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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 217 records · Page 12
All sourcesNASA NTRSDOE OSTI
DOE OSTI2015

sRecovery Act: Geologic Characterization of the South Georgia Rift Basin for Source Proximal CO 2 Storage

This study focuses on evaluating the feasibility and suitability of using the Jurassic/Triassic (J/TR) sediments of the South Georgia Rift basin (SGR) for CO 2 storage in southern South Carolina and southern Georgia The SGR basin in South Carolina (SC), prior to this project, was one of the least understood rift basin along the east coast of the U.S. In the SC part of the basin there was only one well (Norris Lightsey #1) the penetrated into J/TR. Because of the scarcity of data, a scaled approach used to evaluate the feasibility of storing CO 2 in the SGR basin. In the SGR basin, 240 km (~149 mi) of 2-D seismic and 2.6 km2 3-D (1 mi2) seismic data was collected, process, and interpreted in SC. In southern Georgia 81.3 km (~50.5 mi) consisting of two 2-D seismic lines were acquired, process, and interpreted. Seismic analysis revealed that the SGR basin in SC has had a very complex structural history resulting the J/TR section being highly faulted. The seismic data is southern Georgia suggest SGR basin has not gone through a complex structural history as the study area in SC. The project drilled one characterization borehole (Rizer # 1) in SC. The Rizer #1 was drilled but due to geologic problems, the project team was only able to drill to 1890 meters (6200 feet) instead of the proposed final depth 2744 meters (9002 feet). The drilling goals outlined in the original scope of work were not met. The project was only able to obtain 18 meters (59 feet) of conventional core and 106 rotary sidewall cores. All the conventional core and sidewall cores were in sandstone. We were unable to core any potential igneous caprock. Petrographic analysis of the conventional core and sidewall cores determined that the average porosity of the sedimentary material was 3.4% and the average permeability was 0.065 millidarcy. Compaction and diagenetic studies of the samples determined there would not be any porosity or permeability at depth in SC. In Georgia there appears to be porosity in the J/TR section based on neutron log porosity values. The only zones in Rizer #1 that appear to be porous were fractured diabase units where saline formation water was flowing into the borehole. Two geocellular models were created for the SC and GA study area. Flow simulation modeling was performed on the SC data set. The injection simulation used the newly acquired basin data as well as the Petrel 3-D geologic model that included geologic structure. Due to the new basin findings as a result of the newly acquired data, during phase two of the modeling the diabase unit was used as reservoir and the sandstone units were used as caprock. Conclusion are: 1) the SGR basin is composed of numerous sub-basins, 2) this study only looked at portions of two sub-basins, 3) in SC, 30 million tonnes of CO 2 can be injected into the diabase units if the fracture network is continuous through the units, 4) due to the severity of the faulting there is no way of assuring the injected CO 2 will not migrate upward into the overlying Coastal Plain aquifers, 5) in Georgia there appears to porous zones in the J/TR sandstones, 6) as in SC there is faulting in the sub-basin and the seismic suggest the faulting extends upward into the Coastal Plain making that area not suitable for CO 2 sequestration, 7) the complex faulting observed at both study areas appear to be associated with transfer fault zones (Heffner 2013), if sub-basins in the Georgia portion of the SGR basin can be located that are far away from the transfer fault zones there is a strong possibility of sequestering CO 2 in these areas, and 9) the SGR basin covers area in three states and this project only studied two small areas so there is enormous potential for CO 2 sequestration in other portions the basin and further research needs to be done to find these areas.

58 GEOSCIENCES↗
DOE OSTI2022

Predicting Oxygen Off-Stoichiometry and Hydrogen Incorporation in Complex Perovskite Oxides

