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Jiang, Shuai

Publications and source records attributed to Jiang, Shuai.

17 records
All sourcesNASA NTRSDOE OSTI
DOE OSTI2024

A splice method for local-to–nonlocal coupling of weak forms

Here, we propose a method to couple local and nonlocal diffusion models. By inheriting desirable properties such as patch tests, asymptotic compatibility and unintrusiveness from related splice and optimization-based coupling schemes, it enables the use of weak (or variational) formulations, is computationally efficient and straightforward to implement. We prove well-posedness of the coupling scheme and demonstrate its properties and effectiveness in a variety of numerical examples.

97 MATHEMATICS AND COMPUTING↗
DOE OSTI2024

Direct Visualization of Laser-Induced Coalescence and Alloying of Au into Ag Nanowires

Noble metal nanocomposites with controlled morphology and composition have been largely useful in a wide variety of applications like catalysis, plasmonics, and biological applications. Herein, we show pulsed-laser-assisted fabrication of beaded Au-Ag nanowires with a variety of morphologies and compositions via coalescence and alloying of Au nanoparticles (NP) into a Ag nanowire (NW). Direct visualization of the evolution process with in situ laser heating transmission electron microscopy (ILH-TEM) leads to unambiguous insights into the mechanism of formation for the first time. Ag, being a soft material, melts at the surface to bridge the gap between the NP-NW, forming a cup-like morphology underneath the Au NP via capillary action. Progressive laser irradiation leads to wetting of the Au NP with Ag, forming an envelope around the NP. This is associated with the formation of a valley in Ag NW around the NP, which flattens gradually by partial embedding of the NP. Interdiffusion of Au into Ag and vice versa sets in at this stage, leading to the depletion of Au from the Au-rich NP region. Prolonged irradiation leads to gradual intermixing of Au-Ag forming beaded Au-doped Ag nanowires with homogeneous composition. Such a step-by-step understanding of the coalescence and alloying process has implications in nanowelding, which holds the future in designing efficient transparent conductors and printed electronics.

Isik, Tugba↗
DOE OSTI2020

Human XPG nuclease structure, assembly, and activities with insights for neurodegeneration and cancer from pathogenic mutations

Xeroderma pigmentosum group G (XPG) protein is both a functional partner in multiple DNA damage responses (DDR) and a pathway coordinator and structure-specific endonuclease in nucleotide excision repair (NER). Different mutations in the XPG gene ERCC5 lead to either of two distinct human diseases: Cancer-prone xeroderma pigmentosum (XP-G) or the fatal neurodevelopmental disorder Cockayne syndrome (XP-G/CS). To address the enigmatic structural mechanism for these differing disease phenotypes and for XPG’s role in multiple DDRs, here we determined the crystal structure of human XPG catalytic domain (XPGcat), revealing XPG-specific features for its activities and regulation. Furthermore, XPG DNA binding elements conserved with FEN1 superfamily members enable insights on DNA interactions. Notably, all but one of the known pathogenic point mutations map to XPGcat, and both XP-G and XP-G/CS mutations destabilize XPG and reduce its cellular protein levels. Mapping the distinct mutation classes provides structure-based predictions for disease phenotypes: Residues mutated in XP-G are positioned to reduce local stability and NER activity, whereas residues mutated in XP-G/CS have implied long-range structural defects that would likely disrupt stability of the whole protein, and thus interfere with its functional interactions. Combined data from crystallography, biochemistry, small angle X-ray scattering, and electron microscopy unveil an XPG homodimer that binds, unstacks, and sculpts duplex DNA at internal unpaired regions (bubbles) into strongly bent structures, and suggest how XPG complexes may bind both NER bubble junctions and replication forks. Collective results support XPG scaffolding and DNA sculpting functions in multiple DDR processes to maintain genome stability.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2018

Influence of Iron Content on Microstructure and Magnetic Properties of Sr{sub 0.3}La{sub 0.4}Ca{sub 0.3}n(Fe{sub 2}O{sub 3})Co{sub 0.4}

In this work, the hexagonal ferrite Sr{sub 0.3}La{sub 0.4}Ca{sub 0.3}n (Fe{sub 2}O{sub 3})Co{sub 0.4}, where n ranging from 5.5 to 6.0 with a step of 0.1, and magnetic powders and magnets were synthesized by solid-states reaction. The microstructure of the magnetic powders was investigated by X-ray diffraction (XRD). And then we can found that a single magnetoplumbite phase is obtained for magnetic powders as a result when 5.6 ≤ n ≤ 5.8. When the iron content in the magnetic powders increased continuously, the diffraction peaks of α-Fe{sub 2}O{sub 3} were observed. Scanning electron microcopy (SEM) was used to explore the micrographs of the magnets and the hexagonal-shaped crystals were found obviously. The magnetic properties of the M-type hexagonal ferrites Sr{sub 0.3}La{sub 0.4}Ca{sub 0.3}n(Fe{sub 2}O{sub 3})Co{sub 0.4} were studied by using vibrating sample magnetometry. The saturation magnetization (M{sub s}) first increased and then began to decrease with the n increasing. While the coercivity first decreased with the n from 5.5 to 5.9 and then increased when n ≥5.9. The coercivity (H{sub c}) of the hexagonal ferrite Sr{sub 0.3}La{sub 0.4}Ca{sub 0.3}n(Fe{sub 2}O{sub 3})Co{sub 0.4} reaches the maximum value (H{sub c} = 1130 Oe) when the iron content (n = 5.5).

