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Wu, Ying

Publications and source records attributed to Wu, Ying.

At least 19 records
All sourcesNASA NTRSDOE OSTI
DOE OSTI2026

Two-mirror resonator for next-generation Compton gamma-ray source

The next-generation Compton gamma-ray sources (CGSs) based on storage rings require a high-power, well-focused laser beam as a photon driver, which can be realized using a Fabry-Perot cavity (FPC). In this work, we reexamine the behavior and performance of a two-mirror, nearly concentric resonator by introducing a new figure of merit representing the cavity’s proximity to instability. This figure of merit is used to analyze various aspects of the cavity design, including misalignment, beam coupling limitations, and beam size scaling. We then examine several factors affecting the gamma-ray flux, such as the interaction area, crossing angle for collision, frequency matching between the electron and laser beams, and intrabeam scattering effects. Using an example CGS, we demonstrate how to make improved design choices for a two-mirror resonator to enhance the gamma-ray beam flux. This work shows that simple two-mirror Fabry-Perot cavities are well suited as the laser driver for the next-generation storage ring-based CGS, while offering superior advantages in gamma-ray beam polarization control compared to more complex four-mirror, nonplanar resonators.

Delooze, Will↗
DOE OSTI2023

BUZZ : an essential gene for postinitiation root hair growth and a mediator of root architecture in Brachypodium distachyon

Here, we discover a player in root development. Recovered from a forward-genetic screen in Brachypodium distachyon, the buzz mutant initiates root hairs but they fail to elongate. In addition, buzz roots grow twice as fast as wild-type roots. Also, lateral roots show increased sensitivity to nitrate, whereas primary roots are less sensitive to nitrate. Using whole-genome resequencing, we identified the causal single nucleotide polymorphism as occurring in a conserved but previously uncharacterized cyclin-dependent kinase (CDK)-like gene. The buzz mutant phenotypes are rescued by the wild-type B. distachyon BUZZ coding sequence and by an apparent homolog in Arabidopsis thaliana. Moreover, T-DNA mutants in A. thaliana BUZZ have shorter root hairs. BUZZ mRNA localizes to epidermal cells and develops root hairs and, in the latter, partially colocalizes with the NRT1.1A nitrate transporter. Based on qPCR and RNA-Seq, buzz overexpresses ROOT HAIRLESS LIKE SIX-1 and -2 and misregulates genes related to hormone signaling, RNA processing, cytoskeletal, and cell wall organization, and to the assimilation of nitrate. Overall, these data demonstrate that BUZZ is required for tip growth after root hair initiation and root architectural responses to nitrate.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2020

Base pairing, structural and functional insights into N 4 -methylcytidine (m 4 C) and N 4 ,N 4 -dimethylcytidine (m 4 2 C) modified RNA

The N 4 -methylation of cytidine (m 4 C and m 4 2 C) in RNA plays important roles in both bacterial and eukaryotic cells. In this work, we synthesized a series of m 4 C and m 4 2 C modified RNA oligonucleotides, conducted their base pairing and bioactivity studies, and solved three new crystal structures of the RNA duplexes containing these two modifications. Our thermostability and X-ray crystallography studies, together with the molecular dynamic simulation studies, demonstrated that m 4 C retains a regular C:G base pairing pattern in RNA duplex and has a relatively small effect on its base pairing stability and specificity. By contrast, the m 4 2 C modification disrupts the C:G pair and significantly decreases the duplex stability through a conformational shift of native Watson-Crick pair to a wobble-like pattern with the formation of two hydrogen bonds. This double-methylated m 4 2 C also results in the loss of base pairing discrimination between C:G and other mismatched pairs like C:A, C:T and C:C. The biochemical investigation of these two modified residues in the reverse transcription model shows that both mono- or di-methylated cytosine bases could specify the C:T pair and induce the G to T mutation using HIV-1 RT. In the presence of other reverse transcriptases with higher fidelity like AMV-RT, the methylation could either retain the normal nucleotide incorporation or completely inhibit the DNA synthesis. These results indicate the methylation at N 4 -position of cytidine is a molecular mechanism to fine tune base pairing specificity and affect the coding efficiency and fidelity during gene replication.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2020

Cyclic Topology Enhancing Structural Ordering and Stability of Comb-Shaped Polypeptoid Thin Films against Melt-Induced Dewetting

