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DOE OSTI2025

Evaluation of DNA Extraction Efficiency in Diverse Algae Strains Using Commercial Kits and Lysis Approaches

Efficient DNA extraction is essential for accurately monitoring microalgae communities in large-scale cultivation systems such as raceway ponds and wastewater ponds. Traditional phenol chloroform extracts are a staple in microbiology but are obsolete for routine sampling due to its high toxicity reagents and time intensive setups. Commercial DNA extraction kits are more favorable for the microbes found in these ponds, but lack specific kits made for these communities. Little is known about which kits perform the best, leading researchers to use a variety of different kits with inconsistent results. This project compared one precipitation based commercial kit (Lucigen Masterpure) and five wash based kits (Monarch, Zymo Quick-DNA, and three Qiagen DNeasy kits) using four brackish algae strains to determine which methods yield the greatest quantity and quality of genomic DNA. Extractions were evaluated using the manufacturers protocol, and additional pretreatment options were administered before a single kit to compare its potential in being added routinely before extractions. Pretreatment options included both cryogenic freeze-thawing and heat incubation using enzymes. DNA was quantified using Qubit fluorometry and NanoDrop purity ratios. Overall, the Qiagen PowerWater kit provided the highest DNA yield and purity, but at a significantly higher cost then the precipitation-based kit (MasterPure). It was also noted that while the precipitation-based kit was significantly cheaper, provided similar results, it took significantly more time to complete a single run. Cryogenic pretreatment (6x cycles) increased average DNA yields by up to 80%, whereas enzymatic pretreatment most improved purity ratios without substantially improving quantity. The results suggest that it may be more cost and time efficient to use Qiagen kits with the addition of lysis pretreatments to procure better results. Future works includes developing a better system to efficiently collect multi variable data, and to upscale to artificial polycultures using similar methodologies alongside sequencing to confirm kit results.

59 BASIC BIOLOGICAL SCIENCES↗

DOE OSTI2020

Primary intrinsic defects and their charge transition levels in β–Ga 2 O 3

A steady-state photocapacitance (SSPC) setup directly connected to the beamline of a MeV ion implanter is utilized to study primary intrinsic defects in β – Ga 2 O 3 generated by He implantation at cryogenic temperatures (120 K). At low temperatures, the migration of defects is suppressed, and hence the generation of primary intrinsic defects is expected to prevail. SSPC measurements reveal defect-related optical transitions in halide vapor-phase epitaxy (HVPE) -grown β – Ga 2 O 3 thin films with onset energies at 1.3 ( T 1 ) , 1.7 ( T 2 ) , 1.9 ( T 3 ) , 2.6 ( T 4 ) , 3.7 ( T 5 ) , and 4.2 eV ( T 6 ) . T 2 , T 4 , T 5 , and T 6 were observed in as-received HVPE-grown β – Ga 2 O 3 thin films, whereby T 2 is only sporadically observed. The introduction rates for T 3 , T 4 , as well as T 6 indicate an origin related to primary intrinsic defects. Notably, T 1 and T 3 are only observed after He implantation at cryogenic temperatures. Hybrid-functional calculations were performed to estimate the optical absorption cross-section spectra for the gallium ( Ga i ) and oxygen ( O i ) interstitials as well as the corresponding vacancies ( V Ga and V O , respectively), and compared with the measured onsets for optical absorption found by SSPC measurements. Indeed, we propose T 3 to be associated with Ga i ( + / + 2 ) and/or V GaI ( - 3 / - 2 ) , while T 4 is suggested to be related to V O K ( 0 / + ) ( K = I , II , III ) and/or V GaII ( - 3 / - 2 ) . Additionally, several further charge-state transition levels associated with V GaI and V GaII may contribute to T 4 and T 6 . We further studied the kinetics of the defects created with He implantation by exposing the sample to room temperature. The kinetics observed for T 3 and T 4 further support the proposed assignments of the corresponding defect signatures.