75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗
DOE OSTI2016

Regulation of oxidized base damage repair by chromatin assembly factor 1 subunit A

Reactive oxygen species (ROS), generated both endogenously and in response to exogenous stress, induce point mutations by mis-replication of oxidized bases and other lesions in the genome. Repair of these lesions via base excision repair (BER) pathway maintains genomic fidelity. Regulation of the BER pathway for mutagenic oxidized bases, initiated by NEIL1 and other DNA glycosylases at the chromatin level remains unexplored. Whether single nucleotide (SN)-BER of a damaged base requires histone deposition or nucleosome remodeling is unknown, unlike nucleosome reassembly which is shown to be required for other DNA repair processes. Here we show that chromatin assembly factor (CAF)-1 subunit A (CHAF1A), the p150 subunit of the histone H3/H4 chaperone, and its partner anti-silencing function protein 1A (ASF1A), which we identified in human NEIL1 immunoprecipitation complex, transiently dissociate from chromatin bound NEIL1 complex in G1 cells after induction of oxidative base damage. CHAF1A inhibits NEIL1 initiated repair in vitro. Subsequent restoration of the chaperone-BER complex in cell, presumably after completion of repair, suggests that histone chaperones sequester the repair complex for oxidized bases in non-replicating chromatin, and allow repair when oxidized bases are induced in the genome.

Biochemistry & Molecular Biology↗
DOE OSTI2015

Paclitaxel Enhances Carboplatin-DNA Adduct Formation and Cytotoxicity

This rapid report focuses on the pharmacodynamic mechanism of the carboplatin/paclitaxel combination and correlates it with its cytotoxicity. Consistent with the synergistic to additive antitumor activity (the combination index ranging from 0.53 to 0.94), cells exposed to this combination had significantly increased carboplatin-DNA adduct formation when compared to that of carboplatin alone (450 ± 30 versus 320 ± 120 adducts per 10 8 nucleotides at 2 h, p = 0.004). Removal of paclitaxel increased the repair of carboplatin-DNA adducts: 39.4 versus 33.1 adducts per 10 8 nucleotides per hour in carboplatin alone (p = 0.021). In conclusion, this rapid report provides the first pharmacodynamics data to support the use of carboplatin/paclitaxel combination in the clinic.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2015

Probing the Structures and Electronic Properties of Dual-Phosphorus-Doped Gold Cluster Anions (AunP-2, n = 1–8): A Density functional Theory Investigation

The geometries of gold clusters doped with two phosphorus atoms, (AunP-2, n = 1–8) were investigated using density functional theory (DFT) methods. Various two-dimensional (2D) and three-dimensional (3D) structures of the doped clusters were studied. The results indicate that the structures of dual-phosphorus-doped gold clusters exhibit large differences from those of pure gold clusters with small cluster sizes. In our study, as for Au6P-2, two cis–trans isomers were found. The global minimum of Au8P-2 presents a similar configuration to that of Au-20, a pyramid-shaped unit, and the potential novel optical and catalytic properties of this structure warrant further attention. The higher stability of AunP-2 clusters relative to Au-n+2 (n = 1–8) clusters was verified based on various energy parameters, and the results indicate that the phosphorus atom can improve the stabilities of the gold clusters. We then explored the evolutionary path of (n = 1–8) clusters. We found that AunP-2 clusters exhibit the 2D–3D structural transition at n = 6, which is much clearer and faster than that of pure gold clusters and single-phosphorus-doped clusters. The electronic properties of AunP-2 (n = 1–8) were then investigated. The photoelectron spectra provide additional fundamental information on the structures and molecular orbitals shed light on the evolution of AunP-2 (n = 1–8). Natural bond orbital (NBO) described the charge distribution in stabilizing structures and revealed the strong relativistic effects of the gold atoms.

