Search NASA⌕ Search

SEARCH · Search NASA

Results for “Active interactions”

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 73 records · Page 4
All sourcesNASA NTRSDOE OSTI
DOE OSTI2025

Host cell and viral protease targets of human SERPINs identified by in silico docking

Serine protease inhibitors (SERPINs) are involved in various physiological processes and diseases, such as inflammation, cancer metastasis, and neurodegeneration. Their role in viral infections is poorly understood, as their expression patterns during infection and the range of proteases they target have yet to be fully characterized. Here, we show widespread expression of human SERPINs in response to respiratory virus infections, both in bronchioalveolar lavages from COVID-19 patients and in polarized human airway epithelial cultures. Using in silico docking of 10 SERPINs to 48 host proteases, we confirm known targets and predict new interactions. Protease activity assays validated selected interactions, confirming the newly predicted host targets for PAI-1 (SERPINE1) and PAI-2 (SERPINB2). PAI-1 inhibits cathepsin L, essential for SARS-CoV-2 maturation, and suppresses multi-cycle replication of both ancestral SARS-CoV-2 WA-1 and its variant Omicron BA.1. In addition, we identify PAI-2 as an antiviral SERPIN that reduces infectivity of human adenovirus 5 by directly inhibiting the adenoviral protease. Our study leverages in silico docking using full-length 3D protein structures to uncover new SERPIN targets, offering a range of candidate targets for therapeutic interventions.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2020

CASSCF with Extremely Large Active Spaces Using the Adaptive Sampling Configuration Interaction Method

The complete active space self-consistent field (CASSCF) method is the principal approach employed for studying strongly correlated systems. However, exact CASSCF can only be performed on small active spaces of ~20 electrons in ~20 orbitals due to exponential growth in the computational cost. Here, we show that employing the Adaptive Sampling Configuration Interaction (ASCI) method as an approximate Full CI solver in the active space allows CASSCF-like calculations within chemical accuracy (<1 kcal/mol for relative energies) in active spaces with more than ~50 active electrons in ~50 active orbitals, significantly increasing the sizes of systems amenable to accurate multiconfigurational treatment. The main challenge with using any selected CI-based approximate CASSCF is the orbital optimization problem; they tend to exhibit large numbers of local minima in orbital space due to their lack of invariance to active–active rotations (in addition to the local minima that exist in exact CASSCF). We highlight methods that can avoid spurious local extrema as a practical solution to the orbital optimization problem. We employ ASCI-SCF to demonstrate a lack of polyradical character in moderately sized periacenes with up to 52 correlated electrons and compare against heat-bath CI on an iron porphyrin system with more than 40 correlated electrons.

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

Measurement of the Triple-Differential Cross Section of Muon Neutrino Charged Current Interactions with Low Hadronic Activity in the NO$\nu$A Near Detector

This dissertation describes the analysis and measurement of the triple-differential cross-section of the $\nu_\mu CC$ interaction with Low Hadronic Activity (maximum kinetic energy of 250 MeV for protons and 175 MeV for pions) in the NOvA Near Detector. This cross-section is reported in bins of Muon Kinematics and available hadronic energy. The data corresponds to an accumulated $14.2\times10^{20}$ protons-on-target (POT) in the neutrino mode of the NuMI beam, with a narrow band of neutrino energies peaked at 1.8 GeV. The analysis provides a sample of neutrino–nucleus interactions with an enhanced fraction of quasi-elastic (QE) and two-particle-two-hole (2p2h) interactions and a suppression of resonant pion production (RES) and deep inelastic scattering (DIS) interactions. This enhancement of QE and 2p2h allows for quantitative comparisons with various models of these processes. We find strong disagreement between data and theory-based models in the forward muon direction, especially for the 0.2-0.4 GeV available hadronic energy region.