36 MATERIALS SCIENCE↗

DOE OSTI2020

Broadband, millimeter-wave antireflection coatings for large-format, cryogenic aluminum oxide optics

Here, we present two prescriptions for broadband (~77 -252 GHz), millimeter-wave antireflection coatings for cryogenic, sintered polycrystalline aluminum oxide optics: one for large-format (700 mm diameter) planar and plano–convex elements, the other for densely packed arrays of quasi-optical elements—in our case, 5 mm diameter half-spheres (called “lenslets”). The coatings comprise three layers of commercially available, polytetrafluoroethylene-based, dielectric sheet material. The lenslet coating is molded to fit the 150 mm diameter arrays directly, while the large-diameter lenses are coated using a tiled approach. We review the fabrication processes for both prescriptions, then discuss laboratory measurements of their transmittance and reflectance. In addition, we present the inferred refractive indices and loss tangents for the coating materials and the aluminum oxide substrate. We find that at 150 GHz and 300 K the large-format coating sample achieves (97±2)% transmittance, and the lenslet coating sample achieves (94±3)% transmittance.

36 MATERIALS SCIENCE↗

DOE OSTI2021

Use of Transmission Electron Microscopy for Analysis of Aerosol Particles and Strategies for Imaging Fragile Particles

For over 25 years, transmission electron microscopy (TEM) has provided a method for the study of aerosol particles with sizes from below the optical diffraction limit to several microns, resolving the particles as well as smaller features. The wide use of this technique to study aerosol particles has contributed important insights about environmental aerosol particle samples and model atmospheric systems. TEM produces an image that is a 2D projection of aerosol particles that have been impacted onto grids and, through associated techniques and spectroscopies, can contribute additional information such as the determination of elemental composition, crystal structure, and 3D particle structures. Soot, mineral dust, and organic/inorganic particles have all been analyzed using TEM and spectroscopic techniques. TEM, however, has limitations that are important to understand when interpreting data including the ability of the electron beam to damage and thereby change the structure and shape of particles, especially in the case of particles composed of organic compounds and salts. In this paper, we concentrate on the breadth of studies that have used TEM as the primary analysis technique. Another focus is on common issues with TEM and cryogenic-TEM. Insights for new users on best practices for fragile particles, that is, particles that are easily susceptible to damage from the electron beam, with this technique are discussed. Tips for readers on interpreting and evaluating the quality and accuracy of TEM data in the literature are also provided and explained.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

DOE OSTI2023

Surface structure studies in 2D and 3D Nb resonators using GI-XRD

Superconductor radio frequency (SRF) Nb-resonators are a key element in the development of new generations of particle accelerators as well as in the fabrication of 3D circuit QED architecture for quantum computing. Nevertheless, Niobium is extremally reactive to light elements such as C, N, O and H, and therefore to the impurities ordering under special conditions, e.g., cryogenic temperatures. Since these resonators are put through a series of metallurgical and chemical processes, the number of impurities in the solid increases in tens of ppm. Upon operational conditions ~1.6 K, Nb become vulnerable to H atoms ordering, which leads to the nucleation of secondary phases such as Nb-hydrides. Thereupon to the energy dissipation and eventually to the superconductivity breakdown known as Q-disease and potentially High-Field Q-slope. In this contribution, we present a detailed structural analysis by high-energy grazing-incidence X-ray diffraction of specimens extracted from 3D Nb resonators to shed light on the kinetic formation of the resulting secondary phases and their crystal phase identification upon cooling and heating cycles. To our knowledge, this is the first study carried out in resonators samples using a light source, shallow angles and temperatures near ~4 K. Consequently, this work opens new routes to understand the chemical and phase composition, crystal and electronic structure of the Nb surface at temperatures near the operating conditions as a strategy to improve the physical and functional properties of Nb superconducting resonators.

