Search NASA⌕ Search

Engineering topics

Xu, Yang

Publications and source records attributed to Xu, Yang.

At least 19 records
All sourcesNASA NTRSDOE OSTI
DOE OSTI2023

Orthogonal spatial coding with stimulated parametric down-conversion

Orthogonal optical coding is widely used in classical multi-user communication networks. Using the phase conjugation property of stimulated parametric down-conversion, we extend the current time-domain orthogonal optical coding scheme to the spatial domain to encode and decode image information. In this process, the idler beam inherits the complex conjugate of the field information encoded in the seed beam. An encoding phase mask introduced onto the input seed beam blurs the image transferred to the idler. The original image is restored by passing the coded transferred image through a corrective phase mask placed in the momentum space of the idler beam. We expect that this scheme can also inspire new techniques in secure image transmission, aberration cancellation, and frequency conversion imaging.

Xu, Yang↗
DOE OSTI2023

Gate-Tunable Multiband Transport in ZrTe 5 Thin Devices

Interest in ZrTe 5 has been reinvigorated in recent years owing to its potential for hosting versatile topological electronic states and intriguing experimental discoveries. However, the mechanism of many of its unusual transport behaviors remains controversial: for example, the characteristic peak in the temperature-dependent resistivity and the anomalous Hall effect. Here, through employing a clean dry-transfer fabrication method in an inert environment, we successfully obtain high-quality ZrTe 5 thin devices that exhibit clear dual-gate tunability and ambipolar field effects. Such devices allow us to systematically study the resistance peak as well as the Hall effect at various doping densities and temperatures, revealing the contribution from electron–hole asymmetry and multiple-carrier transport. By comparing with theoretical calculations, we suggest a simplified semiclassical two-band model to explain the experimental observations. Finally, our work helps to resolve the longstanding puzzles on ZrTe 5 and could potentially pave the way for realizing novel topological states in the two-dimensional limit.

75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗
DOE OSTI2022

Reconciliation of asynchronous satellite-based $\mathrm{NO_2}$ and $\mathrm{XCO_2}$ enhancements with mesoscale modeling over two urban landscapes

Fossil fuel carbon dioxide (CO 2ff ), the main driver of global warming and climate change, is often co-emitted with nitrogen oxides (NO x ) and precursors to ground-level ozone from anthropogenic sources like power plants or vehicles. In urban and suburban areas, satellite-based NO 2 can be used as a proxy to track the emissions of CO 2ff . Because of NO 2 ’s shorter lifetime, urban NO 2 plumes are more distinguishable from backgrounds and more sensitive to variations in emissions. However, the combination of these two gases is limited by the asynchrony among NO 2 and CO 2 monitoring satellites. We used CO 2ff simulated by the Weather Research and Forecasting model coupled with Chemistry (WRF-Chem) model to reconcile the tropospheric NO 2 vertical column density (VCD) from the Tropospheric Monitoring Instrument (TROPOMI) and column-averaged dry-air mole fractions of carbon dioxide enhancements (ΔXCO 2 ) from Orbiting Carbon Observatory 3 (OCO-3) Snapshot Area Maps (SAMs) over a multicity area, Washington D.C.-Baltimore (DC-Balt), and a basin city, Mexico City. NO 2 /CO 2ff ratios over DC-Balt are smaller than Mexico City, indicative of stricter emission restrictions, a more combustion-efficient vehicle fleet, and higher combustion efficiency due to lower altitude in DC-Balt. For single-track cases, the spatial correlations between NO 2 and ΔXCO 2 over Mexico City are stronger than DC-Balt because the NO 2 and CO 2 are mostly trapped in the valley of Mexico City, while DC-Balt is severely affected by distant sources (i.e., US East Coast cities). Using multi-track averaging, spatial correlation coefficients increase with the number of days used for averaging. The correlations reached a maximum when averaging >12 continuous images for DC-Balt and > 10 continuous images for Mexico City. This finding indicates that multi-track averaging using modeled CO 2ff as a proxy is helpful to filter the noise in single-track images, to cancel the interference from distant sources, and to magnify correlations between NO 2 and CO 2ff . Mexico City showed stronger spatial correlations but weaker temporal correlations than DC-Balt due to biomass burning hot spots and large transport errors caused by the trapping effects of the surrounding mountains. Tracking the 20-day moving average of CO 2ff emissions using TROPOMI NO 2 seems technically feasible, considering the relationship between correlation coefficients and the number of available satellite images.

