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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 163 records · Page 9
All sourcesNASA NTRSDOE OSTI
DOE OSTI2021

SEM petrography of dispersed organic matter in black shales: A review

Organic matter (OM)-hosted pores are important constituents of the pore system of black shales and play a crucial role in determining their methane adsorption capacity and porosity. OM-hosted pores are generally observed and described with scanning electron microscope (SEM) on Ar ion-milled surfaces. However, SEM imaging is not able to reliably distinguish OM types and relate the observed pores to specific macerals. Partly because of this inability to relate organic pores to macerals, the evolution of organic porosity during thermal maturation remains poorly understood. In this paper, we review the petrographic characteristics of dispersed organic matter (DOM) in black shales under the SEM. Organic petrographic classification of DOM developed for reflected-light microscopy is so far the most practical method when describing DOM in black shales under the SEM because this classification has information on the origin of DOM. Therefore, correlative microscopy (combination of reflected-light and electron microscopy) is the most effective method to identify both OM types and OM-hosted pores. This method, however, is not readily available to most researchers. Although identifying OM on the basis of SEM observations is a challenging task, it is achievable provided there is a good understanding of the studied shales, especially their thermal maturity and original OM composition. Therefore, the overall objective of this paper is to review petrographic characteristics of DOM in black shales under the SEM to provide some guidelines for identifying DOM from SEM observations. We also review factors that control the formation and preservation of OM-hosted pores. OM-hosted pores consist of primary and secondary organic pores. Primary organic pores are pores inherited from the biological structure of the original OM. Secondary organic pores develop during hydrocarbon generation and expulsion from oil-prone OM and are hosted by solid bitumen or pyrobitumen. The development of secondary organic pores is controlled by thermal maturity and OM type, and their preservation is subject to thermal maturity, OM content, and mineralogical composition. The presented view of the evolution of micropore and mesopore characteristics of OM with thermal maturity is based on data from the literature. The specific surface area and pore volume of OM in black shales follow a parabolic pattern with increasing thermal maturity (quantified via vitrinite reflectance, R o ). The initial increase reflects development of OM-hosted pores, and the subsequent decrease is due to denser stacking of aromatic units in the macromolecular structure of OM, with maximum values (specific surface area ~ 300 m 2 /g and pore volume ~ 0.3 cm 3 /g) reached at R o values in the 2.5-3.5% range. The contribution of OM-hosted pores to the pore characteristics of black shales depends on OM content, OM type, and thermal maturity.

03 NATURAL GAS↗
DOE OSTI2025

The Elements of Life, Photosynthesis and Genomics

I am a Professor of Biochemistry, Biophysics and Structural Biology and Plant and Microbial Biology at the University of California in Berkeley. I was born and raised in India, emigrated to the United States to attend university, earning a B.S. in Molecular Biology and a Ph.D. in Biochemistry at the University of Wisconsin in Madison. Following post-doctoral studies with Lawrence Bogorad at Harvard University where I became interested in genetic control of trace element quotas, I joined the department of Chemistry and Biochemistry at UCLA. One of the first to appreciate essential trace metals as potential regulators of gene expression, I articulated the details of the nutritional Cu regulon in Chlamydomonas. In parallel, I used genetic approaches to discover the genes governing missing steps in tetrapyrrole metabolism, including the attachment of heme to apocytochromes in the thylakoid lumen and the factors catalyzing the formation of ring V in chlorophyll. After biochemistry and classical genetics, I embraced genomics, taking a leadership role on the Joint Genome Institute’s efforts on the Chlamydomonas genome and more recently, contributing to high quality assemblies of several genomes in the green algal radiation, and large transcriptomic and proteomic datasets — focusing on the diel metabolic cycle in synchronized cultures and acclimation to key environmental and nutritional stressors — that are well-used and appreciated by the community. Finally, a new venture in Berkeley is the promotion of Auxenochlorella protothecoides as the true “green yeast” and as a platform for engineering algae to produce useful bioproducts.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2024