72 PHYSICS OF ELEMENTARY PARTICLES AND FIELDS↗

DOE OSTI2020

Magnetic Microcalorimeter (MMC) Gamma-Ray Detectors with Ultra-High Energy Resolution. Comprehensive Technology Readiness Assessment

Magnetic Microcalorimeter (MMC) gamma ray detectors have demonstrated very high energy resolution of 38 eV FWHM for gamma ray energies below 100 keV. This is an order or magnitude better than conventional HPGe detector and can remove most line-overlap problems in NDA by gamma spectroscopy below ~130 keV. Unlike superconducting transition edge sensors (TESs), MMCs have a reproducible and almost perfectly linear response, which greatly simplifies adding spectra from different detector pixels and reduces systematic errors in quantitative assays. The instrument is currently at TRL-5 but could advance to TRL-6 by improving the signal processing software and using the system for the quantitative analysis of a safeguards sample provided by e.g. the IAEA. Making MMC detectors commercially viable and used more widely then depends on making the technology more reliable, specifically by increasing the device uniformity and yield, and by developing commercial software. This situation is often only half-jokingly referred to as the “valley of death” and could be addressed though the SBIR program. Our collaborators at STAR Cryoelectronics LLC are well qualified to further advance MMC development, and XIA LLC is well-positioned to develop the data acquisition system and write the software for MMC readout. In addition, the advance to TRL-6 would be desirable to increase the visibility and showcase the value of MMC spectrometers, e.g. by placing one of them into the Safeguards Analytical Laboratory (SAL) at the IAEA, whose NDA experts have recently started to show interest in cryogenic detector technology. As a result of this LCP, we also now have an instrument at LLNL that we will use for various applications of MMCs in nuclear safeguards and science. We are confident that as the number of high-profile results increases, so will the interest in and commercial viability of this technology.

42 ENGINEERING↗

DOE OSTI2020

Magnetic Microcalorimeter (MMC) Gamma-Ray Detectors with Ultra-High Energy Resolution. Comprehensive Technology Readiness Assessment

42 ENGINEERING↗

DOE OSTI2022

Plant-specific features of respiratory supercomplex I + III2 from Vigna radiata

Abstract The last steps of cellular respiration—an essential metabolic process in plants—are carried out by mitochondrial oxidative phosphorylation. This process involves a chain of multi-subunit membrane protein complexes (complexes I–V) that form higher-order assemblies called supercomplexes. Although supercomplexes are the most physiologically relevant form of the oxidative phosphorylation complexes, their functions and structures remain mostly unknown. Here we present the cryogenic electron microscopy structure of the supercomplex I + III 2 from Vigna radiata (mung bean). The structure contains the full subunit complement of complex I, including a newly assigned, plant-specific subunit. It also shows differences in the mitochondrial processing peptidase domain of complex III 2 relative to a previously determined supercomplex with complex IV. The supercomplex interface, while reminiscent of that in other organisms, is plant specific, with a major interface involving complex III 2 ’s mitochondrial processing peptidase domain and no participation of complex I’s bridge domain. The complex I structure suggests that the bridge domain sets the angle between the enzyme’s two arms, limiting large-scale conformational changes. Moreover, complex I’s catalytic loops and its response in active-to-deactive assays suggest that, in V. radiata , the resting complex adopts a non-canonical state and can sample deactive- or open-like conformations even in the presence of substrate. This study widens our understanding of the possible conformations and behaviour of complex I and supercomplex I + III 2 . Further studies of complex I and its supercomplexes in diverse organisms are needed to determine the universal and clade-specific mechanisms of respiration.

