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All sources NASA NTRS DOE OSTI

DOE OSTI2022

Dynamics of organic matter molecular composition under aerobic decomposition and their response to the nitrogen addition in grassland soils

Grassland soils store a substantial proportion of the global soil carbon (C) stock. The transformation of C in grassland soils with respect to chemical composition and persistence strongly regulate the predicted terrestrial-atmosphere C flux in global C biogeochemical cycling models. In addition, increasing atmospheric nitrogen (N) deposition alters C chemistry in grassland soils. However, there remains controversy about the importance of mineralogical versus biochemical preservation of soil C, as well as uncertainty regarding how grassland soil C chemistry responds to elevated N. This study used grassland soils with diverse soil organic matter (SOM) chemistries in an 8-month aerobic incubation experiment to evaluate whether the chemical composition of SOM converged across sites over time, and how SOM persistence responded to the N addition. This study demonstrates that over the course of incubation, the richness of labile compounds decreased in soils with less ferrihydrite content, whereas labile compounds were more persistent in ferrihydrite rich soils. In contrast, we found that the richness of more complex compounds increased over the incubation in most sites, independent of soil mineralogy. Moreover, we demonstrate the extent to which the diverse chemical composition of SOM converged among sites in response to microbial decomposition. N fertilization decreased soil respiration and inhibited the convergence of molecular composition across ecosystems by altering N demand for microbial metabolism and chemical interactions between minerals and organic molecules. This study provides original evidence that the decomposition and metabolism of labile organic molecules were largely regulated by soil mineralogy (physicochemical preservation), while the metabolism of more complex organic molecules was controlled by substrate complexity (biochemical preservation) independent to mineral-organic interactions. This study advanced our understanding of the dynamic biogeochemical cycling of C by unveiling that N addition dampened C respiration and diminished the convergence of SOM chemistry across diverse grassland ecosystems.

54 ENVIRONMENTAL SCIENCES↗

DOE OSTI2018

Crystal structure of the catalytic domain of HIV-1 restriction factor APOBEC3G in complex with ssDNA

The human APOBEC3G protein is a cytidine deaminase that generates cytidine to deoxy-uridine mutations in single-stranded DNA (ssDNA), and capable of restricting replication of HIV-1 by generating mutations in viral genome. The mechanism by which APOBEC3G specifically deaminates 5'-CC motifs has remained elusive since structural studies have been hampered due to apparently weak ssDNA binding of the catalytic domain of APOBEC3G. We overcame the problem by generating a highly active variant with higher ssDNA affinity. Here, we present the crystal structure of this variant complexed with a ssDNA substrate at 1.86 Å resolution. This structure reveals atomic-level interactions by which APOBEC3G recognizes a functionally-relevant 5'-TCCCA sequence. This complex also reveals a key role of W211 in substrate recognition, implicating a similar recognition in activation-induced cytidine deaminase (AID) with a conserved tryptophan.

59 BASIC BIOLOGICAL SCIENCES↗

DOE OSTI2022

Crystal Structure of CYP3A4 Complexed with Fluorol Identifies the Substrate Access Channel as a High-Affinity Ligand Binding Site

Cytochrome P450 3A4 (CYP3A4) is a major human drug-metabolizing enzyme, notoriously known for its extreme substrate promiscuity, allosteric behavior, and implications in drug–drug interactions. Despite extensive investigations, the mechanism of ligand binding to CYP3A4 is not fully understood. We determined the crystal structure of CYP3A4 complexed with fluorol, a small fluorescent dye that can undergo hydroxylation. In the structure, fluorol associates to the substrate channel, well suited for the binding of planar polyaromatic molecules bearing polar groups, through which stabilizing H-bonds with the polar channel residues, such as Thr224 and Arg372, can be established. Mutagenesis, spectral, kinetic, and functional data confirmed the involvement but not strict requirement of Thr224 for the association of fluorol. Collectively, our data identify the substrate channel as a high-affinity ligand binding site and support the notion that hydrophobic ligands first dock to the nearby peripheral surface, before migrating to the channel and, subsequently, into the active site.