We investigated the effect of cyclic chain topology on the molecular ordering and thermal stability of comb-shaped polypeptoid thin films on silicon (Si) substrates. Cyclic and linear poly(N-decylglycine) (PNDG) bearing long n-decyl side chains were synthesized by ring-opening polymerization of N-decylglycine-derived N-carboxyanhydrides. When the spin-coated thin films were subjected to thermal annealing at temperatures above the melting temperature (T > T m ), the cyclic PNDG films exhibited significantly enhanced stability against melt-induced dewetting than the linear counterparts (l-PNDG). When recrystallized at temperatures below the crystallization temperature (T < T c ), the homogeneous c-PNDG films exhibit enhanced crystalline ordering relative to the macroscopically dewetted l-PNDG films. Both cyclic and linear PNDG molecules adopt cis-amide conformations in the crystalline film, which transition into trans-amide conformations upon melting. A top-down solvent leaching treatment of both l/c-PNDG films revealed the formation of an irreversibly physisorbed monolayer with similar thickness (ca. 3 nm) on the Si substrate. The physisorbed monolayers are more disordered relative to the respective thicker crystalline films for both cyclic and linear PNDGs. Upon heating above T m , the adsorbed c-PNDG chains adopt trans-amide backbone conformation identical with the free c-PNDG molecules in the molten film. By contrast, the backbone conformations of l-PNDG chains in the adsorbed layers are notably different from those of the free chains in the molten film. We postulate that the conformational disparity between the chains in the physically adsorbed layers versus the free chains in the molten film is an important factor to account for the difference in the thermal stability of PNDG thin films. These findings highlight the use of cyclic chain topology to suppress the melt-induced dewetting in polymer thin films.

36 MATERIALS SCIENCE↗
DOE OSTI2019

Development of Tunable, Precision Permanent Magnet Phase Shifter for X-Ray FEL

In an X-ray free-electron laser (XFEL), a high quality relativistic electron beam from a linear accelerator traverses an array of undulator magnets to generate a high power X-ray beam by allowing the FEL to reach saturation. In many XFELs, phase shifters haven’t been commonly used or included in their designs. The importance of the phase shifter was recognized only recently. A phase shifter can be constructed using either an electromagnet (EM) or a permanent magnet (PM). EM phase shifters are heavy, complex to operate, and take more valuable longitudinal space between the undulators. Compared to EMs, the PMs have several outstanding advantages, including compactness, lighter weights, simple operation, and low maintenance. This project has developed an innovative design of fixed-gap, tunable PM-based compact phase shifter for the XFEL. While keeping the poles and gap fixed, the new design incorporates proven features from the prior work, along with novel field tuning methods, which allow the field strength to be adjusted within a reasonably large range to achieve the desired range of the phase delay control. The PM design without electric currents and power electronics associated with EMs improves reliability by reducing the number of possible points of failure and lowers the operation cost. The compactness makes it possible to use PM phase shifters in the existing XFELs with small gaps between adjacent undulators, as well as in the new XFELs without significantly increasing the FEL length. In Phase I we have accomplished the followings; 1) determined the optimum physics parameters for both weak and strong phase shifters; 2) conducted magnetic design with concrete magnetic and geometrical parameters of actual produced PM materials; 3) provided solutions to achieve precision fine tuning of the magnetic fields with unique methods; 4) elaborated a design based upon ease of manufacturing and cost analysis; and 5) produced rare-earth PM materials, which will be used for prototyping in Phase II. The phase I results provide a foundation for the research and development in the Phase II project, which will aim at building two full-size PM phase shifters and testing at SLAC National Accelerator Laboratory. This project will significantly provide the potential to bring a paradigm change in accelerator technology, replacing conventional electromagnets for many existing accelerator applications and allowing the development of new applications in completely new areas. For example, the PM FEL phase shifters can help significantly improve coherence and power of an XFEL. The proposed use of PM phase shifters will also bring significant cost savings to the construction, operation and maintenance of FEL facilities.

43 PARTICLE ACCELERATORS↗
DOE OSTI2019

The crystal structure of dGTPase reveals the molecular basis of dGTP selectivity

Deoxynucleotide triphosphohydrolases (dNTPases) play a critical role in cellular survival and DNA replication through the proper maintenance of cellular dNTP pools. While the vast majority of these enzymes display broad activity toward canonical dNTPs, such as the dNTPase SAMHD1 that blocks reverse transcription of retroviruses in macrophages by maintaining dNTP pools at low levels, Escherichia coli ( Ec )-dGTPase is the only known enzyme that specifically hydrolyzes dGTP. However, the mechanism behind dGTP selectivity is unclear. Here we present the free-, ligand (dGTP)- and inhibitor (GTP)-bound structures of hexameric Ec- dGTPase, including an X-ray free-electron laser structure of the free Ec- -dGTPase enzyme to 3.2 Å. To obtain this structure, we developed a method that applied UV-fluorescence microscopy, video analysis, and highly automated goniometer-based instrumentation to map and rapidly position individual crystals randomly located on fixed target holders, resulting in the highest indexing rates observed for a serial femtosecond crystallography experiment. Our structures show a highly dynamic active site where conformational changes are coupled to substrate (dGTP), but not inhibitor binding, since GTP locks dGTPase in its apo- form. Moreover, despite no sequence homology, Ec- dGTPase and SAMHD1 share similar active-site and HD motif architectures; however, Ec- dGTPase residues at the end of the substrate-binding pocket mimic Watson–Crick interactions providing guanine base specificity, while a 7-Å cleft separates SAMHD1 residues from dNTP bases, abolishing nucleotide-type discrimination. Furthermore, the structures shed light on the mechanism by which long distance binding (25 Å) of single-stranded DNA in an allosteric site primes the active site by conformationally “opening” a tyrosine gate allowing enhanced substrate binding.