59 BASIC BIOLOGICAL SCIENCES↗

DOE OSTI2024

Neutrons in Structural Biology: Challenges and Opportunities (Workshop Report)

Gaining a thorough understanding of biological systems requires building our knowledge about biological processes from the level of atoms and electrons, and up to whole organisms. Such comprehensive knowledge will allow for a predictive understanding of complex biological systems behavior. It will guide us in the design and development of novel therapeutics and vaccines to tackle existing health threats and to prepare for future pandemics, and it will provide information necessary to create new biomaterials and bio-inspired technologies through manipulation of biological macromolecules, their assemblies, single cells and even microorganisms. Reaching these goals will require a synergistic combination of multiple experimental techniques with molecular calculations and predictive simulations, and the design and development of new techniques and capabilities that bridge current knowledge and technology gaps. Neutron scattering provides unique information about the biomacromolecular structure and function and can play a major role in achieving these goals. A workshop was held to engage the scientific community in identifying pressing challenges in biochemistry, structural biology, enzymology and structure-guided drug design not solved with the current neutron scattering technologies or utilizing other structural biology techniques such as X-ray crystallography, NMR, and cryo-EM. The workshop brought together structural biology, biochemistry and computational experts, as well as early career researchers and students, creating a forum for discussing scientific advancement and collaboration. The workshop included a one-day satellite training workshop where graduate students and postdoctoral researchers were educated in the application of neutron crystallography and small-angle scattering in structural biology. Furthermore, the Instrument Scientific Advisory Board (ISAB) for the development of a macromolecular neutron diffractometer at ORNL’s Second Target Station was introduced at the workshop. The major outcome was that neutrons can provide atomic-level understanding of biomacromolecular structure, function and dynamics which is of paramount importance for addressing the identified challenges. Neutron crystallography, in particular, can resolve long-standing biochemical issues regarding enzyme function by delineating the underlying chemistry and can have a major impact on the design of small-molecule therapeutics, especially in combination with molecular computation (quantum chemistry and molecular dynamics simulations) and the emerging artificial intelligence (AI)-assisted drug design technologies. The unique properties of neutrons, including their high sensitivity to hydrogen and their non-destructive nature, make them ideal probes of biological matter. There is a palpable need in the scientific community to expand and enhance the impact of neutron sciences on biology. Neutron crystallography is the only structural biology method capable of determining positions of all hydrogen atoms in proteins, nucleic acids and their complexes at near-physiological temperatures and of unstable species at cryogenic temperatures. Moreover, neutron analysis is non-ionizing, non-destructive and does not perturb the structure or redox chemistry of active site metal centers and clusters in proteins, which can be invaluable for studying radiation-sensitive metalloprotein complexes. Further, neutron energies used in scattering applications are similar to atomic motions, permitting neutron spectroscopies to characterize the dynamics of biomacromolecules on the picosecond to microsecond timescales. The different sensitivities of neutrons to protium (H) and deuterium (D) isotopes of hydrogen allow enhanced visibility of specific parts of biological complexes through isotopic labeling. The impact of neutrons will be most powerful when neutron scattering is combined with complementary experimental techniques that use photons and electrons, and with high-performance computing. The interconnection and mutuality of the experimental and theoretical capabilities will drive discoveries in biological and health sciences to generate more complete picture of complex biological systems. The major limitation in the field of biological neutron crystallography has been signal-to-noise, demanding large samples that are difficult to produce for the majority of biomacromolecules and limiting the applicability of this technique in biological sciences. A neutron crystallography instrument at the Second Target Station will revolutionize biological science with neutrons by engaging a large scientific community of structural biologists, enabling successful neutron diffraction experiments from radically smaller biomacromolecular crystals, resolving unanswered biochemical questions, and meaningfully contributing to rational drug design. The meeting highlighted 10 grand challenges that will be addressed with this advanced capability over the next decade and beyond, and the recommendations required to help address them are given below.

