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At least 37 records · Page 2

Impact of gas background on XFEL single-particle imaging

Abstract Single-particle imaging (SPI) using X-ray free-electron Lasers (XFELs) offers the potential to determine protein structures at high spatial and temporal resolutions without the need for crystallization or vitrification. However, the technique faces challenges due to weak diffraction signals from single proteins and significant background scattering from gases used for sample delivery. A recent observation of a diffraction pattern from an isolated GroEL protein complex Ekeberg T et al. (Light Sci Appl 13:15, 2024.https://doi.org/10.1038/274s41377-023-01352-7) had similar numbers of signal and background photons. Ongoing efforts aim to reduce the background created by sample delivery, with one approach replacing most of the used gas with helium Yenupuri T et al. (Sci Rep 14:4401, 2024.https://doi.org/10.1038/s41598-024-54605-9). In this study, we investigate the effects of a reduced background on the resolution limits for SPI of isolated proteins under different experiment conditions. As a test case, we used GroEL, and we used experimentally derived parameters for our simulations. We observe that background significantly impacts the achievable resolution, particularly when the signal strength is comparable to the background. This is best exemplified at 6.0 keV, where a background reduction by a factor of 10 leads to a resolution improvement from 1.9 to 1.2 nm, for a dataset of$$10^4$$patterns.

Science & Technology - Other Topics↗

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↗

Test and Validation of the Mars Science Laboratory Robotic Arm

The Mars Science Laboratory Robotic Arm (RA) is a key component for achieving the primary scientific goals of the mission. The RA supports sample acquisition by precisely positioning a scoop above loose regolith or accurately preloading a percussive drill on Martian rocks or rover-mounted organic check materials. It assists sample processing by orienting a sample processing unit called CHIMRA through a series of gravity-relative orientations and sample delivery by positioning the sample portion door above an instrument inlet or the observation tray. In addition the RA facilitates contact science by accurately positioning the dust removal tool, Alpha Particle X-Ray Spectrometer (APXS) and the Mars Hand Lens Imager (MAHLI) relative to surface targets. In order to fulfill these seemingly disparate science objectives the RA must satisfy a variety of accuracy and performance requirements. This paper describes the necessary arm requirement specification and the test campaign to demonstrate these requirements were satisfied.

manipulation↗

Rapid and efficient room-temperature serial synchrotron crystallography using the CFEL TapeDrive

Serial crystallography at conventional synchrotron light sources (SSX) offers the possibility to routinely collect data at room temperature using micrometre-sized crystals of biological macromolecules. However, SSX data collection is not yet as routine and currently takes significantly longer than the standard rotation series cryo-crystallography. Thus, its use for high-throughput approaches, such as fragment-based drug screening, where the possibility to measure at physiological temperatures would be a great benefit, is impaired. On the way to highthroughput SSX using a conveyor belt based sample delivery system – the CFEL TapeDrive – with three different proteins of biological relevance (Klebsiella pneumoniae CTX-M-14 β-lactamase, Nectria haematococca xylanase GH11 and Aspergillus flavus urate oxidase), it is shown here that complete datasets can be collected in less than a minute and only minimal amounts of sample are required.

36 MATERIALS SCIENCE↗

Plug-and-play polymer microfluidic chips for hydrated, room temperature, fixed-target serial crystallography

The practice of serial X-ray crystallography (SX) depends on efficient, continuous delivery of hydrated protein crystals while minimizing background scattering. Of the two major types of sample delivery devices, fixed-target devices offer several advantages over widely adopted jet injectors, including: lower sample consumption, clog-free delivery, and the ability to control on-chip crystal density to improve hit rates. In this study we present our development of versatile, inexpensive, and robust polymer microfluidic chips for routine and reliable room temperature serial measurements at both synchrotrons and X-ray free electron lasers (XFELs). Our design includes highly X-ray-transparent enclosing thin film layers tuned to minimize scatter background, adaptable sample flow layers tuned to match crystal size, and a large sample area compatible with both raster scanning and rotation based serial data collection. The optically transparent chips can be used both for in situ protein crystallization (to eliminate crystal handling) or crystal slurry loading, with prepared samples stable for weeks in a humidified environment and for several hours in ambient conditions. Serial oscillation crystallography, using a multi-crystal rotational data collection approach, at a microfocus synchrotron beamline (SSRL, beamline 12-1) was used to benchmark the performance of the chips. Furthermore, high-resolution structures (1.3–2.7 Å) were collected from five different proteins – hen egg white lysozyme, thaumatin, bovine liver catalase, concanavalin-A (type VI), and SARS-CoV-2 nonstructural protein NSP5. Overall, our modular fabrication approach enables precise control over the cross-section of materials in the X-ray beam path and facilitates chip adaption to different sample and beamline requirements for user-friendly, straightforward diffraction measurements at room temperature.

