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Characterization of Pathogens in Clinical Specimens via Suppression of Host Background for Efficient Second Generation Sequencing Analyses

Branda, Steven; Jebrail, Mais J.; Van De Vreugde, James L.; Langevin, Stanley A.; Bent, Zachary; Curtis, Deanna J.; Lane, Pamela; Carson, Bryan; La Bauve, Elisa; Patel, Kamlesh; Ricken, Bryce; Schoeniger, Joseph S.; Solberg, Owen D.; Williams, Kelly P.; Misra, Milind; Powell, Amy J.; Pattengale, Nicholas D.; May, Elebeoba; Lane, Todd; Lindner, Duane L.; Young, Malin M.; Vandernoot, Victoria A.; Thaitrong, Numrin; Bartsch, Michael S.; Renzi, Ronald F.; Tran-Gyamfi, Mary; Meagher, Robert M.

Abstract not provided.

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TYPE Conference YEAR 2012
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Error estimation for immersed interface solutions

Discrete and Continuous Dynamical Systems - Series B

Vanderlei, Ben A.; Hopkins, Matthew M.; Fauci, Lisa J.

We present an error estimation method for immersed interface solutions of elliptic boundary value problems. As opposed to an asymptotic rate that indicates how the errors in the numerical method converge to zero, we seek a posteriori estimates of the errors, and their spatial distribution, for a given solution. Our estimate is based upon the classical idea of defect corrections, which requires the application of a higher-order discretization operator to a solution achieved with a lower-order discretization. Our model problem will be an elliptic boundary value problem in which the coefficients are discontinuous across an internal boundary.

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TYPE Journal Article YEAR 2012
ScopusOSTI

ML Enhancements via the Calculation of Rigid Body Modes (RBMs) for Mechanics Problems Implemented within the Albany Code Base

Tezaur, Irina K.

The algebraic multigrid approach known as smoothed aggregation is very efficient at solving systems that arise from elasticity problems. In order to construct an efficient algebraic multilevel method, a multigrid solver should be provided with a small set of vectors that represent the error components that are difficult to resolve. It is well-known that for linear elasticity problems, these components correspond to the the so-called rigid body modes (RBMs). The present document summarizes some new development within the Albany code base that has enabled the application of algebraic multigrid preconditioners from the ML package of Trilinos to mechanics problems implemented within Albany via a new function that calculates the RBMs using information about the problem's underlying mesh. The performance of these preconditioners is evaluated on four problems: a 3D static elasticity problem, a 3D non-linear elasticity problem, a 3D thermo-elasticity problem, and a 3D thermo-poro-plasticity problem. The tests reveal the superiority of the ML preconditioners over ILU preconditioners from the Trilinos Ifpack package for mechanics problems in Albany.

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TYPE SAND Report YEAR 2012
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Biochemical production of ethanol and water-immiscible biofuel from lignocellulosic biomass: A comparative analysis of environmental and economic performance

12AIChE - 2012 AIChE Spring Meeting and 8th Global Congress on Process Safety, Conference Proceedings

Paap, Scott M.

Two separate processes to produce either ethanol or a fatty acid ethyl ester (FAEE) - identical to oil-derived biodiesel - via the fermentation of sugars obtained from lignocellulosic materials were analyzed in terms of economic and environmental metrics. Simplified process models were introduced and employed to estimate fuel production, net energy consumption, minimum fuel selling price, and water consumption for both processes. Monte Carlo analyses were carried out to identify the parameters governing process performance, and an analysis of the impact of potential improvements to the FAEE process was performed. The results of the analyses, capturing both the current state of technology development as well as paths to improve the performance of the FAEE process relative to that for producing ethanol, are presented. This is an abstract of a paper presented at the 2012 AIChE Spring National Meeting and 8th Global Congress on Process Safety (Houston, TX 4/1-5/2012).

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TYPE Conference YEAR 2012
OSTIScopus

Self-assembly of artificial microtubules

Soft Matter

Cheng, Shengfeng; Aggarwal, Ankush; Stevens, Mark J.

