Search NASA⌕ Search

SEARCH · Search NASA

Results for “information structures”

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.

Quote a phrase for an exact phrase match. Source license links do not imply unrestricted reuse.

At least 145 records · Page 8
All sourcesNASA NTRSDOE OSTI
DOE OSTI2020

Cryo-EM Structures of Human Drosha and DGCR8 in Complex with Primary MicroRNA

Metazoan microRNAs require specificmaturation steps initiated by Microprocessor, comprising Drosha and DGCR8. Lack of structural information for the assembled complex has hindered an understanding of how Microprocessor recognizes primary microRNA transcripts (pri-miRNAs). In this paper we present a cryoelectron microscopy structure of human Microprocessor with a pri-miRNA docked in the active site, poised for cleavage. The basal junction is recognized by a four-way intramolecular junction in Drosha, triggered by the Belt and Wedge regions that clamp over the ssRNA. The belt is important for efficiency and accuracy of pri-miRNA processing. TwodsRBDs form a molecular ruler tomeasure the stem length between the twodsRNA-ssRNAjunctions. The specific organization of thedsRBDs near the apical junction is independent of Drosha core domains, as observed in a second structure in the partially docked state. Collectively, we derive a molecular model to explain how Microprocessor recognizes a pri-miRNA and accurately identifies the cleavage site.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2023

Aminobenzoic Acid Derivatives Obstruct Induced Fit in the Catalytic Center of the Ribosome

The Escherichia coli (E. coli) ribosome can incorporate a variety of non-l-α-amino acid monomers into polypeptide chains in vitro but with poor efficiency. Although these monomers span a diverse set of compounds, there exists no high-resolution structural information regarding their positioning within the catalytic center of the ribosome, the peptidyl transferase center (PTC). Thus, details regarding the mechanism of amide bond formation and the structural basis for differences and defects in incorporation efficiency remain unknown. Within a set of three aminobenzoic acid derivatives–3-aminopyridine-4-carboxylic acid (Apy), ortho-aminobenzoic acid (oABZ), and meta-aminobenzoic acid (mABZ)–the ribosome incorporates Apy into polypeptide chains with the highest efficiency, followed by oABZ and then mABZ, a trend that does not track with the nucleophilicity of the reactive amines. Here, we report high-resolution cryo-EM structures of the ribosome with each of these three aminobenzoic acid derivatives charged on tRNA bound in the aminoacyl-tRNA site (A-site). The structures reveal how the aromatic ring of each monomer sterically blocks the positioning of nucleotide U2506, thereby preventing rearrangement of nucleotide U2585 and the resulting induced fit in the PTC required for efficient amide bond formation. They also reveal disruptions to the bound water network that is believed to facilitate formation and breakdown of the tetrahedral intermediate. Together, the cryo-EM structures reported here provide a mechanistic rationale for differences in reactivity of aminobenzoic acid derivatives relative to l-α-amino acids and each other and identify stereochemical constraints on the size and geometry of non-monomers that can be accepted efficiently by wild-type ribosomes.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2024

TATB thermal decomposition: Expanding the molecular profile with cryo-focused pyrolysis GC-MS

Understanding the molecular composition of high explosives during thermal decomposition is vital for predicting the sensitivity, safety, and performance of explosive materials. The thermal decomposition of 1,3,5-triamino-2,4,6-trinitrobenzene (TATB) has been linked to the formation of furazans through a series of dehydration reactions of the NO2 and NH2 groups on the phenyl ring, along with breakdown into small molecules (≤120 amu). Molecular identification of compounds formed in this transformation of the furazans to light gases has been lacking. To address this, we have applied a pseudo-confined sampling system in a cryo-focused pyrolysis gas chromatography-mass spectrometry (pyGC-MS) system to molecularly identify these intermediates. By design, sublimation of TATB, which has complicated MS analyses of thermal degradation, was significantly reduced and additional compounds were identified with potential structural information. In addition to the known furazan compounds, one of these compounds forms from the loss of oxygen from benzo-trifurazan (F3) and produces an open ring structure that may be the first step in the formation of lower molecular weight furazan breakdown products. The loss of a nitro group from benzo-monofurazan (F1) was also discovered and implicates the formation of oxidizing NO2 gas in the thermal decomposition mechanism. So these findings are vital for understanding the proper heat flow from energetic materials on a molecular level, necessary when measuring enthalpy and developing decomposition models based on kinetic parameters.