YOLO2U-Net: Detection-guided 3D instance segmentation for microscopy

Microscopy imaging techniques are instrumental for characterization and analysis of biological structures. As these techniques typically render 3D visualization of cells by stacking 2D projections, issues such as out-of-plane excitation and low resolution in the z-axis may pose challenges (even for human experts) to detect individual cells in 3D volumes as these non-overlapping cells may appear as overlapping. In this paper a comprehensive method for accurate 3D instance segmentation of cells in the brain tissue is introduced. The proposed method combines the 2D YOLO detection method with a multi-view fusion algorithm to construct a 3D localization of the cells. Next, the 3D bounding boxes along with the data volume are input to a 3D U-Net network that is designed to segment the primary cell in each 3D bounding box, and in turn, to carry out instance segmentation of cells in the entire volume. The promising performance of the proposed method is shown in comparison with current deep learning-based 3D instance segmentation methods.

3D instance segmentation↗
DOE OSTI2024

Rational Design of Novel Biomimetic Sequence-Defined Polymers for Mineralization Applications

Silica biomineralization is a naturally occurring process, wherein organisms use proteins and other biological structures to direct the formation of complex, hierarchical nanostructures. Discovery and characterization of such proteins and their underlying mechanisms spurred significant efforts to identify routes for biomimetic mineralization that reproduce the exquisite shapes and size selectivities found in nature. A common strategy has been the use of short peptide sequences with chemistry mimicking those found in natural systems, such as the use of the silaffin-derived R5 peptide. While progress has been made using this approach, there are many limitations that have prevented breakthroughs in biomimicry. To advance our ability to use charged macromolecules for silica formation, we propose to use sequence-defined synthetic polymers known as peptoids, or N-substituted polyglycines, which present significant capability for the precise tuning of sequence and structure beyond what can often be achieved with peptides alone. This study presents a computationally predicted design of these polymers that leads to the controlled formation of silica nanomaterials. We investigate surface adsorption and the mineralization process through analysis of binding mechanisms and energetics of the R5 system. Next, we synthesized two R5-inspired peptoids and validated our prediction in the design of mineralization polymers through characterization using surface plasmon resonance and electron microscopy. Here, this computationally guided study holds great promise for designing new sequences with unprecedented control of the placement of chemical functional groups, thus allowing for further unraveling of silicification mechanisms and the eventual design of sequence-defined synthetic polymers leading to the predictive synthesis of nanostructured functional materials.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2023

Characterization of mApple as a Red Fluorescent Protein for Cryogenic Single-Molecule Imaging with Turn-Off and Turn-On Active Control Mechanisms

Single-molecule superresolution microscopy is a powerful tool for the study of biological structures on size scales smaller than the optical diffraction limit. Imaging samples at cryogenic temperatures (77 K) reduces the quantum yield of photobleaching for many fluorescent labels, yielding localization precisions below 10 nm. Cryogenic imaging further enables correlation with cryogenic electron tomography. A key limitation in applying methods such as PALM and STORM to samples maintained at 77 K is the limited number of fluorophores known to undergo efficient turn-on and turn-off mechanisms necessary to control the sparsity of active emitters. Here we find that mApple, a red-emitting fluorescent protein, undergoes a novel turn-off mechanism in response to simultaneous illumination with two colors of light. This turn-off mechanism enables localization of many individual molecules in initially bright samples, but the final density of localizable emitters is limited by relatively inefficient turn-on (photoactivation). Bulk excitation and emission spectroscopy shows that mApple has access to two distinct emissive states as well as dark states accessible optically or through changes in pH. The bright and stable emission of mApple enables widefield collection of single-molecule emission spectra, which highlight the complex nature and environmental sensitivity of states observed in red fluorescent proteins.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2023

Nanomaterials and Sustainability

Nanostructuring adds a tremendous degree of tunability to the optical, electronic, magnetic, tribological, and chemical properties of matter. As a result, nanostructured materials already play major roles in the many technologies and industries that provide the comfort and convenience of our everyday lives. Although there are examples of nanostructured materials that currently enhance sustainable technologies, such as for batteries and electrolyzers, the potential impact of nanoscale materials on sustainability has likely not nearly been realized when one considers that the nanostructure–property–composition exploration phase space is almost infinite. We can find inspiration from nature, which builds and assembles nanostructured materials into hierarchical biological structures to perform the enormously complex functions of life, all the while doing so with a relatively small set of elements that are sustainably sourced. This contrasts with current technology, where performance demands often require a greater and greater diversity of elements from the periodic table, some of which are very challenging to be sustainably sourced or recycled.