54 ENVIRONMENTAL SCIENCES↗
DOE OSTI2022

sciCAN: single-cell chromatin accessibility and gene expression data integration via cycle-consistent adversarial network

The boom in single-cell technologies has brought a surge of high dimensional data that come from different sources and represent cellular systems from different views. With advances in these single-cell technologies, integrating single-cell data across modalities arises as a new computational challenge. Here, we present an adversarial approach, sciCAN, to integrate single-cell chromatin accessibility and gene expression data in an unsupervised manner. We benchmarked sciCAN with 5 existing methods in 5 scATAC-seq/scRNA-seq datasets, and we demonstrated that our method dealt with data integration with consistent performance across datasets and better balance of mutual transferring between modalities than the other 5 existing methods. We further applied sciCAN to 10X Multiome data and confirmed that the integrated representation preserves biological relationships within the hematopoietic hierarchy. Finally, we investigated CRISPR-perturbed single-cell K562 ATAC-seq and RNA-seq data to identify cells with related responses to different perturbations in these different modalities.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2022

Coarse-Grained Simulations for the Characterization and Optimization of Hybrid Protein–DNA Nanostructures

We present here the combination of experimental and computational modeling tools for the design and characterization of protein–DNA hybrid nanostructures. Our work incorporates several features in the design of these nanostructures: (1) modeling of the protein–DNA linker identity and length; (2) optimizing the design of protein–DNA cages to account for mechanical stresses; (3) probing the incorporation efficiency of protein–DNA conjugates into DNA nanostructures. The modeling tools were experimentally validated using structural characterization methods like cryo-TEM and AFM. Our method can be used for fitting low-resolution electron density maps when structural insights cannot be deciphered from experiments, as well as enable in-silico validation of nanostructured systems before their experimental realization. Finally, these tools will facilitate the design of complex hybrid protein–DNA nanostructures that seamlessly integrate the two different biomolecules.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2022

Active conformation of the p97-p47 unfoldase complex

The p97 AAA+ATPase is an essential and abundant regulator of protein homeostasis that plays a central role in unfolding ubiquitylated substrates. Here we report two cryo-EM structures of human p97 in complex with its p47 adaptor. One of the conformations is six-fold symmetric, corresponds to previously reported structures of p97, and lacks bound substrate. The other structure adopts a helical conformation, displays substrate running in an extended conformation through the pore of the p97 hexamer, and resembles structures reported for other AAA unfoldases. These findings support the model that p97 utilizes a “hand-over-hand” mechanism in which two residues of the substrate are translocated for hydrolysis of two ATPs, one in each of the two p97 AAA ATPase rings. Proteomics analysis supports the model that one p97 complex can bind multiple substrate adaptors or binding partners, and can process substrates with multiple types of ubiquitin modification.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2021

Chromosome compartmentalization alterations in prostate cancer cell lines model disease progression

Prostate cancer aggressiveness and metastatic potential are influenced by gene expression and genomic aberrations, features that can be influenced by the 3D structure of chromosomes inside the nucleus. Using chromosome conformation capture (Hi-C), we conducted a systematic genome architecture comparison on a cohort of cell lines that model prostate cancer progression, from normal epithelium to bone metastasis. We describe spatial compartment identity (A-open versus B-closed) changes with progression in these cell lines and their relation to gene expression changes in both cell lines and patient samples. In particular, 48 gene clusters switch from the B to the A compartment, including androgen receptor, WNT5A, and CDK14. These switches are accompanied by changes in the structure, size, and boundaries of topologically associating domains (TADs). Further, compartment changes in chromosome 21 are exacerbated with progression and may explain, in part, the genesis of the TMPRSS2-ERG translocation. These results suggest that discrete 3D genome structure changes play a deleterious role in prostate cancer progression.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2021

Proteins associated with the Arabidopsis thaliana plastid rhomboid-like protein RBL10

Rhomboid-like proteins are intramembrane proteases with a variety of regulatory roles in cells. Though many rhomboid-like proteins are predicted in plants, their detailed molecular mechanisms or cellular functions are not yet known. Of the 13 predicted rhomboids in Arabidopsis thaliana, one, RBL10, affects lipid metabolism in the chloroplast, because in the respective rbl10 mutant the transfer of phosphatidic acid through the inner envelope membrane is disrupted. Here we show that RBL10 is part of a high-molecular-weight complex of 250 kDa or greater in size. Nine likely components of this complex are identified by two independent methods and include Acyl Carrier Protein 4 (ACP4) and Carboxyltransferase Interactor1 (CTI1), which have known roles in chloroplast lipid metabolism. The acp4 mutant has decreased C16:3 fatty acid content of monogalactosyldiacylglycerol, similar to the rbl10 mutant, prompting us to offer a mechanistic model of how an interaction between ACP4 and RBL10 might affect chloroplast lipid assembly. We also demonstrate the presence of a seventh transmembrane domain in RBL10, refining the currently accepted topology of this protein. Taken together, the identity of possible RBL10 complex components as well as insights into RBL10 topology and distribution in the membrane provide a stepping-stone towards a deeper understanding of RBL10 function in Arabidopsis lipid metabolism.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2021

Striking luminescence phenomena of carbon dots and their applications as a double ratiometric fluorescence probes for H2S detection