59 BASIC BIOLOGICAL SCIENCES↗

The Liquid Jet Endstation for Hard X-ray Scattering and Spectroscopy at the Linac Coherent Light Source

The ability to study chemical dynamics on ultrafast timescales has greatly advanced with the introduction of X-ray free electron lasers (XFELs) providing short pulses of intense X-rays tailored to probe atomic structure and electronic configuration. Fully exploiting the full potential of XFELs requires specialized experimental endstations along with the development of techniques and methods to successfully carry out experiments. The liquid jet endstation (LJE) at the Linac Coherent Light Source (LCLS) has been developed to study photochemistry and biochemistry in solution systems using a combination of X-ray solution scattering (XSS), X-ray absorption spectroscopy (XAS), and X-ray emission spectroscopy (XES). The pump–probe setup utilizes an optical laser to excite the sample, which is subsequently probed by a hard X-ray pulse to resolve structural and electronic dynamics at their intrinsic femtosecond timescales. The LJE ensures reliable sample delivery to the X-ray interaction point via various liquid jets, enabling rapid replenishment of thin samples with millimolar concentrations and low sample volumes at the 120 Hz repetition rate of the LCLS beam. This paper provides a detailed description of the LJE design and of the techniques it enables, with an emphasis on the diagnostics required for real-time monitoring of the liquid jet and on the spatiotemporal overlap methods used to optimize the signal. Additionally, various scientific examples are discussed, highlighting the versatility of the LJE.

EXAFS↗

Mars Rover Sample Return mission delivery and return challenges

The Mars Rover Sample Return mission is a robotic exploration mission culminating in the return of atmospheric and surface samples from Mars to Earth. To accomplish this complex mission requires sophisticated autonomous systems for many time-critical operations associated with the delivery and return phases, since the round trip light times preclude Earth-based control of these operations. In addition, there are significant engineering and technology challenges to be addressed to meet the mission science and exploration objectives.

Cohen, Aaron↗

Portable Dew Point Mass Spectrometry System for Real-Time Gas and Moisture Analysis

A portable instrument incorporates both mass spectrometry and dew point measurement to provide real-time, quantitative gas measurements of helium, nitrogen, oxygen, argon, and carbon dioxide, along with real-time, quantitative moisture analysis. The Portable Dew Point Mass Spectrometry (PDP-MS) system comprises a single quadrupole mass spectrometer and a high vacuum system consisting of a turbopump and a diaphragm-backing pump. A capacitive membrane dew point sensor was placed upstream of the MS, but still within the pressure-flow control pneumatic region. Pressure-flow control was achieved with an upstream precision metering valve, a capacitance diaphragm gauge, and a downstream mass flow controller. User configurable LabVIEW software was developed to provide real-time concentration data for the MS, dew point monitor, and sample delivery system pressure control, pressure and flow monitoring, and recording. The system has been designed to include in situ, NIST-traceable calibration. Certain sample tubing retains sufficient water that even if the sample is dry, the sample tube will desorb water to an amount resulting in moisture concentration errors up to 500 ppm for as long as 10 minutes. It was determined that Bev-A-Line IV was the best sample line to use. As a result of this issue, it is prudent to add a high-level humidity sensor to PDP-MS so such events can be prevented in the future.

Arkin, C.↗

Autonomous Measurement of Electrochemical Redox Couples for In-Situ Characterization of Enceladus Plume Samples

A 3D-printed microfluidic electrochemical cell with integrated electrodes was developed to demonstrate autonomous in-situ electrochemical characterization of terrestrial seawater samples. The system is designed to extend the capabilities of the 2008 Phoenix Lander’s Wet Chemistry Laboratory (WCL) that analyzed the soluble chemistry of the Martian soil, by miniaturizing its fluidic architecture for analysis of µL-volume samples as expected from an Enceladus fly-by mission. The microfluidic device has a total fluid volume of 48 µL and includes dual channels each populated with 7 electrodes. Measurement of pH was measured using an iridium oxide electrode. Cyclic voltammetry with Au, Pt, and glassy carbon working electrodes was used to measure redox couples in synthetic seawater that contained inorganic and bio-organic molecules. Glassy carbon was found to have minimal risk of interference from constituents of synthetic seawater when measuring molecular organic redox species; however, care must be used to prevent interference due to potential oxidation or dissolution in the case of Au working electrodes. A completely autonomous end-to-end run including sample delivery was performed, to demonstrate the feasibility of microfluidic-based cyclic voltammetry measurements for in-situ characterization of redox couples in Ocean World samples.