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

RCSB Protein Data Bank: visualizing groups of experimentally determined PDB structures alongside computed structure models of proteins

Recent advances in Artificial Intelligence and Machine Learning (e.g., AlphaFold, RosettaFold, and ESMFold) enable prediction of three-dimensional (3D) protein structures from amino acid sequences alone at accuracies comparable to lower-resolution experimental methods. These tools have been employed to predict structures across entire proteomes and the results of large-scale metagenomic sequence studies, yielding an exponential increase in available biomolecular 3D structural information. Given the enormous volume of this newly computed biostructure data, there is an urgent need for robust tools to manage, search, cluster, and visualize large collections of structures. Equally important is the capability to efficiently summarize and visualize metadata, biological/biochemical annotations, and structural features, particularly when working with vast numbers of protein structures of both experimental origin from the Protein Data Bank (PDB) and computationally-predicted models. Moreover, researchers require advanced visualization techniques that support interactive exploration of multiple sequences and structural alignments. This paper introduces a suite of tools provided on the RCSB PDB research-focused web portal RCSB. org, tailor-made for efficient management, search, organization, and visualization of this burgeoning corpus of 3D macromolecular structure data.

3D visualization↗
DOE OSTI2022

Multiscale mechanical design of the lightweight, stiff, and damage-tolerant cuttlebone: A computational study

Cuttlebone, the endoskeleton of cuttlefish, offers an intriguing biological structural model for designing low-density cellular ceramics with high stiffness and damage tolerance. Cuttlebone is highly porous (porosity ~93%) and lightweight (density less than 20% of seawater), constructed mainly by brittle aragonite (95 wt%), but capable of sustaining hydrostatic water pressures over 20 atmospheres and exhibits energy absorption capability under compression comparable to many metallic foams (~4.4 kJ/kg). Here, in this work, we computationally investigate how such remarkable mechanical efficiency is enabled by the multiscale structure of cuttlebone. Using the common cuttlefish, Sepia Officinalis, as a model system, we first conducted high-resolution synchrotron micro-computed tomography (µ-CT) and quantified the cuttlebone's multiscale geometry, including the 3D asymmetric shape of individual walls, the wall assembly patterns, and the long-range structural gradient of walls across the entire cuttlebone (ca. 38 chambers). The acquired 3D structural information enables systematic finite-element simulations, which further reveal the multiscale mechanical design of cuttlebone: at the wall level, wall asymmetry provides optimized energy absorption while maintaining high structural stiffness; at the chamber level, variation of walls (number, pattern, and waviness amplitude) contributes to progressive damage; at the entire skeletal level, the gradient of chamber heights tailors the local mechanical anisotropy of the cuttlebone for reduced stress concentration. Our results provide integrated insights into understanding the cuttlebone's multiscale mechanical design and provide useful knowledge for the designs of lightweight cellular ceramics.

36 MATERIALS SCIENCE↗
DOE OSTI2026

Visualization of the surface distribution of photocatalytic activity at the anatase/rutile TiO2 interface using X-ray photoelectron emission microscopy

We applied X-ray photoelectron emission microscopy (XPEEM) to visualize the surface distribution of photocatalytic activity at the anatase/rutile (A/R) interface of titanium dioxide. Acetic acid was adsorbed on the surface, and its decomposition and desorption reactions under ultraviolet light irradiation were monitored by observing C 1s spectra, enabling direct observation of the spatial distribution of photocatalytic activity. Complementary crystal structure information was obtained using spatially resolved low-energy electron diffraction, low-energy electron microscopy, X-ray absorption spectroscopy, and micro-focused Raman spectroscopy. Comparison with these structural data allowed for the evaluation of the photocatalytic activity as a function of the distance from the A/R interface. The activity is enhanced in the vicinity of the interface and gradually decreases toward both the anatase and rutile regions. These results demonstrate that XPEEM is an effective technique for spatially resolved mapping of photocatalytic activity, which has\\r\\npreviously been inaccessible using conventional characterization techniques.

