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Chen, Li

Publications and source records attributed to Chen, Li.

At least 37 records · Page 2

Lattice-Symmetry-Assisted Second-Order Topological Superconductors and Majorana Patterns

We propose a realization of the lattice-symmetry-assisted second-order topological superconductors with corner Majorana zero modes (MZM) based on two-dimensional topological insulators (2DTI). The lattice symmetry can naturally lead to the anisotropic coupling of edge states along different directions to the in-plane magnetic field and conventional s -wave pairings, thus leading to a single MZM located at the corners for various lattice patterns. In particular, we focus on the 2DTI with $D_{3d}$ lattice symmetry and found different types of gap opening for the edge states along the armchair and zigzag edges in a broad range of parameters. As a consequence, a single MZM exists at the corner between the zigzag and armchair edges, and is robust against weakly broken lattice symmetry. We propose to realize such corner MZMs in a variety of polygon patterns, such as triangles and quadrilaterals. We further show their potentials in building the Majorana network through constructing the Majorana Y junction under an in-plane magnetic field.

71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗

Valley and Zeeman Splittings in Multilayer Epitaxial Graphene Revealed by Circular Polarization Resolved Magneto-infrared Spectroscopy

Circular-polarization-resolved magneto-infrared studies of multilayer epitaxial graphene (MEG) are performed using tunable quantum cascade lasers in high magnetic fields up to 17.5 T. Landau level (LL) transitions in the monolayer and bilayer graphene inclusions of MEG are resolved, and considerable electron–hole asymmetry is observed in the extracted electronic band structure. For monolayer graphene, a four-fold splitting of the $n$ = 0 to $n$ = 1 LL transition is evidenced and attributed to the lifting of the valley and spin degeneracy of the zeroth LL and the broken electron–hole symmetry. The magnetic field dependence of the splitting further reveals its possible mechanisms. The best fit to experimental data yields effective $g$-factors, $g^*_{vs}$ = 6.7 and $g^*_{ZS}$ = 4.8, for the valley and Zeeman splittings, respectively.

36 MATERIALS SCIENCE↗

A New Fully Covered Irradiation Stent Versus a Partially Covered Irradiation Stent for Unresectable Malignant Dysphagia: A Single-Center Experience

Purpose: To assess the efficacy and safety of a newly developed fully covered irradiation stent (FCIS) compared with a partially covered irradiation stent (PCIS) in patients with unresectable malignant dysphagia. Materials and Methods: Data of 195 patients [158 (81.0%) males, median age of 75 years (range 49–89 years)] who underwent FCIS or PCIS placement for unresectable malignant dysphagia from January 2012 to November 2017 were retrospectively analyzed. The median follow-up time was 181 days (range 4–547 days). Outcomes were measured in terms of recurrent dysphagia (primary), technical success, clinical success, overall survival, and adverse events. Recurrent dysphagia was analyzed by Fine–Gray regression model. Results: The technical success rate was 97.8% (87/89) in the FCIS group and 99.1% (105/106) in the PCIS group (P = 0.59). The clinical success rate was 100.0% in both groups. There was no statistically significant difference in the recurrent dysphagia rate between the FCIS and PCIS groups (21.8% vs. 28.6%; P = 0.12). Compared with PCISs, FCISs were associated with a decrease in tissue/tumor growth rate (11.5% vs. 21.9%; P = 0.01), while stent migration rates were statistically comparable (11.5% vs. 5.7%; P = 0.23). The median overall survivals were comparable between the FCIS and PCIS groups (164 days vs. 162 days; P = 0.70). A dysphagia score of 4 and metastasis were risk factors for survival. No significant differences were observed in the rates of adverse events, including chest pain, fistula formation, hemorrhage, and aspiration pneumonia (P > 0.05). Conclusion: For patients with unresectable malignant dysphagia, this newly developed FCIS can provide efficacy and safety comparable to those of a PCIS. Compared with PCIS, this FCIS is more successful in preventing tissue/tumor growth, with a comparable stent migration rate.

