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At least 145 records · Page 8
All sourcesNASA NTRSDOE OSTI
DOE OSTI2018

A mathematical model to systematically align superconducting radio frequency cavities employing the serial robot kinematic theory

In Superconducting Radio Frequency (SRF) cryomodules, precise alignment of cavities is necessary to ensure high beam quality and to increase the overall energetic efficiency. In the SSR1 (Single Spoke Resonator 1) cryomodule, the cavities are aligned using a system of seven screws which allows to control five Degree of Freedoms (DOFs). The relation between the rotation of each screw and the movement of the cavity is non-linear, thus the aligning process, currently based on a trial-and-error procedure, can be time consuming and affected by human error. In this paper the design of an alignment mathematical model, based on the serial robot kinematic, is described and tested on a SSR1 cavity. Furthermore, the goal of the proposed model is to give a step by step operational procedure that bring the SSR1 cavity to a desired location reducing the uncertainties related to the current operator-driven alignment process.

43 PARTICLE ACCELERATORS↗
DOE OSTI2024

In situ counter-diffusion crystallization and long-term crystal preservation in microfluidic fixed targets for serial crystallography

Compared with batch and vapor diffusion methods, counter diffusion can generate larger and higher-quality protein crystals yielding improved diffraction data and higher-resolution structures. Typically, counter-diffusion experiments are conducted in elongated chambers, such as glass capillaries, and the crystals are either directly measured in the capillary or extracted and mounted at the X-ray beamline. Despite the advantages of counter-diffusion protein crystallization, there are few fixed-target devices that utilize counter diffusion for crystallization. In this article, different designs of user-friendly counter-diffusion chambers are presented which can be used to grow large protein crystals in a 2D polymer microfluidic fixed-target chip. Methods for rapid chip fabrication using commercially available thin-film materials such as Mylar, propylene and Kapton are also detailed. Rules of thumb are provided to tune the nucleation and crystal growth to meet users' needs while minimizing sample consumption. These designs provide a reliable approach to forming large crystals and maintaining their hydration for weeks and even months. This allows ample time to grow, select and preserve the best crystal batches before X-ray beam time. Importantly, the fixed-target microfluidic chip has a low background scatter and can be directly used at beamlines without any crystal handling, enabling crystal quality to be preserved. The approach is demonstrated with serial diffraction of photoactive yellow protein, yielding 1.32 Å resolution at room temperature. Fabrication of this standard microfluidic chip with commercially available thin films greatly simplifies fabrication and provides enhanced stability under vacuum. These advances will further broaden microfluidic fixed-target utilization by crystallographers.

Liu, Zhongrui↗
DOE OSTI2016

In cellulo serial crystallography of alcohol oxidase crystals inside yeast cells

The possibility of using femtosecond pulses from an X-ray free-electron laser to collect diffraction data from protein crystals formed in their native cellular organelle has been explored. X-ray diffraction of submicrometre-sized alcohol oxidase crystals formed in peroxisomes within cells of genetically modified variants of the methylotrophic yeast Hansenula polymorpha is reported and characterized. Furthermore, the observations are supported by synchrotron radiation-based powder diffraction data and electron microscopy. Based on these findings, the concept of in cellulo serial crystallography on protein targets imported into yeast peroxisomes without the need for protein purification as a requirement for subsequent crystallization is outlined.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2025

Robust error calibration for serial crystallography

Serial crystallography is an important technique with unique abilities to resolve enzymatic transition states, minimize radiation damage to sensitive metalloenzymes and perform de novo structure determination from micrometre-sized crystals. This technique requires the merging of data from thousands of crystals, making manual identification of errant crystals unfeasible. cctbx.xfel.merge uses filtering to remove problematic data. However, this process is imperfect, and data reduction must be robust to outliers. We add robustness to cctbx.xfel.merge at the step of uncertainty determination for reflection intensities. This step is a critical point for robustness because it is the first step where the data sets are considered as a whole, as opposed to individual lattices. Robustness is conferred by reformulating the error-calibration procedure to have fewer and less stringent statistical assumptions and incorporating the ability to down-weight low-quality lattices. We then apply this method to five macromolecular XFEL data sets and observe the improvements to each. The appropriateness of the intensity uncertainties is demonstrated through internal consistency. This is performed through theoretical CC 1/2 and I /σ relationships and by weighted second moments, which use Wilson's prior to connect intensity uncertainties with their expected distribution. This work presents new mathematical tools to analyze intensity statistics and demonstrates their effectiveness through the often underappreciated process of uncertainty analysis.

