Search NASA⌕ Search

SEARCH · Search NASA

Results for “Structure activity relationship”

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 343 records · Page 19
All sourcesNASA NTRSDOE OSTI
NASA NTRS1971

Recognition on space photographs of structural elements of Baja California

Gemini and Apollo photographs provide illustrations of known structural features of the peninsula and some structures not recognized previously. An apparent transform relationship between strike-slip and normal faulting is illustrated by the overlapping vertical photographs of northern Baja California. The active Agua Blanca right-lateral strike-slip fault trends east-southeastward to end at the north end of the Valle San Felipe and Valle Chico. The uplands of the high Sierra San Pedro Martir are a low-relief surface deformed by young faults, monoclines, and warps, which mostly produce west-facing steps and slopes; the topography is basically structural. The Sierra Cucapas of northeasternmost Baja California and the Colorado River delta of northwesternmost Sonora are broken by northwest-trending strike-slip faults. A strike-slip fault is inferred to trend northward obliquely from near Cabo San Lucas to La Paz, thence offshore until it comes ashore again as the Bahia Concepcion strike-slip fault.

Hamilton, W.↗
DOE OSTI2025

Structural, functional, and regulatory evaluation of a cysteine post-translationally modified Gcn5-related N -acetyltransferase

Polyamines within the cell are tightly regulated by spermidine/spermine N-acetyltransferase (SSAT) enzymes. While several SSATs have been investigated in different bacterial species, there is still a significant gap in knowledge about which proteins are functional SSATs in many organisms. For example, while it is known that Pseudomonas aeruginosa synthesizes the polyamine spermidine, the SSAT that acetylates this molecule and its importance in regulating intracellular polyamines remains unknown. We previously identified a candidate Gcn5-related N-acetyltransferase (GNAT) protein from P. aeruginosa (PA2271) that could fulfill this role since it acetylates spermidine, but no further studies were conducted. Here, we explored the structure/function relationship of the PA2271 protein by determining its X-ray crystal structure and performing enzyme kinetics assays. We also identified active site residues that are essential for catalysis and substrate binding. As the study progressed, we encountered results that led us to explore the importance of four cysteine residues on enzyme activity and disulfide bond formation or modification of cysteine residues. We found these cysteine residues in PA2271 are important for protein solubility and activity, and there is an interrelationship between cysteine residues that contribute to these effects. Furthermore, we also found disulfide bonds could form between C 121 and C 165 and speculate that these residues may contribute to redox regulation of PA2271 protein activity.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2020

Machine learning uncovers independently regulated modules in the Bacillus subtilis transcriptome

The transcriptional regulatory network (TRN) of Bacillus subtilis coordinates cellular functions of fundamental interest, including metabolism, biofilm formation, and sporulation. Here, we use unsupervised machine learning to modularize the transcriptome and quantitatively describe regulatory activity under diverse conditions, creating an unbiased summary of gene expression. We obtain 83 independently modulated gene sets that explain most of the variance in expression and demonstrate that 76% of them represent the effects of known regulators. The TRN structure and its condition-dependent activity uncover putative or recently discovered roles for at least five regulons, such as a relationship between histidine utilization and quorum sensing. The TRN also facilitates quantification of population-level sporulation states. As this TRN covers the majority of the transcriptome and concisely characterizes the global expression state, it could inform research on nearly every aspect of transcriptional regulation in B. subtilis.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2024

An RNA aptamer exploits exosite-dependent allostery to achieve specific inhibition of coagulation factor IXa

Hemostasis relies on a reaction network of serine proteases and their cofactors to form a blood clot. Coagulation factor IXa (protease) plays an essential role in hemostasis as evident from the bleeding disease associated with its absence. RNA aptamers specifically targeting individual coagulation factors have potential as anticoagulants and as probes of the relationship between structure and function. Here, we report X-ray structures of human factor IXa without a ligand bound to the active site either in the apo-form or in complex with an inhibitory aptamer specific for factor IXa. The aptamer binds to an exosite in the catalytic domain and allosterically distorts the active site. Our studies reveal a conformational ensemble of IXa states, wherein large movements of Trp 215 near the active site drive functional transitions between the closed (aptamer-bound), latent (apo), and open (substrate-bound) states. The latent state of the apo-enzyme may bear on the uniquely poor catalytic activity of IXa compared to other coagulation proteases. The exosite, to which the aptamer binds, has been implicated in binding VIIIa and heparin, both of which regulate IXa function. Our findings reveal the importance of exosite-driven allosteric modulation of IXa function and new strategies to rebalance hemostasis for therapeutic gain.