62 RADIOLOGY AND NUCLEAR MEDICINE↗

Composite fermions in Fock space: Operator algebra, recursion relations, and order parameters

We develop recursion relations, in particle number, for all (unprojected) Jain composite fermion (CF) wave functions. These recursions generalize a similar recursion originally written down by Read for Laughlin states, in mixed first-second quantized notation. In contrast, our approach is purely second-quantized, giving rise to an algebraic, “pure guiding center” definition of CF states that de-emphasizes first quantized many-body wave functions. Key to the construction is a second-quantized representation of the flux attachment operator that maps any given fermion state to its CF counterpart. An algebra of generators of edge excitations is identified. In particular, in those cases where a well-studied parent Hamiltonian exists, its properties can be entirely understood in the present framework, and the identification of edge state generators can be understood as an instance of “microscopic bosonization.” Here, the intimate connection of Read's original recursion with “nonlocal order parameters” generalizes to the present situation, and we are able to give explicit second-quantized formulas for nonlocal order parameters associated with CF states.

75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗

Managing genomic variant calling workflows with Swift/T

Bioinformatics research is frequently performed using complex workflows with multiple steps, fans, merges, and conditionals. This complexity makes management of the workflow difficult on a computer cluster, especially when running in parallel on large batches of data: hundreds or thousands of samples at a time. Scientific workflow management systems could help with that. Many are now being proposed, but is there yet the “best” workflow management system for bioinformatics? Such a system would need to satisfy numerous, sometimes conflicting requirements: from ease of use, to seamless deployment at peta- and exa-scale, and portability to the cloud. We evaluated Swift/T as a candidate for such role by implementing a primary genomic variant calling workflow in the Swift/T language, focusing on workflow management, performance and scalability issues that arise from production-grade big data genomic analyses. In the process we introduced novel features into the language, which are now part of its open repository. Additionally, we formalized a set of design criteria for quality, robust, maintainable workflows that must function at-scale in a production setting, such as a large genomic sequencing facility or a major hospital system. The use of Swift/T conveys two key advantages. (1) It operates transparently in multiple cluster scheduling environments (PBS Torque, SLURM, Cray aprun environment, etc.), thus a single workflow is trivially portable across numerous clusters. (2) The leaf functions of Swift/T permit developers to easily swap executables in and out of the workflow, which makes it easy to maintain and to request resources optimal for each stage of the pipeline. While Swift/T’s data-level parallelism eliminates the need to code parallel analysis of multiple samples, it does make debugging more difficult, as is common for implicitly parallel code. Nonetheless, the language gives users a powerful and portable way to scale up analyses in many computing architectures.

Science & Technology - Other Topics↗

NADPH production by the oxidative pentose-phosphate pathway supports folate metabolism

NADPH donates high-energy electrons for antioxidant defence and reductive biosynthesis. Cytosolic NADP is recycled to NADPH by the oxidative pentose-phosphate pathway (oxPPP), malic enzyme 1 (ME1) and isocitrate dehydrogenase 1 (IDH1). Here we show that any one of these routes can support cell growth, but the oxPPP is uniquely required to maintain a normal NADPH/NADP ratio, mammalian dihydrofolate reductase (DHFR) activity and folate metabolism. These findings are based on CRISPR deletions of glucose-6-phosphate dehydrogenase (G6PD, the committed oxPPP enzyme), ME1, IDH1 and combinations thereof in HCT116 colon cancer cells. Loss of G6PD results in high NADP, which induces compensatory increases in ME1 and IDH1 flux. But the high NADP inhibits DHFR, resulting in impaired folate-mediated biosynthesis, which is reversed by recombinant expression of Escherichia coli DHFR. Conclusively, across different cancer cell lines, G6PD deletion produced consistent changes in folate-related metabolites, suggesting a general requirement for the oxPPP to support folate metabolism.

