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Search indexed NASA NTRS and DOE OSTI research on propulsion, heat transfer, battery materials and energy systems. Follow report and document links to the original sources.

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At least 1,297 records · Page 72
All sourcesNASA NTRSDOE OSTI
DOE OSTI2015

Indexing amyloid peptide diffraction from serial femtosecond crystallography: new algorithms for sparse patterns

Special methods are required to interpret sparse diffraction patterns collected from peptide crystals at X-ray free-electron lasers. Bragg spots can be indexed from composite-image powder rings, with crystal orientations then deduced from a very limited number of spot positions. Still diffraction patterns from peptide nanocrystals with small unit cells are challenging to index using conventional methods owing to the limited number of spots and the lack of crystal orientation information for individual images. New indexing algorithms have been developed as part of the Computational Crystallography Toolbox (cctbx) to overcome these challenges. Accurate unit-cell information derived from an aggregate data set from thousands of diffraction patterns can be used to determine a crystal orientation matrix for individual images with as few as five reflections. These algorithms are potentially applicable not only to amyloid peptides but also to any set of diffraction patterns with sparse properties, such as low-resolution virus structures or high-throughput screening of still images captured by raster-scanning at synchrotron sources. As a proof of concept for this technique, successful integration of X-ray free-electron laser (XFEL) data to 2.5 Å resolution for the amyloid segment GNNQQNY from the Sup35 yeast prion is presented.

75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗
DOE OSTI2015

Capture and X-ray diffraction studies of protein microcrystals in a microfluidic trap array

A microfluidic platform has been developed for the capture and X-ray analysis of protein microcrystals, affording a means to improve the efficiency of XFEL and synchrotron experiments. X-ray free-electron lasers (XFELs) promise to enable the collection of interpretable diffraction data from samples that are refractory to data collection at synchrotron sources. At present, however, more efficient sample-delivery methods that minimize the consumption of microcrystalline material are needed to allow the application of XFEL sources to a wide range of challenging structural targets of biological importance. Here, a microfluidic chip is presented in which microcrystals can be captured at fixed, addressable points in a trap array from a small volume (<10 µl) of a pre-existing slurry grown off-chip. The device can be mounted on a standard goniostat for conducting diffraction experiments at room temperature without the need for flash-cooling. Proof-of-principle tests with a model system (hen egg-white lysozyme) demonstrated the high efficiency of the microfluidic approach for crystal harvesting, permitting the collection of sufficient data from only 265 single-crystal still images to permit determination and refinement of the structure of the protein. This work shows that microfluidic capture devices can be readily used to facilitate data collection from protein microcrystals grown in traditional laboratory formats, enabling analysis when cryopreservation is problematic or when only small numbers of crystals are available. Such microfluidic capture devices may also be useful for data collection at synchrotron sources.

75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗
DOE OSTI2015

Raster-scanning serial protein crystallography using micro- and nano-focused synchrotron beams

A raster scanning serial protein crystallography approach is presented, that consumes as low ∼200–700 nl of sedimented crystals. New serial data pre-analysis software, NanoPeakCell, is introduced. High-resolution structural information was obtained from lysozyme microcrystals (20 µm in the largest dimension) using raster-scanning serial protein crystallography on micro- and nano-focused beamlines at the ESRF. Data were collected at room temperature (RT) from crystals sandwiched between two silicon nitride wafers, thereby preventing their drying, while limiting background scattering and sample consumption. In order to identify crystal hits, new multi-processing and GUI-driven Python-based pre-analysis software was developed, named NanoPeakCell, that was able to read data from a variety of crystallographic image formats. Further data processing was carried out using CrystFEL, and the resultant structures were refined to 1.7 Å resolution. The data demonstrate the feasibility of RT raster-scanning serial micro- and nano-protein crystallography at synchrotrons and validate it as an alternative approach for the collection of high-resolution structural data from micro-sized crystals. Advantages of the proposed approach are its thriftiness, its handling-free nature, the reduced amount of sample required, the adjustable hit rate, the high indexing rate and the minimization of background scattering.