Science & Technology - Other Topics↗
NASA NTRS1989

Influence of solar activity on middle atmosphere associated with phases of equatorial quasi-biennial oscillation

Earlier studies on the influence of solar activity variations within a 11-year solar cycle on temperature changes in the middle atmosphere revealed that while the temperature in the mesosphere showed strong responses to changes in solar activity, the stratosphere remained almost unaffected. Recent studies showed that when the temperature data were grouped into east or west phase of the equatorial quasi-biennial oscillation (QBO) in stratospheric zonal wind, significant relationships of temperature in the lower stratosphere and troposphere could be obtained with 10.7 cm solar radio flux. Positive correlations in high latitude regions and negative correlations in mid-latitude and tropical regions were obtained during winter when the QBO was in its west phase. During the east phase, converse relationships were indicated. These results inspired this study on the response of solar activity in 11-year cycle on the temperature structure of the middle atmosphere in the two phases of equatorial QBO of zonal wind at 50 mb, in tropics, mid-latitude and antarctic regions.

Mohanakumar, K.↗
DOE OSTI2020

Active Learning Accelerated Discovery of Stable Iridium Oxide Polymorphs for the Oxygen Evolution Reaction

The discovery of high-performing and stable materials for sustainable energy applications is a pressing goal in catalysis and materials science. Understanding the relationship between a material’s structure and functionality is an important step in the process, such that viable polymorphs for a given chemical composition need to be identified. Machine-learning-based surrogate models have the potential to accelerate the search for polymorphs that target specific applications. Herein, we report a readily generalizable active-learning (AL) accelerated algorithm for identification of electrochemically stable iridium oxide polymorphs of IrO 2 and IrO 3 . The search is coupled to a subsequent analysis of the electrochemical stability of the discovered structures for the acidic oxygen evolution reaction (OER). Structural candidates are generated by identifying all 956 structurally unique AB2 and AB3 prototypes in existing materials databases (more than 38000). Next, using an active learning approach, we find 196 IrO 2 polymorphs within the thermodynamic amorphous synthesizability limit and reaffirm the global stability of the rutile structure. We find 75 synthesizable IrO 3 polymorphs and report a previously unknown FeF 3 -type structure as the most stable, termed α-IrO 3 . To test the algorithms performance, we compare to a random search of the candidate space and report at least a 2-fold increase in the rate of discovery. Additionally, the AL approach can acquire the most stable polymorphs of IrO 2 and IrO 3 with fewer than 30 density functional theory optimizations. Analysis of the structural properties of the discovered polymorphs reveals that octahedral local coordination environments are preferred for nearly all low-energy structures. Subsequent Pourbaix Ir–H 2 O analysis shows that α-IrO3 is the globally stable solid phase under acidic OER conditions and supersedes the stability of rutile IrO 2 . Calculation of theoretical OER surface activities reveal ideal weaker binding of the OER intermediates on α-IrO 3 than on any other considered iridium oxide. We emphasize that the proposed AL algorithm can be easily generalized to search for any binary metal oxide structure with a defined stoichiometry.

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

Generalized Brønsted‐Evans‐Polanyi Relationships for Reactions on Metal Surfaces from Machine Learning

Abstract Brønsted‐Evans‐Polanyi (BEP) relationships, i. e., a linear scaling between reaction and activation energies, lie at the core of computational design of heterogeneous catalysts. However, BEPs are not general and often require reparameterization for each class of reactions. Here we construct generalized BEPs (gBEPs), which can predict activation energies for a diverse dataset of reactions of C, O, N and H containing molecules on metal surfaces. In a first step we develop a set of descriptors based on scaling relationships that can capture the change in chemical identity of reactants during the reaction. Subsequently, we use the reaction energy, these descriptors and a single descriptor for the surface structure to parameterize machine learning based regression approaches for the prediction of activation energies. The best approach we developed shows a Mean Absolute Error (MAE) of 0.11 eV for the training set (80 % of the data set) and 0.23 eV for the test set (20 % of the data set). The methodology presented here allows to calculate activation energies within fractions of seconds on a typical personal computer and due to its generality, accuracy and simplicity in application it might prove to be useful in transition metal catalyst design.