Understanding the complex self-assembly of biomacromolecules is a major outstanding question. Microtubules are one example of a biopolymer that possesses characteristics quite distinct from standard synthetic polymers that are derived from its hierarchical structure. In order to understand how to design and build artificial polymers that possess features similar to those of microtubules, we have initially studied the self-assembly of model monomers into a tubule geometry. Our model monomer has a wedge shape with lateral and vertical binding sites that are designed to form tubules. We used molecular dynamics simulations to study the assembly process for a range of binding site interaction strengths. In addition to determining the optimal regime for obtaining tubules, we have calculated a diagram of the structures that form over a wide range of interaction strengths. Unexpectedly, we find that the helical tubules form, even though the monomer geometry is designed for nonhelical tubules. We present the detailed dynamics of the tubule self-assembly process and show that the interaction strengths must be in a limited range to allow rearrangement within clusters. We extended previous theoretical methods to treat our system and to calculate the boundaries between different structures in the diagram. © 2012 The Royal Society of Chemistry.

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TYPE Journal Article YEAR 2012
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Actuation for carbon fiber reinforced polymer active optical mirrors

IEEE Aerospace Conference Proceedings

Jungwirth, Matthew; Wick, David V.; Baker, Michael S.; Wilcox, Christopher C.; Dereniak, Eustace L.; Romeo, Robert C.; Martin, Robert N.

Adaptive or active elements can alter their shape to remove aberrations or shift focal points. Carbon fiber reinforced polymer (CFRP) material improves upon current active mirror materials, such as Zerodur, in several ways: low stiffness-to-weight ratio, very low hysteresis, and greater dynamic range of correction. In this paper, we present recent developments in CFRP mirror actuation, i.e., changing the mirror's shape in an accurate and repeatable fashion. Actuation methods are studied both theoretically, using finite element analysis, and experimentally, using interferometric testing. We present results using two annular rings to push against the mirror's back, producing a wavefront with less than 20 waves of total error. Applications for this work include active telescope secondaries, phase diversity, and adaptive zoom systems. © 2012 IEEE.

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TYPE Conference YEAR 2012
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Optimized pulses for the control of uncertain qubits

Physical Review A - Atomic, Molecular, and Optical Physics

Carroll, M.S.; Witzel, Wayne M.

The construction of high-fidelity control fields that are robust to control, system, and/or surrounding environment uncertainties is a crucial objective for quantum information processing. Using the two-state Landau-Zener model for illustrative simulations of a controlled qubit, we generate optimal controls for π/2 and π pulses and investigate their inherent robustness to uncertainty in the magnitude of the drift Hamiltonian. Next, we construct a quantum-control protocol to improve system-drift robustness by combining environment-decoupling pulse criteria and optimal control theory for unitary operations. By perturbatively expanding the unitary time-evolution operator for an open quantum system, previous analysis of environment-decoupling control pulses has calculated explicit control-field criteria to suppress environment-induced errors up to (but not including) third order from π/2 and π pulses. We systematically integrate this criteria with optimal control theory, incorporating an estimate of the uncertain parameter to produce improvements in gate fidelity and robustness, demonstrated via a numerical example based on double quantum dot qubits. For the qubit model used in this work, postfacto analysis of the resulting controls suggests that realistic control-field fluctuations and noise may contribute just as significantly to gate errors as system and environment fluctuations.

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Nanoindentation and TEM Characterization of Ion Irridiated 316L Stainless Steels

Energy Technology 2012: Carbon Dioxide Management and Other Technologies

Hattar, Khalid M.; Buchheit, Thomas E.; Kotula, Paul G.; Mcginnis, Alexander; Brewer, Luke

Understanding the effects of extensive radiation damage in structural metals provides necessary insight for predicting the performance of those metals considered for application in the extreme radiation environment. Predicting mechanical performance after long term radiation exposure is of great importance to extending the life of current nuclear reactors and for developing future materials for the next generation of reactors. A combination of finite element modeling, nanoindentation, and TEM characterization were used to rapidly determine the microstructure and mechanical properties influences of ion irradiation on a standard 316L stainless steel sample. The results of this study found that ion irradiation and small scale mechanical property testing can be used to characterize extensive levels of radiation damage structure, only when significant consideration is given to ion irradiation depth, surface roughness and polishing condition, the irradiation temperature, and.many other experimental parameters. © 2012 The Minerals, Metals, & Materials Society. All rights reserved.

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TYPE Conference YEAR 2012
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Reliable forward walking parameters from head-track data alone

Proceedings - IEEE Virtual Reality

Wendt, Jeremy; Whitton, Mary C.; Adalsteinsson, David; Brooks, Frederick P.

Head motion during real walking is complex: The basic translational path is obscured by head bobbing. Many VE applications would be improved if a bobbing-free path were available. This paper introduces a model that describes head position while walking in terms of a bobbing free path and the head bobs. We introduce two methods to approximate the model from head-track data. © 2012 IEEE.