77 NANOSCIENCE AND NANOTECHNOLOGY↗
DOE OSTI2020

Understanding the Impact of Lignocellulosic Biomass Variability on the Size Reduction Process: A Review

The importance of size reduction to the commercial deployment of biomass utilization technologies cannot be overemphasized. Size reduction is necessary to create good flowing, easily digestible lignocellulosic biomass. However, inefficiencies and inconsistencies have not been well addressed for the process of size reduction. This has motivated quite a few research studies, some of which have reported the influence of process variables and pretreatment on the size reduction performance as well as the development of novel size reduction equipment and empirical mathematical models. In this Perspective, we present a systematic and critical evaluation of the state of lignocellulosic biomass size reduction research to provide insights for engineers and scientists for future development and investigation. We first briefly discuss the structural biology and failure mode of lignocellulosic biomass. Then, we present a comprehensive, data-driven picture of the interactions among lignocellulosic biomass attributes, size reduction process variables, pretreatment processes, and size reduction process performance (as defined by product characteristics and size reduction energy consumption). The sizing equipment tool wear issues are also summarized. Finally, we highlight some existing gaps and future research opportunities for lignocellulosic biomass size reduction to inform the development of newer technologies that could effectively produce high-value lignocellulosic biomass particles.

09 BIOMASS FUELS↗
DOE OSTI2023

Cryo-EM structure of the Saccharomyces cerevisiae Rpd3L histone deacetylase complex

The Rpd3L histone deacetylase (HDAC) complex is an ancient 12-subunit complex conserved in a broad range of eukaryotes that performs localized deacetylation at or near sites of recruitment by DNA-bound factors. Here we describe the cryo-EM structure of this prototypical HDAC complex that is characterized by as many as seven subunits performing scaffolding roles for the tight integration of the only catalytic subunit, Rpd3. The principal scaffolding protein, Sin3, along with Rpd3 and the histone chaperone, Ume1, are present in two copies, with each copy organized into separate lobes of an asymmetric dimeric molecular assembly. The active site of one Rpd3 is completely occluded by a leucine side chain of Rxt2, while the tips of the two lobes and the more peripherally associated subunits exhibit varying levels of flexibility and positional disorder. The structure reveals unexpected structural homology/analogy between unrelated subunits in the fungal and mammalian complexes and provides a foundation for deeper interrogations of structure, biology, and mechanism of these complexes, as well as for the discovery of HDAC complex-specific inhibitors.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2025

Extracellular filaments revealed by affinity capture cryogenic-electron tomography

Cryogenic-electron tomography (cryo-ET) has provided an unprecedented glimpse into the nanoscale architecture of cells by combining cryogenic preservation of biological structures with electron tomography. Micropatterning of extracellular matrix proteins is increasingly used as a method to prepare adherent cell types for cryo-ET as it promotes optimal positioning of cells and subcellular regions of interest for vitrification, cryo-focused ion beam (cryo-FIB) milling, and data acquisition. Here we demonstrate a micropatterning workflow for capturing minimally adherent cell types, human T cells and Jurkat cells, for cryo-FIB and cryo-ET. Our affinity capture system facilitated the nanoscale imaging of Jurkat cells, revealing extracellular filamentous structures. It improved workflow efficiency by consistently producing grids with a sufficient number of well-positioned cells for an entire cryo-FIB session. Affinity capture can be extended to facilitate high-resolution imaging of other adherent and non-adherent cell types with cryo-ET.