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

Adaptive continuity-preserving simplification of street networks

Street network data is widely used to study human-based activities and urban structure. Often, these data are geared towards transportation applications, which require highly granular, directed graphs that capture the complex relationships of potential traffic patterns. While this level of network detail is critical for certain fine-grained mobility models, it represents a hindrance for studies concerned with the morphology of the street network. For the latter case, street network simplification — the process of converting a highly granular input network into its most simple morphological form — is a necessary, but highly tedious preprocessing step, especially when conducted manually. In this manuscript, we develop and present a novel adaptive algorithm for simplifying street networks that is both fully automated and able to mimic results obtained through a manual simplification routine. The algorithm — available in the neatnet Python package — outperforms current state-of-the-art procedures when comparing those methods to manually, human-simplified data, while preserving network continuity.

Python↗
DOE OSTI2021

Sugar phosphate activation of the stress sensor eIF2B

The multi-subunit translation initiation factor eIF2B is a control node for protein synthesis. eIF2B activity is canonically modulated through stress-responsive phosphorylation of its substrate eIF2. The eIF2B regulatory subcomplex is evolutionarily related to sugar-metabolizing enzymes, but the biological relevance of this relationship was unknown. To identify natural ligands that might regulate eIF2B, we conduct unbiased binding- and activity-based screens followed by structural studies. We find that sugar phosphates occupy the ancestral catalytic site in the eIF2Bα subunit, promote eIF2B holoenzyme formation and enhance enzymatic activity towards eIF2. A mutant in the eIF2Bα ligand pocket that causes Vanishing White Matter disease fails to engage and is not stimulated by sugar phosphates. These data underscore the importance of allosteric metabolite modulation for proper eIF2B function. We propose that eIF2B evolved to couple nutrient status via sugar phosphate sensing with the rate of protein synthesis, one of the most energetically costly cellular processes.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2021

QLiG: Query Like a Graph For Subgraph Matching

A graph is a natural and flexible modeling approach to represent entities and relationships between them in real-world. A Knowledge Graphs (KG) is a specialized graph with formal and structured representation of facts, relationships, annotated with semantic descriptions. Subgraph matching is one of the fundamental graph problems to identify relationships, interactions and activities of interest within a large graph. A query specification is a collection of abstract components, operations, and constraints to express a pattern. The specification can be implemented in different ways based on underlying data model. Various graph query specifications have been developed over the years and have led to the development of different open-sourced and vendor-specific query languages. Such specification are modeled as an extension of relational algebra used to develop relational query languages such as SQL. Such relational concepts do not inherently support graph queries. There is a need to represent graph queries in terms on graph-based components to expedite query construction by non-database experts. We present a graph-based query approach QLiG (pronounced cleeg), to perform subgraph matching in Labeled Property Graph. We present the query specifications, salient features, and a use case to show functional examples.

Purohit, Sumit↗
DOE OSTI2021

Molecular Dynamics Simulations of a Catalytic Multivalent Peptide–Nanoparticle Complex

Molecular modeling of a supramolecular catalytic system is conducted resulting from the assembling between a small peptide and the surface of cationic self-assembled monolayers on gold nanoparticles, through a multiscale iterative approach including atomistic force field development, flexible docking with Brownian Dynamics and µs-long Molecular Dynamics simulations. Self-assembly is a prerequisite for the catalysis, since the catalytic peptides do not display any activity in the absence of the gold nanocluster. Atomistic simulations reveal details of the association dynamics as regulated by defined conformational changes of the peptide due to peptide length and sequence. Our results show the importance of a rational design of the peptide to enhance the catalytic activity of peptide–nanoparticle conjugates and present a viable computational approach toward the design of enzyme mimics having a complex structure–function relationship, for technological and nanomedical applications.