Lesmeister, James Ryan [Houston U.]↗
DOE OSTI2024

Accessing metal-specific orbital interactions in C–H activation with resonant inelastic X-ray scattering

Photochemically prepared transition-metal complexes are known to be effective at cleaving the strong C–H bonds of organic molecules in room temperature solutions. There is also ample theoretical evidence that the two-way, metal to ligand (MLCT) and ligand to metal (LMCT), charge-transfer between an incoming alkane C–H group and the transition metal is the decisive interaction in the C–H activation reaction. What is missing, however, are experimental methods to directly probe these interactions in order to reveal what determines reactivity of intermediates and the rate of the reaction. Here, using quantum chemical simulations we predict and propose future time-resolved valence-to-core resonant inelastic X-ray scattering (VtC-RIXS) experiments at the transition metal L-edge as a method to provide a full account of the evolution of metal–alkane interactions during transition-metal mediated C–H activation reactions. For the model system cyclopentadienyl rhodium dicarbonyl (CpRh(CO) 2 ), we demonstrate, by simulating the VtC-RIXS signatures of key intermediates in the C–H activation pathway, how the Rh-centered valence-excited states accessible through VtC-RIXS directly reflect changes in donation and back-donation between the alkane C–H group and the transition metal as the reaction proceeds via those intermediates. We benchmark and validate our quantum chemical simulations against experimental steady-state measurements of CpRh(CO) 2 and Rh(acac)(CO)2 (where acac is acetylacetonate). Our study constitutes the first step towards establishing VtC-RIXS as a new experimental observable for probing reactivity of C–H activation reactions. More generally, the study further motivates the use of time-resolved VtC-RIXS to follow the valence electronic structure evolution along photochemical, photoinitiated and photocatalytic reactions with transition metal complexes.

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

Active virus-host interactions at sub-freezing temperatures in Arctic peat soil

Abstract Background Winter carbon loss in northern ecosystems is estimated to be greater than the average growing season carbon uptake and is primarily driven by microbial decomposers. Viruses modulate microbial carbon cycling via induced mortality and metabolic controls, but it is unknown whether viruses are active under winter conditions (anoxic and sub-freezing temperatures). Results We used stable isotope probing (SIP) targeted metagenomics to reveal the genomic potential of active soil microbial populations under simulated winter conditions, with an emphasis on viruses and virus-host dynamics. Arctic peat soils from the Bonanza Creek Long-Term Ecological Research site in Alaska were incubated under sub-freezing anoxic conditions with H 2 18 O or natural abundance water for 184 and 370 days. We sequenced 23 SIP-metagenomes and measured carbon dioxide (CO 2 ) efflux throughout the experiment. We identified 46 bacterial populations (spanning 9 phyla) and 243 viral populations that actively took up 18 O in soil and respired CO 2 throughout the incubation. Active bacterial populations represented only a small portion of the detected microbial community and were capable of fermentation and organic matter degradation. In contrast, active viral populations represented a large portion of the detected viral community and one third were linked to active bacterial populations. We identified 86 auxiliary metabolic genes and other environmentally relevant genes. The majority of these genes were carried by active viral populations and had diverse functions such as carbon utilization and scavenging that could provide their host with a fitness advantage for utilizing much-needed carbon sources or acquiring essential nutrients. Conclusions Overall, there was a stark difference in the identity and function of the active bacterial and viral community compared to the unlabeled community that would have been overlooked with a non-targeted standard metagenomic analysis. Our results illustrate that substantial active virus-host interactions occur in sub-freezing anoxic conditions and highlight viruses as a major community-structuring agent that likely modulates carbon loss in peat soils during winter, which may be pivotal for understanding the future fate of arctic soils' vast carbon stocks.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2024

Structural basis of transcription: RNA polymerase II substrate binding and metal coordination using a free-electron laser

Catalysis and translocation of multisubunit DNA-directed RNA polymerases underlie all cellular mRNA synthesis. RNA polymerase II (Pol II) synthesizes eukaryotic pre-mRNAs from a DNA template strand buried in its active site. Structural details of catalysis at near-atomic resolution and precise arrangement of key active site components have been elusive. Here, we present the free-electron laser (FEL) structures of a matched ATP-bound Pol II and the hyperactive Rpb1 T834P bridge helix (BH) mutant at the highest resolution to date. The radiation-damage-free FEL structures reveal the full active site interaction network, including the trigger loop (TL) in the closed conformation, bonafide occupancy of both site A and B Mg 2+ , and, more importantly, a putative third (site C) Mg 2+ analogous to that described for some DNA polymerases but not observed previously for cellular RNA polymerases. Molecular dynamics (MD) simulations of the structures indicate that the third Mg 2+ is coordinated and stabilized at its observed position. TL residues provide half of the substrate binding pocket while multiple TL/BH interactions induce conformational changes that could allow translocation upon substrate hydrolysis. Consistent with TL/BH communication, a FEL structure and MD simulations of the T834P mutant reveal rearrangement of some active site interactions supporting potential plasticity in active site function and long-distance effects on both the width of the central channel and TL conformation, likely underlying its increased elongation rate at the expense of fidelity.