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TYPE Conference YEAR 2012
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First-principles modeling of the initial stages of organic solvent decomposition on Li xMn 2O 4(100) surfaces

Journal of Physical Chemistry C

Leung, Kevin

Density functional theory and ab initio molecular dynamics simulations are applied to investigate the initial steps of ethylene carbonate (EC) decomposition on spinel Li 0.6Mn 2O 4(100) surfaces. EC is a key component of the electrolyte used in lithium ion batteries. We predict a slightly exothermic EC bond-breaking event on this oxide facet, which facilitates subsequent EC oxidation and proton transfer to the oxide surface. Both the proton and the partially decomposed EC fragment weaken the Mn-O ionic bonding network. Implications for an interfacial film made of decomposed electrolyte on cathode surfaces, and Li xMn 2O 4 dissolution during power cycling, are discussed. © 2012 American Chemical Society.

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TYPE Journal Article YEAR 2012
DOIOSTIScopus

EPR/PTFE dosimetry for test reactor environments

Journal of ASTM International

Vehar, David W.; Griffin, Patrick J.; Quirk, Thomas J.

In 1992 the Radiation Metrology Laboratory (RML) at Sandia National Laboratories implemented EPR/Alanine capabilities for use in routine and calibration activities at its Co-60 and pulsed-power facilities. At that time it also investigated the usefulness of the system for measurement of absorbed dose in the mixed neutron/photon environments of reactors such as the Sandia Pulsed Reactor and the Annular Core Research Reactor used for hardness testing of electronics. The RML concluded that the neutron response of alanine was a sufficiently high fraction of the overall dosimeter response that the resulting uncertainties in the photon dose would be unacceptably large for silicon-device testing. However, it also suggested that non-hydrogenous materials such as polytetrafluoroethylene (PTFE) would exhibit smaller neutron response and might be useful in mixed environments. Preliminary research with PTFE in photon environments indicated considerable promise, but further development was not pursued at that time. Because of renewed interest in absorbed dose measurements that could better define the individual contributions of photon and neutron components to the overall dose delivered to a test object, the RML has re-initiated the development of an EPR/PTFE dosimetry system. This paper presents a summary of the research, a description of the EPR/PTFE dosimetry system, and recommendations for preparation and fielding of the dosimetry in photon and mixed neutron/photon environments. Copyright © 2012 by ASTM International.

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Solid liner implosions on Z for producing multi-megabar, shockless compressions

Physics of Plasmas

Martin, M.R.; Lemke, Raymond W.; Mcbride, Ryan; Davis, Jean-Paul; Dolan, Daniel H.; Knudson, Marcus D.; Cochrane, K.R.; Sinars, Daniel; Smith, Ian C.; Savage, Mark E.; Stygar, William A.; Killebrew, K.; Flicker, Dawn; Herrmann, Mark H.

Current pulse shaping techniques, originally developed for planar dynamic material experiments on the Z-machine [M. K. Matzen, Phys. Plasmas 12, 055503 (2005)], are adapted to the design of controlled cylindrical liner implosions. By driving these targets with a current pulse shape that prevents shock formation inside the liner, shock heating is avoided along with the corresponding decrease in electrical conductivity ahead of the magnetic diffusion wave penetrating the liner. This results in an imploding liner with a significant amount of its mass in the solid phase and at multi-megabar pressures. Pressures in the solid region of a shaped pulse driven beryllium liner fielded on the Z-machine are inferred to 5.5 Mbar, while simulations suggest implosion velocities greater than 50 kms-1. These solid liner experiments are diagnosed with multi-frame monochromatic x-ray backlighting which is used to infer the material density and pressure. This work has led to a new platform on the Z-machine that can be used to perform off-Hugoniot measurements at higher pressures than are accessible through magnetically driven planar geometries. © 2012 American Institute of Physics.

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TYPE Journal Article YEAR 2012
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Investigating inertial confinement fusion target fuel conditions through x-ray spectroscopy

Physics of Plasmas

Hansen, Stephanie B.

Inertial confinement fusion (ICF) targets are designed to produce hot, dense fuel in a neutron-producing core that is surrounded by a shell of compressing material. The x-rays emitted from ICF plasmas can be analyzed to reveal details of the temperatures, densities, gradients, velocities, and mix characteristics of ICF targets. Such diagnostics are critical to understand the target performance and to improve the predictive power of simulation codes. © 2012 American Institute of Physics.