59 BASIC BIOLOGICAL SCIENCES↗

Peak Annotation and Verification Engine for Untargeted LC–MS Metabolomics

Untargeted metabolomics can detect more than 10 000 peaks in a single LC–MS run. The correspondence between these peaks and metabolites, however, remains unclear. Here in this study, we introduce a Peak Annotation and Verification Engine (PAVE) for annotating untargeted microbial metabolomics data. The workflow involves growing cells in 13 C and 15 N isotope-labeled media to identify peaks from biological compounds and their carbon and nitrogen atom counts. Improved deisotoping and deadducting are enabled by algorithms that integrate positive mode, negative mode, and labeling data. To distinguish metabolites and their fragments, PAVE experimentally measures the response of each peak to weak in-source collision induced dissociation, which increases the peak intensity for fragments while decreasing it for their parent ions. The molecular formulas of the putative metabolites are then assigned based on database searching using both m/z and C/N atom counts. Application of this procedure to Saccharomyces cerevisiae and Escherichia coli revealed that more than 80% of peaks do not label, i.e., are environmental contaminants. More than 70% of the biological peaks are isotopic variants, adducts, fragments, or mass spectrometry artifacts yielding ~2000 apparent metabolites across the two organisms. About 650 match to a known metabolite formula based on m/z and C/N atom counts, with 220 assigned structures based on MS/MS and/or retention time to match to authenticated standards. Lastly, PAVE enables systematic annotation of LC–MS metabolomics data with only ~4% of peaks annotated as apparent metabolites.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Synthesis of Post-fire Monitoring Activities in the Great Basin Desert, Mojave Desert, and Transition Zones

In the deserts of the American Southwest, fire return intervals of centuries to millennia are being replaced by fire return intervals of decades. This increased burn frequency has implications for post-closure management and long-term stewardship for Soils Corrective Action Units (CAUs) and Corrective Action Sites (CASs) on the Nevada National Security Site (NNSS), Tonopah Test Range, and Nevada Test and Training Range for which the U.S. Department of Energy (DOE), Environmental Management-Nevada (EM-NV) is responsible. For many CAUs and CASs, where closure-in-place alternatives were implemented or are being considered, there is a chance that these sites could burn over while they still pose a risk to the environment or human health given the long half-lives of some of the radionuclide contaminants of concern (COCs) (Shafer et al., 2007; Shafer and Gomes, 2009). Although it would have been ideal to conduct a fire-related study at a radionuclide contaminated site on the NNSS to determine how contaminated soils are transported post-fire, it was more practical to examine fires in environments analogous to where Soils Activity CAUs and CASs exist. Therefore, a series of studies were initiated at three radiologically uncontaminated analog sites to better understand the possible effects of wildfire on erosion and sediment transport by wind and water should vegetation at contaminated sites burn at the NNSS. The studies took place at the sites of the Gleason Fire, a prescribed burn that occurred near Ely, Nevada, which is in the Great Basin ecoregion; the White Rock Fire that occurred near Mesquite, Nevada, which is in the Mojave Desert ecoregion; and the Jacob Fire that occurred near Hiko, Nevada, in the transitional zone between the Great Basin Desert and the Mojave Desert. Each site was representative of one of the three ecoregions found on the NNSS. Erosion and vegetation characteristics were measured multiple times post-fire on both burned and unburned test plots at these study sites to compare and monitor the effects of fire over time. However, at the Mojave Desert site, there was an additional burn from nearly 25 years ago that was also compared with the more recent burned areas from 2013. Also, the time elapsed after the fire and the time when sampling began differed among the ecoregions. For example, at the Great Basin site, samples were collected prior to the fire and less than one month after the fire, whereas data collected at the Mojave Desert site did not occur until 22 months after the fire. The differences between the sample measurements and the time that elapsed after the fire may contribute to the variability in the data and the interpretations of the data. Runoff and water erosion were quantified through a series of rainfall and runoff simulation tests in which controlled amounts of water were delivered to the soil surface. Runoff data were collected from different microhabitats (e.g., undercanopies, interspace soils, ridges, and drainage areas). The data showed soil hydrophobicity (i.e., water repellency) on the Great Basin site for up to 12 months after the fire. The soil structure remained changed and weaker on the burned areas compared with the unburned areas for the three-year study period. Although runoff data at both the Great Basin site and transition zone site were highly variable, the post-fire runoff potential did not generally increase at either location after three years of monitoring. Mojave runoff did not differ much between fire ages or between burned and unburned areas, possibly because of the amount of vegetation growing on all three surfaces and because the fire intensity was likely lower relative to other ecoregions due to the amount of space between plants. Additionally, the measurements conducted on the Mojave fire occurred several years after the fire had burned and not within several months of the burn, which may also account for the lack of differences in runoff between burned and unburned locations. Wind erosion was assessed and quantified with a Portable In-Situ Wind ERosion Lab (PI-SWERL) on both the burned and unburned soils of different microhabitats (e.g., ridges, drainages, interspaces between plants, and plant undercanopies). Estimates of emissions (e.g., particulate matter with aerodynamic diameters less than or equal to 10 micrometers, or PM10) at different wind speeds were collected and filter samples were analyzed for chemical composition. The measurements among the fires were similar and the results of the wind erosion measurements indicate that there were seasonal influences on many parameters, but the potential for PM10 windblown dust emissions was higher on burned areas compared with unburned areas. Among the burned areas, drainages produced the most dust emissions, whereas burned ridges were the least emissive. Emissions at the Mojave site and transition zone site were similar between burned and unburned areas approximately three years after the respective fires. Emissions remained much greater on burned soils at the Great Basin site. However, site selection may have also contributed to the differences of emissions among the three study locations. Post-fire vegetation responses were documented for three years following each fire in different microhabitats (e.g., ridge, drainage, undercanopy, and interspace) at the Great Basin and transition zone sites. In 2013, at the Mojave fire site, random permanent plots were established in newly burned areas, areas that burned approximately 25 years ago, and an unburned control area. At each fire site, the regeneration of native plant species dominated the burned areas, but invasive annual grasses were present at each fire site. During the course of each three-year study, the invasive annual grasses increased in density or percentage at both the Great Basin and transition fire sites but not at the Mojave site, where annual invasive grasses remained high throughout the study period. However, the chronosequence data from the Mojave site indicate a transition to different invasive grass species with time. The post-burn vegetation at all three ecoregions is still in the early stages of succession, and shrub size should increase over time and shrub density should decrease over time. However, the recovery of the plant communities to pre-burn compositions may not occur for decades or centuries, or may not occur because of changes in climate and the presence of invasive annual grasses. Results from the three study locations suggested that contaminated soils on the NNSS that experienced wildfire had the potential for soil erosion and transport of contaminated soils. Both wind and soil runoff studies indicated that locations in the Great Basin and transition zone ecoregions were more susceptible to erosion than the Mojave Desert ecoregion, but the highest levels of erosion occurred during the early portions of the study (the first 24 months) and the Mojave Desert was not measured until 22 months after the burn. Additionally, data from the Great Basin indicated deeper soils may increase susceptibility to wind erosion. Historically, the Great Basin and transition zone ecoregions burned more frequently than the Mojave Desert because of fuel abundance and connectivity—and they continue to burn more frequently, particularly after the introduction of invasive grasses (Davies and Nafus, 2013). However, both ecoregions and the transition zone have burned with extensive, high-severity fires when certain weather and fuel conditions are met. For example, the high abundance and productivity of annual grasses and forbs—which are usually produced by above average winter precipitation—combined with early spring and summer warm, dry conditions. Future climate scenarios predict increased temperatures, variable to reduced precipitation, and larger, more extreme wildfires throughout western North America. These predictions suggest that future fires on the NNSS could increase in frequency, intensity, and severity similar to their analog ecosystems throughout the Great Basin and Mojave Desert (Dennison et al., 2014; Abatzoglou andWilliams, 2016; Westerling, 2016).