Barnes, Christopher O.↗
DOE OSTI2018

Efficiently Exploring Adsorption Space to Identify Privileged Adsorbents for Chemical Separations of a Diverse Set of Molecules

Although computational models have been used to predict adsorption of molecules in large libraries of porous adsorbents, previous work of this kind has focused on a small number of molecules as potential adsorbates. In this paper we use molecular simulations to consider the adsorption of a diverse range of molecules in a large collection of metal-organic framework (MOF) materials. Specifically, we obtain 11,304 isotherms from molecular simulations of 24 different adsorbates in 471 MOFs. This information allows us to explore several interesting questions that could not be addressed with previously available data. Here, we introduce highly computationally efficient methods that can predict isotherms for a wide range of adsorbing molecules with far less computation than traditional molecular simulations. By characterizing the 276 binary mixtures defined by the molecules we considered, we show that “privileged” adsorbents exist that are effective for separating many different molecular mixtures. Finally, we show that correlations that have been developed previously to predict molecular solubility in polymers are surprisingly effective in predicting the average properties of molecules adsorbing in MOFs.

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

Crossover of thermal expansion from positive to negative by removing the excess fluorines in cubic ReO 3 -type TiZrF 7-x

Here, we report the crossover of the coefficient of thermal expansion (CTE) from positive to negative by withdrawing the excess fluorines in ReO 3 -type TiZrF 7-x (x = 0, 0.5 and 1) compounds. The average volumetric CTE between 300 K and 623 K changes from 8.07 ppm K -1 for x = 0, to 0.66 ppm K -1 for x = 0.5 and finally to -6.09 ppm K -1 for x = 1. After withdrawing the excess fluorines, the lattice expands and the edge-sharing polyhedra partially transform to corner-sharing ones, which enhances the transverse vibrations of fluorines and thus accounts for the crossover of CTE. Moreover, these compounds are narrow-gap semiconductors with the energy gap decreasing with x. NTE may also be achievable in other fluorine-excess cubic fluorides by removing the excess fluorines, which opens up a new avenue for exploring the NTE in fluorides.

36 MATERIALS SCIENCE↗
DOE OSTI2017

Contorted Octabenzocircumbiphenyl Sorts Semiconducting Single-Walled Carbon Nanotubes with Structural Specificity

Here, we use a nonplanar aromatic molecule, contorted octabenzocircumbiphenyl (c-OBCB), to sort semiconducting single-walled carbon nanotubes (SWNTs) by their chiral angles. From absorption spectroscopy, photoluminescence excitation spectroscopy, and Raman spectroscopy studies, we find that c-OBCB preferentially binds and sorts for a number of semiconducting carbon nanotubes with chiral angles greater than 12°. Molecular dynamics simulations reveal that the contorted aromatic core of c-OBCB binds strongly to only certain SWNTs, especially those with matching curvature, and that this discriminatory binding interaction is reinforced by preferences of the side chains on the c-OBCB to stick to SWNT surface rather than interact with the solvent. This opens the door to side chain/solvent engineering to bias the selection of certain (m,n) SWNT variants. We also investigate the temperature dependence of hole mobility in field-effect transistors comprising c-OBCB-sorted semiconducting carbon-nanotube networks and find hole transport in these networks to be thermally activated.

36 MATERIALS SCIENCE↗
DOE OSTI2016

Computational investigation on CO 2 adsorption in titanium carbide-derived carbons with residual titanium

We develop a new approach for modeling titanium carbide derived-carbon (TiC-CDC) systems with residual titanium by the generation of modified atomistic structures based on a silicon carbide derived-carbon (SiC-CDC) model and the application of weighted combinations of these structures. In our approach, the original SiC-CDC structure is modified by (i) removing carbon, (ii) adding carbon and (iii) adding titanium. The new atomic scale carbide-derived carbon (CDC) structures are investigated using classical molecular dynamics simulations, and their pure CO 2 adsorption isotherms are calculated using grand canonical Monte Carlo simulations. The system of TiC-CDC with residual titanium is modeled as weighted combinations of pure carbon CDC structures, CDC structures with titanium and a TiC crystalline structure. Our modeling is able to produce both structural properties and adsorption isotherms in accordance with experimental data. The fraction of different models in the systems successfully reflects the structural differences in various experimental TiC-CDC samples. The modeling also suggests that in partially etched TiC-CDC systems, the titanium that may be accessible to CO 2 gas at the transitional interface may provide significant interaction sites for CO 2 and may lead to more efficient overall gas adsorption.