Planetary Instruments↗

FMX – the Frontier Microfocusing Macromolecular Crystallography Beamline at the National Synchrotron Light Source II

Two new macromolecular crystallography (MX) beamlines at the National Synchrotron Light Source II, FMX and AMX, opened for general user operation in February 2017 [Schneider et al. (2013). J. Phys. Conf. Ser. 425 , 012003; Fuchs et al. (2014). J. Phys. Conf. Ser. 493 , 012021; Fuchs et al. (2016). AIP Conf. Proc. SRI2015 , 1741 , 030006]. FMX, the micro-focusing Frontier MX beamline in sector 17-ID-2 at NSLS-II, covers a 5–30 keV photon energy range and delivers a flux of 4.0 × 10 12 photons s −1 at 1 Å into a 1 µm × 1.5 µm to 10 µm × 10 µm (V × H) variable focus, expected to reach 5 × 10 12 photons s −1 at final storage-ring current. This flux density surpasses most MX beamlines by nearly two orders of magnitude. The high brightness and microbeam capability of FMX are focused on solving difficult crystallographic challenges. The beamline's flexible design supports a wide range of structure determination methods – serial crystallography on micrometre-sized crystals, raster optimization of diffraction from inhomogeneous crystals, high-resolution data collection from large-unit-cell crystals, room-temperature data collection for crystals that are difficult to freeze and for studying conformational dynamics, and fully automated data collection for sample-screening and ligand-binding studies. FMX's high dose rate reduces data collection times for applications like serial crystallography to minutes rather than hours. With associated sample lifetimes as short as a few milliseconds, new rapid sample-delivery methods have been implemented, such as an ultra-high-speed high-precision piezo scanner goniometer [Gao et al. (2018). J. Synchrotron Rad. 25 , 1362–1370], new microcrystal-optimized micromesh well sample holders [Guo et al. (2018). IUCrJ , 5 , 238–246] and highly viscous media injectors [Weierstall et al. (2014). Nat. Commun. 5 , 3309]. The new beamline pushes the frontier of synchrotron crystallography and enables users to determine structures from difficult-to-crystallize targets like membrane proteins, using previously intractable crystals of a few micrometres in size, and to obtain quality structures from irregular larger crystals.

73 NUCLEAR PHYSICS AND RADIATION PHYSICS↗

Handheld Biosensor for COVID-19 Screening

We have made significant progress toward the development of an integrated nucleic acid amplification system for Autonomous Medical Devices Incorporated (AMDIs) Optikus handheld diagnostic device. In this effort, we developed a set of loop-mediated isothermal amplification (LAMP) primers for SARS-CoV-2 and then demonstrate amplification directly on a surface acoustic wave (SAW) sensor. We built associated hardware and developed a C-code to control the amplification process. The goal of this project was to develop a nucleic amplification assay that is compatible with SAW sensors to enable both nucleic and serological testing in a single handheld diagnostic device. Toward this goal, AMDI is collaborating Sandia National Laboratories to develop a rapid, portable diagnostic screening device that utilizes Sandias unique surface acoustic wave biosensor (SAW) for COVID-19 detection. Previously, the SANDIA- AMDI SAW sensor has successfully detected multiple high-profile bacteria viruses, including Ebola, HIV, Sin Nombre, and Anthrax. Over the last two years, AMDI and SANDIA have significantly improved the sensitivity and detection capability of the SAW biosensor and have also developed a modular hand-held, portable platform called the Optikus, which uses CD microfluidics and handheld instrumentation to automate all sample preparation, reagent introduction, sample delivery, and measurement for a number of different assay targets. We propose to use this platform for the development of a rapid (%3C30 minutes), point-of-care diagnostic test for detection of COVID-19 from nasal swab samples.

