Search NASA⌕ Search

SEARCH · Search NASA

Results for “correlation screening”

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 307 records · Page 17
All sourcesNASA NTRSDOE OSTI
DOE OSTI2018

LncRNA CALML3-AS1 promotes tumorigenesis of bladder cancer via regulating ZBTB2 by suppression of microRNA-4316

An increasing number of studies have elucidated the essential roles of long noncoding RNAs (lncRNAs) in tumor development. LncRNAs are also closely associated with bladder cancer (BCa) progression. In the present study, we screened out a novel lncRNA CALML3-AS1 with increased expression value in BCa tissues. Particularly, we showed that CALML3-AS1 overexpression correlates with advanced staging and an unsatisfactory prognosis. Functional experiments illustrated that CALML3-AS1 knockdown suppressed BCa cell proliferation, arrested cell-cycle progression and impaired migration and invasion while promoting apoptosis. Mechanistic investigation revealed that CALML3-AS1 directly interacts with miR-4316 and inhibits its availability in BCa cells, leading to elevated expression of ZBTB2. Consequently, ZBTB2 promotes BCa tumorigenesis through repressing p21 and facilitating PDK4 transcription. In conclusion, our findings demonstrate a novel CALML3-AS1-mediated process involved in BCa progression and indicate it might be a promising therapeutic target.

60 APPLIED LIFE SCIENCES↗
DOE OSTI2020

Stochastically Realized Observables for Excitonic Molecular Aggregates

In this work, we show that a stochastic approach enables calculations of the optical properties of large 2-dimensional and nanotubular excitonic molecular aggregates. Previous studies of such systems relied on numerically diagonalizing the dense and disordered Frenkel Hamiltonian, which scales approximately as $\mathcal{O}$($N$ 3 ) for $N$ dye molecules. Our approach scales much more efficiently as $\mathcal{O}$($N$ log($N$)), enabling quick study of systems with a million of coupled molecules on the micrometer size scale. We calculate several important experimental observables, including the optical absorption spectrum and density of states, and develop a stochastic formalism for the participation ratio. Quantitative agreement with traditional matrix diagonalization methods is demonstrated for both small- and intermediate-size systems. The stochastic methodology enables the study of the effects of spatial-correlation in site energies on the optical signatures of large 2D aggregates. Our results demonstrate that stochastic methods present a path forward for screening structural parameters and validating experiments and theoretical predictions in large excitonic aggregates.

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

Pan-cancer proteogenomic investigations identify post-transcriptional kinase targets

Identifying genomic alterations of cancer proteins has guided the development of targeted therapies, but proteomic analyses are required to validate and reveal new treatment opportunities. Herein, we develop a new algorithm, OPPTI, to discover overexpressed kinase proteins across 10 cancer types using global mass spectrometry proteomics data of 1,071 cases. OPPTI outperforms existing methods by leveraging multiple co-expressed markers to identify targets overexpressed in a subset of tumors. OPPTI-identified overexpression of ERBB2 and EGFR proteins correlates with genomic amplifications, while CDK4/6, PDK1, and MET protein overexpression frequently occur without corresponding DNA- and RNA-level alterations. Analyzing CRISPR screen data, we confirm expression-driven dependencies of multiple currently-druggable and new target kinases whose expressions are validated by immunochemistry. Identified kinases are further associated with up-regulated phosphorylation levels of corresponding signaling pathways. Collectively, our results reveal protein-level aberrations—sometimes not observed by genomics—represent cancer vulnerabilities that may be targeted in precision oncology.

60 APPLIED LIFE SCIENCES↗
DOE OSTI2015

Low-energy positron scattering by pyrimidine

This work reports elastic integral and differential cross sections for positron collisions with pyrimidine, for energies up to 20 eV. The cross sections were computed with the Schwinger multichannel method in the static plus polarization approximation. We also employed the Born closure procedure to account for the long range potential due to the permanent dipole moment of the molecule. Our results are compared with the experimental total cross section of Zecca et al. [J. Phys. B 43, 215204 (2010)], the experimental grand-total, quasi-elastic integral and differential cross section of Palihawadana et al. [Phys. Rev. A 88, 12717 (2013)]. We also compare our results with theoretical integral and differential cross sections obtained by Sanz et al. [Phys. Rev. A 88, 62704 (2013)] with the R-matrix and the independent atom model with screening-corrected additivity rule methods, and with the results computed by Franz and Gianturco [Phys. Rev. A 88, 042711 (2013)] using model correlation-polarization potentials. The agreement between the theory and the experiment is encouraging.