Chemically and structurally complex solid compounds, including those with significant off-stoichiometry, are rapidly extending new material functionality across a variety of applications. Accelerated development of these compounds requires accurate predictions of material defect properties including effective defect formation energies and equilibrium defect concentrations. Traditional first-principles approaches typically examine dilute defect concentrations and relatively ordered atomic structures to identify the lowest energy defect sites. These approaches are rarely suitable for describing the disorder present in these systems and its influence on defect formation, which can lead to unphysically large predictions for defect concentrations. Here, we demonstrate a new method to accurately predict the temperature and pressure dependence of oxygen vacancy concentrations and proton interstitial concentrations in complex oxides. This method extends standard dilute defect calculations to incorporate atomic and magnetic disorder, employs the ensemble descriptions of defect sites resulting in improved predictions of defect formation energies, and accounts for effects beyond the dilute defect limit. To demonstrate our method, we show that the predicted defect concentrations in perovskites used as ceramic fuel cell cathodes, including Ba0.5Sr0.5Fe0.8Zn0.2O3-d, Ba0.5Sr0.5Co0.8Fe0.2O3-d, and BaCo1-x-y-zFexZryYzO3-d, are in good agreement with experimental values, thereby opening the door for predictive design of complex oxides by these applications.

DFT↗
DOE OSTI2025

Protein-ligand binding affinity prediction using multi-instance learning with docking structures

Recent advances in 3D structure-based deep learning approaches demonstrate improved accuracy in predicting protein-ligand binding affinity in drug discovery. These methods complement physics-based computational modeling such as molecular docking for virtual high-throughput screening. Despite recent advances and improved predictive performance, most methods in this category primarily rely on utilizing co-crystal complex structures and experimentally measured binding affinities as both input and output data for model training. Nevertheless, co-crystal complex structures are not readily available and the inaccurate predicted structures from molecular docking can degrade the accuracy of the machine learning methods. We introduce a novel structure-based inference method utilizing multiple molecular docking poses for each complex entity. Our proposed method employs multi-instance learning with an attention network to predict binding affinity from a collection of docking poses. We validate our method using multiple datasets, including PDBbind and compounds targeting the main protease of SARS-CoV-2. The results demonstrate that our method leveraging docking poses is competitive with other state-of-the-art inference models that depend on co-crystal structures. This method offers binding affinity prediction without requiring co-crystal structures, thereby increasing its applicability to protein targets lacking such data.

97 MATHEMATICS AND COMPUTING↗
DOE OSTI2015

RNA quaternary structure and global symmetry

Many proteins associate into symmetric multisubunit complexes. Structural analyses suggested that, by contrast, virtually all RNAs with complex 3D structures function as asymmetric monomers. Recent crystal structures revealed that several biological RNAs exhibit global symmetry at the level of their tertiary and quaternary structures. Here we survey known examples of global RNA symmetry, including the true quaternary symmetry of the bacteriophage Φ29 prohead RNA (pRNA) and the internal pseudosymmetry of the single-chain flavin mononucleotide (FMN), glycine, and cyclic di-AMP (c-di-AMP) riboswitches. For these RNAs, we report global symmetry stabilizes the RNA fold, coordinates ligand–RNA interactions, and facilitates association with symmetric binding partners.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2021

Lightweight, strong, moldable wood via cell wall engineering as a sustainable structural material

Turning wood into honeycombs Wood is an attractive material for structural applications, but it usually works best as boards or sheets. Xiao et al . have developed a process for engineering hardwood that allows these sheets to be manipulated into complex structures (see the Perspective by Tajvidi and Gardner). The key is to manipulate the cell wall structure by shrinking and blasting open the fibers and vessels by drying and “water-shocking” them. This process creates a window wherein the wood can be manipulated without ripping or tearing. Honeycomb, corrugated, or other complex structures are locked in once the wood dries. —BG