Environmental Molecular Sciences Laboratory↗
DOE OSTI2015

Stability of Hydrated Methylamine: Structural Characteristics and H2N···H–O Hydrogen Bonds

Methylamine is the simplest aliphatic amine found in human urine, blood, and tissues. It is thought to play a significant part in central nervous system disturbances observed during renal and hepatic disease. In this work we have investigated the methylamine hydration clusters using a basin hopping (BH) algorithm with the density functional theory (DFT). The results presented herein yield a detailed understanding of the structure and stability for a system consisting of one methylamine molecule and up to seven waters: the most stable geometries arise from a fusion of tetramer or pentamer rings; by the geometrical parameters and topological parameters analysis, the strengths of the H2N···H–O hydrogen bonds of the global minima increase as the sizes of clusters increase, except for n = 5 where there is a slight fluctuation. This work may shed light on the form mechanism of methylamine existing in organisms and the hydration structures of larger molecules containing amino functional groups and their interaction with the water molecules nearby.

Environmental Molecular Sciences Laboratory↗
DOE OSTI2015

Interaction of Gas Phase Oxalic Acid with Ammonia and its Atmospheric Implications

Oxalic acid is believed to play an important role in the formation and growth of atmospheric organic aerosols. However, as a common organic acid, the understanding of the larger clusters formed by gas phase oxalic acid with multiple ammonia molecules is incomplete. In this work, the structural characteristics and thermodynamics of oxalic acid clusters with up to six ammonia molecules have been investigated at the PW91PW91/6-311++G(3df,3pd) level of theory. We found that oxalic acid forms relatively stable clusters with ammonia molecules, and that ionization events play a key role. The analyses of the thermodynamics and atmospheric relevance indicate that the heterodimer (H2C2O4)(NH3) shows an obvious relative concentration in the atmosphere, and thus likely participates in new particle formation. However, with increasing number of ammonia molecules, the concentration of clusters decreases gradually. Additionally, clusters of oxalic acid with ammonia molecules are predicted to form favorably in low temperature conditions and show high Rayleigh scattering intensities.

Environmental Molecular Sciences Laboratory↗
DOE OSTI2015

A Flexible Transition State Searching Method for Atmospheric Reaction Systems

The precise and rapid exploration of transition states (TSs) is a major challenge when studying atmospheric reactions due to their complexity. In this work, a Monte Carlo Transition State Search Method (MCTSSM), which integrates Monte Carlo sampling technique with transition state optimization methods using an efficient computer script, has been developed for transition state searches. The efficiency and the potential application in atmospheric reactions of this method have been demonstrated by three types of test suits related to the reactions of atmospheric volatile organic compounds (VOCs): (1) OH addition, (2) OH hydrogen-abstraction, and (3) the other reactive group (e.g. Cl, O3, NO3), especially for the reaction of β-pinene-sCI (stabilized Criegee Intermediates) with water. It was shown that the application of this method with effective restricted parameters has greatly simplified the time-consuming and tedious manual search procedure for transition state (TS) of the bimolecular reaction systems.

Aerosol↗
DOE OSTI2015

Properties of Ammonium Ion–Water Clusters: Analyses of Structure Evolution, Noncovalent Interactions, and Temperature and Humidity Effects

Although ammonium ion–water clusters are abundant in the biosphere, some information regarding these clusters, such as their growth route, the influence of temperature and humidity, and the concentrations of various hydrated clusters, is lacking. In this study, theoretical calculations are performed on ammonium ion–water clusters. These theoretical calculations are focused on determining the following characteristics: (1) the pattern of cluster growth; (2) the percentages of clusters of the same size at different temperatures and humidities; (3) the distributions of different isomers for the same size clusters at different temperatures; (4) the relative strengths of the noncovalent interactions for clusters of different sizes. The results suggest that the dipole moment may be very significant for the ammonium ion–water system, and some new stable isomers were found. The nucleation of ammonium ions and water molecules is favorable at low temperatures; thus, the clusters observed at high altitudes might not be present at low altitudes. High humidity can contribute to the formation of large ammonium ion–water clusters, whereas the formation of small clusters may be favorable under low-humidity conditions. The potential energy surfaces (PES) of these different sized clusters are complicated and differ according to the distribution of isomers at different temperatures. Some similar structures are observed between NH4+(H2O)n and M(H2O)n (where M represents an alkali metal ion or water molecule); when n = 8, the clusters begin to form the closed-cage geometry. As the cluster size increases, these interactions become progressively weaker. The successive binding energy at the DF-MP2-F12/VDZ-F12 level is better than that at the PW91PW91/6-311++G(3df, 3pd) level and is consistent with the experimentally determined values.