75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗
DOE OSTI2015

A revised partiality model and post-refinement algorithm for X-ray free-electron laser data

An updated partiality model and post-refinement algorithm for XFEL snapshot diffraction data is presented and confirmed by observing anomalous density for S atoms at an X-ray wavelength of 1.3 Å. Research towards using X-ray free-electron laser (XFEL) data to solve structures using experimental phasing methods such as sulfur single-wavelength anomalous dispersion (SAD) has been hampered by shortcomings in the diffraction models for X-ray diffraction from FELs. Owing to errors in the orientation matrix and overly simple partiality models, researchers have required large numbers of images to converge to reliable estimates for the structure-factor amplitudes, which may not be feasible for all biological systems. Here, data for cytoplasmic polyhedrosis virus type 17 (CPV17) collected at 1.3 Å wavelength at the Linac Coherent Light Source (LCLS) are revisited. A previously published definition of a partiality model for reflections illuminated by self-amplified spontaneous emission (SASE) pulses is built upon, which defines a fraction between 0 and 1 based on the intersection of a reflection with a spread of Ewald spheres modelled by a super-Gaussian wavelength distribution in the X-ray beam. A method of post-refinement to refine the parameters of this model is suggested. This has generated a merged data set with an overall discrepancy (by calculating the R{sub split} value) of 3.15% to 1.46 Å resolution from a 7225-image data set. The atomic numbers of C, N and O atoms in the structure are distinguishable in the electron-density map. There are 13 S atoms within the 237 residues of CPV17, excluding the initial disordered methionine. These only possess 0.42 anomalous scattering electrons each at 1.3 Å wavelength, but the 12 that have single predominant positions are easily detectable in the anomalous difference Fourier map. It is hoped that these improvements will lead towards XFEL experimental phase determination and structure determination by sulfur SAD and will generally increase the utility of the method for difficult cases.

71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗
DOE OSTI2015

A high-transparency, micro-patternable chip for X-ray diffraction analysis of microcrystals under native growth conditions

A highly X-ray-transparent, silicon nitride-based device has been designed and fabricated to harvest protein microcrystals for high-resolution X-ray diffraction data collection using microfocus beamlines and XFELs. Microcrystals present a significant impediment to the determination of macromolecular structures by X-ray diffraction methods. Although microfocus synchrotron beamlines and X-ray free-electron lasers (XFELs) can enable the collection of interpretable diffraction data from microcrystals, there is a need for efficient methods of harvesting small volumes (<2 µl) of microcrystals grown under common laboratory formats and delivering them to an X-ray beam source under native growth conditions. One approach that shows promise in overcoming the challenges intrinsic to microcrystal analysis is to pair so-called ‘fixed-target’ sample-delivery devices with microbeam-based X-ray diffraction methods. However, to record weak diffraction patterns it is necessary to fabricate devices from X-ray-transparent materials that minimize background scattering. Presented here is the design of a new micro-diffraction device consisting of three layers fabricated from silicon nitride, photoresist and polyimide film. The chip features low X-ray scattering and X-ray absorption properties, and uses a customizable blend of hydrophobic and hydrophilic surface patterns to help localize microcrystals to defined regions. Microcrystals in their native growth conditions can be loaded into the chips with a standard pipette, allowing data collection at room temperature. Diffraction data collected from hen egg-white lysozyme microcrystals (10–15 µm) loaded into the chips yielded a complete, high-resolution (<1.6 Å) data set sufficient to determine a high-quality structure by molecular replacement. The features of the chip allow the rapid and user-friendly analysis of microcrystals grown under virtually any laboratory format at microfocus synchrotron beamlines and XFELs.

75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗
DOE OSTI2015

Structure of the human MLH1 N-terminus: implications for predisposition to Lynch syndrome

Mismatch repair prevents the accumulation of erroneous insertions/deletions and non-Watson–Crick base pairs in the genome. Pathogenic mutations in the MLH1 gene are associated with a predisposition to Lynch and Turcot's syndromes. Although genetic testing for these mutations is available, robust classification of variants requires strong clinical and functional support. Here, the first structure of the N-terminus of human MLH1, determined by X-ray crystallography, is described. Lastly, the structure shares a high degree of similarity with previously determined prokaryotic MLH1 homologs; however, this structure affords a more accurate platform for the classification of MLH1 variants.

