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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 37 records · Page 2
All sourcesNASA NTRSDOE OSTI
DOE OSTI2025

PhaseT3M: 3D imaging at 1.6 Å resolution via electron cryo-tomography with nonlinear phase retrieval

Electron cryo-tomography (cryo-ET) enables 3D imaging of complex, radiation-sensitive structures with molecular detail. However, image contrast from the interference of scattered electrons is nonlinear with atomic density and multiple scattering further complicates interpretation. These effects degrade resolution, particularly in conventional reconstruction algorithms, which assume linearity. Particle averaging can reduce such issues but is unsuitable for heterogeneous or dynamic samples ubiquitous in biology, chemistry, and materials sciences. Here, we develop a phase retrieval-based cryo-ET method, PhaseT3M. We experimentally demonstrate its application to an approximately 7 nm Co3O4 nanoparticle on an approximately 30 nm carbon substrate, achieving a maximum resolution of 1.6 Å, surpassing conventional limits using standard cryo-TEM equipment. PhaseT3M uses a multislice model for multiple scattering and Bayesian optimization for alignment and computational aberration correction, with a positivity constraint to recover ‘missing wedge’ information. Applied directly to biological particles, it enhances reconstruction quality and reduces artifacts, establishing a standard for routine 3D imaging with phase contrast.

Biophysics↗
DOE OSTI2024

CryoTRANS: predicting high-resolution maps of rare conformations from self-supervised trajectories in cryo-EM

Cryogenic electron microscopy (cryo-EM) has revolutionized structural biology, enabling efficient determination of structures at near-atomic resolutions. However, a common challenge arises from the severe imbalance among various conformations of vitrified particles, leading to low-resolution reconstructions in rare conformations due to a lack of particle images in these quasi-stable states. We introduce CryoTRANS, a method that predicts high-resolution maps of rare conformations by constructing a self-supervised pseudo-trajectory between density maps of varying resolutions. This trajectory is represented by an ordinary differential equation parameterized by a deep neural network, ensuring retention of detailed structures from high-resolution density maps. By leveraging a single high-resolution density map, CryoTRANS significantly improves the reconstruction of rare conformations and has been validated on four real-world datasets: alpha-2-macroglobulin, actin-binding protein complexes, SARS-CoV-2 spike glycoprotein, and the 70S ribosome. CryoTRANS can also predict high-resolution structures in cryogenic electron tomography maps using a high-resolution cryo-EM map.Cryogenic electron microscopy (cryo-EM) has revolutionized structural biology, enabling efficient determination of structures at near-atomic resolutions. However, a common challenge arises from the severe imbalance among various conformations of vitrified particles, leading to low-resolution reconstructions in rare conformations due to a lack of particle images in these quasi-stable states. We introduce CryoTRANS, a method that predicts high-resolution maps of rare conformations by constructing a self-supervised pseudo-trajectory between density maps of varying resolutions. This trajectory is represented by an ordinary differential equation parameterized by a deep neural network, ensuring retention of detailed structures from high-resolution density maps. By leveraging a single high-resolution density map, CryoTRANS significantly improves the reconstruction of rare conformations and has been validated on four real-world datasets: alpha-2-macroglobulin, actin-binding protein complexes, SARS-CoV-2 spike glycoprotein, and the 70S ribosome. CryoTRANS can also predict high-resolution structures in cryogenic electron tomography maps using a high-resolution cryo-EM map.

47 OTHER INSTRUMENTATION↗
DOE OSTI2025

Lessons from Testing the First Three US HL-LHC Cryo-Assemblies at FNAL

The US High-Luminosity LHC Accelerator Upgrade Project (AUP) collaborates with CERN to deliver 10 cryo-assemblies for the High-Luminosity LHC upgrade at CERN. Those comprise the Q1/Q3 quadrupole optical elements in the accelerator and are based on Nb3Sn technology, for the first time in a large particle accelerator. So far three cryo-assemblies were tested at the Fermilab’s horizontal magnet test facility, specifically redesigned to serve those needs. This work gives an overview of the facility and its necessary evolution as the campaign progressed; main results and observations from the cryo-assembly tests are presented and discussed in the context of overall performance and expectations toward the completion of efforts. Lessons learned after multiple cryo-assembly tests by the same team are critical to ensure continuous success of the whole enterprise – those are openly shared.