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

Mixed Stochastic-Deterministic Approach for Many-Body Perturbation Theory Calculations

Here, we present an approach for GW calculations of quasiparticle energies with quasi-quadratic scaling by approximating high-energy contributions to the Green's function in its Lehmann representation with effective stochastic vectors. The method is easy to implement without altering the GW code, converges rapidly with stochastic parameters, and treats systems of various dimensionality and screening response. Our calculations on a 5.75° twisted MoS 2 bilayer show how large-scale GW methods include geometry relaxations and electronic correlations on an equal basis in structurally nontrivial materials.

36 MATERIALS SCIENCE↗
NASA NTRS2000

Physics of Hard Spheres Experiment: Significant and Quantitative Findings Made

Direct examination of atomic interactions is difficult. One powerful approach to visualizing atomic interactions is to study near-index-matched colloidal dispersions of microscopic plastic spheres, which can be probed by visible light. Such spheres interact through hydrodynamic and Brownian forces, but they feel no direct force before an infinite repulsion at contact. Through the microgravity flight of the Physics of Hard Spheres Experiment (PHaSE), researchers have sought a more complete understanding of the entropically driven disorder-order transition in hard-sphere colloidal dispersions. The experiment was conceived by Professors Paul M. Chaikin and William B. Russel of Princeton University. Microgravity was required because, on Earth, index-matched colloidal dispersions often cannot be density matched, resulting in significant settling over the crystallization period. This settling makes them a poor model of the equilibrium atomic system, where the effect of gravity is truly negligible. For this purpose, a customized light-scattering instrument was designed, built, and flown by the NASA Glenn Research Center at Lewis Field on the space shuttle (shuttle missions STS 83 and STS 94). This instrument performed both static and dynamic light scattering, with sample oscillation for determining rheological properties. Scattered light from a 532- nm laser was recorded either by a 10-bit charge-coupled discharge (CCD) camera from a concentric screen covering angles of 0 to 60 or by sensitive avalanche photodiode detectors, which convert the photons into binary data from which two correlators compute autocorrelation functions. The sample cell was driven by a direct-current servomotor to allow sinusoidal oscillation for the measurement of rheological properties. Significant microgravity research findings include the observation of beautiful dendritic crystals, the crystallization of a "glassy phase" sample in microgravity that did not crystallize for over 1 year in 1g (Earth's gravity), and the emergence of face-centered-cubic (FCC) crystals late in the coarsening process (as small crystallites lost particles to the slow ripening of large crystallites). Significant quantitative findings from the microgravity experiments have been developed describing complex interactions among crystallites during the growth process, as concentration fields overlap in the surrounding disordered phase. Time-resolved Bragg scattering under microgravity captures one effect of these interactions quite conclusively for the sample at a volume fraction of 0.528. From the earliest time until the sample is almost fully crystalline, the size and overall crystallinity grow monotonically, but the number of crystallites per unit volume (number density) falls. Apparently nucleation is slower than the loss of crystallites because of the transfer of particles from small to large crystals. Thus, coarsening occurs simultaneously with growth, rather than following the completion of nucleation and growth as is generally assumed. In the same sample, an interesting signature appears in the apparent number density of crystallites and the volume fraction within the crystallites shortly before full crystallinity is reached. A brief upturn in both indicates the creation of more domains of the size of the average crystallite simultaneous with the compression of the crystallites. Only the emergence of dendritic arms offers a reasonable explanation. The arms would be "seen" by the light scattering as separate domains whose smaller radii of curvature would compress the interior phase. In fiscal year 1999, numerous papers, a doctoral dissertation, and the PHaSE final report were produced. Although this flight project has been completed, plans are in place for a follow-on colloid experiment by Chaikin and Russel that employs a light microscope within Glenn's Fluids and Combustion Facility on the International Space Station. PHaSE is providing us with a deeper understanding of the nure of phase transitions. The knowledge derived has added to the understanding of condensed matter. In addition, the burgeoning study of the dynamics of colloidal self-assembly may lead to the development of a range of photonic materials that control the desirable properties of light. Thus, applications of ordered colloidal structures include not only ultrastructure ceramics, but also photonic crystals and photothermal nanosecond light-switching devices. Industries dealing with semiconductors, electro-optics, ceramics, and composites stand to benefit from such advancements.

