Engineering Papers⌕ Search

SEARCH · Engineering Papers

Results for “affinity”

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 1,549 records · Page 86
All sourcesNASA NTRSDOE OSTI
DOE OSTI2022

Selection and development of aptamers for pyoverdine

The rhizosphere is a small region surrounding plant roots that is enriched in biochemicals from root exudates and populated with fungi, nematode, and bacteria. Interaction of rhizosphere organisms with plants is mainly promoted by exudates from the roots. Root exudates contain biochemicals that come from primary and secondary metabolisms of plants. These biochemicals attract microbes, which influence plant nutrition. The rhizosphere bacteria (microbiome) are vital to plant nutrient uptake and influence biotic and abiotic stress and pathogenesis. Pseudomonas is a genus of gammaproteobacteria known for its ubiquitous presence in natural habitats and its striking ecological, metabolic, and biochemical diversity. Within the genus, members of the Pseudomonas fluorescens group are common inhabitants of soil and plant surfaces, and certain strains function in the biological control of plant disease, protecting plants from infection by soilborne and aerial plant pathogens. The soil bacterium Pseudomonas protegens Pf-5 (also known as Pseudomonas fluorescensPf-5) is a well-characterized biological strain, which is distinguished by its prolific production of the secondary metabolite, pyoverdine. Knowledge of the distribution of P. fluorescens secretory activity around plant roots is very important for understanding the interaction between P. fluorescens and plants and can be achieved by real time tracking of pyoverdine. To achieve the capability of real-time tracking in soil, we have used a structure-switching SELEX strategy to select high affinity ssDNA and 2’ F-Y-RNA aptamers with specificity for pyoverdine over other siderophores. Pyoverdines from various strains possess a conserved chromophore along with strain-specific peptide chain. Some of the isolated aptamers bind to chromophore of pyoverdine. These will identify pyoverdines from a variety of pseudomonads. Identification of aptamers that selectively bind the peptide portion of pyoverdine Pf-5 is underway. The identified aptamers that are broadly and narrowly specific for pyoverdines or Pf-5 will be optimized for integration into an electrochemical biosensor to track, in real time, P fluorescens activity and other pseudomonads in and around the rhizosphere.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2020

Preservation of erniettomorph fossils in clay-rich siliciclastic deposits from the Ediacaran Wood Canyon Formation, Nevada

Three-dimensionally preserved Ediacaran fossils occur globally within sandstone beds. Sandy siliciclastic deposits of the Ediacaran Wood Canyon Formation (WCF) in the Montgomery Mountains, Nevada, contain two fossil morphologies with similar shapes and sizes: one exhibits mm-scale ridges and a distinct lower boundary and the other is devoid of these diagnostic features. We interpret these as taphomorphs of erniettomorphs, soft-bodied organisms with uncertain taxonomic affinities. We explore the cast-and-mould preservation of both taphomorphs by petrography, Raman spectroscopy, X-ray fluorescence microprobe and X-ray diffraction. All fossils and the surrounding sedimentary matrix contain quartz grains, iron-rich chlorite and muscovite. The ridged fossils contain about 70% larger quartz grains compared to the ridgeless taphomorph, indicating a lower abundance of clay minerals in the ridged fossil. Chlorite and muscovite likely originated from smectite and kaolinite precursors that underwent lower greenschist facies metamorphism. Kaolinite and smectite are inferred to have been abundant in sediments around the ridged fossil, which enabled the preservation of a continuous, distinct, clay- and kerogen-rich bottom boundary. The prevalence of quartz in the ridged fossils of the WCF and in erniettomorphs from other localities also suggests a role for this mineral in three-dimensional preservation of erniettomorphs in sandstone and siltstone deposits.