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TYPE Presentation YEAR 2012
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Kinetics and mechanism of metal-organic framework thin film growth: Systematic investigation of HKUST-1 deposition on QCM electrodes

Chemical Science

Stavila, Vitalie; Volponi, Joanne V.; Katzenmeyer, Aaron M.; Dixon, Matthew C.; Allendorf, Mark D.

We describe a systematic investigation of the factors controlling step-by-step growth of the metal-organic framework (MOF) [Cu 3(btc) 2(H 2O) 3]·xH 2O (also known as HKUST-1), using quartz crystal microbalance (QCM) electrodes as an in situ probe of the reaction kinetics and mechanism. Electrodes coated with silica, alumina and gold functionalized with OH- and COOH-terminated self-assembled monolayers (SAMs) were employed to determine the effects of surface properties on nucleation. Deposition rates were measured using the high sensitivity available from QCM-D (D = dissipation) techniques to determine rate constants in the early stage of the process. Films were characterized using grazing incidence XRD, SEM, AFM, profilometry and reflection-absorption IR spectroscopy. The effects of reaction time, concentration, temperature and substrate on the deposition rates, film crystallinity and surface morphology were evaluated. The initial growth step, in which the surface is exposed to copper ions (in the form of an ethanolic solution of copper(ii) acetate) is fast and independent of temperature, after which all subsequent steps are thermally activated over the temperature range 22-62 °C. Using these data, we propose a kinetic model for the Cu 3(btc) 2 growth on surfaces that includes rate constants for the individual steps. The magnitude of the activation energies, in particular the large entropy decrease, suggests an associative reaction with a tight transition state. The measured activation energies for the step-by-step MOF growth are an order of magnitude lower than the value previously reported for bulk Cu 3(btc) 2 crystals. Finally, the results of this investigation demonstrate that the QCM method is a powerful tool for quantitative, in situ monitoring of MOF growth in real time. © 2012 The Royal Society of Chemistry.

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TYPE Journal Article YEAR 2012
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A case for Sandia investment in complex adaptive systems science and technology

Johnson, Curtis M.; Backus, George A.; Brown, Theresa J.; Colbaugh, Richard; Jones, Katherine; Tsao, Jeffrey Y.

This white paper makes a case for Sandia National Laboratories investments in complex adaptive systems science and technology (S&T) -- investments that could enable higher-value-added and more-robustly-engineered solutions to challenges of importance to Sandia's national security mission and to the nation. Complex adaptive systems are ubiquitous in Sandia's national security mission areas. We often ignore the adaptive complexity of these systems by narrowing our 'aperture of concern' to systems or subsystems with a limited range of function exposed to a limited range of environments over limited periods of time. But by widening our aperture of concern we could increase our impact considerably. To do so, the science and technology of complex adaptive systems must mature considerably. Despite an explosion of interest outside of Sandia, however, that science and technology is still in its youth. What has been missing is contact with real (rather than model) systems and real domain-area detail. With its center-of-gravity as an engineering laboratory, Sandia's has made considerable progress applying existing science and technology to real complex adaptive systems. It has focused much less, however, on advancing the science and technology itself. But its close contact with real systems and real domain-area detail represents a powerful strength with which to help complex adaptive systems science and technology mature. Sandia is thus both a prime beneficiary of, as well as potentially a prime contributor to, complex adaptive systems science and technology. Building a productive program in complex adaptive systems science and technology at Sandia will not be trivial, but a credible path can be envisioned: in the short run, continue to apply existing science and technology to real domain-area complex adaptive systems; in the medium run, jump-start the creation of new science and technology capability through Sandia's Laboratory Directed Research and Development program; and in the long run, inculcate an awareness at the Department of Energy of the importance of supporting complex adaptive systems science through its Office of Science.

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TYPE SAND Report YEAR 2012
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Copy of Automated Molecular Biology Platform Enabling Rapid & Efficient SGS Analysis of Pathogens in Clinical Samples

Branda, Steven; Jebrail, Mais J.; Van De Vreugde, James L.; Langevin, Stanley A.; Bent, Zachary; Curtis, Deanna J.; Lane, Pamela; Carson, Bryan; La Bauve, Elisa; Patel, Kamlesh; Ricken, Bryce; Schoeniger, Joseph S.; Solberg, Owen D.; Williams, Kelly P.; Misra, Milind; Powell, Amy J.; Pattengale, Nicholas D.; May, Elebeoba; Lane, Todd; Lindner, Duane L.; Young, Malin M.; Vandernoot, Victoria A.; Thaitrong, Numrin; Bartsch, Michael S.; Renzi, Ronald F.; Tran-Gyamfi, Mary; Meagher, Robert M.