47 OTHER INSTRUMENTATION↗

Serial femtosecond and serial synchrotron crystallography can yield data of equivalent quality: A systematic comparison

For the two proteins myoglobin and fluoroacetate dehalogenase, we present a systematic comparison of crystallographic diffraction data collected by serial femtosecond (SFX) and serial synchrotron crystallography (SSX). To maximize comparability, we used the same batch of micron-sized crystals, the same sample delivery device, and the same data analysis software. Overall figures of merit indicate that the data of both radiation sources are of equivalent quality. For both proteins, reasonable data statistics can be obtained with approximately 5000 room-temperature diffraction images irrespective of the radiation source. The direct comparability of SSX and SFX data indicates that the quality of diffraction data obtained from these samples is linked to the properties of the crystals rather than to the radiation source. Therefore, for other systems with similar properties, time-resolved experiments can be conducted at the radiation source that best matches the desired time resolution.

59 BASIC BIOLOGICAL SCIENCES↗

X-ray Absorption Spectroscopy of Dilute Metalloenzymes at X-ray Free-Electron Lasers in a Shot-by-Shot Mode

X-ray absorption spectroscopy (XAS) of 3d transition metals provides important electronic structure information for many fields. However, X-ray-induced radiation damage under physiological temperature has prevented using this method to study dilute aqueous systems, such as metalloenzymes, as the catalytic reaction proceeds. Here we present a new approach to enable operando XAS of dilute biological samples and demonstrate its feasibility with K-edge XAS spectra from the Mn cluster in photosystem II and the Fe–S centers in photosystem I. This approach combines highly efficient sample delivery strategies and a robust signal normalization method with high-transmission Bragg diffraction-based spectrometers at X-ray free-electron lasers (XFELs) in a damage-free, shot-by-shot mode. These photon-out spectrometers have been optimized for discriminating the metal Mn/Fe Kα fluorescence signals from the overwhelming scattering background present on currently available detectors for XFELs that lack suitable energy discrimination. We quantify the enhanced performance metrics of the spectrometer and discuss its potential applications for acquiring time-resolved XAS spectra of biological samples during their reactions at XFELs.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Calibration and Sequence Development Status for the Sample Analysis at Mars Investigation on the Mars Science Laboratory

The measurement goals of the Sample Analysis at Mars (SAM) instrument suite on the "Curiosity" Rover of the Mars Science Laboratory (MSL) include chemical and isotopic analysis of organic and inorganic volatiles for both atmospheric and solid samples [1,2]. SAM directly supports the ambitious goals of the MSL mission to provide a quantitative assessment of habitability and preservation in Gale crater by means of a range of chemical and geological measurements [3]. The SAM FM combined calibration and environmental testing took place primarily in 2010 with a limited set of tests implemented after integration into the rover in January 2011. The scope of SAM FM testing was limited both to preserve SAM consumables such as life time of its electromechanical elements and to minimize the level of terrestrial contamination in the SAM instrument. A more comprehensive calibration of a SAM-like suite of instruments will be implemented in 2012 with calibration runs planned for the SAM testbed. The SAM Testbed is nearly identical to the SAM FM and operates in a ambient pressure chamber. The SAM Instrument Suite: SAM's instruments are a Quadrupole Mass Spectrometer (QMS), a 6-column Gas Chromatograph (GC), and a 2-channel Tunable Laser Spectrometer (TLS). Gas Chromatography Mass Spectrometry is designed for identification of even trace organic compounds. The TLS [5] secures the C, H, and O isotopic composition in carbon dioxide, water, and methane. Sieved materials are delivered from the MSL sample acquisition and processing system to one of68 cups of the Sample Manipulation System (SMS). 59 of these cups are fabricated from inert quartz. After sample delivery, a cup is inserted into one of 2 ovens for evolved gas analysis (EGA ambient to >9500C) by the QMS and TLS. A portion of the gas released can be trapped and subsequently analyzed by GCMS. Nine sealed cups contain liquid solvents and chemical derivatization or thermochemolysis agents to extract and transform polar molecules such as amino acids, nucleobases, and carboxylic acids into compounds that are sufficiently volatile to transmit through the GC columns. The remaining 6 cups contain calibrants. SAM FM Calibration Overview: The SAM FM calibration in the Mars chamber employed a variety of pure gases, gas mixtures, and solid materials. Isotope calibration runs for the TLS utilized 13C enriched C02 standards and 0 enriched CH4. A variety of fluorocarbon compounds that spanned the entire mass range of the QMS as well as C3-C6 hydrocarbons were utilized for calibration of the GCMS. Solid samples consisting of a mixture of calcite, melanterite, and inert silica glass either doped or not with fluorocarbons were introduced into the SAM FM cups through the SAM inlet funnel/tube system.