59 BASIC BIOLOGICAL SCIENCES↗

DOE OSTI2026

Integrated fluorescence light microscopy-guided cryo-focused ion beam-milling for in situ montage cryo-ET

Cryogenic-electron tomography (cryo-ET) permits the in situ visualization of biological macromolecules at the molecular level. Owing to the variable thickness of cells, tissues and organisms, frozen specimens may need to be thinned by cryo-focused ion beam (FIB) milling to produce thin (<500 nm) cryo-lamellae suitable for cryo-ET. Locating regions of interest remains a challenge because untargeted milling can lead to inadvertent ablation and removal of regions of interest. Correlative light and electron microscopy, combined with cryo-FIB milling, can guide the identification of labeled targets in the cellular milieu. Multiple transfers between cryo-imaging instruments, cumbersome correlation algorithms, limited accuracy and low throughput have hindered the routine adoption of cryo-FIB milling within a multimodal correlative workflow for in situ structural biology. Here, in this study, we present a workflow for 3D correlative cryo-fluorescence light microscopy-FIB-ET that streamlines fluorescence light microscopy-guided FIB milling, improving throughput while preserving both structural and contextual information. The complete integration of hardware and software described here minimizes sample contamination from cross-platform exchanges and greatly enhances the efficiency of 3D targeting in cryo-milling. We then describe procedures for implementing montage parallel array cryo-ET (MPACT), which can be easily adapted to any modern life-science transmission electron microscope. MPACT supports high-throughput cryo-ET acquisitions (10 tilt series in 1.5 h) for structure determination and comprehensive contextual understanding of macromolecules within their native surroundings. A complete session from sample preparation to MPACT data processing takes 5−7 d for an individual experienced in both cryo-EM and cryo-FIB milling.

Yang, Jie E. [Univ. of Wisconsin, Madison, WI (Uni↗

DOE OSTI2020

SuperCDMS Event Reconstruction Using Convolutional Neural Networks [Thesis]

The SuperCDMS experiment uses cryogenic silicon and germanium detectors to search for dark matter candidates such as WIMPs (Weakly Interacting Massive Particles) streaming through the Earth. Collisions in the silicon and germanium crystals are expected to produce phonons whose thermal signatures can be measured. This thesis first describes the integration of a new Signal Distribution Unit (SDU) to the SuperCDMS data acquisition system, which allows for synchronization of multiple detectors and electronic/mechanical noise characterization via accelerometer, antenna, and AC phase measurements. From SuperCDMS detector data it is necessary to reconstruct the energies of the particle events. This thesis explores the use of Convolutional Neural Networks (CNNs) to perform this reconstruction and finds that, although they perform well, changing the noise model breaks the model and requires the neural network to be retrained. In order to mitigate this issue, a new CNN model is proposed which includes the noise Power Spectral Density (PSD) of the data as an additional input to the CNN. While it proves to be effective as a denoising algorithm, it still fails for data with a different noise model. However, including data from multiple PSDs in the neural network training sample allows it to handle data with different types of noise while still maintaining the quality of the reconstruction. Nevertheless, neural networks trained even on multiple PSDs do not robustly handle data taken with PSDs dissimilar to those in the training sample, suggesting that CNNs may need to be retrained whenever the noise environment changes in a significant way.

46 INSTRUMENTATION RELATED TO NUCLEAR SCIENCE AND ↗

DOE OSTI2023

Temperature-dependent elastic constants of thorium dioxide probed using time-domain Brillouin scattering

Herein we report the adiabatic elastic constants of single-crystal thorium dioxide over a temperature range of 77–350 K. Time-domain Brillouin scattering, an all-optical, non-contact picosecond ultrasonic technique, is used to generate and detect coherent acoustic phonons that propagate in the bulk perpendicular to the surface of the crystal. These coherent acoustic lattice vibrations have been monitored in two hydrothermally grown single-crystal thorium dioxide samples along the (100) and (311) crystallographic directions. The three independent elastic constants of the cubic crystal (C 11 , C 12 , and C 44 ) are determined from the measured bulk acoustic velocities. The longitudinal wave along the (100) orientation provided a direct measurement of C 11 . Measurement of C 44 and C 12 was achieved by enhancing the intensity of quasi-shear mode in a (311) oriented crystal by adjusting the polarization angle relative to the crystal axes. We find the magnitude of softening of the three elastic constants to be ~2.5% over the measured temperature range. Good agreement is found between the measured elastic constants with previously reported values at room temperature, and between the measured temperature-dependent bulk modulus with calculated values. We find that semi-empirical models capturing lattice anharmonicity adequately reproduce the observed trend. We also determine the acoustic Grüneisen anharmonicity parameter from the experimentally derived temperature-dependent bulk modulus and previously reported temperature-dependent values of volumetric thermal expansion coefficient and heat capacity. This work presents measurements of the temperature-dependent elasticity in single-crystal thorium dioxide at cryogenic temperature and provides a basis for testing ab initio theoretical models and evaluating the impact of anharmonicity on thermophysical properties.