Stoynev, Stoyan [Fermilab]↗
NASA NTRS2003

Helium Cryo Testing of a SLMS(TM) (Silicon Lightweight Mirrors) Athermal Optical Assembly

SLMS (TM) a thermal technology has been demonstrated in the small 4-foot helium cryogenic test chamber located at the NASA/MSFC X-Ray Calibration Facility (XRCF). A SLMS (TM) Ultraviolet Demonstrator Mirror (UVDM) produced by Schafer under a NASA/MSFC Phase I SBIR was helium cryo tested both free standing and bonded to a Schafer designed prototype carbon fiber reinforced silicon carbide (Cesic) mount. Surface figure data was obtained with a test measurement system that featured an Instantaneous Phase Interferometer (IPI) by ADE Phase Shift. The test measurement system s minimum resolvable differential figure deformation and possible contributions from test chamber ambient to cryo window deformation are under investigation. The free standing results showed differential figure deformation of 10.4 nm rms from 295K to 27K and 3.9 nm rms after one cryo cycle. The surface figure of the UVDM degraded by lambda/70 rms HeNe once it was bonded to the prototype Cesic mount. The change was due to a small astigmatic aberration in the rototype Cesic mount due to lack of finish machining and not the bonding technique. This effect was seen in SLMST (TM) optical assembly results, which showed differential figure deformation of 46.5 nm rms from 294K to 27K, 42.9 nm rms from 294K to 77K, 28.0 nm rms from 294K to 193K and 6.2 nm rms after one cryo cycle.

Jacoby, Marc T.↗
DOE OSTI2026

Deep-learning methods for contrast enhancement and artifact reduction in cryo-electron tomography: a systematic analysis of the state of the art and proposed improvements

Cryo-electron tomography (cryo-ET) has emerged as the preferred technique for visualizing the organization of macromolecular complexes in situ and resolving their structures at subnanometre resolution [Tegunov et al. (2021)View full citation, Nat. Methods, 18, 186–193]. Despite improvements in data quality as a result of advances in detector technology, microscope stability and stage precision, the analysis and interpretation of tomograms remains challenging due to a low signal-to-noise ratio and reconstruction artifacts stemming from experimental constraints in specimen tilt during data collection resulting in a missing wedge in the Fourier space. Recently, self-supervised deep-learning methods have been proposed for contrast enhancement and reduction of resolution anisotropy in reconstructed tomograms. Here, we evaluate several state-of-the-art deep-learning methods which aim to improve the interpretability of cryo-ET reconstructions, with a focus on their performance on downstream tasks of template matching, sub­tomogram averaging and segmentation. We propose new training architectures and a loss function based on Fourier shell correlation that show improved performance over the standard U-Net with L1/L2 losses. We demonstrate our analysis on four diverse experimental datasets: purified 80S ribosomes, in situ Chlamydomonas reinhardtii, immature HIV-1 virus-like particles and INS-1E cells.

contrast enhancement↗
DOE OSTI2026

Multiscale Cryo Electron Microscopy Reveals Interfacial Degradation and Stabilization in Battery Electrodes

Electrochemical interfaces are dynamic systems, evolving based on their local environment and reactant surface structures. The electrode-electrolyte interface in Li-ion batteries can be protective, limiting parasitic reactions with the electrolyte to passivate the surface [1]. Additionally, this interphase has an impact on the Li-ion transport through that layer based on its composition, bonding environment, and thickness. These parameters are challenging to collect and may vary depending on the electrode surface site investigated relative to its spatial position in a coin cell. This study will detail a multiscale cryogenic electron microscopy approach where millimeter-scale cross-sections through the coin cell batteries were made using a cryogenic stage within a fs-laser plasma focused ion beam (laser PFIB) with complementary energy dispersive X-ray spectroscopy able to detect variations in the composition at electrode interfaces [2]. Microscale cross-sectioning and lamella sample preparation of battery electrodes was conducted at the Center for Integrated Nanotechnologies using a Ga-ion focused ion beam (FIB) with air-free and cryo-transfer [3], followed by nanoscale mapping of composition and bonding within the CEI through cryo-scanning transmission electron microscopy (cryo-STEM) electron energy loss spectroscopy [4]. This multiscale approach enabled identification of millimeter-scale features of a battery stack with visualization of degradation in electrodes such as cracks in cathode particles, gas evolution, and SEI evolution; microscale interfacial characteristics, such as heterogeneity in the SEI or barrier layer and identification of electrolyte networks to the electrode surfaces; and nanoscale measurement of the CEI thickness, mapping of transition metal bonding within the cathode particles to identify loss of active materials, and identification of beneficial electrolyte additives incorporated into the CEI structure. This multiscale approach allows for a statistical understanding of the primary mechanisms and parasitic degradation pathways that impact performance by limiting the ion transport pathways within Li+ batteries.

