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At least 73 records · Page 4

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DOE OSTI2018

Three-dimensional (3D) analysis of white etching bands (WEBs) in AISI M50 bearing steel using automated serial sectioning

Dark etching regions (DER) and white etching bands (WEB) form in the subsurface stressed regions of bearing raceways and rolling elements. Also, “butterfly” formations form around non-metallic inclusions and large carbides. The formation of WEBs, DERs and butterfly are dependent on operating conditions, material alloying elements and heat treatment. The DER, WEB and butterfly formations are well studied in two dimensions (2D). The objective of this study was to analyze WEB formation in three dimensions (3D) that will allow better understanding of material transformation after stress cycling. Three rolling contact fatigue (RCF) tested vacuum induction melted vacuum arc re-melted (VIM-VAR) AISI M50 samples (from a bench test, sub-scale test and commercial gas turbine engine) were analyzed using automated serial sectioning to map WEB networks and a butterfly formation in 3D. Automated serial sectioning and 2D optical microstructural data for 3D reconstructions and analysis was done using a fully automated serial sectioning system – Robo-Met.3D®. 3D analysis was performed using Image-Pro Premier 3D. The data set allowed 3D visualization and analysis of the evolution and propagation of WEB and butterfly in M50 bearing steel, including the positive microscopic identification of a ceramic inclusion that was the source of a WEB.

36 MATERIALS SCIENCE↗

DOE OSTI2021

An on-demand, drop-on-drop method for studying enzyme catalysis by serial crystallography

Serial femtosecond crystallography has opened up many new opportunities in structural biology. In recent years, several approaches employing light-inducible systems have emerged to enable time-resolved experiments that reveal protein dynamics at high atomic and temporal resolutions. However, very few enzymes are light-dependent, whereas macromolecules requiring ligand diffusion into an active site are ubiquitous. In this work we present a drop-on-drop sample delivery system that enables the study of enzyme-catalyzed reactions in microcrystal slurries. The system delivers ligand solutions in bursts of multiple picoliter-sized drops on top of a larger crystal-containing drop inducing turbulent mixing and transports the mixture to the X-ray interaction region with temporal resolution. We demonstrate mixing using fluorescent dyes, numerical simulations and time-resolved serial femtosecond crystallography, which show rapid ligand diffusion through microdroplets. The drop-on-drop method has the potential to be widely applicable to serial crystallography studies, particularly of enzyme reactions with small molecule substrates.

59 BASIC BIOLOGICAL SCIENCES↗

DOE OSTI2014

A serial-kinematic nanopositioner for high-speed atomic force microscopy

A flexure-guided serial-kinematic XYZ nanopositioner for high-speed Atomic Force Microscopy is presented in this paper. Two aspects influencing the performance of serial-kinematic nanopositioners are studied in this work. First, mass reduction by using tapered flexures is proposed to increased the natural frequency of the nanopositioner. 25% increase in the natural frequency is achieved due to reduced mass with tapered flexures. Second, a study of possible sensor positioning in a serial-kinematic nanopositioner is presented. An arrangement of sensors for exact estimation of cross-coupling is incorporated in the proposed design. A feedforward control strategy based on phaser approach is presented to mitigate the dynamics and nonlinearity in the system. Limitations in design approach and control strategy are discussed in the Conclusion.

46 INSTRUMENTATION RELATED TO NUCLEAR SCIENCE AND ↗

DOE OSTI2023

All polymer microfluidic chips—A fixed target sample delivery workhorse for serial crystallography

The development of x-ray free electron laser (XFEL) light sources and serial crystallography methodologies has led to a revolution in protein crystallography, enabling the determination of previously unobtainable protein structures and near-atomic resolution of otherwise poorly diffracting protein crystals. However, to utilize XFEL sources efficiently demands the continuous, rapid delivery of a large number of difficult-to-handle microcrystals to the x-ray beam. A recently developed fixed-target system, in which crystals of interest are enclosed within a sample holder, which is rastered through the x-ray beam, is discussed in detail in this Perspective. The fixed target is easy to use, maintains sample hydration, and can be readily modified to allow a broad range of sample types and different beamline requirements. Recent innovations demonstrate the potential of such microfluidic-based fixed targets to be an all-around “workhorse” for serial crystallography measurements. In conclusion, this Perspective will summarize recent advancements in microfluidic fixed targets for serial crystallography, examine needs for future development, and guide users in designing, choosing, and utilizing a fixed-target sample delivery device for their system.