Science & Technology - Other Topics↗
DOE OSTI2017

Selective Se-for-S substitution in Cs-bearing uranyl compounds

Phase formation in the mixed sulfate-selenate aqueous system of uranyl nitrate and cesium nitrate has been investigated. Two types of crystalline compounds have been obtained and characterized using a number of experimental (single crystal XRD, FTIR, SEM) and theoretical (information-based complexity calculations, topological analysis) techniques. No miscibility gaps have been observed for Cs{sub 2}[(UO{sub 2}){sub 2}(TO{sub 4}){sub 3}] (T= S, Se), which crystallizes in tetragonal system, P-42{sub 1}m, a =9.616(1)–9.856(2), c =8.105(1)–8.159(1) Å, V =749.6(2)–792.5(3) Å{sup 3}. Nine phases with variable amount of S and Se have been structurally characterized. The structures of the Cs{sub 2}[(UO{sub 2}){sub 2}(TO{sub 4}){sub 3}] (T= S, Se) compounds are based upon the [(UO{sub 2}){sub 2}(TO{sub 4}){sub 3}]{sup 2-} layers of corner-sharing uranyl pentagonal bipyramids and TO{sub 4} tetrahedra. The layers contain two types of tetrahedral sites: T1 (3-connected, i.e. having three O atoms shared by adjacent uranyl polyhedra) and T2 (4-connected). The Se-for-S substitution in tetrahedral sites is highly selective with smaller S{sup 6+} cation showing a strong preference for the more tightly bonded T2 site. Crystallization in the pure Se system starts with the formation of Cs{sub 2}[(UO{sub 2})(SeO{sub 4}){sub 2}(H{sub 2}O)](H{sub 2}O) crystals, its subsequent dissolution and formation of Cs{sub 2}[(UO{sub 2}){sub 2}(SeO{sub 4}){sub 3}]. The information-based structural complexity calculations for these two phases support the rule that more topologically complex structures form at the latest stages of crystallization. - Graphical abstract: Nine phases representing the Cs{sub 2}[(UO{sub 2}){sub 2}(TO{sub 4}){sub 3}] (T= S, Se) solid solution series with variable amount of S and Se have been prepared by isothermal evaporation from aqueous solutions and characterized using a number of experimental and theoretical techniques. No immiscibility is observed between the pure sulfate and selenate compounds. The Se-for-S substitution in tetrahedral sites is highly selective with smaller S{sup 6+} cation showing a strong preference for the more tightly bonded 4-connected site. - Highlights: • Single crystals of novel mixed sulfate-selenate uranyl oxysalts were prepared by evaporation method. • Topological analysis and information-based complexity calculations were used for structure description. • The selective Se-for-S substitution was observed. • Evolution of phase formation in the aqueous Cs{sup +}–UO{sub 2}{sup 2+}–SO{sub 4}{sup 2–}–SeO{sub 4}{sup 2–} system was analyzed.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2022

Disk Evolution Study through Imaging of Nearby Young Stars (DESTINYS): A Panchromatic View of DO Tau’s Complex Kilo-astronomical-unit Environment

While protoplanetary disks are often treated as isolated systems in planet formation models, observations increasingly suggest that vigorous interactions between Class II disks and their environments are not rare. DO Tau is a T Tauri star that has previously been hypothesized to have undergone a close encounter with the HV Tau system. As part of the DESTINYS ESO Large Programme, we present new Very Large Telescope (VLT)/SPHERE polarimetric observations of DO Tau and combine them with archival Hubble Space Telescope (HST) scattered-light images and Atacama Large Millimeter/submillimeter Array (ALMA) observations of CO isotopologues and CS to map a network of complex structures. The SPHERE and ALMA observations show that the circumstellar disk is connected to arms extending out to several hundred astronomical units. HST and ALMA also reveal stream-like structures northeast of DO Tau, some of which are at least several thousand astronomical units long. These streams appear not to be gravitationally bound to DO Tau, and comparisons with previous Herschel far-IR observations suggest that the streams are part of a bridge-like structure connecting DO Tau and HV Tau. We also detect a fainter redshifted counterpart to a previously known blueshifted CO outflow. While some of DO Tau's complex structures could be attributed to a recent disk–disk encounter, they might be explained alternatively by interactions with remnant material from the star formation process. These panchromatic observations of DO Tau highlight the need to contextualize the evolution of Class II disks by examining processes occurring over a wide range of size scales.

79 ASTRONOMY AND ASTROPHYSICS↗
DOE OSTI2018

Mechanistic View of hnRNPA2 Low-Complexity Domain Structure, Interactions, and Phase Separation Altered by Mutation and Arginine Methylation

hnRNPA2, a component of RNA-processing membraneless organelles, forms inclusions when mutatedin a syndrome characterized by the degeneration of neurons (bearing features of amyotrophic lateral sclerosis [ALS] and frontotemporal dementia), muscle,and bone. In this work we provide a unified structural view of hnRNPA2 self-assembly, aggregation, and interaction and the distinct effects of small chemical changes—disease mutations and arginine methylation—on these assemblies. The hnRNPA2 low-complexity (LC) domain is compact and intrinsically disordered as a monomer, retaining predominant disorder in a liquid-liquid phase-separated form. Disease mutations D290V and P298L induce aggregation by enhancing and extending, respectively, the aggregation-prone region. Co-aggregating in disease inclusions, hnRNPA2 LC directly interacts with and induces phase separation of TDP-43. Conversely, arginine methylation reduces hnRNPA2 phase separation, disrupting arginine-mediated contacts. These results highlight the mechanistic role of specific LC domain interactions and modifications conserved across many hnRNP family members but altered by aggregation-causing pathological mutations.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2017