58 GEOSCIENCES↗
DOE OSTI2020

Molecular mechanism for the interaction between human CPSF30 and hFip1

Most eukaryotic pre-mRNAs must undergo 3'-end cleavage and polyadenylation prior to their export from the nucleus. A large number of proteins in several complexes participate in this 3'-end processing, including cleavage and polyadenylation specificity factor (CPSF) in mammals. The CPSF30 subunit contains five CCCH zinc fingers (ZFs), with ZF2–ZF3 being required for the recognition of the AAUAAA poly(A) signal. ZF4–ZF5 recruits the hFip1 subunit of CPSF, although the details of this interaction have not been characterized. Here we report the crystal structure of human CPSF30 ZF4–ZF5 in complex with residues 161–200 of hFip1 at 1.9 Å resolution, illuminating the molecular basis for their interaction. Unexpectedly, the structure reveals one hFip1 molecule binding to each ZF4 and ZF5, with a conserved mode of interaction. Our mutagenesis studies confirm that the CPSF30–hFip1 complex has 1:2 stoichiometry in vitro. Mutation of each binding site in CPSF30 still allows one copy of hFip1 to bind, while mutation of both sites abrogates binding. Our fluorescence polarization binding assays show that ZF4 has higher affinity for hFip1, with a K d of 1.8 nM. We also demonstrate that two copies of the catalytic module of poly(A) polymerase (PAP) are recruited by the CPSF30–hFip1 complex in vitro, and both hFip1 binding sites in CPSF30 can support polyadenylation.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2024

Structural and biochemical analyses of the nuclear IκBζ protein in complex with the NF-κB p50 homodimer

As part of the efforts to understand nuclear IκB function in NF-κB-dependent gene expression, we report an X-ray crystal structure of the IκBζ ankyrin repeat domain in complex with the dimerization domain of the NF-κB p50 homodimer. IκBζ possesses an N-terminal α helix that conveys domain folding stability. Affinity and specificity of the complex depend on a small portion of p50 at the nuclear localization signal. The model suggests that only one p50 subunit supports binding with IκBζ, and biochemical experiments confirm that IκBζ associates with DNA-bound NF-κB p50:RelA heterodimers. Comparisons of IκBζ:p50 and p50:κB DNA complex crystallographic models indicate that structural rearrangement is necessary for ternary complex formation of IκBζ and p50 with DNA.

Cell Biology↗
DOE OSTI2025

Emission properties of a hybrid metallized diamond(001) photocathode

The spectral emission characteristics of a proof-of-concept hybrid metallized diamond(001) photocathode are presented. The quantum efficiency (QE) is shown to be determined by the photoinjection efficiency across the ohmic contact at the back metallized face, whereas the mean transverse energy (MTE) of the photoemitted electrons is consistent with an (optical)phonon-assisted and momentum-resonant Franck-Condon mechanism [Franck-Condon electron emission from polar semiconductor photocathodes, Phys. Rev. Appl. 23, 054065 (2025)] following electron drift transport to the untreated diamond(001) front emission face. Emission is observed from both the lower and upper conduction bands of diamond with positive and negative electron affinity, respectively. A potential route to the realization of a red-visible photocathode based on this concept with a sub-50 meV MTE and a QE greater than 0.1% is discussed.

Density of states↗
DOE OSTI2023

Injection mechanisms in a III -nitride light-emitting diode as seen by self-emissive electron microscopy

Here, we report on the investigation of an electrically biased high efficiency green III-nitride light-emitting diode (LED) by electron emission microscopy (EEM) using a low-energy electron microscope (LEEM). The surface of the LED was activated to negative electron affinity via deposition of a submonolayer of Cs. With the illumination column of the LEEM turned off, upon electrical injection of the LED, we directly image the hot electrons generated by eeh Auger-Meitner nonradiative processes that diffuse through the top p-Ga N layer and emit out the surface of the biased LED. By determining the source of emitted electrons using complementary electron emission spectroscopy measurements, EEM allows us to effectively map the carrier density within the LED. Using EEM, we observed nonelectron emitting regions with a density of approximately 3 × 10 8 cm -2 , identified as V-shaped defects (V-defects). This is confirmed through the corresponding dark spots of panchromatic cathodoluminescence measurements of the same sample and by plan-view transmission electron microscopy. The absence of electron emission at the sidewall of the V-defects can be attributed to several factors, including reduced carrier density in the sidewall quantum wells due to carriers traveling fast through the semipolar sidewalls before being injected into the planar quantum wells, the reduced population of hot electrons surviving diffusion through the thicker p-GaN filling in the V-defect before emission onto vacuum, and a smaller Auger-Meitner coefficient for the low In content semipolar sidewall quantum wells. The stronger electron emission observed at the ridges of most V-defects compared to the planar quantum well regions indicates larger local injected carrier densities, confirming that V-defect sidewalls allow for strong lateral carrier injection when compared to the weaker vertical injection away from the V-defect as evidenced by the weaker electron emission intensity away from the V-defects.

