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At least 775 records · Page 43

Optimized Expression and Purification for High-Activity Preparations of Algal [FeFe]-Hydrogenase

Recombinant expression and purification of metallo-enzymes, including hydrogenases, at high-yields is challenging due to complex, and enzyme specific, post-translational maturation processes. Low fidelities of maturation result in preparations containing a significant fraction of inactive, apo-protein that are not suitable for biophysical or crystallographic studies. We describe the construction, overexpression and high-yield purification of a fusion protein consisting of the algal [2Fe2S]-ferredoxin PetF (Fd) and [FeFe]-hydrogenase HydA1. The maturation of Fd-HydA1 was optimized through improvements in culture conditions and media components used for expression. We also demonstrated that fusion of Fd to the N-terminus of HydA1, in comparison to the C-terminus, led to increased expression levels that were 4-fold higher. Together, these improvements led to enhanced HydA1 activity and improved yield after purification. The strong binding-affinity of Fd for DEAE allowed for two-step purification by ion exchange and StrepTactin affinity chromatography. In addition, the incorporation of a TEV protease site in the Fd-HydA1 linker allowed for the proteolytic removal of Fd after DEAE step, and purification of HydA1 alone by StrepTactin. In combination, this process resulted in HydA1 purification yields of 5 mg L{sup -1} of culture from E. coli with specific activities of 1000 U (U = 1 {micro}mol hydrogen evolved mg{sup -1} min{sup -1}). The [FeFe]-hydrogenases are highly efficient enzymes and their catalytic sites provide model structures for synthetic efforts to develop robust hydrogen activation catalysts. In order to characterize their structure-function properties in greater detail, and to use hydrogenases for biotechnological applications, reliable methods for rapid, high-yield expression and purification are required.

09 BIOMASS FUELS↗

WSEAT Shock Testing Margin Assessment Using Energy Spectra Final Report

Several programs at Sandia National Laboratories have adopted energy spectra as a metric to relate the severity of mechanical insults to structural capacity. The purpose being to gain insight into the system's capability, reliability, and to quantify the ultimate margin between the normal operating envelope and the likely system failure point -- a system margin assessment. The fundamental concern with the use of energy metrics was that the applicability domain and implementation details were not completely defined for many problems of interest. The goal of this WSEAT project was to examine that domain of applicability and work out the necessary implementation details. The goal of this project was to provide experimental validation for the energy spectra based methods in the context of margin assessment as they relate to shock environments. The extensive test results concluded that failure predictions using energy methods did not agree with failure predictions using S-N data. As a result, a modification to the energy methods was developed following the form of Basquin's equation to incorporate the power law exponent for fatigue damage. This update to the energy-based framework brings the energy based metrics into agreement with experimental data and historical S-N data.

47 OTHER INSTRUMENTATION↗

Power Market Primers

The National Energy Technology Laboratory (NETL) has developed a series of primers on independent system operators (ISOs) and regional transmission organizations (RTOs). The primers primarily explore the history, workings, and types of electricity markets composing the seven ISOs/RTOs in the United States (U.S.) (Exhibit 1-1). The primer series includes sixteen documents. A general introduction to ISOs/RTOs is given in Independent System Operators and Regional Transmission Organizations. Specific details about the seven existing ISOs/RTOs in the United States are given in seven additional primers: California Independent System Operator, ERCOT Independent System Operator, ISO New England Regional Transmission Operator, MISO Regional Transmission Operator, New York Independent System Operator, PJM Regional Transmission Operator, and Southwest Power Pool, Inc. These primers provide a history of each ISO/RTO, short explanations of products and services (different types of electricity markets) offered by ISO/RTO, and the ISO/RTO generation mix. Readers who are not familiar with the different types of markets and their mechanisms can find basic information in six additional primers titled: Power Markets, Energy Market, Capacity Market, Comparisons of Different ISO/RTO Capacity Market Structures, Ancillary Services, and Financial Transmission Rights. Additionally, the primer North American Electric Reliability Corporation introduces the electric reliability organization, which is responsible for reliability of the bulk power system and Federal Energy Regulatory Commission introduces the federal commission responsible for overseeing the nation's electric power markets and related energy and financial markets and issuing market related rules and regulations. All the primers are very short and concise documents. They are accompanied by a Glossary of Terms in which many of the technical terms used in these primers are defined.