25 ENERGY STORAGE↗
DOE OSTI2024

Small, solubilized platinum nanocrystals consist of an ordered core surrounded by mobile surface atoms

In situ structures of Platinum (Pt) nanoparticles (NPs) can be determined with graphene liquid cell transmission electron microscopy. Atomic-scale three-dimensional structural information about their physiochemical properties in solution is critical for understanding their chemical function. We here analyze eight atomic-resolution maps of small (<3 nm) colloidal Pt NPs. Their structures are composed of an ordered crystalline core surrounded by surface atoms with comparatively high mobility. 3D reconstructions calculated from cumulative doses of 8500 and 17,000 electrons/pixel, respectively, are characterized in terms of loss of atomic densities and atomic displacements. Less than 5% of the total number of atoms are lost due to dissolution or knock-on damage in five of the structures analyzed, whereas 10–16% are lost in the remaining three. Less than 5% of the atomic positions are displaced due to the increased electron irradiation in all structures. The surface dynamics will play a critical role in the diverse catalytic function of Pt NPs and must be considered in efforts to model Pt NP function computationally.

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

Nuclear quantum effects on the quasiparticle properties of the chloride anion aqueous solution within the GW approximation

Photoelectron spectroscopy experiments in ionic solutions reveal important electronic structure information, in which the interaction between hydrated ions and water solvent can be inferred. Based on many-body perturbation theory with GW approximation, we theoretically compute the quasiparticle electronic structure of chloride anion solution, which is modeled by path-integral abinitio molecular dynamics simulation by taking account the nuclear quantum effects (NQEs). The electronic levels of hydrated anion as well as water are determined and compared with the recent experimental photoelectron spectra. It is found that NQEs improve the agreement between theoretical prediction and experiment because NQEs effectively weaken the hybridization of the between the Cl – anion and water. Furthermore, our study indicates that NQEs plays a small but non-negligible role in predicting the electronic structure of the aqueous solvation of ions of the Hofmeister series.

75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗
DOE OSTI2025

lllinois Storage Corridor CarbonSAFE Phase III: Pre-drilling Site Assessment: Prairie State Generating Company

The Illinois Storage Corridor project will drill a stratigraphic test well as part of the Illinois Storage Corridor CarbonSAFE Phase 3 project near the Prairie State Generating Company coal-fired power plant near Marissa, Illinois. The pre-drilling site evaluation has considered the primary target reservoirs, the Potosi Dolomite and St. Peter Sandstone, and primary seal, the Maquoketa Group. Data to be collected from the well include core, fluid samples, in situ well tests, geophysical logs intended to provide information on lithologic, geomechanical, and geophysical characteristics to determine the feasibility for the geologic sequestration of 50 million metric tons or more of injected carbon dioxide. The planned drilling site has been evaluated using available subsurface geologic data and analyses from the Illinois Basin. These data provide lithologic and structural information, shallow groundwater resource distribution, location of known nearby wellbores, and regional drilling characteristics. The data were used to generate geologic structure and isopach maps for the target reservoir and caprock strata and for prognosing the tops of major lithologic units to aid drilling and coring procedures. The regional analyses indicate that no known structural features are expected to negatively impact the target storage reservoir or caprock. No protected and sensitive areas, groundwater resources, or existing resource development are expected to be impacted by the proposed well drilling activities. The well is planned to be drilled to a total depth of approximately 5,600 feet (1,707 m) and terminate in the Precambrian. Cores (up to 5 intervals) will be collected from the Maquoketa Group, confining units above the St. Peter Sandstone, St. Peter Sandstone, confining units of the Potosi Dolomite and the Potosi Dolomite. Water samples will be attempted to be collected from the St. Peter Sandstone and Potosi Dolomite. Potential impact on drilling progress is a lost circulation zone in the Potosi Dolomite, which has been demonstrated to have intermittent cavernous porosity from karstification elsewhere in the Illinois Basin. This document also presents a preliminary coring and sampling program, proposed logging suite, and well testing program, all of which will be reviewed during drilling.