36 MATERIALS SCIENCE↗
DOE OSTI2016

Radiation pressure induced difference-sideband generation beyond linearized description

We investigate radiation-pressure induced generation of the frequency components at the difference-sideband in an optomechanical system, which beyond the conventional linearized description of optomechanical interactions between cavity fields and the mechanical oscillation. We analytically calculate amplitudes of these signals, and identify a simple square-root law for both the upper and lower difference-sideband generation which can describe the dependence of the intensities of these signals on the pump power. Further calculation shows that difference-sideband generation can be greatly enhanced via achieving the matching conditions. The effect of difference-sideband generation, which may have potential application for manipulation of light, is especially suited for on-chip optomechanical devices, where nonlinear optomechanical interaction in the weak coupling regime is within current experimental reach.

71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗
DOE OSTI2016

Transmission electron microscopy for the evaluation and optimization of crystal growth

The crystallization of protein samples remains the most significant challenge in structure determination by X-ray crystallography. Here, the effectiveness of transmission electron microscopy (TEM) analysis to aid in the crystallization of biological macromolecules is demonstrated. It was found that the presence of well ordered lattices with higher order Bragg spots, revealed by Fourier analysis of TEM images, is a good predictor of diffraction-quality crystals. Moreover, the use of TEM allowed (i) comparison of lattice quality among crystals from different conditions in crystallization screens; (ii) the detection of crystal pathologies that could contribute to poor X-ray diffraction, including crystal lattice defects, anisotropic diffraction and crystal contamination by heavy protein aggregates and nanocrystal nuclei; (iii) the qualitative estimation of crystal solvent content to explore the effect of lattice dehydration on diffraction and (iv) the selection of high-quality crystal fragments for microseeding experiments to generate reproducibly larger sized crystals. Applications to X-ray free-electron laser (XFEL) and micro-electron diffraction (microED) experiments are also discussed.

Stevenson, Hilary P.↗
DOE OSTI2015

Optical nonreciprocal transmission in an asymmetric silicon photonic crystal structure

An optical nonreciprocal transmission (ONT) is realized by employing the nonlinear effects in a compact asymmetric direct-coupled nanocavity-waveguide silicon photonic crystal structure with a high loaded quality factor (Q{sub L}) of 42 360 and large extinction ratio exceeding 30 dB. Applying a single step lithography and successive etching, the device can realize the ONT in an individual nanocavity, alleviating the requirement to accurately control the resonance of the cavities. A maximum nonreciprocal transmission ratio of 21.1 dB as well as a working bandwidth of 280 pm in the telecommunication band are obtained at a low input power of 76.7 μW. The calculated results by employing a nonlinear coupled-mode model are in good agreement with the experiment.

71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗
DOE OSTI2015

Erbium and nitrogen co-doped SrTiO{sub 3} with highly visible light photocatalytic activity and stability by solvothermal synthesis

Highlights: • Er/N co-doped SrTiO{sub 3} was prepared by a solvothermal process at low temperature. • The co-doping induces the band gap narrowing and prominent absorbance in visible light region. • The samples show excellent catalytic activity and stability under visible light irradiation. - Abstract: Erbium–nitrogen co-doped SrTiO{sub 3} photocatalysts have been synthesized by a facile solvothermal method. The resulting samples were analyzed by FE-SEM, XRD, BET-surface area and UV–vis. The UV–vis absorption spectra of these powders indicated that erbium–nitrogen co-doped SrTiO{sub 3} possessed stronger absorption bands in the visible light region in comparison with that of pure SrTiO{sub 3}. The occurrence of the erbium–nitrogen co-doped cubic SrTiO{sub 3} induced the higher photocatalytic activities for the degradation of methyl orange (MO) under irradiation by ultraviolet light and visible light, respectively, being superior to that of pure SrTiO{sub 3} and commercial TiO{sub 2} (P-25) powders. In addition, the Er–N co-doped SrTiO{sub 3} (initial molar ratios of Sr/Er/N = 1:0.015:0.1, designated as S5) sample showed the best photocatalytic activity with the degradation rate as high as 98% after 30 min under the visible light irradiation. After five cycles, the photocatalytic activity of the S5 catalyst showed no significant decrease, which indicated that the photocatalysts were stable under visible light irradiation.

36 MATERIALS SCIENCE↗