Science & Technology - Other Topics↗
DOE OSTI2024

Combinatorial transcription factor binding encodes cis -regulatory wiring of mouse forebrain GABAergic neurogenesis

Transcription factors (TFs) bind combinatorially to cis-regulatory elements, orchestrating transcriptional programs. Although studies of chromatin state and chromosomal interactions have demonstrated dynamic neurodevelopmental cis-regulatory landscapes, parallel understanding of TF interactions lags. To elucidate combinatorial TF binding driving mouse basal ganglia development, we integrated chromatin immunoprecipitation sequencing (ChIP-seq) for twelve TFs, H3K4me3-associated enhancer-promoter interactions, chromatin and gene expression data, and functional enhancer assays. We identified sets of putative regulatory elements with shared TF binding (TF-pRE modules) that orchestrate distinct processes of GABAergic neurogenesis and suppress other cell fates. The majority of pREs were bound by one or two TFs; however, a small proportion were extensively bound. These sequences had exceptional evolutionary conservation and motif density, complex chromosomal interactions, and activity as in vivo enhancers. Our results provide insights into the combinatorial TF-pRE interactions that activate and repress expression programs during telencephalon neurogenesis and demonstrate the value of TF binding toward modeling developmental transcriptional wiring.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2020

Breaking Simple Scaling Relations through Metal–Oxide Interactions: Understanding Room-Temperature Activation of Methane on M/CeO 2 (M = Pt, Ni, or Co) Interfaces

The clean activation of methane at low temperatures remains an eminent challenge and a field of competitive research. In particular, on late transition metal surfaces such as Pt(111) or Ni(111), higher temperatures are necessary to activate the hydrocarbon molecule, but a massive deposition of carbon makes the metal surface useless for catalytic activity. However, on very low-loaded M/CeO 2 (M = Pt, Ni, or Co) surfaces, the dissociation of methane occurs at room temperature, which is unexpected considering simple linear scaling relationships. This intriguing phenomenon has been studied using a combination of experimental techniques (ambient-pressure X-ray photoelectron spectroscopy, time-resolved X-ray diffraction, and X-ray absorption spectroscopy) and density functional theory-based calculations. The experimental and theoretical studies show that the size and morphology of the supported nanoparticles together with strong metal–support interactions are behind the deviations from the scaling relations. These findings point toward a possible strategy for circumventing scaling relations, producing active and stable catalysts that can be employed for methane activation and conversion.

03 NATURAL GAS↗
DOE OSTI2021

Monolayer Support Control and Precise Colloidal Nanocrystals Demonstrate Metal-Support Interactions in Heterogeneous Catalysts

We report that electronic and geometric interactions between active and support phases are critical in determining the activity of heterogeneous catalysts, but metal-support interactions are challenging to study. Here, it is demonstrated how the combination of the monolayer-controlled formation using atomic layer deposition (ALD) and colloidal nanocrystal synthesis methods leads to catalysts with sub-nanometer precision of active and support phases, thus allowing for the study of the metal-support inter-actions in detail. The use of this approach in developing a fundamental understanding of support effects in Pd-catalyzed methane combustion is demonstrated. Uniform Pd nanocrystals are deposited onto Al2O 3 /SiO 2 spherical supports prepared with control over morphology and Al 2 O 3 layer thicknesses ranging from sub-monolayer to a ≈4 nm thick uniform coating. Dramatic changes in catalytic activity depending on the coverage and structure of Al 2 O 3 situated at the Pd/Al 2 O 3 interface are observed, with even a single monolayer of alumina contributing an order of magnitude increase in reaction rate. By building the Pd/Al 2 O 3 interface up layer-by-layer and using uniform Pd nanocrystals, this work demonstrates the importance of controlled and tunable materials in determining metal-support interactions and catalyst activity.