71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗
DOE OSTI2025

Franck-Condon electron emission from polar semiconductor photocathodes

An analytical formulation of (optical-)phonon-mediated and momentum-resonant Franck-Condon emission of photoexcited electrons from polar semiconductors is shown to be very consistent with (i) the observed emission properties of a cesiated Ga⁢As⁢(001) photocathode at 808 nm [J. Phys. D: Appl. Phys. 54, 205301 (2021)] and (ii) the measured spectral emission properties of a Ga⁢N(0001) photocathode from just below its bandgap energy to 5 eV. The theoretical analysis in the parabolic band approximation predicts the form of both the quantum efficiency and mean transverse energy of photoemission as a function of the photocathode’s electron affinity and the electron temperature in the vicinity of its emission face. The good agreement between theory and experimental data also suggests that sub-10-nm rms surface roughness effects are not significant for polar semiconductor photocathodes.

71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗
DOE OSTI2023

Spectral emission properties of a nitrogen-doped diamond (001) photocathode: Hot electron transport and transverse momentum filtering

The electron emission properties of a single-crystal nitrogen-doped diamond(001) photocathode inserted in a 10 kV DC photoelectron gun are determined using a tunable (235–410 nm) ultraviolet laser radiation source for photoemission from both the back nitrogen-doped substrate face and the front homoepitaxially grown and undoped diamond crystal face. Here, the measured spectral trends of the mean transverse energy and quantum efficiency of the emitted electrons are both anomalous and nonmonotonic, but are shown to be consistent with (i) the known physics of electron photoexcitation from the nitrogen substitution states into the conduction bands of diamond, (ii) the energy position and dispersion characteristics of the conduction bands of diamond in the (001) emission direction, (iii) the effective electron affinity of the crystal faces, (iv) the strong electron-(optical)phonon coupling in diamond, and (v) the associated hot electron transport dynamics under energy equipartition with the optical phonons. Notably, the observed hot electron emission is shown to be restricted parallel to the photocathode surface by the low transverse effective masses of the emitting band states—a transverse momentum filtering effect.

36 MATERIALS SCIENCE↗
DOE OSTI2025

Trap-assisted Auger-Meitner recombination in GaN p-i-n diodes

Most properties of semiconductor devices are dominated by shallow impurities. However, deep defects often play an important role, for instance, in recombination processes or high field transport. While a variety of techniques are available to assess the density and energy levels of impurities, other properties, such as the recombination mechanisms of the defects, escape observation. We report on the direct measurement of hot electrons generated by trap-assisted Auger-Meitner recombination (TAAR) in GaN p-i-n diodes. By performing electron emission spectroscopy (EES) on diodes with surfaces activated to negative electron affinity by cesium, we observe the expected overflow electrons of p-i-n diodes under low current injection. However, when operating the devices at higher current densities, as low as ∼25 A/c⁢m 2 , we measure the emission of high-energy electrons. At variance with the observed hot electrons in light-emitting diodes (LEDs) using EES, the hot electrons generated in p-i-n diodes at our tested currents cannot be from eeh Auger-Meitner recombination due to the diodes' significantly lower carrier densities compared to those in LEDs. During our measurements, we observe the emission of accumulated electrons with energies ∼0.42 eV, ∼0.99 eV, ∼1.43 eV, and ∼2.32 eV above the conduction-band minimum (CBM) at various bias conditions, suggesting the existence of conduction-band features in GaN at these energies where electrons can be long-lived, such as satellite-valley minima and inflection points. We also measure incompletely relaxed hot electrons approaching energies 1.97 ± 0.13 eV and 2.94 ± 0.13 eV above the CBM, as the diodes are biased to high currents, suggesting at least some of the TAAR partaking defects have an energy level ≳1.97 eV and ≳2.94 eV away from either the conduction or valence band edges. Additionally, at our highest operating currents, we measure hot electrons with energies 3.28 ± 0.13 eV above the CBM, providing direct evidence of TAAR processes involving shallow impurities. This unexpected observation of TAAR in GaN p-i-n diodes spotlights the importance of further studies of defects in GaN and the necessity to incorporate the multi-phonon emission, radiative, and TAAR capture steps of defect-assisted recombination cycles into device modeling. Furthermore, this experiment demonstrates the applicability of the simplest semiconductor structures, p-i-n diodes, as a test bed to study the rich recombination physics of semiconductor materials.

75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗
DOE OSTI2022

Nonaffine Strains Control Ductility of Metallic Glasses

The origin of limited plasticity in metallic glasses is elusive, with no apparent link to their atomic structure. In this study, we propose that the response of the glassy structure to applied stress, not the original structure itself, provides a gauge to predict the degree of plasticity. We carried out high-energy x-ray diffraction on various bulk metallic glasses (BMGs) under uniaxial compression within the elastic limit and evaluated the anisotropic pair distribution function. We show that the extent of local deviation from the affine (uniform) deformation in the elastic regime is strongly correlated with the plastic behavior of BMGs beyond yield, across chemical compositions and sample history. The results suggest that the propensity for collective local atomic rearrangements under stress promotes plasticity.