Mahaffy, Paul R.↗

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↗

Optimization of a Mixed Fleet of Aerial Drones for Medical Supplies: A Case Study of Blood Delivery Logistics

Aerial drones have emerged as an innovative solution for faster transportation of time-sensitive items (e.g., emergency medical supplies), potentially reducing the transmission of contagious diseases and enhancing healthcare availability through contactless autonomous delivery. We study fleet sizing and efficient scheduling of a mixed fleet of drones for delivering time-sensitive medical items having distinct release and due times to minimize the required fleet size and fleet composition, the required number of additional batteries, and the total energy consumption. We continuously track the remaining battery energy of drones to determine the optimal timing for battery replacement, rather than replacing the battery at each node. Using actual drone flight test data, we employed a machine learning (ML) method to estimate the energy consumption of different drone types during flight segments for different operating parameters. We present a novel mixed-integer programming model to efficiently formulate the problem that integrates the estimated energy consumption functions from ML. We propose a new greedy heuristic (GH) algorithm and a customized genetic algorithm (GA) for solving large-scale instances of this problem faster. Results demonstrate that the GH algorithm is substantially faster than the accelerated CPLEX and the GA, while sacrificing the solution quality by a small amount. Results based on an actual blood sample delivery case study from Pendleton, Oregon, United States, show that using a mixed fleet of drones reduces the total cost and total energy consumption up to 18.18% and 28.7%, respectively, compared to using a homogeneous fleet.

29 - ENERGY PLANNING, POLICY AND ECONOMY↗

Soft X‐Ray Absorption Spectroscopy With a Flat Liquid Jet in Vacuum Using a Table‐Top Laser‐Induced Plasma Source

ABSTRACT In this work, we demonstrate the integration of a flat liquid jet sample delivery system into a compact soft x‐ray absorption spectrometer using a table‐top laser‐induced plasma source. A high‐speed flat liquid sheet is formed by the collision of two cylindrical jets. This micrometer‐thin lamella can ideally be utilized for transmission‐mode soft x‐ray absorption spectroscopy using krypton plasma emission. Detailed analysis of the jet's thickness profile is achieved applying Lambert–Beer's law. Measurements on water, focusing on the oxygen K‐edge, reveal a lamella thickness profile ranging from 500 nm to 1 μm over a length of 3.8 mm. Additionally, we have investigated aqueous solutions of iron salts, capturing near edge x‐ray absorption fine structure spectra over a broad spectral range from the nitrogen K‐edge to the iron L‐edge. Focused analysis on iron species in aqueous solutions enabled us to distinguish quantitatively between the oxidation states of Fe 2+ and Fe 3+ at the iron L‐edge. Our results are compared with measurements obtained under similar conditions at a synchrotron.

Holburg, Jonathan [Department Optics/Short Wavelen↗

Predicting the oxidation states of Mn ions in the oxygen-evolving complex of photosystem II using supervised and unsupervised machine learning

Abstract Serial Femtosecond Crystallography at the X-ray Free Electron Laser (XFEL) sources enabled the imaging of the catalytic intermediates of the oxygen evolution reaction of Photosystem II (PSII). However, due to the incoherent transition of the S-states, the resolved structures are a convolution from different catalytic states. Here, we train Decision Tree Classifier and K-means clustering models on Mn compounds obtained from the Cambridge Crystallographic Database to predict the S-state of the X-ray, XFEL, and CryoEM structures by predicting the Mn’s oxidation states in the oxygen-evolving complex. The model agrees mostly with the XFEL structures in the dark S 1 state. However, significant discrepancies are observed for the excited XFEL states (S 2 , S 3, and S 0 ) and the dark states of the X-ray and CryoEM structures. Furthermore, there is a mismatch between the predicted S-states within the two monomers of the same dimer, mainly in the excited states. We validated our model against other metalloenzymes, the valence bond model and the Mn spin densities calculated using density functional theory for two of the mismatched predictions of PSII. The model suggests designing a more optimized sample delivery and illumiation systems are crucial to precisely resolve the geometry of the advanced S-states to overcome the noncoherent S-state transition. In addition, significant radiation damage is observed in X-ray and CryoEM structures, particularly at the dangler Mn center (Mn4). Our model represents a valuable tool for investigating the electronic structure of the catalytic metal cluster of PSII to understand the water splitting mechanism.

Plant Sciences↗