Doherty, Michael P.↗
DOE OSTI2018

Representing local atomic environment using descriptors based on local correlations

Statistical learning of material properties is an emerging topic of research and has been tremendously successful in areas such as representing complex energy landscapes as well as in technologically relevant areas, like identification of better catalysts and electronic materials. However, analysis of large data sets to efficiently learn characteristic features of a complex energy landscape, for example, depends on the ability of descriptors to effectively screen different local atomic environments. Thus, discovering appropriate descriptors of bulk or defect properties and the functional dependence of such properties on these descriptors remains a difficult and tedious process. To this end, we develop here a framework to generate descriptors based on many-body correlations that can effectively capture intrinsic geometric features of the local environment of an atom. These descriptors are based on the spectrum of two-body, three-body, four-body, and higher order correlations between an atom and its neighbors and are evaluated by calculating the corresponding two-body, three-body, and four-body overlap integrals. They are invariant to global translation, global rotation, reflection, and permutations of atomic indices. By systematically testing the ability to capture the local atomic environment, it is shown that the local correlation descriptors are able to successfully reconstruct structures containing 10-25 atoms which was previously not possible.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2026

Production and Evaluation of Fluorophore-Doped Polymer Substrates to Screen for Plastic-Degrading Enzymes

Fast and sensitive analytical methods are the key to efficient screening of plastic-degrading enzymes. Here, we present a streamlined and affordable approach to assess the enzymatic deconstruction of insoluble synthetic polymers by blending them with a fluorescent dye, rhodamine 6G, and we evaluate this screening method using poly(ethylene terephthalate) (PET) as a model material. Our results indicate that enzymatic depolymerization of the rhodamine-doped PET can be observed in a high-throughput fashion by following release of the fluorophore. The fluorescence data obtained during the hydrolysis of rhodamine-doped PET by 14 PET hydrolases, produced with a robotic platform, correlated with the quantitative chromatographic analysis of PET degradation products. Remarkably, the use of the rhodamine-loaded PET substrate resulted in negligibly low background signals even when detecting PETase activity in crude cell lysates, suggesting suitability for screening of a wide variety of samples. Encouraged by these results, we next produced a selection of polyethylene- and nylon-based materials loaded with rhodamine 6G. While rapid leaching of fluorophore observed with nylon substrates limits the utility of the method for detecting nylonase activity, the rhodamine-loaded polyethylene showed promising performance in passive diffusion tests, indicating that this latter substrate may be used to screen for polyolefin-degrading enzymes.

09 BIOMASS FUELS↗
DOE OSTI2025

Breakdown of the Static Dielectric Screening Approximation of Coulomb Interactions in Atomically Thin Semiconductors

Coulomb interactions in atomically thin materials are remarkably sensitive to variations in the dielectric screening of the environment, which can be used to control exotic quantum many-body phases and engineer exciton potential landscapes. For decades, static or frequency-independent approximations of the dielectric response, where increased dielectric screening is predicted to cause an energy redshift of the exciton resonance, have been sufficient. These approximations were first applied to quantum wells and were more recently extended with initial success to layered transition metal dichalcogenides (TMDs). Here, we use charge-tunable exciton resonances to investigate screening effects in TMD monolayers embedded in materials with low-frequency dielectric constants ranging from 4 to more than 1000, a range of 2 orders of magnitude larger than in previous studies. In contrast to the redshift predicted by static models, we observe a blueshift of the exciton resonance exceeding 30 meV in higher dielectric constant environments. We explain our observations by introducing a dynamical screening model based on a solution to the Bethe-Salpeter equation (BSE). When dynamical effects are strong, we find that the exciton binding energy remains mostly controlled by the low-frequency dielectric response, while the exciton self-energy is dominated by the high-frequency one. Our results supplant the understanding of screening in layered materials and their heterostructures, introduce a knob to tune selected many-body effects, and reshape the framework for detecting and controlling correlated quantum many-body states and designing optoelectronic and quantum devices.