59 BASIC BIOLOGICAL SCIENCES↗
NASA NTRS1985

Shock effects on hydrous minerals and implications for carbonaceous meteorites

The effect of shock loading over the pressure range of 29-59 GPa on the shock-recovered specimens of antigorite serpentine, Mg3Si2O5(OH)4, were investigated employing infrared (IR) spectroscopy, thermogravimetric analysis, and optical and scanning electron microscopy. With increasing shock pressure, there was an increase in H2O IR absorption peaks at the expense of OH peaks, while the changes in SiO bond vibration modes were identical to those seen for other, nonhydrous minerals. Thermogravimetric results on vented assembly samples showed linear relationships between the shock pressure and both the length of dehydration interval and the effective activation energy for releasing post-shock structural water. Optical and scanning electron microscopy revealed gas bubbles, which appeared to be injected into zones of partial melting, and vesicular dark veins distributed throughout the shocked samples. It is suggested that shock loading of hydrous minerals would release and redistribute free water in the regoliths of carbonaceous chondrite parent bodies, giving rise to observed hydrous alterations.

Lange, M. A.↗
NASA NTRS2000

Extragalactic Radio Jets and Intergalactic Medium 2

During the mid 1990s, the ROSAT satellite provided the highest resolution X-ray imaging, with useful X-ray spectroscopy, and excellent sensitivity. ROSAT"s PSPC and HRI instruments gave us our first high-quality data on the AGN phenomenon in nearby galaxies - the central theme of this research project. Initially this project concentrated on separating the AGN-related component of the X-ray emission from thermal radiation from the surrounding atmospheres in radio galaxies. There was ample reason to believe that this separation would be possible, although earlier work had taken the view that the X-ray emission from radio galaxies is either wholly AGN-related (and hence of sub-arcsec scale), or wholly from the galaxy and cluster atmospheres (and hence of scales - 10 arcsec or more in the low-redshift radio galaxies that we chose to study). First with the PSPC, and then with the HRI, we proved that a wide range of AGN core X ray emissivities could be found, and that the generic radio galaxy produces both AGN-related and atmosphere-related X-radiation. We demonstrated that there is a close relationship between the core X-ray power and the core radio power, and found instances in which the hot atmospheres of the galaxies must be participating in cooling flows, and other cases where those atmospheres are relatively stable. In some cases, there is a clear active relationship between the extended radio emission and the X-ray atmospheres: thus in NGC 326, we interpret the distorted radio structure as evidence of buoyancy as the radio plasma rises through the cluster atmosphere. In 3C 449, we can see that the radio plasma is displacing the X-ray emitting gas. In a further case (NGC 1265), we hoped that the motion of a radio galaxy through a cluster atmosphere would be apparent though the wake that it might establish - unfortunately, other structure in the atmosphere of the Perseus cluster tends to dominate our X-ray image, and no useful limits could be placed on the strength of the wake. In the light of so-called "unified" models of AGN, it is expected that the low-power radio galaxies studied under these programmes are the unbeamed counterparts of BL Lac objects. Accordingly, we predicted that BL Lac objects, as a class, should show X-ray halos from atmospheres similar to those associated with radio galaxies. The difficulty with studying this is that BL Lac objects tend to be X-ray bright, and the halos then vanish under the wings of the point response function. We found a BL Lac with less of a dynamic range problem, mapped it with the ROSAT HRI, and duly found an atmosphere (Hardcastle et al. 1999). Unfortunately for unification models, this atmosphere is exceptionally dense, so that it must be participating in an intense cooling flow. The implications of this for unification models are far from clear, and further work is under way.

Birkinshaw, Mark↗
NASA NTRS2021

Interaction of Saturn’s Hexagon with Convective Storms

In March 2020 a convective storm erupted at planetographic latitude 76°N in the southern flank of Saturn’s long-lived hexagonal wave. The storm reached a zonal size of 4,500 km and developed a tail extending zonally 33,000 km. Two new short-lived storms erupted in May in the hexagon edge. These storms formed after the convective storms that took place in 2018 in nearby latitudes. There were no noticeable changes in the zonal profile of Saturn's polar winds in 2018-2020. Measurements of the longitude position of the vertices of the hexagon throughout this period yield a value for its period of rotation equal to that of System III of radio-rotation measured at the time of Voyagers. We report changes in the hexagon clouds related to the activity of the storms. Our study reinforces the idea that Saturn’s hexagon is a well rooted structure with a possible direct relationship with the bulk rotation of the planet.

