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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 181 records · Page 10
All sourcesNASA NTRSDOE OSTI
DOE OSTI2025

Observation of early events in the photoactivation of Myxobacterial phytochrome using time-resolved serial femtosecond crystallography

Myxobacteria are non-photosynthetic, soil-dwelling bacteria distinguished by a multicellular stage in their life cycle known as fruiting bodies that are stimulated by light. Myxobacterial phytochromes are candidates for the perception of red-light. The mechanism how light is perceived and converted to a physiological response is unknown. Here, time-resolved serial femtosecond crystallographic (TR-SFX) experiments were conducted on microcrystals of the photosensory core module of the Stigmatella aurantiaca bacteriophytochrome 2 (SaBphP2). Initial events of the Z to E isomerization reaction of the covalently bound, open-chain tetrapyrrole biliverdin (BV) chromophore were determined. At 3 ps after light activation, the BV ring-D assumes a configuration needed for the isomerization. At 100 ps, a mixture of BV in the Z or E configuration is observed in subunit A, while in the other subunit the chromophore remains in the Z configuration. In conjunction with prior results, these structures reveal the molecular mechanism of phytochrome activation in the photomorphogenesis of the myxobacteria and provide the molecular foundation for physiological responses to red light in other bacteria.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2014

Fixed-target protein serial microcrystallography with an x-ray free electron laser

We present results from experiments at the Linac Coherent Light Source (LCLS) demonstrating that serial femtosecond crystallography (SFX) can be performed to high resolution (,2.5 Å) using protein microcrystals deposited on an ultra-thin silicon nitride membrane and embedded in a preservation medium at room temperature. Data can be acquired at a high acquisition rate using x-ray free electron laser sources to overcome radiation damage, while sample consumption is dramatically reduced compared to flowing jet methods. We achieved a peak data acquisition rate of 10 Hz with a hit rate of ,38%, indicating that a complete data set could be acquired in about one 12-hour LCLS shift using the setup described here, or in even less time using hardware optimized for fixed target SFX. This demonstration opens the door to ultra low sample consumption SFX using the technique of diffraction-before-destruction on proteins that exist in only small quantities and/or do not produce the copious quantities of microcrystals required for flowing jet methods.

77 NANOSCIENCE AND NANOTECHNOLOGY↗
DOE OSTI2017

Double-flow focused liquid injector for efficient serial femtosecond crystallography

Serial femtosecond crystallography requires reliable and efficient delivery of fresh crystals across the beam of an X-ray free-electron laser over the course of an experiment. We introduce a double-flow focusing nozzle to meet this challenge, with significantly reduced sample consumption, while improving jet stability over previous generations of nozzles. We demonstrate its use to determine the first room-temperature structure of RNA polymerase II at high resolution, revealing new structural details. Furthermore, the double flow-focusing nozzles were successfully tested with three other protein samples and the first room temperature structure of an extradiol ring-cleaving dioxygenase was solved by utilizing the improved operation and characteristics of these devices.

71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗
DOE OSTI2018

Crystal-on-crystal chips for in situ serial diffraction at room temperature

Recent developments in serial crystallography have been driven by two scientific goals – first, static structure determination from nano or microcrystals that are difficult for cryocrystallography, and second, direct observations of transient structural species in biochemical reactions at near atomic resolution.

Ren, Zhong↗
DOE OSTI2014

Controllable optomechanical coupling in serially-coupled triple resonators

Radiation pressure can efficiently couple mechanical modes with optical modes in an optical cavity. The coupling efficiency is quite dependent on the interaction between the optical mode and mechanical mode. In this report, we investigate a serially-coupled triple resonator system, where a freestanding beam is placed in the vicinity of the middle resonator. In this coupled system, we demonstrate that the mechanical mode of the free-standing beam can be selectively coupled to different resonance supermodes through the near field interaction.

36 MATERIALS SCIENCE↗
DOE OSTI2023

Low-pass spectral analysis of time-resolved serial femtosecond crystallography data

Low-pass spectral analysis (LPSA) is a recently developed dynamics retrieval algorithm showing excellent retrieval properties when applied to model data affected by extreme incompleteness and stochastic weighting. In this work, we apply LPSA to an experimental time-resolved serial femtosecond crystallography (TR-SFX) dataset from the membrane protein bacteriorhodopsin (bR) and analyze its parametric sensitivity. While most dynamical modes are contaminated by nonphysical high-frequency features, we identify two dominant modes, which are little affected by spurious frequencies. The dynamics retrieved using these modes shows an isomerization signal compatible with previous findings. We employ synthetic data with increasing timing uncertainty, increasing incompleteness level, pixel-dependent incompleteness, and photon counting errors to investigate the root cause of the high-frequency contamination of our TR-SFX modes. By testing a range of methods, we show that timing errors comparable to the dynamical periods to be retrieved produce a smearing of dynamical features, hampering dynamics retrieval, but with no introduction of spurious components in the solution, when convergence criteria are met. Using model data, we are able to attribute the high-frequency contamination of low-order dynamical modes to the high levels of noise present in the data. Finally, we propose a method to handle missing observations that produces a substantial dynamics retrieval improvement from synthetic data with a significant static component. Reprocessing of the bR TR-SFX data using the improved method yields dynamical movies with strong isomerization signals compatible with previous findings.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2026

Suppressing proximity effects during rapid serial two-photon lithography through tuning of reaction–diffusion kinetics

The ability of two-photon lithography (TPL) to print deterministic nanoporous 3D structures is highly valuable for many applications. However, it is challenging to print such structures rapidly due to the proximity effects that cause closely spaced features to enlarge and merge. A key challenge is the limited understanding of the origins and spatiotemporal dynamics of the long-range proximity effects that extend beyond the optical focal spot. Here, we empirically investigate these proximity effects in serial TPL using custom-made acrylate-based photoresists. We demonstrate that the complex spatiotemporal dynamics of the proximity effects can be explained through the kinetics of the reaction–diffusion photopolymerization mechanisms that underlie the curing process. Specifically, we show that the proximity effects arise due to comparable timescales of reaction and diffusion of oxygen. Furthermore, we demonstrate that long-range proximity effects can be suppressed by introducing phenolic inhibitors, which reduce oxygen consumption through non-inhibiting side reactions and promote faster termination of curing reactions. These insights enabled improving the linewidths from >400 to 260 nm during printing of nanoporous 3D woodpiles at scanning speeds of 50 mm s −1 . Thus, the knowledge generated here can be applied to deterministically tune the proximity effects and enable rapid printing of high-resolution nanoporous 3D structures.

36 MATERIALS SCIENCE↗
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↗