01 COAL, LIGNITE, AND PEAT↗
DOE OSTI2025

Standardized Residue Numbering and Secondary Structure Nomenclature in the Class D β-Lactamases

Over 1370 class D β-lactamases are currently known, and they pose a serious threat to the effective treatment of many infectious diseases, particularly in some pathogenic bacteria where evolving carbapenemase activity has been reported. Detailed understanding of their molecular biology, enzymology, and structural biology are critically important, but the lack of a standardized residue numbering scheme and inconsistent secondary structure annotation has made comparative analyses sometimes difficult and cumbersome. Compounding this, in the post-AlphaFold world where we currently find ourselves, an extraordinary wealth of detailed structural information on these enzymes is literally at our fingertips; therefore it is vitally important that a standard numbering system is in place to facilitate the accurate and straightforward analysis of their structures. In conclusion, here we present a residue numbering and secondary structure scheme for the class D enzymes based on the sequence and structure of OXA-48 and apply it to test targets to demonstrate the ease with which it can be used.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2022

Charge-ordered state satisfying the Anderson condition in LiRh 2 O 4 arising from local dimer order

Here we report on the charge-ordered structure of LiRh 2 O 4 arising below the metal-insulator transition at 170 K. Structural studies using synchrotron x rays have revealed that the charge-ordered states of Rh 3+ and Rh 4+ with dimerization are realized in the low-temperature phase below 170 K. Although the low-temperature ground state resembles that of CuIr 2 S 4 , a charge-ordering pattern satisfying the Anderson condition is realized in LiRh 2 O 4 . Based on structural information such as the short-range order of dimers appearing above the transition temperature and the weakening of the correlation between rhodium one-dimensional chains appearing in the crystal structure, we argue that the Coulomb interaction plays an important role in determining the charge-ordering patterns.

36 MATERIALS SCIENCE↗
DOE OSTI2025

CSGL: chemical synthesis graph learning for molecule representation

Abstract Motivation Molecule representation learning (MRL) translates molecules into a real vector space, serving as input to downstream tasks in biology, chemistry, and computer science. This article introduces a chemical synthesis graph learning (CSGL) framework, which enhances MRL by considering both the atomic structures of molecules and their roles in chemical reactions through a hierarchical graph representation. Specifically, molecules are first modeled based on their molecular graphs, which capture atomic-level structural information. They are then further refined using a chemical synthesis graph, where nodes represent reactant and product molecule sets, and edges encode chemical transformations between reactants and products (e.g. changes in molecular structures). CSGL optimizes molecular embeddings of reactant and product nodes in a fashion that ensures the embeddings conform to a chemical balance constraint. Results Experimental results show that our method CSGL achieves strong performance on a variety of tasks, including product prediction, reaction classification, and molecular property prediction. Availability and implementation https://github.com/li-2023/CSGL.

Biochemistry & Molecular Biology↗
DOE OSTI2024

Strong-Field Bloch Electron Interferometry for Band-Structure Retrieval

When Bloch electrons in a solid are exposed to a strong optical field, they are coherently driven in their respective bands where they acquire a quantum phase as the imprint of the band shape. If an electron approaches an avoided crossing formed by two bands, it may be split by undergoing a Landau-Zener transition. We here employ subsequent Landau-Zener transitions to realize strong-field Bloch electron interferometry (SFBEI), allowing us to reveal band structure information. In particular, we measure the Fermi velocity (band slope) of graphene in the vicinity of the K points as 1.07±0.04 nm fs –1 . As a result, we expect SFBEI for band structure retrieval to apply to a wide range of material systems and experimental conditions, making it suitable for studying transient changes in band structure with femtosecond temporal resolution at ambient conditions.

75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗
DOE OSTI2020

Structure of a paramyxovirus polymerase complex reveals a unique methyltransferase-CTD conformation

Paramyxoviruses are enveloped, nonsegmented, negative-strand RNA viruses that cause a wide spectrum of human and animal diseases. The viral genome, packaged by the nucleoprotein (N), serves as a template for the polymerase complex, composed of the large protein (L) and the homo-tetrameric phosphoprotein (P). The ~250-kDa L possesses all enzymatic activities necessary for its function but requires P in vivo. Structural information is available for individual P domains from different paramyxoviruses, but how P interacts with L and how that affects the activity of L is largely unknown due to the lack of high-resolution structures of this complex in this viral family. In this study we determined the structure of the L–P complex from parainfluenza virus 5 (PIV5) at 4.3-Å resolution using cryoelectron microscopy, as well as the oligomerization domain (OD) of P at 1.4-Å resolution using X-ray crystallography. P-OD associates with the RNA-dependent RNA polymerase domain of L and protrudes away from it, while the X domain of one chain of P is bound near the L nucleotide entry site. The methyltransferase (MTase) domain and the C-terminal domain (CTD) of L adopt a unique conformation, positioning the MTase active site immediately above the poly-ribonucleotidyltransferase domain and near the likely exit site for the product RNA 5' end. Our study reveals a potential mechanism that mononegavirus polymerases may employ to switch between transcription and genome replication. This knowledge will assist in the design and development of antivirals against paramyxoviruses.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2021