24 POWER TRANSMISSION AND DISTRIBUTION↗

One-Way Coupled Flow-Induced Vibration Analysis for a Twisted-Tube Heat Exchanger

The NEAMS program aims to develop an integrated multi-physics simulation capability “pellet-to-plant” for the design and analysis of future generations of nuclear power plants. In particular, the Reactor Product Line code suite's multi-resolution hierarchy is being designed to ultimately span the full range of length and time scales present in relevant reactor design and safety analyses, as well as scale from desktop to petaflop computing platforms. Flow-induced vibration (FIV) is a widespread problem in energy systems because they rely on fluid movement for energy conversion. Vibrating structures may be damaged as fatigue or wear occurs. Given the importance of reliable components in the nuclear industry, flow-induced vibration has long been a major concern in safety and operation of nuclear reactors. Nuclear fuel rods and steam generators have been known to suffer from flow-induced vibration and related failures.

22 GENERAL STUDIES OF NUCLEAR REACTORS↗

The Star Formation Histories of Disk Galaxies: The Live, the Dead, and the Undead

We reexamine the properties of local galaxy populations using published surveys of star formation, structure, and gas content. After recalibrating star formation measures, we are able to reliably measure specific star formation rates well below that of the so-called “main sequence” of star formation versus mass. We find an unexpectedly large population of quiescent galaxies with star formation rates intermediate between the main sequence and passive populations and with disproportionately high star formation rates. We demonstrate that a tight main sequence is a natural outcome of most histories of star formation and has little astrophysical significance but that the quiescent population requires additional astrophysics to explain its properties. Using a simple model for disk evolution based on the observed dependence of star formation on gas content in local galaxies, and assuming simple histories of cold gas inflow, we show that the evolution of galaxies away from the main sequence can be attributed to the depletion of gas due to star formation after a cutoff of gas inflow. The quiescent population is composed of galaxies in which the density of disk gas has fallen below a threshold for star formation probably set by disk stability. The evolution of galaxies beyond the quiescent state to gas exhaustion and the end of star formation requires another process, probably wind-driven mass loss. The environmental dependence of the three galaxy populations is consistent with recent numerical modeling, which indicates that cold gas inflows into galaxies are truncated at earlier epochs in denser environments.

79 ASTRONOMY AND ASTROPHYSICS↗

Modeling most likely pathways for smuggling radioactive and special nuclear materials on a worldwide multi-modal transportation network

Nuclear weapons proliferation is an existing and growing worldwide problem. To help with devising strategies and supporting decisions to interdict the transport of nuclear material, we developed the Pathway Analysis, Threat Response and Interdiction Options Tool (PATRIOT) that provides an analytical approach for evaluating the probability that an adversary smuggling radioactive or special nuclear material will be detected during transit. We incorporate a global, multi-modal transportation network, explicit representation of designed and serendipitous detection opportunities, and multiple threat devices, material types, and shielding levels. This paper presents the general structure of PATRIOT, all focuses on the theoretical framework used to model the reliabilities of all network components that are used to predict the most likely pathways to the target.

98 NUCLEAR DISARMAMENT, SAFEGUARDS, AND PHYSICAL P↗

An Overview of Recent Results from CLAS

The unique capabilities of the CLAS detector to measure exclusive meson electroproduction off protons, with almost complete coverage of the final hadron phase space, has extended our knowledge of excited baryon structure. Consistent results from Np and Npp final states provide convincing evidence for reliable extraction of N* electrocouplings. Theoretical analyses of these results, using self-consistent dynamical calculations using an internal quark core and an external meson-baryon cloud suggest that meson-baryon dressing amplitudes need to be included. The meson-baryon dressing was already shown to be necessary to get agreement between calculations and data on the D resonance transition magnetic moment at low Q{sup 2}. Similarly, a new measurement of the transition magnetic moment for strange baryons also disagrees with quark models, suggesting the need for meson-baryon dressings. In the near future, the CLAS detector will be replaced with CLAS12, providing new high-precision data.