11 NUCLEAR FUEL CYCLE AND FUEL MATERIALS↗

DOE OSTI2022

Electron microscopy holdings of the Protein Data Bank: the impact of the resolution revolution, new validation tools, and implications for the future

Abstract As a discipline, structural biology has been transformed by the three-dimensional electron microscopy (3DEM) “Resolution Revolution” made possible by convergence of robust cryo-preservation of vitrified biological materials, sample handling systems, and measurement stages operating a liquid nitrogen temperature, improvements in electron optics that preserve phase information at the atomic level, direct electron detectors (DEDs), high-speed computing with graphics processing units, and rapid advances in data acquisition and processing software. 3DEM structure information (atomic coordinates and related metadata) are archived in the open-access Protein Data Bank (PDB), which currently holds more than 11,000 3DEM structures of proteins and nucleic acids, and their complexes with one another and small-molecule ligands (~ 6% of the archive). Underlying experimental data (3DEM density maps and related metadata) are stored in the Electron Microscopy Data Bank (EMDB), which currently holds more than 21,000 3DEM density maps. After describing the history of the PDB and the Worldwide Protein Data Bank (wwPDB) partnership, which jointly manages both the PDB and EMDB archives, this review examines the origins of the resolution revolution and analyzes its impact on structural biology viewed through the lens of PDB holdings. Six areas of focus exemplifying the impact of 3DEM across the biosciences are discussed in detail (icosahedral viruses, ribosomes, integral membrane proteins, SARS-CoV-2 spike proteins, cryogenic electron tomography, and integrative structure determination combining 3DEM with complementary biophysical measurement techniques), followed by a review of 3DEM structure validation by the wwPDB that underscores the importance of community engagement.

Burley, Stephen K. (ORCID:0000000224879713)↗

DOE OSTI2023

Compact, high-power superconducting radio-frequency accelerators for environmental applications

Electron-beam irradiation has been proven to destructively reduce or eliminate a wide variety of organic chemicals, viruses and bacteria from wastewater, as well as reducing sulfur and nitrous oxides emission from coal-fired power plants. It is estimated that there are approximately 30,000 such particle accelerators in use worldwide for industrial processes including surface and bulk processing of material, medical sterilization, and environmental remediation. Maximum beam power from accelerators used in these applications is currently limited to less than 500 kW, and a higher beam power is needed to reduce treatment costs. The market availability of continuous-wave (CW) electron-beam accelerators with power of the order of ~100 kW is also very limited. Superconducting radio-frequency (SRF) linear accelerators (linacs) are commonly used at basic research laboratories throughout the world due to their exceptionally high efficiency as compared to current industrial varieties. Recent advances in cryogenics, SRF thin films and high-power magnetrons allow for the design of increasingly compact and efficient CW SRF electron linacs in the energy range 1-10 MeV, with up to 1 MW of beam power. A new class of compact, high-efficiency electron-beam accelerators may provide cost-effective solutions for a range of industrial and environmental remediation applications, particularly with respect to tackling one such class of contaminants so-called forever chemicals, including per- and polyfluoroalkyl substances (PFASs), which are ubiquitous in a wide range of products and for which there is currently no effective destruction technology. We have recently demonstrated the key technologies required for such accelerators by: 1) operating a Nb3Sn SRF accelerating cavity cooled by commercial cryocoolers up to an accelerating gradient of 12.4 MV/m and 2) demonstrating the phase-locking as well as a high-efficiency power combining scheme for industrial magnetron transmitters. In this presentation, we will introduce the principles and benefits of MW-class SRF linacs, based on the conduction-cooled SRF technology that we have demonstrated for environmental remediation. We propose the development of a 4 MeV, 20 kW prototype to be built at Jefferson Lab as a first accelerator demonstrator unit. We will also present the results from samples study on the effect of electron-beam irradiation on so-called forever chemicals such as 1,4-dioxane and PFAS, using an existing multi-purpose 10 MeV, low-power, CW SRF linac at Jefferson Lab.

