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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 397 records · Page 22
All sourcesNASA NTRSDOE OSTI
DOE OSTI2021

Positron Emission Tomography Imaging of Functional Transforming Growth Factor β (TGFβ) Activity and Benefit of TGFβ Inhibition in Irradiated Intracranial Tumors

Transforming growth factor β (TGFβ) promotes cell survival by endorsing DNA damage repair and mediates an immunosuppressive tumor microenvironment. Thus, TGFβ activation in response to radiation therapy is potentially targetable because it opposes therapeutic control. Strategies to assess this potential in the clinic are needed.

62 RADIOLOGY AND NUCLEAR MEDICINE↗
DOE OSTI2024

Analytic Nuclear Gradients for Complete Active Space Linearized Pair-Density Functional Theory

Accurately modeling photochemical reactions is difficult due to the presence of conical intersections and locally avoided crossings, as well as the inherently multiconfigurational character of excited states. As such, one needs a multistate method that incorporates state interaction in order to accurately model the potential energy surface at all nuclear coordinates. The recently developed linearized pair-density functional theory (L-PDFT) is a multistate extension of multiconfiguration PDFT, and it has been shown to be a cost-effective post-MCSCF method (as compared to more traditional and expensive multireference many-body perturbation methods or multireference configuration interaction methods) that can accurately model potential energy surfaces in regions of strong nuclear–electronic coupling in addition to accurately predicting Franck–Condon vertical excitations. Here, in this paper, we report the derivation of analytic gradients for L-PDFT and their implementation in the PySCF-forge software, and we illustrate the utility of these gradients for predicting ground- and excited-state equilibrium geometries and adiabatic excitation energies for formaldehyde, s-trans-butadiene, phenol, and cytosine.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2020

Potential Control of Oxygen Non-Stoichiometry in Cerium Oxide and Phase Transition Away from Equilibrium

Cerium oxide (ceria, CeO 2 ) is a technologically important material for energy conversion applications. Its activities strongly depend on redox states and oxygen vacancy concentration. Understanding the functionality of chemical active species and behavior of oxygen vacancy during operation, especially in high-temperature solid-state electrochemical cells, is the key to advance future material design. Herein, the structure evolution of ceria is spatially resolved using bulk-sensitive operando X-ray diffraction and spectroscopy techniques. During water electrolysis, ceria undergoes reduction, and its oxygen non-stoichiometry shows a dependence on the electrochemical current. Cerium local bonding environments vary concurrently to accommodate oxygen vacancy formation, resulting in changes in Ce-O coordination number and Ce 3+ /Ce 4+ redox couple. When reduced enough, a crystallographic phase transition occurs from α to an α' phase with more oxygen vacancies. Nevertheless, the transition behavior is intriguingly different from the one predicted in the standard phase diagram of ceria. This work demonstrates a feasible means to control oxygen non-stoichiometry in ceria via electrochemical potential. It also sheds light on the mechanism of phase transitions induced by electrochemical potential. For electrochemical systems, effects from a large-scale electrical environment should be taken into consideration, besides effective oxygen partial pressure and temperature.

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

Chloroplast SRP43 autonomously protects chlorophyll biosynthesis proteins against heat shock

The assembly of light-harvesting chlorophyll-binding proteins (LHCPs) is coordinated with chlorophyll biosynthesis during chloroplast development. The ATP-independent chaperone known as chloroplast signal recognition particle 43 (cpSRP43) mediates post-translational LHCP targeting to the thylakoid membrane and also participates in tetrapyrrole biosynthesis (TBS). How these distinct actions of cpSRP43 are controlled has remained unclear. Here, we demonstrate that cpSRP43 effectively protects several TBS proteins from heat-induced aggregation and enhances their stability during leaf greening and heat shock. While the substrate-binding domain of cpSRP43 is sufficient for chaperoning LHCPs, the stabilization of TBS clients requires the chromodomain 2 of the protein. Strikingly, cpSRP54—which activates cpSRP43’s LHCP-targeted function—inhibits the chaperone activity of cpSRP43 towards TBS proteins. High temperature weakens the interaction of cpSRP54 with cpSRP43, thus freeing cpSRP43 to interact with and protect the integrity of TBS proteins. Our data indicate that the temperature sensitivity of the cpSRP43–cpSRP54 complex enables cpSRP43 to serve as an autonomous chaperone for the thermoprotection of TBS proteins.

