanced magnetic properties (open access)

Harnessing microbial subsurface metal reduction activities to synthesise nanoscale cobalt ferrite with enhanced magnetic properties

Nanoscale ferrimagnetic particles have a diverse range of uses from directed cancer therapy and drug delivery systems to magnetic recording media and transducers. Such applications require the production of monodisperse nanoparticles with well-controlled size, composition, and magnetic properties. To fabricate these materials purely using synthetic methods is costly in both environmental and economical terms. However, metal-reducing microorganisms offer an untapped resource to produce these materials. Here, the Fe(III)-reducing bacterium Geobacter sulfurreducens is used to synthesize magnetic iron oxide nanoparticles. A combination of electron microscopy, soft X-ray spectroscopy, and magnetometry techniques was employed to show that this method of biosynthesis results in high yields of crystalline nanoparticles with a narrow size distribution and magnetic properties equal to the best chemically synthesized materials. In particular, it is demonstrated here that cobalt ferrite (CoFe{sub 2}O{sub 4}) nanoparticles with low temperature coercivity approaching 8 kOe and an effective anisotropy constant of {approx} 10{sup 6} erg cm{sup -3} can be manufactured through this biotechnological route. The dramatic enhancement in the magnetic properties of the nanoparticles by the introduction of high quantities of Co into the spinel structure represents a significant advance over previous biomineralization studies in this area using magnetotactic bacteria. The successful production of …
Date: March 24, 2009
Creator: Coker, Victoria S.; Telling, Neil D.; van der Laan, Gerrit; Pattrick, Richard A.D.; Pearce, Carolyn I.; Arenholz, Elke et al.
System: The UNT Digital Library
High quality ZnO:Al transparent conducting oxide films synthesized by pulsed filtered cathodic arc deposition (open access)

High quality ZnO:Al transparent conducting oxide films synthesized by pulsed filtered cathodic arc deposition

Aluminum-doped zinc oxide, ZnO:Al or AZO, is a well-known n-type transparent conducting oxide with great potential in a number of applications currently dominated by indium tin oxide (ITO). In this study, the optical and electrical properties of AZO thin films deposited on glass and silicon by pulsed filtered cathodic arc deposition are systematically studied. In contrast to magnetron sputtering, this technique does not produce energetic negative ions, and therefore ion damage can be minimized. The quality of the AZO films strongly depends on the growth temperature while only marginal improvements are obtained with post-deposition annealing. The best films, grown at a temperature of about 200?C, have resistivities in the low to mid 10-4 Omega cm range with a transmittance better than 85percent in the visible part of the spectrum. It is remarkable that relatively good films of small thickness (60 nm) can be fabricated using this method.
Date: April 24, 2009
Creator: Anders, Andre; Lim, Sunnie H.N.; Yu, Kin Man; Andersson, Joakim; Rosen, Johanna; McFarland, Mike et al.
System: The UNT Digital Library
High quality copy number and genotype data from FFPE samples using Molecular Inversion Probe (MIP) microarrays (open access)

High quality copy number and genotype data from FFPE samples using Molecular Inversion Probe (MIP) microarrays

A major challenge facing DNA copy number (CN) studies of tumors is that most banked samples with extensive clinical follow-up information are Formalin-Fixed Paraffin Embedded (FFPE). DNA from FFPE samples generally underperforms or suffers high failure rates compared to fresh frozen samples because of DNA degradation and cross-linking during FFPE fixation and processing. As FFPE protocols may vary widely between labs and samples may be stored for decades at room temperature, an ideal FFPE CN technology should work on diverse sample sets. Molecular Inversion Probe (MIP) technology has been applied successfully to obtain high quality CN and genotype data from cell line and frozen tumor DNA. Since the MIP probes require only a small ({approx}40 bp) target binding site, we reasoned they may be well suited to assess degraded FFPE DNA. We assessed CN with a MIP panel of 50,000 markers in 93 FFPE tumor samples from 7 diverse collections. For 38 FFPE samples from three collections we were also able to asses CN in matched fresh frozen tumor tissue. Using an input of 37 ng genomic DNA, we generated high quality CN data with MIP technology in 88% of FFPE samples from seven diverse collections. When matched fresh frozen …
Date: February 24, 2009
Creator: Wang, Yuker; Carlton, Victoria E. H.; Karlin-Neumann, George; Sapolsky, Ronald; Zhang, Li; Moorhead, Martin et al.
System: The UNT Digital Library
A New Class of Non-Linear, Finite-Volume Methods for Vlasov Simulation (open access)

A New Class of Non-Linear, Finite-Volume Methods for Vlasov Simulation

Methods for the numerical discretization of the Vlasov equation should efficiently use the phase space discretization and should introduce only enough numerical dissipation to promote stability and control oscillations. A new high-order, non-linear, finite-volume algorithm for the Vlasov equation that discretely conserves particle number and controls oscillations is presented. The method is fourth-order in space and time in well-resolved regions, but smoothly reduces to a third-order upwind scheme as features become poorly resolved. The new scheme is applied to several standard problems for the Vlasov-Poisson system, and the results are compared with those from other finite-volume approaches, including an artificial viscosity scheme and the Piecewise Parabolic Method. It is shown that the new scheme is able to control oscillations while preserving a higher degree of fidelity of the solution than the other approaches.
Date: November 24, 2009
Creator: Banks, J W & Hittinger, J A
System: The UNT Digital Library
Quantitative assessment of electrostatic embedding in Density Functional Theory calculations of biomolecular systems (open access)

Quantitative assessment of electrostatic embedding in Density Functional Theory calculations of biomolecular systems

We evaluate the accuracy of density functional theory quantum calculations of biomolecular subsystems using a simple electrostatic embedding scheme. Our scheme is based on dividing the system of interest into a primary and secondary subsystem. A finite difference discretization of the Kohn-Sham equations is used for the primary subsystem, while its electrostatic environment is modeled with a simple one-electron potential. Force-field atomic partial charges are used to generate smeared Gaussian charge densities and to model the secondary subsystem. We illustrate the utility of this approach with calculations of truncated dipeptide chains. We analyze quantitatively the accuracy of this approach by calculating atomic forces and comparing results with fullQMcalculations. The impact of the choice made in terminating dangling bonds at the frontier of the QM region is also investigated.
Date: April 24, 2009
Creator: Fattebert, J.; Law, R. J.; Bennion, B.; Lau, E. Y.; Schwegler, E. & Lightstone, F. C.
System: The UNT Digital Library