Antibacterial Properties of Metallocenyl-7-ADCA Derivatives and Structure in Complex with CTX-M β -Lactamase

We report a series of six novel metallocenyl-7-ADCA (metallocenyl = ferrocenyl or ruthenocenyl; 7-ADCA = 7- aminodesacetoxycephalosporanic acid) conjugates were synthesized and their antibacterial properties evaluated by biochemical and microbiological assays. The ruthenocene derivatives showed a higher level of inhibition of DDcarboxypeptidase 64-575, a penicillin binding protein (PBP), than the ferrocene derivatives and the reference compound penicillin G. Protein X-ray crystallographic analysis revealed a covalent acyl–enzyme complex of a ruthenocenyl compound with CTX-M β-lactamase E166A mutant, corresponding to a similar complex with PBPs responsible for the bactericidal activities of these compounds. Most interestingly, an intact compound was captured at the crystal-packing interface, elucidating for the first time the structure of a metallocenyl β-lactam compound that previously eluded small-molecule crystallography. We propose that protein crystals, even from biologically unrelated molecules, can be utilized to determine structures of small molecules.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2025

VHH antibody loop guides design of a synthetic macrocyclic peptide that potently blocks influenza virus membrane fusion

Abstract Miniaturizing biologically complex structural motifs to produce synthetic functional mimetics holds significant promise for development of new therapeutic modalities. Here, we demonstrate a unique approach using the key binding loop of the single variable domain of a heavy chain (V H H) llama antibody as a starting point for peptide design. V H H antibodies of camelids and sharks generally have longer, but more ligand-efficient complementarity determining region 3 (CDR3) loops and are relatively stable structures. We harnessed these attributes as templates for design of a series of synthetic macrocyclic peptides. The designed peptides exhibit nanomolar binding to influenza hemagglutinin (HA) and heterosubtypic in vitro neutralization breadth against influenza A viruses by inhibiting the low pH mediated HA conformational changes that lead to membrane fusion. X-ray structures of peptide-HA complexes reveal high structural mimicry with the parent V H H antibody. One such macrocycle peptide candidate is promising for further development of broad protection against influenza A group 1 viruses.

Kadam, Rameshwar U.↗
DOE OSTI2014

Engineering yeast consortia for surface-display of complex cellulosome structures

As our society marches toward a more technologically advanced future, energy and environmental sustainability are some of the most challenging problems we face today. Biomass is one of the most abundant renewable-feedstock for sustainable production of biofuels. However, the main technological obstacle to more widespread uses of this resource is the lack of low-cost technologies to overcome the recalcitrant nature of the cellulosic structure, especially the hydrolysis step on highly ordered celluloses. In this proposal, we successfully engineered several efficient and inexpensive whole-cell biocatalysts in an effort to produce economically compatible and sustainable biofuels, namely cellulosic ethanol. Our approach was to display of a highly efficient cellulolytic enzyme complex, named cellulosome, on the surface of a historical ethanol producer Saccharomyces cerevisiae for the simultaneous and synergistic saccharification and fermentation of cellulose to ethanol. We first demonstrated the feasibility of assembling a mini-cellulosome by incubating E. coli lysates expressing three different cellulases. Resting cells displaying mini-cellulosomes produced 4-fold more ethanol from phosphoric acid-swollen cellulose (PASC) than cultures with only added enzymes. The flexibility to assemble the mini-cellulosome structure was further demonstrated using a synthetic yeast consortium through intracellular complementation. Direct ethanol production from PASC was demonstrated with resting cell cultures. To create a microorganism suitable for a more cost-effective process, called consolidated bioprocessing (CBP), a synthetic consortium capable of displaying mini-cellulosomes on the cell surface via intercellular complementation was created. To further improve the efficiency, a new adaptive strategy of employing anchoring and adaptor scaffoldins to amplify the number of enzymatic subunits was developed, resulting in the creation of an artificial tetravalent cellulosome on the yeast surface and a significant improvement in cellulosic ethanol production. Although this adaptive strategy is ideal for assembling more complex cellulosome for large-scale production of cellulosic ethanol, a substantially larger number of enzymes (up to 10 to 12) is needed to better mimic the natural cellulosome structures for practical usage of the technology.