36 MATERIALS SCIENCE↗
NASA NTRS2016

Cryo-Temp Data Logger

Biological experiments on the ISS are frequently frozen at ultra-low temperatures on orbit prior to return to Earth for analysis. Recording temperatures during the freezing process, and subsequent handling to the point of post-flight processing, can provide important information of sample integrity to the scientist. The MadgeTech Cryo-Temp Data Logger has been modified for space flight applications by the Payload Development Team at Kennedy Space Center. This ultra-low temperature data logger is rated for temperatures from -86 C to +35 C with 0.1 C resolution and +/-1 C accuracy, but has been successfully tested at Kennedy Space Centers Cryogenic Lab down to -100 C. The logger provides date and time stamped temperature recordings and can be set with logging intervals from 5 seconds up to 30 minutes using the MadgeTech Data Logger Software. Data can be recorded, depending on logging interval, for greater than 90 days. The Cryo-Temp Data logger will first be flown on Space X-12 in the BRIC-Petri Dish Fixation Unit (PDFU) canister hardware, recording temperature data for a Space Life and Physical Sciences (SLPS) flight experiment. The modified Cryo-Temp Data Logger is small in size (Figure 1) and is the ideal temperature monitoring solution for any application involving independent temperature data logging.

Logger↗
DOE OSTI2025

Key Intermediate Nanostructures in the Self-Assembly of Amphiphilic Polypeptoids Revealed by Cryo-TEM

Amphiphilic copolypeptoids are known to form a variety of nanostructures (fibers, tubes, sheets, etc.), but the assembly mechanisms and key intermediates remain underexplored. This study investigates the intermediate structures formed during the early stages of self-assembly in diblock copolypeptoids using cryo-transmission electron microscopy (cryo-TEM). Here we focused on two diblock copolypeptoids, one with a free N-terminus and the other with a capped N-terminus, which ultimately form less-ordered nanofibers and well-ordered nanosheets, respectively. Through cryo-TEM imaging of vitrified solutions at various time points during the self-assembly process, the study identified micelles and vesicles as key intermediate structures. Notably, the formation of vesicles as intermediates is unusual in crystallization-driven self-assembly and suggests a unique pathway in polypeptoid self-assembly. The study provides direct imaging evidence of key intermediates in polypeptoid self-assembly, advancing the understanding of their self-assembly mechanisms.

59 BASIC BIOLOGICAL SCIENCES↗
NASA NTRS2003

Hot Views on Cold Crystals: The Application of Thermal Imaging in Cryo-crystallography

In the past we have used thermal imaging techniques to visualize the cryocooling processes of macromolecular crystals. From these images it was clear that a cold wave progresses through a crystal starting at the face closest to the origin of the cold stream and ending at the point furthest away. During these studies we used large volume crystals, which were clearly distinguished from the loop holding them. These large crystals, originally grown for neutron diffraction studies, were chosen deliberately to enhance the imaging. As an extension to this work, we present used thermal imaging to study small crystals, held in a cryo-loop, in the presence of vitrified mother liquor. The different infrared transmission and reflectance properties of the crystal in comparison to the mother liquor surrounding it are thought to be the parameter that produces the contrast that makes the crystal visible. An application of this technology may be the determination of the exact location of small crystals in a cryo-loop. Data from initial tests in support of application development was recorded for lysozyme crystals and for bFGF/dna complex crystals, which were cryo-cooled and imaged in large loops, both with visible light and with infrared radiation. The crystals were clearly distinguished from the vitrified solution in the infrared spectrum, while in the case of the bFGF/dna complex the illumination had to be carefully manipulated to make the crystal visible in the visible spectrum. These results suggest that the thermal imaging may be more sensitive than visual imaging for automated location of small crystals. However, further work on small crystals robotically mounted at SSRL did not clearly visualize those crystals. The depth of field of the camera proved to be limiting and a different cooling geometry was used, compared to the previous, successful experiments. Analysis to exploit multiple images to improve depth of field and experimental work to understand cooling geometry effects is ongoing. These results will be presented along with advantages and disadvantages of the technique and a discussion of how it might be applied.