36 MATERIALS SCIENCE↗
DOE OSTI2024

Observing Chemical and Morphological Changes in a Cu@TiO x Core@Shell Catalyst: Impact of Reversible Metal-Oxide Interactions on CO 2 Activation and Hydrogenation

A combination of several in-situ techniques (XRD, XAS, AP-XPS, E-TEM) was used to explore links between the structural and chemical properties of a Cu@TiO x catalyst under CO 2 hydrogenation conditions. The active phase of the catalyst involved an inverse oxide/metal configuration, but the initial core@shell motif was disrupted during the pre-treatment in H 2 . As a consequence of strong metal-support interactions, the titania shell cracked and Cu particles migrated from the core to on top of the oxide with the simultaneous formation of a Cu-Ti-O x phase. The generated Cu particles had a diameter of 20-40 nm and were decorated by small clusters of TiO x (< 5 nm in size). Results of in-situ XAS and XRD and images of E-TEM showed a very dynamic system, where the inverse oxide/metal configuration promoted the reactivity of the system towards CO 2 and H 2 . At room temperature, CO 2 oxidized the Cu nanoparticles (CO 2,gas → CO gas + O oxide ) inducing a redistribution of the TiO x clusters and big modifications in catalyst surface morphology. The generated oxide overlayer disappeared at elevated temperatures (> 180 °C) upon exposure to H 2 , producing a transient surface that was very active for the reverse water-gas shift reaction (CO 2 + H 2 → CO + H 2 O) but was not stable at 250 °C. When oxidation and reduction occurred at the same time, under a mixture of CO 2 and H 2 , the surface structure evolved toward a dynamic equilibrium that strongly depended on the temperature. Neither CO 2 nor H 2 can be considered as passive reactants. In the Cu@TiO x system, morphological changes were linked to variations in the composition of metal-oxide interfaces which were reversible with temperature or chemical environment and affected the catalytic activity of the system. Finally, the present study illustrates the dynamic nature of phenomena associated with the trapping and conversion of CO 2 .

36 MATERIALS SCIENCE↗
DOE OSTI2023

Metal-ligand interactions in a redox active ligand system. Electrochemistry and spectroscopy of [M(dipyvd) 2 ] n+ (M=Zn, Ni, n =0, 1, 2)

Reaction of nickel and zinc triflates with the tridentate leucoverdazyl 1-isopropyl-3,5-di (2'-pyridyl)-6-oxo-2H-tetrazine (dipyvdH) and triethylamine resulted in the neutral coordination compounds M(dipyvd) 2 (M = Ni,Zn). In acetonitrile, both compounds undergo two one electron oxidation processes, Zn (dipyvd) 2 at -0.28 V and -0.12 V and Ni(dipyvd) 2 at -0.32 V and -0.15 V vs ferrocene/ferricenium. Oxidations are ligand based resulting in an intermediate mixed valence species and a cationic bis(verdazyl) compound respectively. Oxidation of the ligand changes a localized, antiaromatic, non-planar 8π electron anion to a planar, delocalized 7π electron radical. The change in ligand structure results in an increase in the octahedral ligand field splitting from 10,500 cm –1 to ~13,000 cm –1 , suggesting an increase in the pi acceptor character of the ligand. In the mixed valence species, spectroscopic data suggests minimal interaction between ligands mediated by the metal center; i.e., these are class I-II systems in the Robin-Day classification.