Mittan-Moreau, David W.↗
DOE OSTI2024

Robust Data-Driven Predictive Run-to-Run Control for Automated Serial Sectioning

This letter presents a one-step predictive run-to-run controller (R2R-MPC) for the automation of mechanical serial sectioning (MSS), a destructive material analysis process. To address the inherent uncertainty and disturbances in the MSS process, a robust closed-loop approach is presented. Here, the robust R2R-MPC models the uncertainty of the MSS process using a linear differential inclusion. As an analytical model of the MSS process is unavailable, the differential inclusion is identified from historical data. The R2R-MPC is posed as an optimization problem that computes incremental changes to the control input which minimize the worst-case material removal errors. This optimization-based controller is combined with a run-to-run controller to provide integral action that rejects constant disturbances and tracks constant reference removal rates. To demonstrate the efficacy of our robust R2R-MPC, we present simulation results which compare the presented controller with a conventional non-robust R2R.

42 ENGINEERING↗
DOE OSTI2015

Implications of the focal beam profile in serial femtosecond crystallography

The photon density profile of an X-ray free-electron laser (XFEL) beam at the focal position is a critical parameter for serial femtosecond crystallography (SFX), but is difficult to measure because of the destructive power of the beam. A novel high intensity radiation induced phasing method (HIRIP) has been proposed as a general experimental approach for protein structure determination, but has proved to be sensitive to variations of the X-ray intensity, with uniform incident fluence desired for best performance. Here we show that experimental SFX data collected at the nano-focus chamber of the Coherent X-ray Imaging end-station at the Linac Coherent Light Source using crystals with a limited size distribution suggests an average profile of the X-ray beam that has a large variation of intensity. We propose a new method to improve the quality of high fluence data for HI-RIP, by identifying and removing diffraction patterns from crystals exposed to the low intensity region of the beam. The method requires crystals of average size comparable to the width of the focal spot.

43 PARTICLE ACCELERATORS↗
DOE OSTI2014

TU-F-12A-01: Quantitative Non-Linear Compartment Modeling of 89Zr- and 124I- Labeled J591 Monoclonal Antibody Kinetics Using Serial Non-Invasive Positron Emission Tomography Imaging in a Pre-Clinical Human Prostate Cancer Mouse Model

Purpose: To examine the binding kinetics of human IgG monoclonal antibody J591 which targets prostate-specific membrane antigen (PSMA) in a pre-clinical mouse cancer model using quantitative PET compartmental analysis of two radiolabeled variants. Methods: PSMA is expressed in normal human prostate, and becomes highly upregulated in prostate cancer, making it a promising therapeutic target. Two forms of J591, radiolabeled with either {sup 89}Zr or {sup 124}I, were prepared. {sup 89}Zr is a radiometal that becomes trapped in the cell upon internalization by the antigen-antibody complex, while radioiodine leaves the cell. Mice with prostate cancer xenografts underwent non-invasive serial imaging on a Focus 120 microPET up to 144 hours post-injection of J591. A non-linear compartmental model describing the binding and internalization of antibody in tumor xenograft was developed and applied to the PET-derived time-activity curves. The antibody-antigen association rate constant (ka), total amount of antigen per gram tumor (Ag-total), internalization rate of antibody-antigen complex, and efflux rate of radioisotope from tumor were fitted using the model. The surface-bound and the internalized activity were also estimated. Results: Values for ka, Ag-total, and internalization rate were found to be similar regardless of radiolabel payload used. The efflux rate, however, was ∼ 9-fold higher for {sup 124}I-J591 than for {sup 89}Zr-J591. Time-dependent surface-bound and internalized radiotracer activity were similar for both radiolabels at early times post-injection, but clearly differed beyond 24 hours. Conclusion: Binding and internalization of J591 to PSMA-expressing tumor xenografts were similar when radiolabeled with either {sup 89}Zr or {sup 124}I payload. The difference in efflux of radioactivity from tumor may be attributable to differential biological fate intracellularly of the radioisotopes. This has great significance for radioimmunotherapy and antibody-drug conjugates. Further exploration using the model will examine binding and radioisotope residence as antibody dose is increased to antigen saturation. The Center for Targeted Radioimmunotherapy and Theranostics, Ludwig Center for Cancer Immunotherapy, Memorial Sloan Kettering Cancer Center (MSK), NIH (R25-CA096945). Technical services provided by the MSK Small-Animal Imaging Core Facility were supported by the NIH (R24-CA83084, P30-CA08748, and P50-CA92629; Zanzonico). NCI, Center to Reduce Cancer Health Disparity (R21 CA153177-03; Osborne)