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

Understanding the effect of density functional choice and van der Waals treatment on predicting the binding configuration, loading, and stability of amine-grafted metal organic frameworks

Metal organic frameworks (MOFs) are crystalline, three-dimensional structures with high surface areas and tunable porosities. Made from metal nodes connected by organic linkers, the exact properties of a given MOF are determined by node and linker choice. MOFs hold promise for numerous applications, including gas capture and storage. M2(4,4′-dioxidobiphenyl-3,3′-dicarboxylate)—henceforth simply M2(dobpdc), with M = Mg, Mn, Fe, Co, Ni, Cu, or Zn—is regarded as one of the most promising structures for CO2 capture applications. Further modification of the MOF with diamines or tetramines can significantly boost gas species selectivity, a necessity for the ultra-dilute CO2 concentrations in the direct-air capture of CO2. There are countless potential diamines and tetramines, paving the way for a vast number of potential sorbents to be probed for CO2 adsorption properties. The number of amines and their configuration in the MOF pore are key drivers of CO2 adsorption capacity and kinetics, and so a validation of computational prediction of these quantities is required to suitably use computational methods in the discovery and screening of amine-functionalized sorbents. In this work, we study the predictive accuracy of density functional theory and related calculations on amine loading and configuration for one diamine and two tetramines. In particular, we explore the Perdew–Burke–Ernzerhof (PBE) functional and its formulation for solids (PBEsol) with and without the Grimme-D2 and Grimme-D3 pairwise corrections (PBE+D2/3 and PBEsol+D2/3), two revised PBE functionals with the Grimme-D2 and Grimme-D3 pairwise corrections (RPBE+D2/3 and revPBE+D2/3), and the nonlocal van der Waals correlation (vdW-DF2) functional. We also investigate a universal graph deep learning interatomic potential’s (M3GNet) predictive accuracy for loading and configuration. These results allow us to identify a useful screening procedure for configuration prediction that has a coarse component for quick evaluation and a higher accuracy component for detailed analysis. Our general observation is that the neural network-based potential can be used as a high-level and rapid screening tool, whereas PBEsol+D3 gives a completely qualitatively predictive picture across all systems studied, and can thus be used for high accuracy motif predictions. We close by briefly exploring the predictions of relative thermal stability for the different functionals and dispersion corrections.

Chemistry↗
DOE OSTI2024

Strongly coupled edge states in a graphene quantum Hall interferometer

Electronic interferometers using the chiral, one-dimensional (1D) edge channels of the quantum Hall effect (QHE) can demonstrate a wealth of fundamental phenomena. The recent observation of phase jumps in a Fabry-Pérot (FP) interferometer revealed anyonic quasiparticle exchange statistics in the fractional QHE. When multiple integer edge channels are involved, FP interferometers have exhibited anomalous Aharonov-Bohm (AB) interference frequency doubling, suggesting putative pairing of electrons into 2e quasiparticles. Here, we use a highly tunable graphene-based QHE FP interferometer to observe the connection between interference phase jumps and AB frequency doubling, unveiling how strong repulsive interaction between edge channels leads to the apparent pairing phenomena. By tuning electron density in-situ from filling factor v < 2 to v > 7, we tune the interaction strength and observe periodic interference phase jumps leading to AB frequency doubling. Our observations demonstrate that the combination of repulsive interaction between the spin-split v = 2 edge channels and charge quantization is sufficient to explain the frequency doubling, through a near-perfect charge screening between the localized and extended edge channels. Our results show that interferometers are sensitive probes of microscopic interactions and enable future experiments studying correlated electrons in 1D channels using density-tunable graphene.