54 ENVIRONMENTAL SCIENCES↗

Entangled Pauli principles: The DNA of quantum Hall fluids

A formalism is developed for the rigorous study of solvable fractional quantum Hall parent Hamiltonians with Landau-level mixing. The idea of organization through “generalized Pauli principles” is expanded to allow for root-level entanglement, giving rise to “entangled Pauli principles.” Through the latter, aspects of the effective field theory description become ingrained in exact microscopic solutions for a great wealth of phases for which no similar single Landau-level description is known. We discuss in detail braiding statistic, edge theory, and rigorous zero-mode counting for the Jain-221 state as derived from a microscopic Hamiltonian. As a result, the relevant root-level entanglement is found to feature an Affleck-Kennedy-Lieb-Tasaki (AKLT)-type matrix-product ground states structure associated with an emergent SU(2) symmetry.

75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗

A novel phosphor CaZnGe2O6:Bi3+ with persistent luminescence and photo-stimulated luminescence

Highlights: • The CaZnGe{sub 2}O{sub 6}: Bi{sup 3+} with the emission bands at 468 nm. • The afterglow emission band (300–650 nm) almost covering the UV–vis spectral region. • A afterglow time can last 12 h in the dark after ceasing the 254 nm irradiation. • The excitation of VIS-NIR incoherent light can get the photo-stimulated luminescence. - Abstract: Bi{sup 3+}-activated phosphor with ultraviolet-visible persistent luminescence and photo-stimulated luminescence is synthesized via high temperature solid phase reaction. This phosphor shows a broad emission band from 300 nm to 700 nm, a bright persistent luminescence over 12 h after ceasing the excitation and the photo-stimulated luminescence under the excitation of visible to near-infrared light. This paper reports that the operational waveband of long persistent phosphor, CaZnGe{sub 2}O{sub 6}: Bi{sup 3+}, has been extended into the short-wavelength spectral region.