72 PHYSICS OF ELEMENTARY PARTICLES AND FIELDS↗

WHOLE CELL TOMOGRAPHY/MOLECULAR BIOLOGY/STRUCTURAL BIOLOGY: Affordable x-ray microscopy with nanoscale resolution

Biological research spans 10 orders of magnitude from angstroms to meters. While electron microscopy can reveal structural details at most of these spatial length scales, transmission electron tomography only reliably reconstructs three-dimensional (3-D) volumes of cellular material with a spatial resolution between 1-5 nm from samples less than 500 nm thick1. Most biological cells are 2-30 times thicker than this threshold, which means that a cell must be cut into consecutive slices with each slice reconstructed individually in order to approximate the contextual information of the entire cell. Fortunately, due to a larger penetration depth2, X-ray computed tomography bypasses the need to physically section a cell and enables imaging of intact cells and tissues on the micrometer or larger scale with tens to hundreds of nanometer spatial resolution. While the technique of soft x-ray microscopy has been extensively developed in synchrotron facilities, advancements in laboratory x-ray source designs now increase its accessibility by supporting commercial systems suitable for a standard laboratory. In this paper, we highlight a new commercial compact cryogenic soft x-ray microscope designed for a standard laboratory setting and explore its capabilities for mesoscopic investigations of intact prokaryotic and eukaryotic cells.

femtosecond crystallography↗

High-Performance I/O: HDF5 for Lattice QCD

Practitioners of lattice QCD/QFT have been some of the primary pioneer users of the state-of-the-art high-performance-computing systems, and contribute towards the stress tests of such new machines as soon as they become available. As with all aspects of high-performance-computing, I/O is becoming an increasingly specialized component of these systems. In order to take advantage of the latest available high-performance I/O infrastructure, to ensure reliability and backwards compatibility of data files, and to help unify the data structures used in lattice codes, we have incorporated parallel HDF5 I/O into the SciDAC supported USQCD software stack. Here we present the design and implementation of this I/O framework. Our HDF5 implementation outperforms optimized QIO at the 10-20% level and leaves room for further improvement by utilizing appropriate dataset chunking.

Kurth, Thorsten↗

High-Performance I/O: HDF5 for Lattice QCD

Practitioners of lattice QCD/QFT have been some of the primary pioneer users of the state-of-the-art high-performance-computing systems, and contribute towards the stress tests of such new machines as soon as they become available. As with all aspects of high-performance-computing, I/O is becoming an increasingly specialized component of these systems. In order to take advantage of the latest available high-performance I/O infrastructure, to ensure reliability and backwards compatibility of data files, and to help unify the data structures used in lattice codes, we have incorporated parallel HDF5 I/O into the SciDAC supported USQCD software stack. Here we present the design and implementation of this I/O framework. Our HDF5 implementation outperforms optimized QIO at the 10-20% level and leaves room for further improvement by utilizing appropriate dataset chunking.

97 MATHEMATICS AND COMPUTING↗

Viscoelastic Material Characterization and Modeling of Photovoltaic Module Packaging Materials for Direct Finite-Element Method Input

Numerical tools, such as the finite-element method, are increasingly used to design and evaluate the photovoltaic (PV) modules, providing for the reduction of development time and improved performance and reliability. However, high-fidelity material models are necessary to accurately model the complex structural behavior of the involved packaging materials. A common simplification used in recent years is to model the polymer materials (i.e., encapsulant and backsheet) as linear elastic, which will lead to inaccurate results. Therefore, in this work, we present a thorough characterization of the time- and temperature-dependent mechanical response of predominant PV module encapsulant and backsheet materials. Based on this material characterization, we developed and experimentally validated generalized Maxwell models to describe each material's viscoelastic response. In addition, we included measurements of the coefficient of thermal expansion and presented all material models in such a fashion for direct input into commercial finite-element method modeling software.