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

Shape-driven, emergent behavior in active particle mixtures

Abstract Active particle systems can vary greatly from one-component systems of spheres to mixtures of particle shapes at different composition ratios. We investigate computationally the combined effect of anisotropy and stoichiometry on the collective behavior of two-dimensional active colloidal mixtures of polygons. We uncover three emergent phenomena not yet reported in active Brownian particle systems. First, we find that mixtures containing hexagons exhibit micro-phase separation with large grains of hexagonal symmetry. We quantify a measurable, implicit ‘steric attraction’ between the active particles as a result of shape anisotropy and activity. This calculation provides further evidence that implicit interactions in active systems, even without explicit attraction, can lead to an effective preferential attraction between particles. Next, we report stable fluid clusters in mixtures containing one triangle or square component. We attribute the fluidization of the dense cluster to the interplay of cluster destabilizing particles, which introduce grain boundaries and slip planes into the system, causing solid-like clusters to break up into fluid clusters. Third, we show that fluid clusters can coexist with solid clusters within a sparse gas of particles in a steady state of three coexisting phases. Our results highlight the potential for a wide variety of behavior to be accessible to active matter systems and establish a route to control active colloidal systems through simple parameter designs.

72 PHYSICS OF ELEMENTARY PARTICLES AND FIELDS↗
DOE OSTI2022

“Did you eat a MOLEcule today?” An Interactive Demonstration of Molecular Weight with Real-Time Breath Analysis Using Mass Spectrometry for All Ages

Although mass spectrometry is a widely used analytical tool, age-appropriate, interactive outreach activities for laboratory visitors, especially children, are lacking. Furthermore, the presented interactive demonstration, “Did you eat a MOLEcule today?”, introduces all ages to molecular weight concepts and mass spectrometry in a research laboratory, while connecting the concepts to real-world applications. Through real-time breath analysis, participants explore the concepts of molecular weight, electrostatic field manipulation of charged molecules, and analyte identification by mass analysis. This module is rapid and highly adaptable for outreach activities but also includes age- or classroom-appropriate variations to decrease or increase difficulty levels. The presented interactive demonstration has repeatedly been implemented, with over 2300 participants during six annual “Take Our Daughters & Sons to Work Day” and two corporate “Family Day” outreach activities, successfully engaging, exciting, and educating both kids and parents.

36 MATERIALS SCIENCE↗
DOE OSTI2024

Analytical model for the motion and interaction of two-dimensional active nematic defects

Here, we develop an approximate, analytical model for the velocity of defects in active nematics by combining recent results for the velocity of topological defects in nematic liquid crystals with the flow field generated from individual defects in active nematics. Importantly, our model takes into account the long-range interactions between defects that result from the flows they produce as well as the orientational coupling between defects inherent in nematics. Our work complements previous studies of active nematic defect motion by introducing a linear approximation that allows us to treat defect interactions as two-body interactions and incorporates the hydrodynamic screening length as a tuning parameter. We show that the model can analytically predict bound states between two +1/2 winding number defects, effective attraction between two –1/2 defects, and the scaling of a critical unbinding length between ±1/2 defects with activity. The model also gives predictions for the trajectories of defects, such as the scattering of +1/2 defects by –1/2 defects at a critical impact parameter that depends on activity. In the presence of circular confinement, the model predicts a braiding motion for three +1/2 defects that was recently seen in experiments, as well as stable and ergodic trajectories for four or more defects.

36 MATERIALS SCIENCE↗
DOE OSTI2025

Deciphering Catalyst–Support Interaction via Doping for Highly Active and Durable Oxygen Evolution Catalysis

The design of oxygen evolution reaction (OER) electrocatalysts demands a delicate balance between activity and stability. Here, in this study, we present a rational design approach that leverages catalyst-support interactions to enhance both the intrinsic activity and durability of Ir-based catalysts. Our study reveals that while Mo doping energetically promotes the formation of high-valent Ir species, enhancing intrinsic catalytic activity, it also leads to a reduction in electrical conductivity. These findings emphasize that supporting doping can introduce both beneficial and limiting effects, highlighting the need for a carefully balanced design strategy to optimize the overall OER performance. Simultaneously, in situ analytical techniques and comparative evaluation reveal the crucial role of oxide supports in stabilizing the catalyst. These findings highlight the pivotal role of interface engineering in maintaining catalyst integrity and the need for support materials that balance dopant-driven electronic promotion with structural and electrochemical robustness. These interconnected degradation pathways highlight the need to move beyond a catalyst-centric view and instead adopt a system-level understanding of the stability. Our approach offers a strong foundation for the rational design and evaluation of high-performance OER electrocatalysts for electrochemical energy applications.

Kim, Jinyeop [Korea Advanced Inst. Science and Tec↗