Environmental Molecular Sciences Laboratory↗
DOE OSTI2015

On the properties of Au2₂P₃ z (z = -1, 0, +1): analysis of geometry, interaction, and electron density

Au₂P₃, the only metastable binary phase of gold phosphide, has been discovered to exhibit remarkable semiconductor properties among metal phosphides. A systematic study on the geometry, the transformation of Au₂P₃ into different valence states and the different interactions among the atoms of the species is performed by using the density functional theory (DFT) method. The global minimum of Au₂P₃- is a 3D structure with C s symmetry. This structure could be distorted from a planar configuration of Au₂P₃ which decreases the steric effect on it and leads to a new stable configuration. An analogous planar configuration, a local minimum rather than a global minimum, is also found in Au₂P₃⁺, due to the electron effect acting on the structure. Natural bond orbital (NBO) analysis reveals the re-distribution progression of the charge within the species. The central located Au atom and another no. 5 positioned P atom play significant roles on the structures. P5, as an electron adjuster, balances the electron distribution at different valence states of the structures. Deformation density analysis supplies information about charge transfer and the bonding type between two adjacent atoms as well. Looking deep into the bonding types, as electron localization function (ELF) suggests, the interaction between two adjacent P atoms (P3 and P4) of Au₂P₃ belongs to a strong covalent bond. The Au–P interactions among the configurations could be classified as weak classical covalent bonds through the atoms in molecules (AIM) dual parameter analysis. And for the first time, the weak interaction between the two adjacent Au atoms (Au1 and Au2) of the charged states of Au₂P₃ (Au₂P₃⁻ and Au₂P₃⁺), are verified and different from the neutral Au₂P₃ through the reduced density gradient (RDG) analysis.

Environmental Molecular Sciences Laboratory↗
DOE OSTI2013

Structure, stability, and electronic property of carbon-doped gold clusters Au{sub n}C{sup −} (n = 1–10): A density functional theory study

The equilibrium geometric structures, relative stabilities, and electronic properties of Au{sub n}C{sup −} and Au{sub n+1}{sup −} (n = 1–10) clusters are systematically investigated using density functional theory with hyper-generalized gradient approximation. The optimized geometries show that one Au atom capped on Au{sub n−1}C{sup −} clusters is a dominant growth pattern for Au{sub n}C{sup −} clusters. In contrast to Au{sub n+1}{sup −} clusters, Au{sub n}C{sup −} clusters are most stable in a quasi-planar or three-dimensional structure because C doping induces the local non-planarity while the rest of the structure continues to grow in a planar mode, resulting in an overall non-2D configuration. The relative stability calculations show that the impurity C atom can significantly enhance the thermodynamic stability of pure gold clusters. Moreover, the effect of C atom on the Au{sub n}{sup −} host decreases with the increase of cluster size. The HOMO-LUMO gap curves show that the interaction of the C atom with Au{sub n}{sup −} clusters improves the chemical stability of pure gold clusters, except for Au{sub 3}{sup −} and Au{sub 4}{sup −} clusters. In addition, a natural population analysis shows that the charges in corresponding Au{sub n}C{sup −} clusters transfer from the Au{sub n}{sup −} host to the C atom. Meanwhile, a natural electronic configuration analysis also shows that the charges mainly transfer between the 2s and 2p orbitals within the C atom.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2013

Transcriptome and Proteome Exploration to Provide a Resource for the Study of Agrocybe aegerita

Agrocybe aegerita, the black poplar mushroom, has been highly valued as a functional food for its medicinal and nutritional benefits. Several bioactive extracts from A. aegerita have been found to exhibit antitumor and antioxidant activities. However, limited genetic resources for A. aegerita have hindered exploration of this species. To facilitate the research on A. aegerita, we established a deep survey of the transcriptome and proteome of this mushroom. We applied high-throughput sequencing technology (Illumina) to sequence A. aegerita transcriptomes from mycelium and fruiting body. The raw clean reads were de novo assembled into a total of 36,134 expressed sequences tags (ESTs) with an average length of 663 bp. These ESTs were annotated and classified according to Gene Ontology (GO), Clusters of Orthologous Groups (COG), and Kyoto Encyclopedia of Genes and Genomes (KEGG) metabolic pathways. Gene expression profile analysis showed that 18,474 ESTs were differentially expressed, with 10,131 up-regulated in mycelium and 8,343 up-regulated in fruiting body. Putative genes involved in polysaccharide and steroid biosynthesis were identified from A. aegerita transcriptome, and these genes were differentially expressed at the two stages of A. aegerita. Based on one-dimensional gel electrophoresis (1-DGE) coupled with electrospray ionization liquid chromatography tandem MS (LC-ESI-MS/MS), we identified a total of 309 non-redundant proteins. And many metabolic enzymes involved in glycolysis were identified in the protein database. This is the first study on transcriptome and proteome analyses of A. aegerita. The data in this study serve as a resource of A. aegerita transcripts and proteins, and offer clues to the applications of this mushroom in nutrition, pharmacy and industry.

59 BASIC BIOLOGICAL SCIENCES↗