09 BIOMASS FUELS↗
DOE OSTI2016

The interplay of covalency, hydrogen bonding, and dispersion leads to a long range chiral network: The example of 2-butanol

The assembly of complex structures in nature is driven by an interplay between several intermolecular interactions, from strong covalent bonds to weaker dispersion forces. Understanding and ultimately controlling the self-assembly of materials requires extensive study of how these forces drive local nanoscale interactions and how larger structures evolve. Surface-based self-assembly is particularly amenable to modeling and measuring these interactions in well-defined systems. This study focuses on 2-butanol, the simplest aliphatic chiral alcohol. 2-butanol has recently been shown to have interesting properties as a chiral modifier of surface chemistry; however, its mode of action is not fully understood and a microscopic understanding of the role non-covalent interactions play in its adsorption and assembly on surfaces is lacking. In order to probe its surface properties, we employed high-resolution scanning tunneling microscopy and density functional theory (DFT) simulations. We found a surprisingly rich degree of enantiospecific adsorption, association, chiral cluster growth and ultimately long range, highly ordered chiral templating. Firstly, the chiral molecules acquire a second chiral center when adsorbed to the surface via dative bonding of one of the oxygen atom lone pairs. This interaction is controlled via the molecule’s intrinsic chiral center leading to monomers of like chirality, at both chiral centers, adsorbed on the surface. The monomers then associate into tetramers via a cyclical network of hydrogen bonds with an opposite chirality at the oxygen atom. The evolution of these square units is surprising given that the underlying surface has a hexagonal symmetry. Our DFT calculations, however, reveal that the tetramers are stable entities that are able to associate with each other by weaker van der Waals interactions and tessellate in an extended square network. This network of homochiral square pores grows to cover the whole Au(111) surface. Our data reveal that the chirality of a simple alcohol can be transferred to its surface binding geometry, drive the directionality of hydrogen-bonded networks and ultimately extended structure. Furthermore, this study provides the first microscopic insight into the surface properties of this important chiral modifier and provides a well-defined system for studying the network’s enantioselective interaction with other molecules.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2019

Economic Optimization of the Modular Structure of Complex Objects

In the design of complex objects, modular principles are of great interest. That approach has both negative and positive consequences. It clearly affects the cost of acquiring the required stock of equipment and, in particular, the spare parts necessary for its maintenance. Optimization of the modular structure of industrial equipment may best be approached in economic terms. Smart information systems for the support of management decisions prove very useful. A structure is proposed for such a system. Examples of such optimization in the aviation industry are presented, and practical experience is noted.

42 ENGINEERING↗
DOE OSTI2023

Chemical structure and complex growth modes of magnesium silicate hydrate: Nanoparticle orientation, aggregation, and fusion

The extent of utilization of magnesium silicate hydrate (MSH) in construction is limited partly because of insufficient data ascertaining the kinetics of its precipitation. In this report MSH grown homogeneously or heterogeneously in the range of magnesium to silicon solution molar concentration ratios, [Mg]/[Si] = 0.5-1.5, and temperature = 25-80 °C was analyzed for its chemical structure and morphology. Infrared spectroscopy and geochemical modeling show that increasing the [Mg]/[Si] ratio results in less silicate polymerization in MSH. Atomic force microscopy reveals the presence of nanoparticles that aggregate and fuse to form films. Oriented attachment of nanoparticles and features indicative of enhanced crystallinity were observed at higher temperatures and longer reaction times. These data provide direct evidence for the persistence of hierarchical structures (i.e., nanoparticles forming 3D microparticles and 2D film layers) at the nanoscale to mesoscale. These findings offer insights into the precise chemical synthesis of MSH and its widespread use as a binder for construction purposes.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