60 APPLIED LIFE SCIENCES↗
DOE OSTI2025

Serial-femtosecond crystallography reveals how a phytochrome variant couples chromophore and protein structural changes

The photoreaction and commensurate structural changes of a chromophore within biological photoreceptors elicit conformational transitions of the protein promoting the switch between deactivated and activated states. We investigated how this coupling is achieved in a bacterial phytochrome variant, Agp2-PAiRFP2. Contrary to classical protein crystallography, which only allows probing (cryo-trapped) stable states, we have used time-resolved serial femtosecond x-ray crystallography (tr-SFX) and pump-probe techniques with various illumination and delay times with respect to photoexcitation of the parent Pfr state. Thus, structural data for seven time frames were sorted into groups of molecular events along the reaction coordinate. They range from chromophore isomerization to the formation of Meta-F, the intermediate that precedes the functional relevant secondary structure transition of the tongue. Structural data for the early events were used to calculate the photoisomerization pathway to complement the experimental data. Late events allow identifying the molecular switch that is linked to the intramolecular proton transfer as a prerequisite for the following structural transitions.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2014

Time-resolved serial crystallography captures high-resolution intermediates of photoactive yellow protein

We report that serial femtosecond crystallography using ultrashort pulses from X-ray Free Electron Lasers (XFELs) offers the possibility to study light-triggered dynamics of biomolecules. Using microcrystals of the blue light photoreceptor, photoactive yellow protein, as a model system, we present high resolution, time-resolved difference electron density maps of excellent quality with strong features, which allow the determination of structures of reaction intermediates to 1.6 Å resolution. These results open the way to the study of reversible and non-reversible biological reactions on time scales as short as femtoseconds under conditions which maximize the extent of reaction initiation throughout the crystal.

47 OTHER INSTRUMENTATION↗
DOE OSTI2023

Evaluation of Serial Testing After Exposure to COVID-19 in Early Care and Education Facilities, Illinois, March–May 2022

Objective: To understand SARS-CoV-2 transmission in early care and education (ECE) settings, we implemented a Test to Stay (TTS) strategy, which allowed children and staff who were close contacts to COVID-19 to remain in person if they agreed to test twice after exposure. We describe SARS-CoV-2 transmission, testing preferences, and the number of in-person days saved among participating ECE facilities. Methods: From March 21 through May 27, 2022, 32 ECE facilities in Illinois implemented TTS. Unvaccinated children and staff who were not up to date with COVID-19 vaccination could participate if exposed to COVID-19. Participants received 2 tests within 7 days after exposure and were given the option to test at home or at the ECE facility. Results: During the study period, 331 TTS participants were exposed to index cases (defined as people attending the ECE facility with a positive SARS-CoV-2 test result during the infectious period); 14 participants tested positive, resulting in a secondary attack rate of 4.2%. No tertiary cases (defined as a person with a positive SARS-CoV-2 test result within 10 days after exposure to a secondary case) occurred in the ECE facilities. Most participants (366 of 383; 95.6%) chose to test at home. Remaining in-person after an exposure to COVID-19 saved approximately 1915 in-person days among children and staff and approximately 1870 parent workdays. Conclusion: SARS-CoV-2 transmission rates were low in ECE facilities during the study period. Serial testing after COVID-19 exposure among children and staff at ECE facilities is a valuable strategy to allow children to remain in person and parents to avoid missing workdays.

Public, Environmental & Occupational Health↗
DOE OSTI2013

Development, Manufacturing, and Preparation for Serial Production of Low Noise Seismometers (CRADA Final Report)