42 ENGINEERING↗
DOE OSTI2024

Delocalization error poisons the density-functional many-body expansion

The many-body expansion is a fragment-based approach to large-scale quantum chemistry that partitions a single monolithic calculation into manageable subsystems. This technique is increasingly being used as a basis for fitting classical force fields to electronic structure data, especially for water and aqueous ions, and for machine learning. Here, we show that the many-body expansion based on semilocal density functional theory affords wild oscillations and runaway error accumulation for ion–water interactions, typified by F − (H 2 O) N with N ≳ 15. We attribute these oscillations to self-interaction error in the density-functional approximation. The effect is minor or negligible in small water clusters, explaining why it has not been noticed previously, but grows to catastrophic proportion in clusters that are only moderately larger. This behavior can be counteracted with hybrid functionals but only if the fraction of exact exchange is ≳50%, whereas modern meta-generalized gradient approximations including ωB97X-V, SCAN, and SCAN0 are insufficient to eliminate divergent behavior. Other mitigation strategies including counterpoise correction, density correction (i.e., exchange–correlation functionals evaluated atop Hartree–Fock densities), and dielectric continuum boundary conditions do little to curtail the problematic oscillations. In contrast, energy-based screening to cull unimportant subsystems can successfully forestall divergent behavior. These results suggest that extreme caution is warranted when the many-body expansion is combined with density functional theory.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2018

Time-resolved electron spectroscopy for chemical analysis of photodissociation: Photoelectron spectra of Fe(CO) 5 , Fe(CO) 4 , and Fe(CO) 3

The prototypical photoinduced dissociation of Fe(CO) 5 in the gas phase is used to test time-resolved x-ray photoelectron spectroscopy for studying photochemical reactions. Upon one-photon excitation at 266 nm, Fe(CO) 5 successively dissociates to Fe(CO) 4 and Fe(CO) 3 along a pathway where both fragments retain the singlet multiplicity of Fe(CO) 5 . The x-ray free-electron laser FLASH is used to probe the reaction intermediates Fe(CO) 4 and Fe(CO) 3 with time-resolved valence and core-level photoelectron spectroscopy, and experimental results are interpreted with ab initio quantum chemical calculations. Changes in the valence photoelectron spectra are shown to reflect changes in the valence-orbital interactions upon Fe–CO dissociation, thereby validating fundamental theoretical concepts in Fe–CO bonding. Chemical shifts of CO 3σ inner-valence and Fe 3p core-level binding energies are shown to correlate with changes in the coordination number of the Fe center. We interpret this with coordination-dependent charge localization and core-hole screening based on calculated changes in electron densities upon core-hole creation in the final ionic states. This extends the established capabilities of steady-state electron spectroscopy for chemical analysis to time-resolved investigations. Lastly, it could also serve as a benchmark for how charge and spin density changes in molecular dissociation and excited-state dynamics are expressed in valence and core-level photoelectron spectroscopy.

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

Universal dynamics of coarsening during polymer-polymer thin-film spinodal dewetting kinetics

The dewetting dynamics of a supported bilayer polymer thin film on a solid substrate is investigated using grazing incidence x-ray photon correlation spectroscopy. We find that the top layer dewets via the spinodal mechanism. The kinetics of the dewetting is studied by monitoring the time evolution of the surface diffuse x-ray scattering intensity. We study the time evolution of fluctuations about the average surface structure by measuring the two-time x-ray intensity fluctuation correlation functions. Using these two-time correlation functions we quantify the crossover from early-time diffusive dynamics to hydrodynamics. The early diffusive regime satisfies dynamic universality. The two-time correlation functions also quantify the onset of hydrodynamic effects. The hydrodynamic regime is observed during the spinodal dewetting process as these interactions are not screened.