Biochemistry↗
DOE OSTI2021

Small-angle X-ray and neutron scattering

Small-angle scattering (SAS) is a technique that is able to probe the structural organization of matter and quantify its response to changes in external conditions. X-ray and neutron scattering profiles measured from bulk materials or materials deposited at surfaces arise from nanostructural inhomogeneities of electron or nuclear density. Furthermore, the analysis of SAS data from coherent scattering events provides information about the length scale distributions of material components. Samples for SAS studies may be prepared in situ or under near-native conditions and the measurements performed at various temperatures, pressures, flows, shears or stresses, and in a time-resolved fashion. In this Primer, we provide an overview of SAS, summarizing the types of instrument used, approaches for data collection and calibration, available data analysis methods, structural information that can be obtained using the method, and data depositories, standards and formats. Recent applications of SAS in structural biology and the soft-matter and hard-matter sciences are also discussed.

72 PHYSICS OF ELEMENTARY PARTICLES AND FIELDS↗
DOE OSTI2021

Efficiency analysis of helium-cooled MAS DNP: case studies of surface-modified nanoparticles and homogeneous small-molecule solutions

Despite the growing number of successful applications of dynamic nuclear polarization (DNP)-enhanced magic-angle spinning (MAS) NMR in structural biology and materials science, the nuclear polarizations achieved by current MAS DNP instrumentation are still considerably lower than the theoretical maximum. Here, the method could be significantly strengthened if experiments were performed at temperatures much lower than those currently widely used (~100 K). Recently, the prospects of helium (He)-cooled MAS DNP have been increased with the instrumental developments in MAS technology that uses cold helium gas for sample cooling. Despite the additional gains in sensitivity that have been observed with He-cooled MAS DNP, the performance of the technique has not been evaluated in the case of surfaces and interfaces that benefit the most from DNP. Herein, we studied the efficiency of DNP at temperatures between ~30 K and ~100 K for organically functionalized silica material and a homogeneous solution of small organic molecules at a magnetic field B 0 = 16.4 T. We recorded the changes in signal enhancement, paramagnet-induced quenching and depolarization effects, DNP build-up rate, and Boltzmann polarization. For these samples, the increases in MAS-induced depolarization and DNP build-up times at around 30 K were not as severe as anticipated. In the case of the surface species, we determined that MAS DNP at 30 K provided ~10 times higher sensitivity than MAS DNP at 90 K, which corresponds to the acceleration of experiments by multiplicative factors of up to 100.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2021

Prospects for sub-nanometer scale imaging of optical phenomena using electron microscopy

Imaging of optical phenomena at the sub-nanometer scale can offer fundamental insights into the electronic or vibrational states in atomic-scale defects, molecules, and nanoparticles, which are important in quantum information, heterogeneous catalysis, optoelectronics, and structural biology. Several techniques have surpassed the traditional Abbe diffraction limit and attained spatial resolutions down to a few nanometers, but sub-nanometer scale optics has remained elusive. Here, we propose an approach that combines spectrally specific photoabsorption with sub-nanometer scale resolution transmission electron microscopy (TEM) of photoexcited electrons. We first estimate the signal level and conditions required for imaging nanoscale optical phenomena in core-shell quantum dots (QDs) like CdS/CdTe. Furthermore, we show the possibility of imaging photoexcited states of atomic-scale defects in a monolayer hexagonal boron nitride (h-BN) using ab initio and high resolution (HR)TEM simulations. The ability to directly visualize photoexcited states at the sub-nanometer scale opens opportunities to study properties of individual quantum dots and atomic defects.