Abstract not provided.

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TYPE Presentation YEAR 2012
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Automated Molecular Biology Platform Enabling Rapid & Efficient SGS Analysis of Pathogens in Clinical Samples

Branda, Steven; Jebrail, Mais J.; Van De Vreugde, James L.; Langevin, Stanley A.; Bent, Zachary; Curtis, Deanna J.; Lane, Pamela; Carson, Bryan; La Bauve, Elisa; Patel, Kamlesh; Ricken, Bryce; Schoeniger, Joseph S.; Solberg, Owen D.; Williams, Kelly P.; Misra, Milind; Powell, Amy J.; Pattengale, Nicholas D.; May, Elebeoba; Lane, Todd; Lindner, Duane L.; Young, Malin M.; Vandernoot, Victoria A.; Thaitrong, Numrin; Bartsch, Michael S.; Renzi, Ronald F.; Tran-Gyamfi, Mary; Meagher, Robert M.

Abstract not provided.

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TYPE Conference YEAR 2012
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Strategic partnerships final LDRD report : nanocomposite materials for efficient solar hydrogen production

Miller, James E.

This 'campus executive' project sought to advance solar thermochemical technology for producing the chemical fuels. The project advanced the common interest of Sandia National Laboratories and the University of Arizona in creating a sustainable and viable alternative to fossil fuels. The focus of this effort was in developing new methods for creating unique monolithic composite structures and characterizing their performance in thermochemical production of hydrogen from water. The development and processing of the materials was undertaken in the Materials Science and Engineering Department at the University of Arizona; Sandia National Laboratories performed the thermochemical characterization. Ferrite/yttria-stabilized zirconia composite monoliths were fabricated and shown to have exceptionally high utilization of the ferrite for splitting CO{sub 2} to obtain CO (a process analogous to splitting H{sub 2}O to obtain H{sub 2}).

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TYPE SAND Report YEAR 2012
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Loop-to-loop coupling

Warne, Larry K.; Basilio, Lorena I.; Langston, William L.; Salazar, Robert A.; Coleman, Phillip D.; Lucero, Larry

This report estimates inductively-coupled energy to a low-impedance load in a loop-to-loop arrangement. Both analytical models and full-wave numerical simulations are used and the resulting fields, coupled powers and energies are compared. The energies are simply estimated from the coupled powers through approximations to the energy theorem. The transmitter loop is taken to be either a circular geometry or a rectangular-loop (stripline-type) geometry that was used in an experimental setup. Simple magnetic field models are constructed and used to estimate the mutual inductance to the receiving loop, which is taken to be circular with one or several turns. Circuit elements are estimated and used to determine the coupled current and power (an equivalent antenna picture is also given). These results are compared to an electromagnetic simulation of the transmitter geometry. Simple approximate relations are also given to estimate coupled energy from the power. The effect of additional loads in the form of attached leads, forming transmission lines, are considered. The results are summarized in a set of susceptibility-type curves. Finally, we also consider drives to the cables themselves and the resulting common-to-differential mode currents in the load.

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Development of chemiresponsive sensors for detection of common homemade explosives

Brotherton, Christopher M.; Wheeler, David R.

Field-structured chemiresistors (FSCRs) are polymer based sensors that exhibit a resistance change when exposed to an analyte of interest. The amount of resistance change depends on the polymer-analyte affinity. The affinity can be manipulated by modifying the polymer within the FSCRs. In this paper, we investigate the ability of chemically modified FSCRs to sense hydrogen peroxide vapor. Five chemical species were chosen based on their hydrophobicity or reactivity with hydrogen peroxide. Of the five investigated, FSCRs modified with allyl methyl sulfide exhibited a significant response to hydrogen peroxide vapor. Additionally, these same FSCRs were evaluated against a common interferrant in hydrogen peroxide detection, water vapor. For the conditions investigated, the FSCRs modified with allyl methyl sulfide were able to successfully distinguish between water vapor and hydrogen peroxide vapor. A portion of the results presented here will be submitted to the Sensors and Actuators journal.

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Results 63601–63800 of 99,299
Results 63601–63800 of 99,299