Convective storms↗
DOE OSTI2021

Effects of Ink Formulation on Construction of Catalyst Layers for High-Performance Polymer Electrolyte Membrane Fuel Cells

Rational design of catalyst layers in a membrane electrode assembly (MEA) is crucial for achieving high-performance polymer electrolyte membrane fuel cells. Establishing a clear understanding of the property (catalyst ink)–structure (catalyst layer)–performance (MEA) relationship lays the foundation for this rational design. Here, a synergistic approach was taken to correlate the ink formulation, the microstructure of catalyst layers, and the resulting MEA performance to establish such a property–structure–performance relationship. The solvent composition (n-PA/H 2 O mixtures) demonstrated a strong influence on the performance of the MEA fabricated with an 830-EW (Aquivion) ionomer, especially polarization losses of cell activation and mass transport. The performance differences were studied in terms of how the solvent composition affects the catalyst/ionomer interface, ionomer network, and pore structure of the resulting catalyst layers. The ionomer aggregates mainly covered the surface of catalyst aggregates acting as oxygen reduction reaction active sites, and the aggregate sizes of the ionomer and catalyst (revealed by ultrasmall angle X-ray scattering and cryo-transmission electron microscopy) were dictated by tuning the solvent composition, which in turn determined the catalyst/ionomer interface (available active sites). In n-PA/H 2 O mixtures with 50~90 wt % H 2 O, the catalyst agglomerates could be effectively broken up into small aggregates, leading to enhanced kinetic activities. The boiling point of the mixed solvents determined the pore structure of ultimate catalyst layers, as evidenced by mercury porosimetry and scanning electron microscopy. For mixed solvents with a higher boiling point, the catalyst–ionomer aggregates in the ink tend to agglomerate during the solvent evaporation process and finally form larger catalyst–ionomer aggregates in the ultimate catalyst layer, resulting in more secondary pores and thus lower mass transport resistance. Both the enlarged catalyst/ionomer interface and appropriate pore structure were achieved with the catalyst layer fabricated from an n-PA/H 2 O mixture with 90 wt % H 2 O, leading to the best MEA performance.

25 ENERGY STORAGE↗
NASA NTRS1989

Rheologically interesting polysaccharides from yeasts

We have examined the relationships between primary, secondary, and tertiary structures of polysaccharides exhibiting the rheological property of friction (drag) reduction in turbulent flows. We found an example of an exopolysaccharide from the yeast Cryptococcus laurentii that possessed high molecular weight but exhibited lower than expected drag reducing activity. Earlier correlations by Hoyt showing that beta 1 --> 3, beta 2 --> 4, and alpha 1 --> 3 linkages in polysaccharides favored drag reduction were expanded to include correlations to secondary structure. The effect of sidechains in a series of gellan gums was shown to be related to sidechain length and position. Disruption of secondary structure in drag reducing polysaccharides reduced drag reducing activity for some but not all exopolysaccharides. The polymer from C. laurentii was shown to be more stable than xanthan gum and other exopolysaccharides under the most vigorous of denaturing conditions. We also showed a direct relationship between extensional viscosity measurements and the drag reducing coefficient for four exopolysaccharides.

Friction↗
DOE OSTI2025

Operando TEM study of a working copper catalyst during ethylene oxidation

Active catalysts are typically metastable, and their surface state depends on the gas-phase chemical potential and reaction kinetics. To gain relevant insights into structure-performance relationships, it is essential to investigate catalysts under their operational conditions. Here, we use operando TEM combining real-time observations with online mass spectrometry (MS) to study a Cu catalyst during ethylene oxidation. We identify three distinct regimes characterized by varying structures and states that show different selectivities with temperature, and elucidate the reaction pathways with the aid of theoretical calculations. Our findings reveal that quasi-static Cu 2 O at low temperatures is selective towards ethylene oxide (EO) and acetaldehyde (AcH) via an oxometallacycle (OMC) pathway. In the dynamic Cu 0 /Cu 2 O oscillation regime at medium temperatures, partially reduced and strained oxides decrease the activation energies associated with partial oxidation. At high temperatures, the catalyst is predominantly Cu 0 , partially covered by a monolayer Cu 2 O. While Cu 0 is extremely efficient in dehydrogenation and eventual combustion, the monolayer oxide favors direct EO formation. These results challenge conclusions drawn from ultra-high vacuum studies that suggested metallic copper would be a selective epoxidation catalyst and highlight the need for operando study under realistic conditions.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