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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 55 records · Page 3
All sourcesNASA NTRSDOE OSTI
DOE OSTI2020

Preventing Bio-Bloopers and XFEL Follies: Best Practices from your Friendly Instrument Staff

Serial Femtosecond Crystallography (SFX) at X-ray Free electron Lasers (XFELs) is a relatively new field promising to deliver unparalleled spatial and temporal resolution on biological systems and there dynamics. Over the past decade, though, there have been a handful of results that have truly delivered on these promises. Why? SFX has many paradigm shifting techniques not seen in typical structural biology arenas, such as creating a concentrated slurry of microcrystals rather than a handful of loopable prisms worthy of a catalog photo. Then taking that slurry and high speed jetting them towards the vacuum or helium interation region to destroy less than 1% of your sample and waste the other 99. The literature is full of techniques and methods promising to cure what ails your experiment, yet as an instrument scientist will tell you –and a first author might admit after a few drinks at the conference happy hour—is that there are a lot more failures than the success we published, results may vary. We will walk through a best practices on how to prepare your sample and chose a sample delivery technique that will amerliorate your studies rather than undermine your hardwork and hopefully lead to better experimental planning and execution, inching you closer to that scientific goal and that call from Stockholm. This will be written in a more editorialized fashion and is meant to give the reader an idea of what to try or how they should be thinking. Welcome to SFX, now what?

47 OTHER INSTRUMENTATION↗
DOE OSTI2024

Speckle contrast from the split-and-delay unit with seeded X-ray pulses of the MID instrument at European XFEL

We report on the coherence properties and characteristics of the split- and-delay unit at the Materials Imaging and Dynamics instrument of the European XFEL under seeded-beam conditions. Our investigation focuses on the speckle contrast extracted from the scattering patterns from static scatterers and pulse splitting characteristics. Seeded-beam operation enabled a high throughput of the split-and-delay unit. We highlight the invaluable potential of the split-and-delay unit for experimental investigations for enhancing our understanding of ultrafast phenomena in molecular liquids, such as water and aqueous solutions.

Fuoss, Paul↗
DOE OSTI2022

Complementarity of neutron, XFEL and synchrotron crystallography for defining the structures of metalloenzymes at room temperature

Room-temperature macromolecular crystallography allows protein structures to be determined under close-to-physiological conditions, permits dynamic freedom in protein motions and enables time-resolved studies. In the case of metalloenzymes that are highly sensitive to radiation damage, such room-temperature experiments can present challenges, including increased rates of X-ray reduction of metal centres and site-specific radiation-damage artefacts, as well as in devising appropriate sample-delivery and data-collection methods. It can also be problematic to compare structures measured using different crystal sizes and light sources. In this study, structures of a multifunctional globin, dehaloperoxidase B (DHP-B), obtained using several methods of room-temperature crystallographic structure determination are described and compared. Here, data were measured from large single crystals and multiple microcrystals using neutrons, X-ray free-electron laser pulses, monochromatic synchrotron radiation and polychromatic (Laue) radiation light sources. These approaches span a range of 18 orders of magnitude in measurement time per diffraction pattern and four orders of magnitude in crystal volume. The first room-temperature neutron structures of DHP-B are also presented, allowing the explicit identification of the hydrogen positions. The neutron data proved to be complementary to the serial femtosecond crystallography data, with both methods providing structures free of the effects of X-ray radiation damage when compared with standard cryo-crystallography. Comparison of these room-temperature methods demonstrated the large differences in sample requirements, data-collection time and the potential for radiation damage between them. With regard to the structure and function of DHP-B, despite the results being partly limited by differences in the underlying structures, new information was gained on the protonation states of active-site residues which may guide future studies of DHP-B.

36 MATERIALS SCIENCE↗
DOE OSTI2019

SAD phasing of XFEL data depends critically on the error model

A nonlinear least-squares method for refining a parametric expression describing the estimated errors of reflection intensities in serial crystallographic (SX) data is presented. This approach, which is similar to that used in the rotation method of crystallographic data collection at synchrotrons, propagates error estimates from photon-counting statistics to the merged data. Here, it is demonstrated that the application of this approach to SX data provides better SAD phasing ability, enabling the autobuilding of a protein structure that had previously failed to be built. Estimating the error in the merged reflection intensities requires the understanding and propagation of all of the sources of error arising from the measurements. One type of error, which is well understood, is the counting error introduced when the detector counts X-ray photons. Thus, if other types of random errors (such as readout noise) as well as uncertainties in systematic corrections (such as from X-ray attenuation) are completely understood, they can be propagated along with the counting error, as appropriate. In practice, most software packages propagate as much error as they know how to model and then include error-adjustment terms that scale the error estimates until they explain the variance among the measurements. If this is performed carefully, then during SAD phasing likelihood-based approaches can make optimal use of these error estimates, increasing the chance of a successful structure solution. In serial crystallography, SAD phasing has remained challenging, with the few examples of de novo protein structure solution each requiring many thousands of diffraction patterns. Here, the effects of different methods of treating the error estimates are estimated and it is shown that using a parametric approach that includes terms proportional to the known experimental uncertainty, the reflection intensity and the squared reflection intensity to improve the error estimates can allow SAD phasing even from weak zinc anomalous signal.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2021