36 MATERIALS SCIENCE↗

Estimation of bare soil evaporation for different depths of water table in the wind-blown sand area of the Ordos Basin, China

Soil surface evaporation is a significant component of the hydrological cycle, occurring at the interface between the atmosphere and vadose zone, but it is affected by factors such as groundwater level, soil properties, solar radiation and others. In order to understand the soil evaporation characteristics in arid regions, a field experiment was conducted in the Ordos Basin, central China, and high accuracy sensors of soil moisture, moisture potential and temperature were installed in three field soil profiles with water-table depths (WTDs) of about 0.4, 1.4 and 2.2 m. Soil-surface-evaporation values were estimated by observed data combined with Darcy’s law. Results showed that: (1) soil-surface-evaporation rate is linked to moisture content and it is also affected by air temperature. When there is sufficient moisture in the soil profile, soil evaporation increases with rising air temperature. For a WTD larger than the height of capillary rise, the soil evaporation is related to soil moisture content, and when air temperature is above 25 °C, the soil moisture content reduces quickly and the evaporation rate lowers; (2) phreatic water contributes to soil surface evaporation under conditions in which the WTD is within the capillary fringe. This indicates that phreatic water would not participate in soil evaporation for a WTD larger than the height of capillary rise. This finding developed further the understanding of phreatic evaporation, and this study provides valuable information on recognized soil evaporation processes in the arid environment.

58 GEOSCIENCES↗

xxing9703/PAVE

Untargeted metabolomics can detect more than 10 000 peaks in a single LC–MS run. The correspondence between these peaks and metabolites, however, remains unclear. Here, we introduce a Peak Annotation and Verification Engine (PAVE) for annotating untargeted microbial metabolomics data. The workflow involves growing cells in 13C and 15N isotope-labeled media to identify peaks from biological compounds and their carbon and nitrogen atom counts. Improved deisotoping and deadducting are enabled by algorithms that integrate positive mode, negative mode, and labeling data. To distinguish metabolites and their fragments, PAVE experimentally measures the response of each peak to weak in-source collision induced dissociation, which increases the peak intensity for fragments while decreasing it for their parent ions. The molecular formulas of the putative metabolites are then assigned based on database searching using both m/z and C/N atom counts. Application of this procedure to Saccharomyces cerevisiae and Escherichia coli revealed that more than 80% of peaks do not label, i.e., are environmental contaminants. More than 70% of the biological peaks are isotopic variants, adducts, fragments, or mass spectrometry artifacts yielding ∼2000 apparent metabolites across the two organisms. About 650 match to a known metabolite formula based on m/z and C/N atom counts, with 220 assigned structures based on MS/MS and/or retention time to match to authenticated standards. Thus, PAVE enables systematic annotation of LC–MS metabolomics data with only ∼4% of peaks annotated as apparent metabolites.

Xing, Xi↗

Pore-scale study of effects of macroscopic pores and their distributions on reactive transport in hierarchical porous media

For applications of reactive transport in porous media, optimal porous structures should possess both high surface area for reactive sites loading and low mass transport resistance. Hierarchical porous media with a combination of pores at different scales are designed for this purpose. In this paper, using the lattice Boltzmann method, pore-scale numerical studies are conducted to investigate diffusion-reaction processes in 2D hierarchical porous media generated by self-developed reconstruction scheme. Complex interactions between porous structures and reactive transport are revealed under different conditions. Simulation results show that adding macropores can greatly enhance the mass transport, but at the same time reduce the reactive surface, leading to complex change trend of the total reaction rate. Effects of gradient distribution of macropores within the porous medium are also investigated. It is found that a front-loose, back-tight (FLBT) hierarchical structure is desirable for enhancing mass transport, increasing total reaction rate, and improving catalyst utilization. Finally, on the whole, from the viewpoint of reducing cost and improving material performance, hierarchical porous structures, especially gradient structures with the size of macropores gradually decreasing along the transport direction, are desirable for catalyst application.

42 ENGINEERING↗