75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗
DOE OSTI2015

An active site-tail interaction in the structure of hexahistidine-tagged Thermoplasma acidophilum citrate synthase

Citrate synthase (CS) plays a central metabolic role in aerobes and many other organisms. The CS reaction comprises two half-reactions: a Claisen aldol condensation of acetyl-CoA (AcCoA) and oxaloacetate (OAA) that forms citryl-CoA (CitCoA), and CitCoA hydrolysis. Protein conformational changes that `close' the active site play an important role in the assembly of a catalytically competent condensation active site. CS from the thermoacidophile Thermoplasma acidophilum (TpCS) possesses an endogenous Trp fluorophore that can be used to monitor the condensation reaction. The 2.2 Å resolution crystal structure of TpCS fused to a C-terminal hexahistidine tag (TpCSH6) reported here is an `open' structure that, when compared with several liganded TpCS structures, helps to define a complete path for active-site closure. One active site in each dimer binds a neighboring His tag, the first nonsubstrate ligand known to occupy both the AcCoA and OAA binding sites. Solution data collectively suggest that this fortuitous interaction is stabilized by the crystalline lattice. In conclusion, as a polar but almost neutral ligand, the active site-tail interaction provides a new starting point for the design of bisubstrate-analog inhibitors of CS.

75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗
DOE OSTI2015

Analysis of rapidly synthesized guest-filled porous complexes with synchrotron radiation: practical guidelines for the crystalline sponge method

This report describes complete practical guidelines and insights for the crystalline sponge method, which have been derived through the first use of synchrotron radiation on these systems, and includes a procedure for faster synthesis of the sponges. These guidelines will be applicable to crystal sponge data collected at synchrotrons or in-house facilities, and will allow researchers to obtain reliable high-quality data and construct chemically and physically sensible models for guest structural determination. A detailed set of synthetic and crystallographic guidelines for the crystalline sponge method based upon the analysis of expediently synthesized crystal sponges using third-generation synchrotron radiation are reported. The procedure for the synthesis of the zinc-based metal–organic framework used in initial crystal sponge reports has been modified to yield competent crystals in 3 days instead of 2 weeks. These crystal sponges were tested on some small molecules, with two being unexpectedly difficult cases for analysis with in-house diffractometers in regard to data quality and proper space-group determination. These issues were easily resolved by the use of synchrotron radiation using data-collection times of less than an hour. One of these guests induced a single-crystal-to-single-crystal transformation to create a larger unit cell with over 500 non-H atoms in the asymmetric unit. This led to a non-trivial refinement scenario that afforded the best Flack x absolute stereochemical determination parameter to date for these systems. The structures did not require the use of PLATON/SQUEEZE or other solvent-masking programs, and are the highest-quality crystalline sponge systems reported to date where the results are strongly supported by the data. A set of guidelines for the entire crystallographic process were developed through these studies. In particular, the refinement guidelines include strategies to refine the host framework, locate guests and determine occupancies, discussion of the proper use of geometric and anisotropic displacement parameter restraints and constraints, and whether to perform solvent squeezing/masking. The single-crystal-to-single-crystal transformation process for the crystal sponges is also discussed. The presented general guidelines will be invaluable for researchers interested in using the crystalline sponge method at in-house diffraction or synchrotron facilities, will facilitate the collection and analysis of reliable high-quality data, and will allow construction of chemically and physically sensible models for guest structural determination.

75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗
DOE OSTI2016

Recent applications of hard x-ray photoelectron spectroscopy

Recent applications of hard x-ray photoelectron spectroscopy (HAXPES) demonstrate its many capabilities in addition to several of its limitations. Examples are given, including measurement of buried interfaces and materials under in situ or in operando conditions, as well as measurements under x-ray standing-wave and resonant excitation. Physical considerations that differentiate HAXPES from photoemission measurements utilizing soft x-ray and ultraviolet photon sources are also presented.