Ciovati, Gianluigi↗

DOE OSTI2022

Development of Quantum Computing Interconnect Based on Aerosol Jet Printing and Electrochemical Deposition of Rhenium

The electrodeposition of rhenium on to a metal seed layer on flexible substrates is presented as a means to creating superconducting flexible cable connectors in an enabling plug-and-play approach for quantum computing. Cryogenic quantum electronics are currently connected using masses of stainless-steel coaxial cables that are bulky, rigid - both in form and design - and lead to significant joule heating, thermal noise, and cross talk. Here, we present an unprecedented approach to integrate an aerosol jet printed (AJP) metal seed layer with rhenium electrodeposition on a flexible substrate in the advancement of superconducting interconnect technologies. Silver and gold were printed using the ‘Nanojet’ aerosol jet printer on Kapton films. Adhesion of gold was found to be far superior to that of silver and adhesion on roughened Kapton surpassed that of its smooth counterpart. Electrodeposition of rhenium was successful on both silver and gold and an amorphous Re film was confirmed by XRD. Results for both materials are presented however due to the poor adhesion of silver to Kapton it was ruled out as a viable candidate. Composite materials were characterized by profilometry, EDS, XRD and FIBSEM. Electrical measurements of the composite at ambient temperature showed a critical temperature (T c ), where the resistance drops to 0, of 5.8 K, well above 4.2 K, the temperature of liquid helium. Stress-strain tests of the Ag-Re and Au-Re composites on roughened and smooth Kapton were completed. Cyclic flexure testing (200 cycles) to 1.25% strain showed smooth Kapton samples reach a stress of ~16 MPa, while Kapton roughened with sandpaper, reaches ~20MPa of stress for the same 1.25% strain.

36 MATERIALS SCIENCE↗

DOE OSTI2024

Subcellular Feature-Based Classification of α and β Cells Using Soft X-ray Tomography

The dysfunction of α and β cells in pancreatic islets can lead to diabetes. Many questions remain on the subcellular organization of islet cells during the progression of disease. Existing three-dimensional cellular mapping approaches face challenges such as time-intensive sample sectioning and subjective cellular identification. To address these challenges, we have developed a subcellular feature-based classification approach, which allows us to identify α and β cells and quantify their subcellular structural characteristics using soft X-ray tomography (SXT). We observed significant differences in whole-cell morphological and organelle statistics between the two cell types. Additionally, we characterize subtle biophysical differences between individual insulin and glucagon vesicles by analyzing vesicle size and molecular density distributions, which were not previously possible using other methods. These sub-vesicular parameters enable us to predict cell types systematically using supervised machine learning. We also visualize distinct vesicle and cell subtypes using Uniform Manifold Approximation and Projection (UMAP) embeddings, which provides us with an innovative approach to explore structural heterogeneity in islet cells. This methodology presents an innovative approach for tracking biologically meaningful heterogeneity in cells that can be applied to any cellular system.