59 BASIC BIOLOGICAL SCIENCES↗

DOE OSTI2022

Serial-Refine Method for Fast Wake-Steering Yaw Optimization

In this paper we present the Serial-Refine method for quickly finding the optimal yaw angles in wake steering. The method optimizes turbine angles serially from upstream to downstream using a small number of candidate angles. The presented results show that Serial-Refine finds solutions that are at least as good as former conventional optimization approaches but that require much less computation time.

17 WIND ENERGY↗

DOE OSTI2015

In meso in situ serial X-ray crystallography of soluble and membrane proteins

A method for performing high-throughput in situ serial X-ray crystallography with soluble and membrane proteins in the lipid cubic phase is described. It works with microgram quantities of protein and lipid (and ligand when present) and is compatible with the most demanding sulfur SAD phasing. The lipid cubic phase (LCP) continues to grow in popularity as a medium in which to generate crystals of membrane (and soluble) proteins for high-resolution X-ray crystallographic structure determination. To date, the PDB includes 227 records attributed to the LCP or in meso method. Among the listings are some of the highest profile membrane proteins, including the β{sub 2}-adrenoreceptor–G{sub s} protein complex that figured in the award of the 2012 Nobel Prize in Chemistry to Lefkowitz and Kobilka. The most successful in meso protocol to date uses glass sandwich crystallization plates. Despite their many advantages, glass plates are challenging to harvest crystals from. However, performing in situ X-ray diffraction measurements with these plates is not practical. Here, an alternative approach is described that provides many of the advantages of glass plates and is compatible with high-throughput in situ measurements. The novel in meso in situ serial crystallography (IMISX) method introduced here has been demonstrated with AlgE and PepT (alginate and peptide transporters, respectively) as model integral membrane proteins and with lysozyme as a test soluble protein. Structures were solved by molecular replacement and by experimental phasing using bromine SAD and native sulfur SAD methods to resolutions ranging from 1.8 to 2.8 Å using single-digit microgram quantities of protein. That sulfur SAD phasing worked is testament to the exceptional quality of the IMISX diffraction data. The IMISX method is compatible with readily available, inexpensive materials and equipment, is simple to implement and is compatible with high-throughput in situ serial data collection at macromolecular crystallography synchrotron beamlines worldwide. Because of its simplicity and effectiveness, the IMISX approach is likely to supplant existing in meso crystallization protocols. It should prove particularly attractive in the area of ligand screening for drug discovery and development.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

DOE OSTI2015

Accounting for partiality in serial crystallography using ray-tracing principles

Serial crystallography generates partial reflections from still diffraction images. Partialities are estimated with EVAL ray-tracing simulations, thereby improving merged reflection data to a similar quality as conventional rotation data. Serial crystallography generates ‘still’ diffraction data sets that are composed of single diffraction images obtained from a large number of crystals arbitrarily oriented in the X-ray beam. Estimation of the reflection partialities, which accounts for the expected observed fractions of diffraction intensities, has so far been problematic. In this paper, a method is derived for modelling the partialities by making use of the ray-tracing diffraction-integration method EVAL. The method estimates partialities based on crystal mosaicity, beam divergence, wavelength dispersion, crystal size and the interference function, accounting for crystallite size. It is shown that modelling of each reflection by a distribution of interference-function weighted rays yields a ‘still’ Lorentz factor. Still data are compared with a conventional rotation data set collected from a single lysozyme crystal. Overall, the presented still integration method improves the data quality markedly. The R factor of the still data compared with the rotation data decreases from 26% using a Monte Carlo approach to 12% after applying the Lorentz correction, to 5.3% when estimating partialities by EVAL and finally to 4.7% after post-refinement. The merging R{sub int} factor of the still data improves from 105 to 56% but remains high. This suggests that the accuracy of the model parameters could be further improved. However, with a multiplicity of around 40 and an R{sub int} of ∼50% the merged still data approximate the quality of the rotation data. The presented integration method suitably accounts for the partiality of the observed intensities in still diffraction data, which is a critical step to improve data quality in serial crystallography.