09 BIOMASS FUELS↗
DOE OSTI2021

Simulation of adiabatic quantum computing for molecular ground states

Quantum computation promises to provide substantial speedups in many practical applications with a particularly exciting one being the simulation of quantum many-body systems. Adiabatic state preparation (ASP) is one way that quantum computers could recreate and simulate the ground state of a physical system. In this paper, we explore a novel approach for classically simulating the time dynamics of ASP with high accuracy and with only modest computational resources via an adaptive sampling configuration interaction scheme for truncating the Hilbert space to only the most important determinants. We verify that this truncation introduces negligible error and use this new approach to simulate ASP for sets of small molecular systems and Hubbard models. Furthermore, we examine two approaches to speeding up ASP when performed on quantum hardware: (i) using the complete active space configuration interaction (CASCI) wave function instead of the Hartree–Fock initial state and (ii) a nonlinear interpolation between the initial and target Hamiltonians. We find that starting with a CASCI wave function with a limited active space yields substantial speedups for many of the systems examined, while nonlinear interpolation does not. In additional, we observe interesting trends in the minimum gap location (based on the initial state) as well as how state preparation time can depend on certain molecular properties, such as the number of valence electrons. Importantly, we find that the required state preparation times do not show an immediate exponential wall that would preclude an efficient run of ASP on actual hardware.

Kremenetski, Vladimir↗
NASA NTRS1985

Thermionic noise measurements for on-line dispenser cathode diagnostics for linear beam microwave tubes

A test stand has been set up to measure the current fluctuation noise properties of B- and M-type dispenser cathodes in a typical TWT gun structure. Noise techniques were used to determine the work function distribution on the cathode surfaces. Significant differences between the B and M types and significant changes in the work function distribution during activation and life are found. In turn, knowledge of the expected work function can be used to accurately determine the cathode-operating temperatures in a TWT structure. Noise measurements also demonstrate more sensitivity to space charge effects than the Miram method. Full automation of the measurements and computations is now required to speed up data acquisition and reduction. The complete set of equations for the space charge limited diode were programmed so that given four of the five measurable variables (J, J sub O, T, D, and V) the fifth could be computed. Using this program, we estimated that an rms fluctuation in the diode spacing d in the frequency range of 145 Hz about 20 kHz of only about 10 to the -5 power A would account for the observed noise in a space charge limited diode with 1 mm spacing.

Holland, C.↗
DOE OSTI2020

Oxidative dehydrogenation of propane on the oxygen adsorbed edges of boron nitride nanoribbons

Metal-free boron nitride has recently been reported to exhibit high catalytic activity and selectivity towards oxidative dehydrogenation of propane (ODHP). Despite several experimental studies, the exact nature and function of the active sites in this emerging catalyst are unknown. In the present work, density functional theory calculations are combined with microkinetic modeling to systematically explore the ODHP on oxygen passivated boron nitride nanoribbons (BNNRs). Here, the relative stabilities of different edge structures of BNNR were examined using ab initio thermodynamic analysis, and the most stable oxygen passivated edge structure was used for a mechanistic study. Microkinetic analysis revealed that a N 2 O or NO x -type active site is active and selective for the conversion of propane to propene. In addition to a heterogeneous catalytic cycle, the proposed N 2 O/NO x -type active sites are expected to be able to generate gas phase C 3 H 7 ˙, which in turn can trigger gas phase reactions of ODHP as experimentally speculated.

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

Network-level encoding of local neurotransmitters in cortical astrocytes

Abstract Astrocytes, the most abundant non-neuronal cell type in the mammalian brain, are crucial circuit components that respond to and modulate neuronal activity through calcium (Ca 2+ ) signalling 1–7 . Astrocyte Ca 2+ activity is highly heterogeneous and occurs across multiple spatiotemporal scales—from fast, subcellular activity 3,4 to slow, synchronized activity across connected astrocyte networks 8–10 —to influence many processes 5,7,11 . However, the inputs that drive astrocyte network dynamics remain unclear. Here we used ex vivo and in vivo two-photon astrocyte imaging while mimicking neuronal neurotransmitter inputs at multiple spatiotemporal scales. We find that brief, subcellular inputs of GABA and glutamate lead to widespread, long-lasting astrocyte Ca 2+ responses beyond an individual stimulated cell. Further, we find that a key subset of Ca 2+ activity—propagative activity—differentiates astrocyte network responses to these two main neurotransmitters, and may influence responses to future inputs. Together, our results demonstrate that local, transient neurotransmitter inputs are encoded by broad cortical astrocyte networks over a minutes-long time course, contributing to accumulating evidence that substantial astrocyte–neuron communication occurs across slow, network-level spatiotemporal scales 12–14 . These findings will enable future studies to investigate the link between specific astrocyte Ca 2+ activity and specific functional outputs, which could build a consistent framework for astrocytic modulation of neuronal activity.