Here, we report some new observations on the luminescence of carbon dots (CDs) that are passivated with polyethylene glycol, and explored them, for the first time, as highly sensitive H2S detection probe. The as-prepared CDs have an ultraviolet (UV) emission at 350 nm and a green emission at 540 nm when excited at 270 nm, but they have only a green emission at 523 nm when excited at 365 nm. As Na2S is added to the CDs, the UV emission decreases gradually, while the green emission increases slightly, and interestingly a new emission appears at 455 nm is increased linearly in intensity with the increase of Na2S concentration. The blue emission at 455 nm is from the intrinsic core of CDs, and the green emissions at 540 or 523 nm are from their surface states, while the UV emission at 350 nm is from the anchored PEG. Both the emission intensity ratios of F-450/F-350 and F-455/F-523 show an excellent linear relationship with the Na2S concentration in the range of 0-800 mu M, and the detection limit estimated from both of them is approximately 7.0 nM, indicating our method is the most sensitive H2S CDs based detection method reported thus far. Furthermore, the detection was tested successfully for H2S imaging in live cells. We propose that the interactions of H2S with the CDs and the anchored ligands, as well as the energy transfer between the ligands and the CDs, are responsible for the luminescence responses for H2S detection. Our studies enrich the world of carbon dots with plenty of potential applications. (C) 2020 Elsevier Ltd. All rights reserved.

Bioimaging↗
DOE OSTI2020

Multilayered microstructures with shape memory effects for vertical deployment

This paper presents a fabrication and characterization of multilayered microstructures with shape memory effects enabling large vertical deployment under electro-thermal actuation. Our previous research demonstrated vertical deployment of such microstructures by the effect of thermal mismatch. Development of equiatomic NiTi layers in the multilayered microstructure is investigated further for shape memory effects. Multilayered microstructures are built by sputtered NiTi layers and a lift-off process. Negative photoresist ma-N1420 enables clean lift-off of 500 nm thick NiTi layers by forming a significant undercut profile after development. The parametric study on co-sputter powers for Ti and Ni 50 Ti 50 targets suggests that 100 W RF on Ti target and 200 W DC on Ni 50 Ti 50 target can deposit Ni 49.62 Ti 50.38 layers. X-Ray Diffraction (XRD) and Atomic Force Microscopy (AFM) were used to study the crystal structures and surface topography of NiTi layers. XRD results of post-annealed Ni 49.62 Ti 50.38 layers show coexistence of austenite and martensitic phases at room temperature, suggesting that the transformation temperature of such NiTi layers should be approximate 20 °C. The surface topography of Ni 49.62 Ti 50.38 layers reveals substantial increase of surface roughness at ambient conditions after the annealing. Experimental verification of the multilayered microstructure for vertical deployment was carried out by Signatone Probe Station and Dual Scanning Electron Microscope/Focused Ion Beam (SEM/FIB) system. Finally, a vertical deployment of the two-dimensional (2D) multilayered microstructures for three-dimensional (3D) can be detected by applying a constant voltage of 0.04 V, and the expected 3D deployment displacement is enlarged from 2 μm to 10 μm by introducing the shape memory effect.

42 ENGINEERING↗
DOE OSTI2020

Gate field effects on the topological insulator BiSbTeSe 2 interface

Interfaces between two topological insulators are of fundamental interest in condensed matter physics. Inspired by experimental efforts, we study interfacial processes between two slabs of BiSbTeSe 2 (BSTS) via first principles calculations. Topological surface states are absent for the BSTS interface in its equilibrium separation, but our calculations show that they appear if the inter-slab distance is greater than 6 Å. More importantly, we find that topological interface states can be preserved by inserting two or more layers of hexagonal boron nitride between the two BSTS slabs. In experiments, the electric current tunneling through the interface is insensitive to back gate voltage when the bias voltage is small. Using a first-principles based method that allows us to simulate the gate field, we show that at low bias, the extra charge induced by a gate voltage resides on the surface that is closest to the gate electrode, leaving the interface almost undoped. This provides clues to understand the origin of the observed insensitivity of transport properties to back voltage at low bias. Our study resolves a few questions raised in experiment, which does not yet offer a clear correlation between microscopic physics and transport data. We provide a road map for the design of vertical tunneling junctions involving the interface between two topological insulators.

75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗
DOE OSTI2018

Photoreduction of gaseous oxidized mercury changes global atmospheric mercury speciation, transport and deposition

Anthropogenic mercury (Hg(0)) emissions oxidize to gaseous Hg(II) compounds, before deposition to Earth surface ecosystems. Atmospheric reduction of Hg(II) competes with deposition, thereby modifying the magnitude and pattern of Hg deposition. Global Hg models have postulated that Hg(II) reduction in the atmosphere occurs through aqueous-phase photoreduction that may take place in clouds. Here we report that experimental rainfall Hg(II) photoreduction rates are much slower than modelled rates. We compute absorption cross sections of Hg(II) compounds and show that fast gas-phase Hg(II) photolysis can dominate atmospheric mercury reduction and lead to a substantial increase in the modelled, global atmospheric Hg lifetime by a factor two. Models with Hg(II) photolysis show enhanced Hg (0) deposition to land, which may prolong recovery of aquatic ecosystems long after Hg emissions are lowered, due to the longer residence time of Hg in soils compared with the ocean. Fast Hg(II) photolysis substantially changes atmospheric Hg dynamics and requires further assessment at regional and local scales.

54 ENVIRONMENTAL SCIENCES↗