59 BASIC BIOLOGICAL SCIENCES↗

DOE OSTI2017

Ballistic magnetotransport in a suspended two-dimensional electron gas with periodic antidot lattices

The magnetoresistance of suspended semiconductor nanostructures with a two-dimensional electron gas structured by periodic square antidot lattices is studied. It is shown that the ballistic regime of electron transport is retained after detaching the sample from the substrate. Direct comparative analysis of commensurability oscillations of magnetoresistance and their temperature dependences in samples before and after suspension is performed. It is found that the temperature dependences are almost identical for non-suspended and suspended samples, whereas significant differences are observed in the nonlinear regime, caused by direct current passage. Commensurability oscillations in the suspended samples are more stable with respect to exposure to direct current, which can be presumably explained by electron–electron interaction enhancement after detaching nanostructures from the high-permittivity substrate.

36 MATERIALS SCIENCE↗

DOE OSTI2023

Characterization of a Low-Temperature Plasma (LTP) Ambient Ionization Source Using Temporally Resolved Monochromatic Imaging Spectrometry

The low-temperature plasma (LTP) probe is a common plasma-based source used for ambient desorption–ionization mass spectrometry (MS). While the LTP probe has been characterized in detail with MS, relatively few studies have used optical spectroscopy. In this paper, two-dimensional (2D) imaging at selected wavelengths is used to visualize important species in the LTP plasma jet. First, 2D steady-state images of the LTP plume for N 2 + (391.2 nm), He I (706.5 nm), and N 2 (337.1 nm) emissions were recorded under selected plasma conditions. Second, time-resolved 2D emission maps of radiative species in the LTP plasma jet were recorded through the use of a 200 ns detection gate and varying gate delays with respect to the LTP trigger pulse. Emission from He I, N 2 + , and N 2 in the plasma jet region was found to show a transient behavior (often referred to as plasma bullets) lasting only a few microseconds. The N 2 + and He I maps were highly correlated in spatial and temporal structure. Further, emission from N 2 showed two maxima in time, one before and one after the maximum emission for N 2 + and He I, due to an initial electronic excitation wave and ion–electron recombination, respectively. Third, the interaction of the LTP probe with a sample substrate and an electrically grounded metallic needle was studied. Emission from a fluorophore on the sample substrate showed an initial photon-induced excitation from plasma-generated photons followed by electronic excitation by other plasma species. The presence of a grounded needle near the plasma jet significantly extended the plasma jet lifetime and also generated a long-lived corona discharge on the needle. The effect of LTP operating parameters on emission spectra was correlated with mass-spectral results including reagent-ion signals. Lastly, five movies provide a side-by-side comparison of the temporal behavior of emitting species and insights into the interactions of the emission clouds with a sample surface as well as an external needle. Temporally and spatially resolved imaging provided insights into important processes in the LTP plasma jet, which will help improve analyte ion sampling in LTP–MS.

Chan, George C. -Y.↗

DOE OSTI2016

Monolithic active pixel radiation detector with shielding techniques

A monolithic active pixel radiation detector including a method of fabricating thereof. The disclosed radiation detector can include a substrate comprising a silicon layer upon which electronics are configured. A plurality of channels can be formed on the silicon layer, wherein the plurality of channels are connected to sources of signals located in a bulk part of the substrate, and wherein the signals flow through electrically conducting vias established in an isolation oxide on the substrate. One or more nested wells can be configured from the substrate, wherein the nested wells assist in collecting charge carriers released in interaction with radiation and wherein the nested wells further separate the electronics from the sensing portion of the detector substrate. The detector can also be configured according to a thick SOA method of fabrication.

46 INSTRUMENTATION RELATED TO NUCLEAR SCIENCE AND ↗

DOE OSTI2018

Monolithic active pixel radiation detector with shielding techniques

47 OTHER INSTRUMENTATION↗

DOE OSTI2020

Rational synthesis of atomically precise graphene nanoribbons directly on metal oxide surfaces

Atomically precise graphene nanoribbons (GNRs) attract great interest because of their highly tunable electronic, optical, and transport properties. However, on-surface synthesis of GNRs is typically based on metal surface–assisted chemical reactions, where metallic substrates strongly screen their designer electronic properties and limit further applications. In this work, we present an on-surface synthesis approach to forming atomically precise GNRs directly on semiconducting metal oxide surfaces. The thermally triggered multistep transformations preprogrammed in our precursors’ design rely on highly selective and sequential activations of carbon-bromine (C-Br) and carbon-fluorine (C-F) bonds and cyclodehydrogenation. The formation of planar armchair GNRs terminated by well-defined zigzag ends is confirmed by scanning tunneling microscopy and spectroscopy, which also reveal weak interaction between GNRs and the rutile titanium dioxide substrate.