75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗

DOE OSTI2018

Rapid sample delivery for megahertz serial crystallography at X-ray FELs

Liquid microjets are a common means of delivering protein crystals to the focus of X-ray free-electron lasers (FELs) for serial femtosecond crystallography measurements. The high X-ray intensity in the focus initiates an explosion of the microjet and sample. With the advent of X-ray FELs with megahertz rates, the typical velocities of these jets must be increased significantly in order to replenish the damaged material in time for the subsequent measurement with the next X-ray pulse. Here in this paper, this work reports the results of a megahertz serial diffraction experiment at the FLASH FEL facility using 4.3 nm radiation. The operation of gas-dynamic nozzles that produce liquid microjets with velocities greater than 80 m s -1 was demonstrated. Furthermore, this article provides optical images of X-ray-induced explosions together with Bragg diffraction from protein microcrystals exposed to trains of X-ray pulses repeating at rates of up to 4.5 MHz. Finally, the results indicate the feasibility for megahertz serial crystallography measurements with hard X-rays and give guidance for the design of such experiments.

36 MATERIALS SCIENCE↗

DOE OSTI2014

MO-C-17A-10: Comparison of Dose Deformable Accumulation by Using Parallel and Serial Approaches

Purpose: The uncertainty of dose accumulation over multiple CT datasets with deformable fusion may have significant impact on clinical decisions. In this study, we investigate the difference of two dose summation approaches involving deformable fusion. Methods: Five patients, four external beam and one brachytherapy(BT), were chosen for the study. The BT patient was treated with CT-based HDR. The CT image sets acquired in the imageguidance process (8-11 CTs/patient) were used to determine the dose delivered to the four external beam patients. (prostate, pelvis, lung and head and neck). For the HDR patient (cervix), five CT image sets and the corresponding BT plans were used. In total 44 CT datasets and RT dose/plans were imported into the image fusion software MiM (6.0.4) for analysis.For each of the five clinical cases, the dose from each fraction was accumulated into the primary CT dataset by using both Parallel and Serial approaches. The dose-volume histogram (DVH) for CTV and selected organs-at-risks (OAR) were generated. The D95(CTV), OAR(mean) and OAR(max) for the four external beam cases the D90(CTV), and the max dose to bladder and rectum for the BT case were compared. Results: For the four external beam patients, the difference in D95(CTV) were <1.2% PD between the parallel and the serial approaches. The differences of the OAR(mean) and the OAR(max ) range from 0 to 3.7% and <1% PD respectively. For the HDR patient, the dose difference for D90 is 11% PD while that of the max dose to bladder and rectum were 11.5% and 23.3% respectively. Conclusion: For external beam treatments, the parallel and serial approaches have <5% difference probably because tumor volume and OAR have less changes from fraction to fraction. For the brachytherapy case, >10% dose difference between the two approaches was observed as significant volume changes of tumor and OAR were observed among treatment fractions.

60 APPLIED LIFE SCIENCES↗

NASA NTRS1989

A unifying framework for rigid multibody dynamics and serial and parallel computational issues

A unifying framework for various formulations of the dynamics of open-chain rigid multibody systems is discussed. Their suitability for serial and parallel processing is assessed. The framework is based on the derivation of intrinsic, i.e., coordinate-free, equations of the algorithms which provides a suitable abstraction and permits a distinction to be made between the computational redundancy in the intrinsic and extrinsic equations. A set of spatial notation is used which allows the derivation of the various algorithms in a common setting and thus clarifies the relationships among them. The three classes of algorithms viz., O(n), O(n exp 2) and O(n exp 3) or the solution of the dynamics problem are investigated. Researchers begin with the derivation of O(n exp 3) algorithms based on the explicit computation of the mass matrix and it provides insight into the underlying basis of the O(n) algorithms. From a computational perspective, the optimal choice of a coordinate frame for the projection of the intrinsic equations is discussed and the serial computational complexity of the different algorithms is evaluated. The three classes of algorithms are also analyzed for suitability for parallel processing. It is shown that the problem belongs to the class of N C and the time and processor bounds are of O(log2/2(n)) and O(n exp 4), respectively. However, the algorithm that achieves the above bounds is not stable. Researchers show that the fastest stable parallel algorithm achieves a computational complexity of O(n) with O(n exp 4), respectively. However, the algorithm that achieves the above bounds is not stable. Researchers show that the fastest stable parallel algorithm achieves a computational complexity of O(n) with O(n exp 2) processors, and results from the parallelization of the O(n exp 3) serial algorithm.