This was a collaborative effort between Lawrence Livermore National Security, LLC as manager and operator of Lawrence Livermore National Laboratory (LLNL) and Refraction Technology, Inc. (REF TEK), to collaborate on the development of a broadband, competitive low-noise seismometer, rugged and easy to use for field deployments. The work involved collaborative work between LLNL, REF TEK and a group led by Federal State Unitary Enterprise, Research Institute of Pulse Technique (RIPT), Moscow, Russia. The proposed work focused on bringing an improved version of the Russian SDSE seismometer from development phase to production in two versions. The first was a very low cost, rugged, broadband seismometer for field deployment that would achieve noise levels comparable to the standard earth low noise model (LNM) of the USGS. All three components were integrated into one case, and have sensitivity near 2000 v/m/s, and analog output with bandwidth of .01 to 40 Hz with high coherence. The second phase of development combined the results of previous instruments and these tests, and lowered the internal noise according to class A of standard Advanced National Seismic System (ANSS) within the band of 0.01 to 50 Hz for a dynamic range 143 - 128 dB. The second phase extended the development using improved electronics and modifications suggested by these tests of the earlier prototypes. These sensors would also be very competitive and aimed towards major improvements in their ruggedness compared to existing sensors from other manufacturers. Prototypes would undergo extensive testing at low-noise field sites for durability and functionality. The development would yield production prototypes capable of serial production at RPZ in Moscow. The collaboration between the Russian and US partners would improve the availability of rugged, broadband seismometers for commercial applications, research applications, seismic networks operated by our government and international organizations, and a spur collaboration on the development of additional types of seismometers.

Vergino, Eileen S.↗
DOE OSTI2021

Fixed Target Serial Data Collection at Diamond Light Source

Serial data collection is a relatively new technique for synchrotron users. A user manual for fixed target data collection at I24, Diamond Light Source is presented with detailed step-by-step instructions, figures, and videos for smooth data collection.

Horrell, Sam↗
DOE OSTI2016

Apparatus and method for nanoflow liquid jet and serial femtosecond x-ray protein crystallography

Techniques for nanoflow serial femtosecond x-ray protein crystallography include providing a sample fluid by mixing a plurality of a first target of interest with a carrier fluid and injecting the sample fluid into a vacuum chamber at a rate less than about 4 microliters per minute. In some embodiments, the carrier fluid has a viscosity greater than about 3 centipoise.

36 MATERIALS SCIENCE↗
DOE OSTI2016

Serial interpolation for secure membership testing and matching in a secret-split archive

The various technologies presented herein relate to analyzing a plurality of shares stored at a plurality of repositories to determine whether a secret from which the shares were formed matches a term in a query. A threshold number of shares are formed with a generating polynomial operating on the secret. A process of serially interpolating the threshold number of shares can be conducted whereby a contribution of a first share is determined, a contribution of a second share is determined while seeded with the contribution of the first share, etc. A value of a final share in the threshold number of shares can be determined and compared with the search term. In the event of the value of the final share and the search term matching, the search term matches the secret in the file from which the shares are formed.

97 MATHEMATICS AND COMPUTING↗
DOE OSTI2017

Unobtrusive Multi-Static Serial LiDAR Imager (UMSLI) First Generation Shape-Matching Based Classifier for 2D Contours

A multi-static serial LiDAR system prototype was developed under DE-EE0006787 to detect, classify, and record interactions of marine life with marine hydrokinetic generation equipment. This software implements a shape-matching based classifier algorithm for the underwater automated detection of marine life for that system. In addition to applying shape descriptors, the algorithm also adopts information theoretical learning based affine shape registration, improving point correspondences found by shape descriptors as well as the final similarity measure.

Cao, Zheng↗
DOE OSTI2015

Virus Evolution Serial

This is the first code, designed to run on a desktop, which models the intracellular replication and the cell-to-cell infection and demonstrates virus evolution at the molecular level. This code simulates the infection of a population of "idealized biological cells" (represented as objects that do not divide or have metabolism) with "virus" (represented by its genetic sequence), the replication and simultaneous mutation of the virus which leads to evolution of the population of genetically diverse viruses. The code is built to simulate single-stranded RNA viruses. The input for the code is 1. the number of biological cells in the culture, 2. the initial composition of the virus population, 3. the reference genome of the RNA virus, 4. the coordinates of the genome regions and their significance and, 5. parameters determining the dynamics of virus replication, such as the mutation rate. The simulation ends when all cells have been infected or when no more infections occurs after a given number of attempts. The code has the ability to simulate the evolution of the virus in serial passage of cell "cultures", i.e. after the end of a simulation, a new one is immediately scheduled with a new culture of infected cells. The code outputs characteristics of the resulting virus population dynamics and genetic composition of the virus population, such as the top dominant genomes, percentage of a genome with specific characteristics.

Vassilevska, Tanya↗
DOE OSTI2019

High resolution, non-contact removal rate module for serial sectioning

The present invention relates to a metallographic system including a measurement module configured to provide precise differential measurements of a sample after serial sectioning, as well as methods of employing such a module. In particular example, the measurement module provides differential measurement(s) without contacting the surface of a sample, thereby minimizing contamination of the sample surface.

36 MATERIALS SCIENCE↗