36 MATERIALS SCIENCE↗

DOE OSTI2022

Evaluation of different getter substrates using two-dimensional gas chromatography with time of flight mass spectrometry

We report while understanding hydrogen uptake by organic based getters such as 1,4-bis(phenylethynyl)benzene (DEB) combined with a palladium(0)bis(dibenzylideneacetone) (Pd(dba) 2 ) catalyst is essential, another crucial element to understand is the decomposition of the DEB, Pd(dba) 2 , and/or substrate material. The breakdown of these materials may create unwanted volatiles, which may interact with and lead to deterioration of sensitive materials. Moreover, it is critical to understand if different substrates cause the getter and/or catalyst to degrade in different manners. Utilizing comprehensive two-dimensional gas chromatography (GC×GC) with time-of-flight mass spectrometry (TOFMS), the presence of volatiles located in the headspace of various DEB/Pd(dba) 2 getter substrates is examined. These samples include a getter infused silicone foam, a hydrogenated getter infused silicone foam, an activated carbon getter pellet, and a hydrogenated activated carbon getter pellet. Application of Fisher ratio (F-ratio) analyses lead to the identification of several compounds that are generated or consumed through the hydrogenation process. These include benzene derivatives such as bibenzyl, benzaldehyde, and vinyl benzoate in the activated carbon pellets and 1,5-diphenyl-3-pentanone, toluene, styrene, and 1–1'(2-pentene 1,5-diyl)bis benzene in the silicone foams, and alkane/alkene derivatives such undecane, 4-tridecene, and decane in the activated carbon pellets and 2,6-dimethyl undecane in the silicone foams. Further comparison of the different hydrogenated getter substrates (e.g. activated carbon pellet and silicone foam) indicates that the different substrates alter the decomposition products created from the degradation of the DEB and Pd(dba) 2 .

47 OTHER INSTRUMENTATION↗

DOE OSTI2019

Intrinsic interfacial van der Waals monolayers and their effect on the high-temperature superconductor FeSe / SrTiO 3

The sensitive dependence of monolayer materials on their environment often gives rise to unexpected properties. It was recently demonstrated that monolayer FeSe on a SrTiO 3 substrate exhibits a much higher superconducting critical temperature TC than the bulk material. Here, we examine the interfacial structure of FeSe / SrTiO 3 and the effect of an interfacial Ti 1+x O 2 layer on the increased T C using a combination of scanning transmission electron microscopy and density functional theory. We find Ti 1+x O 2 forms its own quasi-two-dimensional layer, bonding to both the substrate and the FeSe film by van der Waals interactions. The excess Ti in this layer electron-dopes the FeSe monolayer in agreement with experimental observations. Moreover, the interfacial layer introduces symmetry-breaking distortions in the FeSe film that favor a T C increase. These results suggest that this common substrate may be functionalized to modify the electronic structure of a variety of thin films and monolayers.

75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗

DOE OSTI2015

The structure of the Caenorhabditis elegans manganese superoxide dismutase MnSOD-3-azide complex

C. elegans MnSOD-3 has been implicated in the longevity pathway and its mechanism of catalysis is relevant to the aging process and carcinogenesis. The structures of MnSOD-3 provide unique crystallographic evidence of a dynamic region of the tetrameric interface (residues 41–54). We have determined the structure of the MnSOD-3-azide complex to 1.77-Å resolution. The analysis of this complex shows that the substrate analog, azide, binds end-on to the manganese center as a sixth ligand and that it ligates directly to a third and new solvent molecule also positioned within interacting distance to the His30 and Tyr34 residues of the substrate access funnel. This is the first structure of a eukaryotic MnSOD-azide complex that demonstrates the extended, uninterrupted hydrogen-bonded network that forms a proton relay incorporating three outer sphere solvent molecules, the substrate analog, the gateway residues, Gln142, and the solvent ligand. This configuration supports the formation and release of the hydrogen peroxide product in agreement with the 5-6-5 catalytic mechanism for MnSOD. The high product dissociation constant k₄ of MnSOD-3 reflects low product inhibition making this enzyme efficient even at high levels of superoxide.