Fijany, Amir↗

NASA NTRS1987

Charge-coupled-device parallel-to-serial converter

A CCD parallel-to-serial converter comprising two successions of charge transfer stages, recurrently side-loaded with respective ones of parallelly supplied charge packets, then serially unloaded by time-interleaved respective shift register operations. The charge packets converted to time-division-multiplexed serial form are supplied to a shared electrometer, and the electrometer response is de-multiplexed. Preferably, shift register operations are carried forward concurrently at the same rate, but with the final charge transfer stages clocked in phases staggered in time.

Tower, John R.↗

NASA NTRSDate not supplied

Spectrally Dependent Radiometric Measurement Errors Due to Ccd Serial Pixel-to-Pixel Readout Interference in the Ocean Color Instrument of the NASA PACE Mission

The Ocean Color Instrument on NASA’s PACE mission is a 322 887 nm hyperspectral imager with 1 km x 1 km nadir spatial resolution and 5 nm spectral resolution utilizing charge-coupled devices (CCDs) operating in Time Delay Integration (TDI) mode where each TDI column represents a different wavelength in 0.625 nm increments. After TDI, the charge is moved into serial output pixels and read out. The spatial resolution requires an 8.5 MHz readout rate. This only allows 59 ns for the CCD reset and video to be asserted and settled before sampling. The response exhibits serial pixel-to-pixel readout interference due to the lack of full settling. Each serial pixel value has a dependence on the value of the preceding pixel value. This leads to a spectrally dependent radiometric measurement error of up to 0.3 %. We explain the operation of the detection system, the behavior of the interference, and show the resulting measurement error based on data from both ground testing and on-orbit characterization.

Remote Sensing↗

NASA NTRS2024

Spectrally Dependent Radiometric Measurement Errors Due to CCD Serial Pixel-to-Pixel Readout Interference in the Ocean Color Instrument of the NASA PACE Mission

Remote Sensing↗

DOE OSTI2015

Mechanical Serial-Sectioning Data Assistant

Mechanical Serial-Sectioning Data Assistant (MECH-SSDA) is a real-time data analytics software with graphical user-interface that; 1) tracks and visualizes material removal rates for mechanical serial-sectioning experiments using at least two height measurement methods; 2) tracks process time for specific segments of the serial-sectioning experiment; and 3) alerts the user to anomalies in expected removal rate, process time or unanticipated operational pauses

Poulter, Gregory A.↗

DOE OSTI2020

RD53A: A large-scale prototype chip for the phase II upgrade in the serially powered HL-LHC pixel detectors

The phase II upgrade of the HL-LHC experiments within the LHC intends to deepen the studies of the Higgs boson and to allow the discovery of further particles by adding an integrated luminosity of about 4000 fb -1 over 10 years of operation. This upgrade would overwhelm the installed pixel detector readout chips with higher hit rates and radiation levels than ever before. To match these extreme requirements the RD53 collaboration, a joint effort between ATLAS and CMS, developed RD53A, a new generation pixel detector readout chip prototype manufactured in a 65 nm CMOS technology. It is half the size of the final pixel chips and designed to meet requirements in the face of 3 GHz/cm 2 hit rate after irradiation to 500 Mrad. The detector is able to use 50×50 μm 2 or 25×100 μm 2 pixels with high readout speed of up to 4 links per chip with 1.28 Gbit/s each. Shunt–LDO regulators integrated on the bottom of the chip provide the required voltages to the two power domains, analog and digital. These regulators enable serial powering of the pixel modules, which is the only feasible, radiation hard scheme to ensure acceptable power cable losses and to stay within the material budget for the future pixel detectors. Finally, an overview of the status and challenges of serial powering and the Shunt–LDO regulator development will be given.