75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗
DOE OSTI2014

Effect of burst and recombination models for Monte Carlo transport of interacting carriers in a-Se x-ray detectors on Swank noise

Purpose: The authors describe the modification to a previously developed Monte Carlo model of semiconductor direct x-ray detector required for studying the effect of burst and recombination algorithms on detector performance. This work provides insight into the effect of different charge generation models for a-Se detectors on Swank noise and recombination fraction. Methods: The proposed burst and recombination models are implemented in the Monte Carlo simulation package, ARTEMIS, developed byFang et al. [“Spatiotemporal Monte Carlo transport methods in x-ray semiconductor detectors: Application to pulse-height spectroscopy in a-Se,” Med. Phys. 39(1), 308–319 (2012)]. The burst model generates a cloud of electron-hole pairs based on electron velocity, energy deposition, and material parameters distributed within a spherical uniform volume (SUV) or on a spherical surface area (SSA). A simple first-hit (FH) and a more detailed but computationally expensive nearest-neighbor (NN) recombination algorithms are also described and compared. Results: Simulated recombination fractions for a single electron-hole pair show good agreement with Onsager model for a wide range of electric field, thermalization distance, and temperature. The recombination fraction and Swank noise exhibit a dependence on the burst model for generation of many electron-hole pairs from a single x ray. The Swank noise decreased for the SSA compared to the SUV model at 4 V/μm, while the recombination fraction decreased for SSA compared to the SUV model at 30 V/μm. The NN and FH recombination results were comparable. Conclusions: Results obtained with the ARTEMIS Monte Carlo transport model incorporating drift and diffusion are validated with the Onsager model for a single electron-hole pair as a function of electric field, thermalization distance, and temperature. For x-ray interactions, the authors demonstrate that the choice of burst model can affect the simulation results for the generation of many electron-hole pairs. The SSA model is more sensitive to the effect of electric field compared to the SUV model and that the NN and FH recombination algorithms did not significantly affect simulation results.

46 INSTRUMENTATION RELATED TO NUCLEAR SCIENCE AND ↗
DOE OSTI2015

Magnetic field, frequency and temperature dependence of complex conductance of ultrathin La1.65Sr0.45CuO4/La2CuO4 films and the organic superconductors κ-(BEDT-TTF)2Cu[N(CN)2]Br

We used atomic-layer molecular beam epitaxy (ALL-MBE) to synthesize bilayer films of a cuprate metal (La1.65Sr0.45CuO4La1.65Sr0.45CuO4, LSCO) and a cuprate insulator (La2CuO4La2CuO4, LCO), in which interface superconductivity occurs in a layer that is just one-half unit cell thick. We have studied the magnetic field and temperature dependence of the complex sheet conductance, σ(ω)σ(ω), of these films, and compared them to κκ-(BEDT-TTF)2Cu[N(CN)2]Br2Cu[N(CN)2]Br single crystals. The magnetic field HH was applied both parallel and perpendicular to the 2D conducting layers. Experiments have been carried out at frequencies between 23 kHz and 50 MHz using either two-coil mutual inductance technique, or the LC resonators with spiral or rectangular coils. The real and the imaginary parts of the mutual-inductance M(T,ω)M(T,ω) between the coil and the sample were measured and converted to complex conductivity. For HH perpendicular to the conducting layers, we observed almost identical behavior in both films and κκ-Br single crystals: (i) the transition onset in the inductive response, L-1kLk-1(T) occurs at a temperature lower by 2 K than in Reσ(T)Reσ(T), (ii) this shift is almost constant with magnetic field up to 8 T; (iii) the vortex diffusion constant D(T)D(T) is exponential due to pinning of vortex cores. These results can be described by the extended dynamic theory of the Berezinski–Kosterlitz–Thouless (BKT) transition and dynamics of bound vortex–antivortex pairs with short separation lengths.