38 RADIATION CHEMISTRY, RADIOCHEMISTRY, AND NUCLEA↗

DOE OSTI2023

Structure of puromycin-sensitive aminopeptidase and polyglutamine binding

Puromycin-sensitive aminopeptidase (E.C. 3.4.11.14, UniProt P55786), a zinc metallopeptidase belonging to the M1 family, degrades a number of bioactive peptides as well as peptides released from the proteasome, including polyglutamine. We report the crystal structure of PSA at 2.3 Å. Overall, the enzyme adopts a V-shaped architecture with four domains characteristic of the M1 family aminopeptidases, but it is in a less compact conformation compared to most M1 enzymes of known structure. A microtubule binding sequence is present in a C-terminal HEAT repeat domain of the enzyme in a position where it might serve to mediate interaction with tubulin. In the catalytic metallopeptidase domain, an elongated active site groove lined with aromatic and hydrophobic residues and a large S1 subsite may play a role in broad substrate recognition. The structure with bound polyglutamine shows a possible interacting mode of this peptide, which is supported by mutation.

59 BASIC BIOLOGICAL SCIENCES↗

DOE OSTI2016

In vitro and in vivo evaluations of the P-glycoprotein-mediated efflux of dibenzoylhydrazines

P-glycoprotein (P-gp) is a member of the ATP-binding cassette transporter family. It actively transports a wide variety of compounds out of cells to protect humans from xenobiotics. Thus, determining whether chemicals are substrates and/or inhibitors of P-gp is important in risk assessments of pharmacokinetic interactions among chemicals because P-gp-mediated transport processes play a significant role in their absorption and disposition. We previously reported that dibenzoylhydrazines (DBHs) such as tebufenozide and methoxyfenozide (agrochemicals) stimulated P-gp ATPase activity. However, it currently remains unclear whether these derivatives are transport substrates of P-gp and inhibit transport of other chemicals by P-gp. In the present study, in order to evaluate the interactions of DBHs with other chemicals in humans, we determined whether DBHs are P-gp transport substrates using both the in vitro bidirectional transport assay and the in vivo study of rats. In the in vivo study, we investigated the influence of P-gp inhibitors on the brain to plasma ratio of methoxyfenozide in rats. We also examined the inhibitory effects of DBHs on quinidine (a P-gp substrate) transport by P-gp in order to ascertain whether these derivatives are inhibitors of P-gp. Based on the results, DBHs were concluded to be weak P-gp transport substrates and moderate P-gp inhibitors. However, the risk of DBHs caused by interaction with other chemicals including drugs was considered to be low by considering the DBHs' potential as the substrates and inhibitors of P-gp as well as their plasma concentrations as long as DBHs are properly used. - Highlights: • Transport of DBHs by P-gp was not detected in in vitro bidirectional transport assay. • DBHs were weak P-gp transport substrates based on in vivo studies in rats. • The in vivo studies are useful methods for evaluating P-gp transport substrates. • DBHs inhibit quinidine transport by P-gp in in vitro bidirectional transport assay.

60 APPLIED LIFE SCIENCES↗

NASA NTRS1987

Interactions of amorphous Ta(x)Cu(1-x) (x = 0.93 and 0.80) alloy films with Au overlayers and GaAs substrates

Amorphous Ta(93)Cu(7) and Ta(80)Cu(20) alloy films are prepared by cosputtering of pure Ta and pure Cu targets with a rotating sample holder table. To investigate the possible application of these materials as diffusion barriers for the Au-GaAs system, vacuum annealings are made in the temperature range from 200 to 800 C. Resistivity change, X-ray diffraction, and Auger electron spectroscopy measurements are performed to find the chemical and metallurgical stabilities of these materials in this system. The reaction temperature for Ta(x)Cu(1-x) in contact with GaAs lies between 500 and 700 C. For Au in contact with Ta(x)Cu(1-x) the reaction occurs at about 600 C. Amorphous Ta(93)Cu(7) shows different interdiffusion characteristics with surrounding elements than does Ta(80)Cu(20).