Short-Lived Intermediate in the N2O Generation by P450 NO Reductase Captured by Time-Resolved IR Spectroscopy and XFEL Crystallography

Diffraction images were collected using an MX300-HS CCD detector. For each cryoloop, 2D raster scan with 50 μm step in each direction was performed twice. In the second pass, the raster-scan grid was shifted 25 μm in each direction. In cheetah directory, - {puck_name}/{pin_id}_hits.h5 correspond to the first scan, and - {puck_name}/{pin_id}-2_hits.h5 correspond to the second scan.

BL3↗
DOE OSTI2023

Development of diamond-based diagnostics for next-generation XFELs

The composition and performance of three different diamond sensor based pass-through diagnostics are presented. A position-sensitive quadrant sensor was designed and characterized using the XPP beam at the SLAC LCLS, demonstrating a generated-charge resolution of 0.025 pC and a position sensitivity of 2 μm, measurable pulse-by-pulse at a repetition rate of up to 50 MHz. A compact signal path capable of repetition rates up to 1 GHz was used to characterize the charge collection properties of diamond sensors as a function of the density of electron-hole pairs created within the sensor, finding a limit of approximately 10 16 electron-hole pairs per cm 3 beyond which the collection efficiency and time began to degrade. Finally, a proposed scheme for measuring ionizing radiation at multi-GHz rates is presented, along with results preliminarily demonstrating signal transport capability in excess of 5 GHz.

46 INSTRUMENTATION RELATED TO NUCLEAR SCIENCE AND ↗
DOE OSTI2023

XFEL Microcrystallography of Self-Assembling Silver n -Alkanethiolates

New synthetic hybrid materials and their increasing complexity have placed growing demands on crystal growth for single-crystal X-ray diffraction analysis. Unfortunately, not all chemical systems are conducive to the isolation of single crystals for traditional characterization. Here, small-molecule serial femtosecond crystallography (smSFX) at atomic resolution (0.833 Å) is employed to characterize microcrystalline silver n-alkanethiolates with various alkyl chain lengths at X-ray free electron laser facilities, resolving long-standing controversies regarding the atomic connectivity and odd–even effects of layer stacking. smSFX provides high-quality crystal structures directly from the powder of the true unknowns, a capability that is particularly useful for systems having notoriously small or defective crystals. We present crystal structures of silver n-butanethiolate (C4), silver n-hexanethiolate (C6), and silver n-nonanethiolate (C9). We show that an odd–even effect originates from the orientation of the terminal methyl group and its role in packing efficiency. We also propose a secondary odd–even effect involving multiple mosaic blocks in the crystals containing even-numbered chains, identified by selected-area electron diffraction measurements. Finally, we conclude with a discussion of the merits of the synthetic preparation for the preparation of microdiffraction specimens and compare the long-range order in these crystals to that of self-assembled monolayers.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2024

Ionization by XFEL radiation produces distinct structure in liquid water

In the warm dense matter (WDM) regime, where condensed, gas, and plasma phases coexist, matter frequently exhibits unusual properties that cannot be described by contemporary theory. Experiments reporting phenomena in WDM are therefore of interest to advance our physical understanding of this regime, which is found in dwarf stars, giant planets, and fusion ignition experiments. Using 7.1 keV X-ray free electron laser radiation (nominally 5×10 5 J/cm 2 ), we produced and probed transient WDM in liquid water. Wide-angle X-ray scattering (WAXS) from the probe reveals a new ~9 Å structure that forms within 75 fs. By 100 fs, the WAXS peak corresponding to this new structure is of comparable magnitude to the ambient water peak, which is attenuated. Simulations suggest that the experiment probes a superposition of two regimes. In the first, fluences expected at the focus severely ionize the water, which becomes effectively transparent to the probe. In the second, out-of-focus pump radiation produces O 1+ and O 2+ ions, which rearrange due to Coulombic repulsion over 10 s of fs. Our simulations account for a decrease in ambient water signal and an increase in low-angle X-ray scattering but not the experimentally observed 9 Å feature, presenting a new challenge for theory.

70 PLASMA PHYSICS AND FUSION TECHNOLOGY↗