FEM↗

ModBase, a database of annotated comparative protein structure models and associated resources

ModBase (http://salilab.org/modbase) is a database of annotated comparative protein structure models. The models are calculated by ModPipe, an automated modeling pipeline that relies primarily on Modeller for fold assignment, sequence-structure alignment, model building and model assessment (http://salilab.org/modeller/). ModBase currently contains almost 30 million reliable models for domains in 4.7 million unique protein sequences. ModBase allows users to compute or update comparative models on demand, through an interface to the ModWeb modeling server (http://salilab.org/ modweb). ModBase models are also available through the Protein Model Portal (http://www.prote inmodelportal.org/). Recently developed associated resources include the AllosMod server for modeling ligand-induced protein dynamics (http://salilab.org/ allosmod), the AllosMod-FoXS server for predicting a structural ensemble that fits an SAXS profile (http://salilab.org/allosmod-foxs), the FoXSDock server for protein–protein docking filtered by an SAXS profile (http://salilab.org/foxsdock), the SAXS Merge server for automatic merging of SAXS profiles (http://salilab.org/saxsmerge) and the Pose & Rank server for scoring protein–ligand complexes (http://salilab.org/poseandrank). In this update, we also highlight two applications of ModBase: a PSI:Biology initiative to maximize the structural coverage of the human alpha-helical transmembrane proteome and a determination of structural determinants of human immunodeficiency virus-1 protease specificity.

59 BASIC BIOLOGICAL SCIENCES↗

Computational analysis of pathogen-borne metallo β-lactamases reveals discriminating structural features between B1 types

Background: Genes conferring antibiotic resistance to groups of bacterial pathogens are cause for considerable concern, as many once-reliable antibiotics continue to see a reduction in efficacy. The recent discovery of the metallo b-lactamase blaNDM-1 gene, which appears to grant antibiotic resistance to a variety of Enterobacteriaceae via a mobile plasmid, is one example of this distressing trend. The following work describes a computational analysis of pathogen-borne MBLs that focuses on the structural aspects of characterized proteins. Results: Using both sequence and structural analyses, we examine residues and structural features specific to various pathogen-borne MBL types. This analysis identifies a linker region within MBL-like folds that may act as a discriminating structural feature between these proteins, and specifically resistance-associated acquirable MBLs. Recently released crystal structures of the newly emerged NDM-1 protein were aligned against related MBL structures using a variety of global and local structural alignment methods, and the overall fold conformation is examined for structural conservation. Conservation appears to be present in most areas of the protein, yet is strikingly absent within a linker region, making NDM-1 unique with respect to a linker-based classification scheme. Variability analysis of the NDM-1 crystal structure highlights unique residues in key regions as well as identifying several characteristics shared with other transferable MBLs. Conclusions: A discriminating linker region identified in MBL proteins is highlighted and examined in the context of NDM-1 and primarily three other MBL types: IMP-1, VIM-2 and ccrA. The presence of an unusual linker region variant and uncommon amino acid composition at specific structurally important sites may help to explain the unusually broad kinetic profile of NDM-1 and may aid in directing research attention to areas of this protein, and possibly other MBLs, that may be targeted for inactivation or attenuation of enzymatic activity.

59 BASIC BIOLOGICAL SCIENCES↗

Defining Threshold Values of Encapsulant and Backsheet Adhesion for PV Module Reliability

The width-tapered cantilever beam method is used to quantify the debond energy (adhesion) of encapsulant and backsheet structures of 32 modules collected from the field. The collected population of modules contains both those that have remained intact and those with instances of either or both encapsulant and backsheet delamination. From this survey, initial threshold values (an adhesion value above which a module should remain intact throughout its lifetime) for encapsulant and backsheet interfaces are proposed. For encapsulants this value is ~ 160J/m 2 and for backsheets ~ 10J/m 2 . Here, it is expected that these values will continue to be refined and evolve as the width-tapered cantilever beam method gets adopted by the PV industry, and that they may aid in the future improvement of accelerated lifetime tests and the development of new, low-cost materials.