Oh, Jae E.↗

NASA NTRS1998

Substrate Effects on Electronic Properties of Atomic Chains

Atomic chains, precise structures of adatoms created on an atomically regulated surface, are candidates for constituent elements in future electronics. It was predicted that Si chains were metallic and Mg chains were semiconducting, and a doping method was also discussed. The substrate was assumed to work as a non-interacting template holding the adatoms. However, this scheme requires a low-temperature environment so that the adatoms will not displace from their ideal positions due to unwanted thermal agitation. For better structural stability, we may seek a scheme to allow the adatoms to form chemical bonding with the substrate atoms and secure their positions. The chemical bonding has two major effects on the chain electronic properties. First, only the remaining s and p orbitals in an adatom not used for the chemical bonding can decide chain band structures, rather than the full set of orbitals previously assumed. Second, because of a possible HOMO energy difference between adatom and substrate atom, semiconducting chains are unintentionally doped. These effects are studied with a self-consistent tight-binding method with universal parameters. With one adatom per unit cell, adatom chains are semiconducting: (1) if adatoms are of group III and form one chemical bond per adatom, or (2) if adatoms are of group IV and form two chemical bonds. 'Me previous result [I I of realizing semiconducting chains by group II adatoms without chemical bonds is consistent with this picture. When the HOMO energy in an adatom is shallower than that in a substrate atom, the entire chain is positively polarized, unintentionally achieving p-type doping. When deeper, the chain is negatively charged, achieving n-type doping.

Yamada, Toshishige↗

NASA NTRS1981

Passivation layer for steel substrate of solar cell

Solar cell is fabricated on commerical sheet-steel substrate passivated with tungsten layer. Layer prevents constituents of steel from interacting with semiconductor materials in MOS thin-film solar cell. Thin plating of nickel on steel improves bonding of tungsten. Use of steel as substrate reduces materials cost of solar cell construction.

Stirn, R. J.↗

DOE OSTI2022

Phonons in complex twisted crystals: Angular momenta, interactions, and topology

We report phonons and their interactions are critically important for a variety of energy-relevant applications ranging from low thermal resistance substrates to thermal barrier coatings. Fundamental insights into the nature of phonons and allowed interactions are governed by the underlying symmetries of the crystal lattice. In this paper, we provide a comprehensive and detailed description of lattice dynamics derived from twist symmetries of chiral and achiral crystals—twist dynamics. Phonon bands naturally carry quantized crystal angular momentum derived from rotational phases, which give insights into the nature of band crossings and avoided crossings, selection rules for phonon interactions, and topological band crossing behaviors. Twist dynamics is demonstrated for a variety of materials covering a range of space groups, symmetry operations, twist axis orientations, and constituent elements. Furthermore, twist symmetry offers insights into peculiar features observed in scattering measurements. In this context, we present inelastic neutron scattering measurements for rutile TiO 2 and explain them using twist dynamics.

75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗

DOE OSTI2017

Active bialkali photocathodes on free-standing graphene substrates

Here, the hexagonal structure of graphene gives rise to the property of gas impermeability, motivating its investigation for a new application: protection of semiconductor photocathodes in electron accelerators. These materials are extremely susceptible to degradation in efficiency through multiple mechanisms related to contamination from the local imperfect vacuum environment of the host photoinjector. Few-layer graphene has been predicted to permit a modified photoemission response of protected photocathode surfaces, and recent experiments of single-layer graphene on copper have begun to confirm these predictions for single crystal metallic photocathodes. Unlike metallic photoemitters, the integration of an ultra-thin graphene barrier film with conventional semiconductor photocathode growth processes is not straightforward. A first step toward addressing this challenge is the growth and characterization of technologically relevant, high quantum efficiency bialkali photocathodes on ultra-thin free-standing graphene substrates. Photocathode growth on free-standing graphene provides the opportunity to integrate these two materials and study their interaction. Specifically, spectral response features and photoemission stability of cathodes grown on graphene substrates are compared to those deposited on established substrates. In addition, we observed an increase of work function for the graphene encapsulated bialkali photocathode surfaces, which is predicted by our calculations. The results provide a unique demonstration of bialkali photocathodes on free-standing substrates, and indicate promise towards our goal of fabricating high-performance graphene encapsulated photocathodes with enhanced lifetime for accelerator applications.

36 MATERIALS SCIENCE↗