75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗
DOE OSTI2012

Summary of Booster Development and Qualification Report

This report outlines booster development work done at Los Alamos National Laboratory from 2007 to present. The booster is a critical link in the initiation train of explosive assemblies, from complex devices like nuclear weapons to conventional munitions. The booster bridges the gap from a small, relatively sensitive detonator to an insensitive, but massive, main charge. The movement throughout the explosives development community is to use more and more insensitive explosive components. With that, more energy is needed out of the booster. It has to initiate reliably, promptly, powerfully and safely. This report is divided into four sections. The first provides a summary of a collaborative effort between LANL, LLNL, and AWE to identify candidate materials and uniformly develop a testing plan for new boosters. Important parameters and the tests required to measure them were defined. The nature of the collaboration and the specific goals of the participating partners has changed over time, but the booster development plan stands on its own merit as a complete description of the test protocol necessary to compare and qualify booster materials, and is discussed in its entirety in this report. The second section describes a project, which began in 2009 with the Department of Defense to develop replacement booster formulations for PBXN-7. Replacement of PBXN-7 was necessary because it contained Triaminotrinitrobenzene (TATB), which was becoming unavailable to the DoD and because it contained Cyclotrimethylenetrinitramine (RDX), which was sensitive and toxic. A LANL-developed explosive, Diaminoazoxyfurazan (DAAF), was an important candidate. This project required any replacement formulation be a drop-in replacement in existing munitions. This project was timely, in that it made use of the collaborative booster development project, and had the additional constraint of matching shock sensitivity. Additionally it needed to be a safety improvement, and a performance improvement, especially at cold temperatures. The requirements of this project necessitated novel test development and a different approach to ranking booster qualities. Results of this project have been documented to the DoD and the relevant portions are included within. The third section of this booster report outlines testing related to main charge initiation merit. Initiability can be evaluated by looking at critical diameter, run distance, and shock sensitivity. Once a booster is initiated, it needs to be powerful enough to initiate the main charge symmetrically and evenly. Main charge initiability is evaluated directly by observing detonation wave symmetry, curvature, and first break out over the surface of a charge. Furthermore it must be insensitive to accidents and insults, and safe and reliable across a range of temperatures. These effects, tests, and results will be discussed individually in the context of DAAF and other explosives similarly tested. The last section provides a conclusion and summary of our experimental work and recommendations for the path forward. References and additional supporting documentation and results are provided in the appendices at the end of this report.

36 MATERIALS SCIENCE↗
DOE OSTI2012

Mastering Uncertainty and Risk at Multiple Time Scales in the Future Electrical Grid

Today's electrical grids enjoy a relatively clean separation of spatio-temporal scales yielding a compartmentalization of grid design, optimization, control and risk assessment allowing for the use of conventional mathematical tools within each area. In contrast, the future grid will incorporate time-intermittent renewable generation, operate via faster electrical markets, and tap the latent control capability at finer grid modeling scales; creating a fundamentally new set of couplings across spatiotemporal scales and requiring revolutionary advances in mathematics techniques to bridge these scales. One example is found in decade-scale grid expansion planning in which today's algorithms assume accurate load forecasts and well-controlled generation. Incorporating intermittent renewable generation creates fluctuating network flows at the hourly time scale, inherently linking the ability of a transmission line to deliver electrical power to hourly operational decisions. New operations-based planning algorithms are required, creating new mathematical challenges. Spatio-temporal scales are also crossed when the future grid's minute-scale fluctuations in network flows (due to intermittent generation) create a disordered state upon which second-scale transient grid dynamics propagate effectively invalidating today's on-line dynamic stability analyses. Addressing this challenge requires new on-line algorithms that use large data streams from new grid sensing technologies to physically aggregate across many spatial scales to create responsive, data-driven dynamic models. Here, we sketch the mathematical foundations of these problems and potential solutions.

24 POWER TRANSMISSION AND DISTRIBUTION↗
DOE OSTI2012

Science Campaign-1 Pulsed Power Efforts [Slides]

The PHELIX portable pulsed-power driver is discussed. It is composed of two air-insulated, single Marx modules capable of storing 300 kJ of electrical energy. The Marx are cable coupled to a toroidal transformer with a 4:1 winding ratio. The experimental load is located at the center of the transformer. The components are mounted in a 8’x10’x18’ boxcar which can be moved in and out of the beam line at the LANL proton radiography facility and prevents EMI within the facility. PHELIX has successfully completed two liner implosion experiments with full diagnostic return from flash X-ray imaging, optical Faraday load current, and multi-channel PDV. Computational modeling with both the legacy 1D MHD code RAVEN and the LANL ASC-LAP FLAG code show good agreement with data.