Snell, E. H.↗
DOE OSTI2026

Cryo-EM visualization of viruses from partially irrigated soils

Viruses are numerically the most abundant forms on Earth, and most are present in soil. Even though viruses are highly abundant in soil and critical to rhizosphere function, visualizing the diverse morphotypes within soil has been challenging. The difficulty is primarily due to the heterogenous nature of isolated suspensions that typically contain nanometer to micron scale debris which renders protein crystallography for structural studies unfeasible and hinders cryo-electron microscopy due to ice thickness and contrast issues. Here we employed and compared a simple spin filtration method to cleanup solutions of extracted viruses for direct observation with cryo-electron microscopy. The method employs common physical biochemical separation steps to remove large and small debris which dramatically improves image quality and preservation of structural features to permit visualizing morphotypes not typically seen with conventional negative stain approaches. In addition to tailed and non-tailed polyhedral phages, several under reported or novel morphotypes of soil viruses are directly visualized as a particle library with both 2D and 3D information.

cryo-EM↗
DOE OSTI2025

Foam-insulated cryo-compressed hydrogen storage vessels for buses

Here, large reductions (40 % vs. compressed gaseous hydrogen vessels and 17 % vs. vacuum insulated cryo-compressed vessels) in hydrogen storage system cost are possible by operating buses with foam-insulated cryo-compressed hydrogen (CcH 2 ) vessels. Detailed thermodynamic analysis reveals that large size and rapid H 2 consumption in buses compensate for the poor performance of foam insulation (∼100 times more conductive than vacuum multilayer insulation), resulting in compact and inexpensive H 2 storage systems with sufficient H 2 capacity for the longest routes (500 km) while maintaining previously identified advantages of CcH 2 systems: increased autonomy, rapid high density refueling, and improved safety, while simultaneously avoiding vacuum insulation stability problems resulting from composite resin outgassing.

Cryo-compressed↗
NASA NTRS2016

Cryo-vacuum testing of the JWST Integrated Science Instrument Module (SPIE)

In late 2015/early 2016, a major cryo-vacuum test was carried out for the Integrated Science Instrument Module (ISIM) of the James Webb Space Telescope (JWST). This test comprised the final cryo-certification and calibration test of the ISIM, after its ambient environmental test program (vibration, acoustics, EMI/EMC), and before its delivery for integration with the rest of the JWST observatory. Over the 108-day period of the round-the-clock test program, the full complement of ISIM flight instruments, structure, harness radiator, and electronics were put through a comprehensive program of thermal, optical, electrical, and operational tests. The test verified the health and excellent performance of the instruments and ISIM systems, proving the ISIM element's readiness for integration with the telescope. We report here on the context, goals, setup, execution, and key results for this critical JWST milestone.

James Webb Space Telescope (JWST)↗
NASA NTRS2016

Cryo-Vacuum Testing of the JWST Integrated Science Instrument Module

In late 2015 early 2016, a major cryo-vacuum test was carried out for the Integrated Science Instrument Module (ISIM) of the James Webb Space Telescope. This test comprised the final cryo-certification and calibration test of the ISIM before its delivery for integration with the rest of the JWST observatory. Over the roughly 100-day period of the round-the-clock test program, the full complement of ISIM flight instruments, structure, harness radiator, and electronics were put through a comprehensive program of thermal, optical, electrical, and operational tests. We briefly summarize the goals, setup, execution, and key results for this critical JWST milestone.

cryo-vacuum test↗
DOE OSTI2025

Continuity of Mitochondrial Budding: Insights from BS-C-1 Cells by In Situ Cryo-electron Tomography

Mitochondrial division is a fundamental biological process essensial for cellular functionality and vitality. The prevailing hypothesis that dynamin related protein 1 (Drp1) provides principal control in mitochondrial division, in which it also involves the endoplasmic reticulum (ER) and the cytoskeleton, does not account for all the observations. Therefore. the hypothesis may be incomplete. Our previous study in HeLa cells led to a new hypothesis of mitochondrial division by budding. To follow-up our previous study, we employed in situ cryo-electron tomography to visualize mitochondrial budding in the intact healthy monkey kidney cells (BS-C-1 cells). Our findings reaffirm single and multiple mitochondrial budding, consistent with our observations in HeLa cells. Notably, the budding regions vary significantly in diameter and length, which may represent different stages of budding. More interestingly, neither rings nor ring-like structures, nor the wrapping of ER tubes was observed in the budding regions, suggesting mitochondrial budding is independent from Drp1 and ER. Meanwhile, we uncovered direct interactions between mitochondria and large vesicles that are distinct from small mitochondrial-derived vesicles and extracellular mitovesicles. In conclusion, we propose that these interacting vesicles may have mitochondrial origins.