36 MATERIALS SCIENCE↗
DOE OSTI2017

A Comprehensive Docking and MM/GBSA Rescoring Study of Ligand Recognition upon Binding Antithrombin

A high-throughput virtual screening pipeline has been extended from single energetically minimized structure Molecular Mechanics/Generalized Born Surface Area (MM/GBSA) rescoring to ensemble-average MM/GBSA rescoring. The correlation coefficient (R2) of calculated and experimental binding free energies for a series of antithrombin ligands has been improved from 0.36 to 0.69 when switching from the single-structure MM/GBSA rescoring to ensemble-average one. The electrostatic interactions in both solute and solvent are identified to play an important role in determining the binding free energy after the decomposition of the calculated binding free energy. Furthermore, the increasing negative charge of the compounds provides a more favorable electrostatic energy change but creates a higher penalty for the solvation free energy. Such a penalty is compensated by the electrostatic energy change, which results in a better binding affinity. A highly hydrophobic ligand is determined by the docking program to be a non-specific binder. Finally, these results have demonstrated that it is very important to keep a few top poses for rescoring, if the binding is non-specific or the binding mode is not well determined by the docking calculation.

59 BASIC BIOLOGICAL SCIENCES↗
NASA NTRS1995

Pulse-echo ultrasonic imaging method for eliminating sample thickness variation effects

A pulse-echo, immersion method for ultrasonic evaluation of a material is discussed. It accounts for and eliminates nonlevelness in the equipment set-up and sample thickness variation effects employs a single transducer, automatic scanning and digital imaging to obtain an image of a property of the material, such as pore fraction. The nonlevelness and thickness variation effects are accounted for by pre-scan adjusments of the time window to insure that the echoes received at each scan point are gated in the center of the window. This information is input into the scan file so that, during the automatic scanning for the material evaluation, each received echo is centered in its time window. A cross-correlation function calculates the velocity at each scan point, which is then proportionalized to a color or grey scale and displayed on a video screen.

Roth, Don J.↗
NASA NTRS1997

Pulse-Echo Ultrasonic Imaging Method for Eliminating Sample Thickness Variation Effects

A pulse-echo, immersion method for ultrasonic evaluation of a material which accounts for and eliminates nonlevelness in the equipment set-up and sample thickness variation effects employs a single transducer and automatic scanning and digital imaging to obtain an image of a property of the material, such as pore fraction. The nonlevelness and thickness variation effects are accounted for by pre-scan adjustments of the time window to insure that the echoes received at each scan point are gated in the center of the window. This information is input into the scan file so that, during the automatic scanning for the material evaluation, each received echo is centered in its time window. A cross-correlation function calculates the velocity at each scan point, which is then proportionalized to a color or grey scale and displayed on a video screen.

Roth, Don J.↗
NASA NTRS1999

Determination of Radiative Forcing of Saharan Dust using Combined TOMS and ERBE Data

The direct radiative forcing of Saharan dust aerosols has been determined by combining aerosol information derived from Nimbus-7 TOMS with radiation measurements observed at the top of atmosphere (TOA) by NOAA-9 ERBE made during February-July 1985. Cloud parameters and precipitable water derived from the NOAA-9 HIRS2 instrument were used to aid in screening for clouds and water vapor in the analyses. Our results indicate that under "cloud-free" and "dry" conditions there is a good correlation between the ERBE TOA outgoing longwave fluxes and the TOMS aerosol index measurements over both land and ocean in areas under the influence of airborne Saharan dust. The ERBE TOA outgoing shortwave fluxes were also found to correlate well with the dust loading derived from TOMS over ocean. However, the calculated shortwave forcing of Saharan dust aerosols is very weak and noisy over land for the range of solar zenith angle viewed by the NOAA-9 ERBE in 1985. Sensitivity factors of the TOA outgoing fluxes to changes in aerosol index were estimated using a linear regression fit to the ERBE and TOMS measurements. The ratio of the shortwave-to-longwave response to changes in dust loading over the ocean is found to be roughly 2 to 3, but opposite in sign. The monthly averaged "clear-sky" TOA direct forcing of airborne Saharan dust was also calculated by multiplying these sensitivity factors by the TOMS monthly averaged "clear-sky" aerosol index. Both the observational and theoretical analyses indicate that the dust layer height, ambient moisture content as well as the presence of cloud all play an important role in determining the TOA direct radiative forcing due to mineral aerosols.

Hsu, N. Christina↗