14 SOLAR ENERGY↗

Development of a reliable Potting process for Photoconductive Semiconductor Switches (PCSS)

Electrical potting is an important process to protect semiconductor devices from damaging external elements (mechanical stress, moisture, high voltage, etc.) and provides structural support for delicate devices for electrical connectivity to a larger platform. This internship will focus on the development of a universal potting jig for photoconductive semiconductor switches (PCSS). The goal is to design a reliable compression jig that is cross compatible with various PCSS designs that allow for easy potting of devices with a high dielectric breakdown strength material. The challenge with the current potting jig is that the design is only compatible with one style of PCSS and applies uneven pressure that can lead to leakage of potting material. Our approach is to move from a design that applies pressure by binder clip to utilizing a micrometer based compressing jig for a reliable packaging process that can pot a variety of devices without having to have a unique compressing jig for each of style of PCSS. Possible roadblocks with the new design include epoxy leakage into the optical path and misalignment of the electrode – metal contact bond.

42 ENGINEERING↗

Revenue Sufficiency and Reliability in a Zero Marginal Cost Future: Preprint

Features of existing wholesale electricity markets, such as administrative pricing rules and policy-based reliability standards, can distort market incentives from allowing generators sufficient opportunities to recover both fixed and variable costs. Moreover, these challenges can be amplified by other factors, including (1) inelastic demand resulting from a lack of price signal clarity, (2) low- or near-zero marginal cost generation, particularly arising from low natural gas fuel prices and variable generation (VG), such as wind and solar, and (3) the variability and uncertainty of this VG. As power systems begin to incorporate higher shares of VG, many questions arise about the suitability of the existing marginal-cost-based price formation, primarily within an energy-only market structure, to ensure the economic viability of resources that might be needed to provide system reliability. This article discusses these questions and provides a summary of completed and ongoing modelling-based work at the National Renewable Energy Laboratory to better understand the impacts of evolving power systems on reliability and revenue sufficiency.

29 ENERGY PLANNING, POLICY, AND ECONOMY↗

Revenue Sufficiency and Reliability in a Zero Marginal Cost Future

Features of existing wholesale electricity markets, such as administrative pricing rules and policy-based reliability standards, can distort market incentives from allowing generators sufficient opportunities to recover both fixed and variable costs. Moreover, these challenges can be amplified by other factors, including (1) inelastic demand resulting from a lack of price signal clarity, (2) low- or near-zero marginal cost generation, particularly arising from low natural gas fuel prices and variable generation (VG), such as wind and solar, and (3) the variability and uncertainty of this VG. As power systems begin to incorporate higher shares of VG, many questions arise about the suitability of the existing marginal-cost-based price formation, primarily within an energy-only market structure, to ensure the economic viability of resources that might be needed to provide system reliability. This article discusses these questions and provides a summary of completed and ongoing modelling-based work at the National Renewable Energy Laboratory to better understand the impacts of evolving power systems on reliability and revenue sufficiency.

29 ENERGY PLANNING, POLICY, AND ECONOMY↗

Techniques for Achieving High Reliability Operation of the Spallation Neutron Source High Power Radio-Frequency System

The Spallation Neutron Source (SNS) high power radiofrequency (HPRF) system operates with high reliability to support the goals of the SNS user program. In recent operational periods the availability of the HPRF system has exceeded 97 percent while the neutron source availability overall is typically greater than 90 percent. SNS has a unique set of 92 HPRF stations that operate at either 402.5 MHz or 805 MHz with peak output power ranging from 550 kW to 5 MW and average power ranging from 49.5 kW to 450 kW. The HPRF transmitters consist of chassis-mounted power supplies, solid-state amplifiers and other equipment that support the operation of the klystrons that ultimately provide the RF power to the accelerating structures. Management of the operation and maintenance of the HPRF system has increasingly focused on reliability and sustainability in recent years. Techniques for klystron lifetime preservation and optimization of transmitter reliability have been developed and will be described.

Moss, John↗