(Cryo-EM)↗
DOE OSTI2024

Evaluating Cryo–TEM Reconstruction Accuracy of Self–Assembled Polymer Nanostructures

Cryogenic transmission electron microscopy (cryo–TEM) combined with single particle analysis (SPA) is an emerging imaging approach for soft materials. However, the accuracy of SPA–reconstructed nanostructures, particularly those formed by synthetic polymers, remains uncertain due to potential packing heterogeneity of the nanostructures. In this study, the combination of molecular dynamics (MD) simulations and image simulations is utilized to validate the accuracy of cryo–TEM 3D reconstructions of self–assembled polypeptoid fibril nanostructures. Using CryoSPARC software, image simulations, 2D classifications, ab initio reconstructions, and homogenous refinements are performed. By comparing the results with atomic models, the recovery of molecular details is assessed, heterogeneous structures are identified, and the influence of extraction location on the reconstructions is evaluated. In conclusion, these findings confirm the fidelity of single particle analysis in accurately resolving complex structural characteristics and heterogeneous structures, exhibiting its potential as a valuable tool for detailed structural analysis of synthetic polymers and soft materials.

36 MATERIALS SCIENCE↗
DOE OSTI2024

Non-averaged single-molecule tertiary structures reveal RNA self-folding through individual-particle cryo-electron tomography

Large-scale and continuous conformational changes in the RNA self-folding process present significant challenges for structural studies, often requiring trade-offs between resolution and observational scope. Here, we utilize individual-particle cryo-electron tomography (IPET) to examine the post-transcriptional self-folding process of designed RNA origami 6-helix bundle with a clasp helix (6HBC). By avoiding selection, classification, averaging, or chemical fixation and optimizing cryo-ET data acquisition parameters, we reconstruct 120 three-dimensional (3D) density maps from 120 individual particles at an electron dose of no more than 168 e - Å -2 , achieving averaged resolutions ranging from 23 to 35 Å, as estimated by Fourier shell correlation (FSC) at 0.5. Each map allows us to identify distinct RNA helices and determine a unique tertiary structure. Statistical analysis of these 120 structures confirms two reported conformations and reveals a range of kinetically trapped, intermediate, and highly compacted states, demonstrating a maturation folding landscape likely driven by helix-helix compaction interactions.

36 MATERIALS SCIENCE↗
DOE OSTI2025

Naturally ornate RNA-only complexes revealed by cryo-EM

The structures of natural RNAs remain poorly characterized and may hold numerous surprises. Here we report three-dimensional structures of three large ornate bacterial RNAs using cryo-electron microscopy (cryo-EM). GOLLD (Giant, Ornate, Lake- and Lactobacillales-Derived), ROOL (Rumen-Originating, Ornate, Large) and OLE (Ornate Large Extremophilic) RNAs form homo-oligomeric complexes whose stoichiometries are retained at lower concentrations than measured in cells. OLE RNA forms a dimeric complex with long co-axial pipes spanning two monomers. Both GOLLD and ROOL form distinct RNA-only multimeric nanocages with diameters larger than the ribosome, each empty except for a disordered loop. Extensive intramolecular and intermolecular A-minor interactions, kissing loops, an unusual A–A helix and other interactions stabilize the three complexes. Sequence covariation analysis of these large RNAs reveals evolutionary conservation of intermolecular interactions, supporting the biological importance of large, ornate RNA quaternary structures that can assemble without any involvement of proteins.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2024

AUP First Pre-Series Cryo-Assembly Design Production and Test Overview

New high field and large-aperture quadrupole magnets for the low-beta inner triplets (Q1, Q2, Q3) have been built and tested as part of the high-luminosity upgrade of the Large Hadron Collider (HL-LHC). These new quadrupole magnets are based on Nb3Sn superconducting technology. The US Accelerator Upgrade Project (US-AUP) is producing the Q1 and Q3 Cryo-Assemblies: a pair of ~5 m long magnet structures installed in a stainless-steel helium vessel (Cold Mass) and surrounded by cryostat shields, piping, and a vacuum vessel. In conclusion, this paper gives an overview of the design, production, and the results of the horizontal test of the first pre-series Q1/Q3 Cryo-Assembly.

43 PARTICLE ACCELERATORS↗