70 PLASMA PHYSICS AND FUSION TECHNOLOGY↗
DOE OSTI2012

High Energy-Density Materials with Fast Energy Release: Molecular scale shock response of explosives (DTRA Basic Research Final Report 2012)

The principle goal of this $\$$150K/yr, 3-yr. project was to experimentally measure the time evolution of shock induced chemistry in the explosive RDX. Since direct measurements of shock induced chemistry in RDX, or any other explosive, have eluded researchers for several decades, new techniques had to be developed. Transient absorption was coupled to laser shock loading to probe the possible role of electronic excitations in the chemistry of RDX. Transient absorption signatures turned out to be a good indication of the relative degree of chemical reaction versus time, but were not conclusive regarding whether electronic excitation was an important factor in shock initiation. Preliminary efforts to sensitize shock induced chemistry with ultraviolet pulsed excitation were performed, but are not yet conclusive. The bulk of the effort of the project was directed at development of femtosecond stimulated Raman spectroscopy (FSRS) as a diagnostic of temperature in the presence of chemistry. This effort was significantly more difficult than initially anticipated. While we had planned to apply the method to single shot laser experiments, the sensitivity achieved during the project duration was insufficient to measure the sub-nanogram amounts of material shocked. Despite the difficulties applying this measurement to our current small scale laser shock experiments, it shows significant promise for measurements where there is more volume of material shocked. We have established the theoretical framework and experimentally validated FSRS as a sub-picosecond molecular vibrational temperature measurement diagnostic. We have also followed the shock induced chemistry of RDX through transient absorption spectroscopy and established the shock stresses required to achieve sub-nanosecond reaction rates. The project led to 3 peer reviewed journal articles, 4 conference proceedings, 3 invited talks at conferences, 2 contributed talks at conferences, and a number of other presentations.

36 MATERIALS SCIENCE↗
DOE OSTI2012

Zone Refining for Low Loss Plutonium Purification

In an effort to enhance plutonium purification capabilities at Los Alamos National Laboratory, further develop of the currently existing zone refining capabilities is needed to create a functional low loss processing option in support of programmatic and materials science research activities. Currently, the most effective process for converting impure plutonium dioxide (~96% pure) to high-purity plutonium metal (>99.9%), consists of the following steps: (1) reducing the dioxide to an impure Plutonium metal with calcium metal in molten calcium chloride, (2) casting the impure metal into an anode and (3) electrorefining the impure metal to produce high-purity plutonium metal. The final step in this method is only 83% efficient as compared to the >95% efficiency of the other processing steps. Other more efficient processing methods are desirable to enhance current purification activities, thereby, reducing waste generation and conserving precious materials in need of purification. Although zone refining has been used extensively to purify many lanthanides and actinides, its usefulness in purifying plutonium has yet to be fully realized.

36 MATERIALS SCIENCE↗
DOE OSTI2012

Sesame Equation of State Number 2100 for Scandium

An equation of state (EOS) for scandium has been constructed using the OpenSesame code and was placed in the SESAME library as material number 2100. The cold curve was constructed with a Mie-Grüneisen model fitted to the high pressure Hugoniot data and to the zero pressure bulk sound speed, the nuclear contribution was calculated from JD Johnson nuclear model and the electronic thermal contribution from the Thomas-Fermi-Dirac statistical model. The EOS behaves reasonably well over a wide range of densities, pressures and temperatures, and compares fairly with the available experimental data. Of the 5 solid phases present in scandium at room temperature, however, only the first one, the hcp phase, is assumed to occur. Also the transition to bcc at room pressure just before melting is ignored. We plan to construct a multiphase EOS as the next step. The purpose of the present calculation was mostly for learning purposes, as is reflected by the way the report is written.

36 MATERIALS SCIENCE↗