3D cell mapping↗

DOE OSTI2020

Data-guided Multi-Map variables for ensemble refinement of molecular movies

Driving molecular dynamics simulations with data-guided collective variables offer a promising strategy to recover thermodynamic information from structure-centric experiments. In this study, the three-dimensional electron density of a protein, as it would be determined by cryo-EM or x-ray crystallography, is used to achieve simultaneously free-energy costs of conformational transitions and refined atomic structures. Unlike previous density-driven molecular dynamics methodologies that determine only the best map-model fits, our work employs the recently developed Multi-Map methodology to monitor concerted movements within equilibrium, non-equilibrium, and enhanced sampling simulations. Construction of all-atom ensembles along the chosen values of the Multi-Map variable enables simultaneous estimation of average properties, as well as real-space refinement of the structures contributing to such averages. Using three proteins of increasing size, we demonstrate that biased simulation along the reaction coordinates derived from electron densities can capture conformational transitions between known intermediates. The simulated pathways appear reversible with minimal hysteresis and require only low-resolution density information to guide the transition. The induced transitions also produce estimates for free energy differences that can be directly compared to experimental observables and population distributions. The refined model quality is superior compared to those found in the Protein Data Bank. We find that the best quantitative agreement with experimental free-energy differences is obtained using medium resolution density information coupled to comparatively large structural transitions. Practical considerations for probing the transitions between multiple intermediate density states are also discussed.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

DOE OSTI2023

Advancements in High-Q development for novel medium-velocity 644 MHz 5-cell elliptical superconducting RF cavities for continuous-wave operation in heavy-ion linacs

The Facility for Rare Isotope Beams is a world-leading center for experimental nuclear physics research, and relies on a first-in-kind superconducting RF driver linac to supply 400 kW beams of a uniquely large range of particles, from protons through the heaviest uranium ions. The FRIB400 project proposes to double the end energy of the current superconducting FRIB linac for the heaviest uranium ions from 200 MeV per nucleon (MeV/u) to 400 MeV/u, which equates to approximately 1 GeV for protons. The increased rare isotope production from higher-energy drive beams would deliver new and exciting capabilities to FRIB users, which include extending the facility's reach along the neutron drip-line, greatly increasing the facility's rare isotope yield, and significantly improving the precision of parameter measurements for the nuclear matter equation of state, which is a particularly timely complement to the recent advent of multi-messenger astronomy, and the study of neutron star mergers. The unique set of design parameters defined by the 400 MeV/u (uranium) energy goal, the physical size, continuous-wave operation, and cryogenic capacity of the extant facilities at FRIB, requires development of a first-in-kind beta = v/c = 0.65, 644 MHz 5-cell elliptical superconducting RF (SRF) cavity, with field-leading efficiency, measured by the cavity's intrinsic quality factor, Q_0. The field of SRF has recently experienced a very active period of development, which demonstrated the potential to raise the Q_0 of 1.3 GHz cavities by factors of two to three or more. In addition to uncovering fascinating new properties of the fundamental physics of superconducting RF phenomena, these improvements suggest substantial improvements could be made over the minimum Q_0 of the proposed FRIB400 upgrade SRF cavities, if these new techniques can be adapted to the beta = 0.65, 644 MHz regime. This work presents the first validation of the the novel beta = 0.65, 644 MHz 5-cell elliptical superconducting RF cavity design, and the first results of both conventional and advanced RF surface preparation techniques. In particular, this work focuses on two recently-developed high-Q_0 recipes: N-doping, and furnace baking, setting the current world-record Q_0 for this type of resonant cavity at 3.8 x 10^10 at the FRIB400 operating gradient of 17.5 MV/m. We also find evidence that these results may be further improved upon, and make the case for further RF surface preparation recipe optimization. We then pair these high-power RF investigations with techniques borrowed from material science to try to better understand the ways in which specific properties of the niobium material, such as grain structure and superconducting flux pinning force, can be related to its superconducting RF performance. These experiments better elucidate the effects of high-temperature annealing on niobium samples, which suggest methods of further optimizing cavity flux expulsion and thus SRF performance.Read

McGee, Kellen E.↗