3-dimensional systems↗
DOE OSTI2022

Numerical Evidence for a Haagerup Conformal Field Theory

We numerically study an anyon chain based on the Haagerup fusion category and find evidence that it leads in the long-distance limit to a conformal field theory whose central charge is ~2. Fusion categories generalize the concept of finite group symmetries to noninvertible symmetry operations, and the Haagerup fusion category is the simplest one which comes from neither finite groups nor affine Lie algebras. As such, ours is the first example of conformal field theories which have truly exotic generalized symmetries. Basically the same result was independently obtained in the preceding Letter [Phys. Rev. Lett. 128, 231602 (2022)].

75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗
DOE OSTI2022

Localization Effect in Photoelectron Transport Induced by Alloy Disorder in Nitride Semiconductor Compounds

Near-band-gap photoemission spectroscopy experiments were performed on p-GaN and p-InGaN/GaN photocathodes activated to negative electron affinity. Here, the photoemission quantum yield of the InGaN samples with more than 5% of indium drops by more than 1 order of magnitude when the temperature is decreased while it remains constant for lower indium content. This drop is attributed to a freezing of photoelectron transport in p-InGaN due to electron localization in the fluctuating potential induced by the alloy disorder. This interpretation is supported by the disappearance at low temperature of the peak in the photoemission spectrum that corresponds to the contribution of the photoelectrons relaxed at the bottom of the InGaN conduction band.

75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗
DOE OSTI2023

Nonmonotonic effect of chemical heterogeneity on interfacial crack growth at high-angle grain boundaries in Fe-Ni-Cr alloys

Here, an intermittent pattern is observed in the modeling of interfacial cyclic-loading crack growth at high-angle grain boundaries in ternary Fe-Ni-Cr alloys. Different from conventional wisdom of stress-intensity factor, the abrupt crack advances are found driven by extreme value statistics—namely, the aggregation of atoms with most compressive residual stresses. In addition, inherently non-affine atomic stress fluctuations are discovered, and the fluctuations peak at intermediate level of chemical heterogeneity, causing the fastest crack growth. Implications of such nonmonotonic mechanism in regard to the origin of intermediate-temperature embrittlement phenomena are also discussed.

36 MATERIALS SCIENCE↗
DOE OSTI2024

Optical tuning of the diamond Fermi level measured by correlated scanning probe microscopy and quantum defect spectroscopy

Quantum technologies based on quantum point defects in crystals require control over the defect charge state. Here we tune the charge state of shallow nitrogen-vacancy and silicon-vacancy centers by locally oxidizing a hydrogenated surface with moderate optical excitation and simultaneous spectral monitoring. The loss of conductivity and change in work function due to oxidation are measured in atmosphere using conductive atomic force microscopy and Kelvin probe force microscopy (KPFM). We correlate these scanning probe measurements with optical spectroscopy of the nitrogen-vacancy and silicon-vacancy centers created via implantation 15–25 nm beneath the diamond surface and annealing. The observed charge state of the defects as a function of optical exposure demonstrates that laser oxidation provides a way to precisely tune the Fermi level over a range of at least 2.00 eV. We also observe a significantly larger oxidation rate for implanted surfaces compared to unimplanted surfaces under ambient conditions. Here, combined with knowledge of the electron affinity of a surface, these results suggest KPFM is a powerful, high-spatial-resolution technique to advance surface Fermi level engineering for charge stabilization of quantum defects.

36 MATERIALS SCIENCE↗
DOE OSTI2025

Geometric origin of the energy-momentum tensor improvement terms

In a flat background, the canonical energy momentum tensor of Lorentz and conformally invariant matter field theories can be improved to a symmetric and traceless tensor that gives the same conserved charges. We argue that the geometric origin of this improvement process is unveiled when the matter theory is coupled to metric-affine gravity. In particular, we show that the Belinfante-Rosenfeld improvement terms correspond to the matter theory’s hypermomentum. The improvement terms in conformally invariant matter theories are also related to the hypermomentum; however, a general proof would require an extended investigation. We demonstrate our results through various examples, such as the free massless scalar, the Maxwell field, Abelian p-forms, the Dirac field, and a nonunitary massless scalar field. Possible applications of our method for theories that break Lorentz or special conformal invariance are briefly discussed.