Science & Technology - Other Topics↗
NASA NTRS2004

DNA in a Tunnel: A Comfy Spot for Recognition - or -The Structure of BsoBI Complexed with DNA. What can we Learn about Function via Structure Determination and how can this be Applied to Bone or Muscle Biology?

The structure and function of a biologically active molecule are related. To understand its function, it is necessary (but not always sufficient) to know the structure of the molecule. There are many ways of relating the molecular function with the structure. Mutation analysis can identify pertinent amino acids of an enzyme, or alternatively structure comparison of the of two similar molecules with different function may lead to understanding which parts are responsible for a functional aspect, or a series of "structural cartoons" - enzyme structure, enzyme plus substrate, enzyme with transition state analog, and enzyme with product - may give insight in the function of a molecule. As an example we will discuss the structure and function of the restriction enzyme BsoBI from Bacillus stearothemzophilus in complex with its cognate DNA. The enzyme forms a unique complex with DNA in that it completely encircles the DNA. The structure reveals the enzyme-DNA contacts, how the DNA is distorted compared with the canonical forms, and elegantly shows how two distinct DNA sequences can be recognized with the same efficiency. Based on the structure we may also propose a hypothesis how the enzymatic mechanism works. The knowledge gained thru studies such as this one can be used to alter the function by changing the molecular structure. Usually this is done by design of inhibitors specifically active against and fitting into an active site of the enzyme of choice. In the case of BsoBI one of the objectives of the study was to alter the enzyme specificity. In bone biology there are many candidates available for molecular study in order to explain, alter, or (temporarily) suspend activity. For example, the understanding of a pathway that negatively regulates bone formation may be a good target for drug design to stimulate bone formation and have good potential as the basis for new countermeasures against bone loss. In principle the same approach may aid muscle atrophy, radiation damage, immune response changes and other risks identified for long-duration Space travel.

vanderWoerd, Mark↗
NASA NTRS2021

Predicting the Functional State of Protein Kinases Using Interpretable Graph Neural Networks

Kinases are a family of proteins that function as molecular switches, regulating several essential cellular activities such as cell proliferation. Dysfunctional kinases are implicated in several types of cancers and hence they are actively pursued as drug targets. Given the vast number of complex kinase structures that are available in the protein data bank (PDB), there is a necessity to develop methodologies that can identify structurally important moieties of the kinases in an automated fashion, for such techniques can be instrumental in identifying novel drug targets. In this work, we develop a graph neural network (GNN) based deep learning framework for classifying the functionally active and inactive states of a large set of eukaryotic protein kinases, making use of their 3D structure from the PDB. We show that GNN based machine learning models can classify protein states with an accuracy greater than 97%. We further use the GNN models to automatically identify regions of the kinases that are important for its function. For this purpose, Gradient-weighted Class Activation Mapping (Grad-CAM) was implemented on the protein graphs. Remarkably, Grad-CAM consistently identifies the highly conserved DFG motif as the most important part of the protein across the entire kinome, without any prior input. Other regions of the hydrophobic core such as the HRD motif were also identified by the interpretable GNN framework, consistent with the literature. We discuss the significance of each of these regions in detail.

Ashwin Ravichandran↗
NASA NTRS1974

Determination of natural and cosmic ray induced radionuclides in Apollo 17 lunar samples

Natural and cosmic ray induced radionuclides have been determined in 15 rocks and 7 soils from the Apollo 17 mission by nondestructive gamma-ray spectroscopy. The Th and K contents of these rocks and soils are shown to be linear functions of the U contents. Large amounts of Co-56, Sc-46, and Mn-54 were found in these samples due to the large proton-accelerating flares which occurred between August 2 and 6, 1972. The behavior of the Co-56 activity as a function of the Mn-54 activity seems to be the result of variation in surface to volume ratios among the samples and exposure angle. It is not necessary to invoke an asymetric solar flare flux to explain this behavior.

Keith, J. E.↗
DOE OSTI2024

Nanotube-Supported Phospholipid Bilayers (Final Technical Report)

The overarching goal of this project was to attain fundamental understanding of structural organization, self-assembly, and function of redox-active enzymes and biological energy transduction systems localized at biological (cellular membranes) as well as manmade bio-nano interfaces. During this project we developed (1) nanopore surfaces suitable to stabilization of functional redox active enzymes and (2) experimental protocols for loading for loading of redox active enzymes into nanopores and taking advantage of self-assembly for forming layer(s) of redox active enzymes inside the nanochannels formed in anodic aluminum oxide (AAO) substrates.

14 SOLAR ENERGY↗
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↗