74 ATOMIC AND MOLECULAR PHYSICS↗
DOE OSTI2026

Impact of atomic substitution on core-hole relaxation dynamics: A study of Br 2 and IBr

Understanding inner-shell decay processes in heavy-element molecules is essential for unraveling x-ray-induced photodynamics and advancing molecular imaging techniques. Here, in this study, we investigate the influence of atomic substitution on core-hole relaxation dynamics and molecular fragmentation in Br 2 and IBr, initiated by x-ray ionization absorption at the Br K-edge. Using a combination of x-ray/ion coincidence measurements and Monte Carlo/molecular dynamics simulations, we track the charge distribution and the kinetic energy release (KER) of fragment ions with a total charge from 2+ to 8+. For both molecules, the simulated KER values show good agreement with experiment across different fragmentation channels. Our comparison reveals that substituting Br with the heavier I atom in IBr has a minimal impact on the inner-shell electronic decay process but significantly influences nuclear motion, leading to slower dissociation and thus a KER close to the Coulomb limit—an effect attributed to the atomic mass. These findings highlight the interplay between electronic and nuclear effects in molecular fragmentation, particularly in heavy-element species, and provide new insights into medical therapies, structural biology, and astrophysics.

Bhat, Nivedita [Argonne National Laboratory (ANL),↗
DOE OSTI2020

Structure-based development of a subtype-selective orexin 1 receptor antagonist

Orexin receptors belong to the superfamily of G-protein–coupled receptors (GPCRs) which represent the largest class of drug targets in humans. Despite the recent progress in structural biology, the development of subtype-selective orexin receptor and GPCR ligands in general remains challenging, due to the high sequence similarity among individual receptor subtypes. However, subtype-selective molecules are key to discerning the individual contributions of receptor subtypes to (patho-)physiology. Starting from the clinically used, non–subtype-selective orexin receptor antagonist suvorexant, we demonstrate how docking, crystallography, medicinal chemistry, and in vitro pharmacology can be combined to exploit single amino acid sequence differences for the discovery of subtype-selective probes. Such compounds will help to better understand orexin receptor pharmacology and develop promising drug candidates.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2021

Kinetic proofreading of lipochitooligosaccharides determines signal activation of symbiotic plant receptors

Plant cell surface receptors perceive carbohydrate signaling molecules and hereby establish communication with surrounding microbes. Genetic studies have identified two different classes of lysin motif receptor kinases as gatekeepers that together trigger the symbiotic pathway in plants; however, no structural or functional data of the perception mechanisms switching these receptors from resting state into activation is known. In this study, we use structural biology, biochemical, and genetic approaches to demonstrate how the NFP/NFR5 class of lipochitooligosaccharide (LCO) receptors discriminate bacterial symbionts based on a kinetic proofreading mechanism that controls receptor activation and signaling specificity. We show that the LCO binding site can be engineered to support symbiotic functions, which greatly advance future opportunities for receptor engineering in legumes and nonlegumes.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2025

Ultracold cryogenic TEM with liquid helium and high stability

Cryogenic transmission electron microscopy has revolutionized structural biology and materials science. To image below liquid nitrogen temperatures, various liquid helium stages have been constructed but have proven to be complex and unstable, making high-resolution imaging challenging. This problem is even more pronounced in side-entry specimen holders common on modern transmission electron microscopes. Here, we introduce an ultracold liquid helium transmission electron microscope side-entry specimen holder, featuring continuous cryogen flow and vibration decoupling. This instrument is compatible with modern aberration-corrected microscopes and achieves sub-25 K base temperature, ±2 mK thermal stability over many hours, and atomic resolution—setting the stage for a new era of cryogenic electron microscopy.

42 ENGINEERING↗
DOE OSTI2026

Embedded EPICS server for PowerPMAC motion controllers

An embedded server layer of Experimental Physics and Industrial Control System (EPICS) for PowerPMAC motion controllers has been developed and deployed at two undulator beamlines of the National Institute of General Medical Sciences and the National Cancer Institute (GM/CA) Structural Biology Facility at the Advanced Photon Source (APS). This compact, open source solution makes the power and versatility of PowerPMAC motion controls directly accessible to distributed EPICS clients. At GM/CA the system controls about 200 servo and stepper motors — both encoded and unencoded — and multiple digital and analog I/O accessories. The server stack comprises two sublayers: a lower-level driver and database that communicates directly with PowerPMAC, and a facility-specific soft sublayer built on top. The paper describes installing EPICS on PowerPMAC, the implementation of both layers and client examples, including on-the-fly scanning.

EPICS↗