Advanced Energy Approaches for Mixed-Use Developments in the Front Range Urban Corridor

The primary objective of the document is to present example technical approaches and strategies that planners and developers can reference for all-electric mixed-use developments in the Rocky Mountain Front Range urban corridor that are considering advanced energy performance goals such as high levels of energy efficiency and renewable integration. The strategies are tailored toward the vision for a zero energy, all-electric, district thermal system-connected starter district. In this example, on-site solar generation is emphasized as a strategy that can be combined with electrical and thermal energy storage for enhanced community resilience and demand flexibility. Opportunities for utilizing or adapting these strategies include: sharing with vertical developers for potential integration of strategies into vertical design guidelines; incorporation into Owner Project Requirements (OPRs); providing example strategies to design teams as a starting point for design; informing structure of agenda for a building design charrette; comparing building designs to example strategies at various points in the design process to evaluate design progression. While the technical strategies outlined in this document can help inform the development of guidelines for projects in the Front Range urban corridor, this document does not set requirements for any rating, certification, program, or policy.

32 ENERGY CONSERVATION, CONSUMPTION, AND UTILIZATI↗
DOE OSTI2024

Quenching of the quantum p -strength in light exotic nuclei

One-nucleon spectroscopic overlaps, their strength or spectroscopic factors (SFs), and nucleon removal cross sections for light nuclei in the mass range A≤12 were evaluated using the fully correlated Quantum Monte Carlo (QMC) wave functions (WFs). Harder (AV18+UX) and softer (NV2+3) bare interactions were used providing consistent results. The SFs were also taken from simple Shell Model (SM) calculations. This structure information was incorporated in the standard three-body Faddeev/Alt-Grassberger-Sandhas reaction formalism to evaluate the (p,pN) cross sections. The results further our understanding of the quenching of the quantum p-shell strength obtained from structure and reactions. We have found the ratios of the total QMC sums of SFs to the SM ones to be uniform and ∼ 3/4. The corresponding ratios of the sums Below Particle Threshold (BPT) of SFs, as well as of total cross sections, deviate strikingly from the uniform trend in some special cases. We find these ratios to be close to unit for 9 Li → 8 Li + n and 9 C → 8 B + p. In contrast, they are strongly reduced for 11 C → 10 C + n and 11 B → 10 Be + p mirror transitions, resulting from the quenching of the strength for low-lying 2 + final state transitions. The QMC theoretical cross section BPT for 11 C(p,pn) is about two times smaller than the experimental data.

(p,pN) reactions↗
DOE OSTI2020

Excited nucleon spectrum and structure studies with CLAS and CLAS12

The study of the spectrum and structure of excited nucleon states employing the electroproduction of exclusive reactions is an important avenue for exploring the nature of the non-perturbative strong interaction. The CLAS detector in Hall B has provided the dominant part of the available world data on most relevant meson electroproduction channels off the nucleon in the resonance region for Q2 up to 5 GeV2. Analyses of CLAS data for the exclusive channels πN, ηN, and π+π-p on a proton target have provided the only results available on the Q2 evolution of the electro-excitation amplitudes for the transitions from the initial photon-proton to the final N* states in the mass range up to W =1.8 GeV. These electrocouplings allow for exploration of the internal structure of the produced excited nucleon states. This work has made it clear that consistent results from independent analyses of several exclusive channels with different resonance hadronic decay parameters and non-resonant backgrounds but the same N* electro-excitation amplitudes, is essential to have confidence in the extracted results. Starting in early 2018, a program to study the spectrum and structure of N* states in various exclusive electroproduction channels using the new CLAS12 spectrometer commenced. These studies will probe the structure of N* states in the mass range up to W =3 GeV and for Q2 as low as 0.05 GeV2 and as high as 10-12 GeV2, thus providing a means to access N* structure information spanning a broad range of distance scales. Quasi-real photoproduction studies are also planned to search for additional N* states, the so-called hybrid baryons, for which the glue serves as an active structural component. In this talk the N* programs from both CLAS and CLAS12 will be reviewed.

Carman, D. S.↗