46 INSTRUMENTATION RELATED TO NUCLEAR SCIENCE AND ↗

DOE OSTI2020

Radiation damage and dose limits in serial synchrotron crystallography at cryo- and room temperatures

Radiation damage limits the accuracy of macromolecular structures in X-ray crystallography. Cryogenic (cryo-) cooling reduces the global radiation damage rate and, therefore, became the method of choice over the past decades. The recent advent of serial crystallography, which spreads the absorbed energy over many crystals, thereby reducing damage, has rendered room temperature (RT) data collection more practical and also extendable to microcrystals, both enabling and requiring the study of specific and global radiation damage at RT. Here, we performed sequential serial raster-scanning crystallography using a microfocused synchrotron beam that allowed for the collection of two series of 40 and 90 full datasets at 2- and 1.9-Å resolution at a dose rate of 40.3 MGy/s on hen egg white lysozyme (HEWL) crystals at RT and cryotemperature, respectively. The diffraction intensity halved its initial value at average doses ( D 1/2 ) of 0.57 and 15.3 MGy at RT and 100 K, respectively. Specific radiation damage at RT was observed at disulfide bonds but not at acidic residues, increasing and then apparently reversing, a peculiar behavior that can be modeled by accounting for differential diffraction intensity decay due to the nonuniform illumination by the X-ray beam. Specific damage to disulfide bonds is evident early on at RT and proceeds at a fivefold higher rate than global damage. The decay modeling suggests it is advisable not to exceed a dose of 0.38 MGy per dataset in static and time-resolved synchrotron crystallography experiments at RT. This rough yardstick might change for proteins other than HEWL and at resolutions other than 2 Å.

36 MATERIALS SCIENCE↗

DOE OSTI2014

Mapping the continuous reciprocal space intensity distribution of X-ray serial crystallography

Serial crystallography using X-ray free-electron lasers enables the collection of tens of thousands of measurements from an equal number of individual crystals, each of which can be smaller than 1 mm in size. This manuscript describes an alternative way of handling diffraction data recorded by serial femtosecond crystallography, by mapping the diffracted intensities into three-dimensional reciprocal space rather than integrating each image in two dimensions as in the classical approach. We call this procedure ‘three-dimensional merging’. This procedure retains information about asymmetry in Bragg peaks and diffracted intensities between Bragg spots. This intensity distribution can be used to extract reflection intensities for structure determination and opens up novel avenues for post-refinement, while observed intensity between Bragg peaks and peak asymmetry are of potential use in novel direct phasing strategies.

71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗

DOE OSTI2015

Low- Z polymer sample supports for fixed-target serial femtosecond X-ray crystallography

X-ray free-electron lasers (XFELs) offer a new avenue to the structural probing of complex materials, including biomolecules. Delivery of precious sample to the XFEL beam is a key consideration, as the sample of interest must be serially replaced after each destructive pulse. The fixed-target approach to sample delivery involves depositing samples on a thin-film support and subsequent serial introduction via a translating stage. Some classes of biological materials, including two-dimensional protein crystals, must be introduced on fixed-target supports, as they require a flat surface to prevent sample wrinkling. A series of wafer and transmission electron microscopy (TEM)-style grid supports constructed of low- Z plastic have been custom-designed and produced. Aluminium TEM grid holders were engineered, capable of delivering up to 20 different conventional or plastic TEM grids using fixed-target stages available at the Linac Coherent Light Source (LCLS). As proof-of-principle, X-ray diffraction has been demonstrated from two-dimensional crystals of bacteriorhodopsin and three-dimensional crystals of anthrax toxin protective antigen mounted on these supports at the LCLS. In conclusion, the benefits and limitations of these low- Z fixed-target supports are discussed; it is the authors' belief that they represent a viable and efficient alternative to previously reported fixed-target supports for conducting diffraction studies with XFELs.

59 BASIC BIOLOGICAL SCIENCES↗