classical solutions in field theory↗
DOE OSTI2020

Compensatory Guaiacyl Lignin Biosynthesis at the Expense of Syringyl Lignin in 4CL1 -Knockout Poplar -Knockout Poplar

The lignin biosynthetic pathway is highly conserved in angiosperms, yet pathway manipulations give rise to a variety of taxon-specific outcomes. Knockout of lignin-associated 4-coumarate:CoA ligases (4CLs) in herbaceous species mainly reduces guaiacyl (G) lignin and enhances cell wall saccharification. In this work we show that CRISPR-knockout of 4CL1 in poplar (Populus tremula x alba) preferentially reduced syringyl (S) lignin, with negligible effects on biomass recalcitrance. Concordant with reduced S-lignin was downregulation of ferulate 5-hydroxylases (F5Hs). Lignification was largely sustained by 4CL5, a low-affinity paralog of 4CL1 typically with only minor xylem expression or activity. Levels of caffeate, the preferred substrate of 4CL5, increased in line with significant upregulation of caffeoyl shikimate esterase1. Upregulation of caffeoyl-CoA O-methyltransferase1 and downregulation of F5Hs are consistent with preferential funneling of 4CL5 products toward G-lignin biosynthesis at the expense of S-lignin. Thus, transcriptional and metabolic adaptations to 4CL1-knockout appear to have enabled 4CL5 catalysis at a level sufficient to sustain lignification. Finally, genes involved in sulfur assimilation, the glutathione-ascorbate cycle, and various antioxidant systems were upregulated in the mutants, suggesting cascading responses to perturbed thioesterification in lignin biosynthesis.

09 BIOMASS FUELS↗
DOE OSTI2023

Quantifying molecular deformation in polymer melts by a generalized Zimm plot approach

The Zimm plot has been widely used to characterize the molecular dimensions of polymers from small-angle scattering experiments, where the reciprocal intensity is analyzed as a function of the square of the magnitude of the scattering wavevector Q. Here, this work explores the benefits of analyzing the reciprocal scattering intensity from deformed polymers, extending the original Zimm plot to anisotropic materials. In the small-angle limit, a tensorial extension of the Guinier law is found for the gyration tensor and the reciprocal single-chain structure factor. In the high-Q limit, application of the spherical harmonic expansion technique to the reciprocal structure factor permits direct model-independent analysis of spatially dependent molecular deformation of polymers. Additionally, the contributions from high-order spherical harmonics become insignificant in the reciprocal-intensity representation. The proposed generalized Zimm plot approach is demonstrated computationally with the affine deformation model and the Rouse model, and experimentally with small-angle neutron scattering measurements of deformed polystyrene melts.

36 MATERIALS SCIENCE↗
DOE OSTI2022

Diffuse X-ray scattering from polished silicon: application of the distorted wave Born approximation

Measured diffuse X-ray scattering data for a `smooth' as well as for a `rough' silicon sample were fit to theoretical expressions within the distorted wave Born approximation (DWBA). Data for the power spectral density (PSD) for both samples were also obtained by means of atomic force microscopy and optical interferometry. The Fourier transforms of trial correlation functions were fit to the PSD data and then applied to the DWBA formalism. The net correlation functions needed to fit the PSD data for each sample comprised the sum of two terms with different cutoff lengths and different self-affine fractal exponents. At zero distance these correlation functions added up to yield net values of σ 2 = (2) 2 and (71) 2 Å 2 for the smooth and rough samples, respectively. X-ray scattering data were obtained at beamline 1-BM of the Advanced Photon Source. Data and fits at values of q z = 0.05 and 0.10 Å −1 for the smooth sample are reported. Good fits for the smooth sample were obtained at both q z values simultaneously, that is, identical fitting parameters were applied at both values of q z . The smooth sample also exhibited weak Yoneda wings and a clear distinction between the strong specular scattering and the weak diffuse scattering. Data for the rough sample were qualitatively different and exhibited very weak scattering at the specular condition in contrast to extremely large Yoneda wings. Fits for the rough sample are reported for q z = 0.04, 0.05, and 0.06 Å −1 . Although the large Yoneda wings could be fit quite well in both position and amplitude, scattering near the specular condition could not be equally well fit by applying the same fitting parameters at all values of q z . Albeit imperfect, best-fitting results at the specular condition were obtained by invoking only diffuse scattering, that is, without including a separate theoretical expression for specular scattering.

73 NUCLEAR PHYSICS AND RADIATION PHYSICS↗