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Here, in this presentation, we demonstrate the operation and applications of a custom-built automation program to acquire high-resolution data on an aberration-corrected STEM.
PCR-based assays have become the benchmark for detecting pathogens of poultry and other livestock; however, these techniques are limited in their ability to detect multiple infecting agents, provide limited genetic information on the pathogen, and, for RNA viruses, must be reviewed frequently to assure high sensitivity and specificity. In contrast, untargeted, high-throughput sequencing can rapidly detect all infecting agents in a sample while providing genomic sequence information to allow more in-depth characterization of viruses. Although next-generation sequencing (NGS) offers many advantages, one of its primary limitations is low sensitivity to pathogens given the abundance of host and other non-target sequences in sequencing libraries. We explored methods for improving the sensitivity of NGS to detect respiratory and enteric viruses in poultry from RNA extracts of swab samples. We employed commercial and custom-designed negative enrichment strategies to selectively deplete the most abundant rRNA reads from the host and non-target bacteria; host RNA was diminished from up to 40% of total reads to as low as 3%, and the total number of reads assigned to abundant bacterial classes were reduced greatly. Our treatment resulted in up to a 700-fold increase in the number of viral reads, detection of a greater number of viral agents, and higher average genome coverage for pathogens. Depletion assays added only 2 h to the NGS library preparation workflow. Custom depletion probe design offered significant cost savings (US$7–12 per sample) compared to commercial kits (US$30–50 per sample).
Increasing landscape heterogeneity (composition and configuration) can enhance natural enemy populations and support pest suppression in agricultural landscapes. Using a network-based data mining approach, we examined independent gradients of landscape composition and configuration at six spatial scales that were associated with pest suppression services measured at 32 sites in Michigan and Wisconsin, USA. We compared the relative effects of landscape composition and configuration across scales with those of local crop type (corn or grassland). We found that multiple gradients of configurational heterogeneity were independent of composition and strongly associated with pest suppression, with different configuration metrics being predictive of pest suppression depending on the spatial scales and regions considered. Landscapes that were more configurationally heterogeneous at smaller spatial scales consistently supported higher pest suppression. In Michigan, pest suppression increased in landscapes with high edge contrast between annual crops and surrounding habitats and high edge density of grassland within 250-500 m radii. In Wisconsin, pest suppression increased with large core area of grassland and high field density within a 250 m radius. The main compositional effect we found was a positive relationship between grassland cover and pest suppression occurring at larger spatial scales (1000-1500 m) and occurring in Wisconsin but not in Michigan. Our findings demonstrate that effects of landscape composition and configuration on pest suppression differ across spatial scales and vary regionally. The network-based data mining techniques used here could be useful for disentangling intercorrelated landscape metrics in a variety of other contexts in landscape ecology.
We theoretically investigate the fluorescence intensity correlation (FIC) of Ar clusters and Mo-doped iron oxide nanoparticles subjected to intense, femtosecond, and sub-femtosecond x-ray free-electron laser pulses for high-resolution and elemental contrast imaging. We present the FIC of Kα and Kαh emission in Ar clusters and discuss the impact of sample damage on retrieving high-resolution structural information and compare the obtained structural information with those from the coherent diffractive imaging (CDI) approach. We found that, while sub-femtosecond pulses will substantially benefit the CDI approach, few-femtosecond pulses may be sufficient for achieving high-resolution information with the FIC. Furthermore, we show that the fluorescence intensity correlation computed from the fluorescence of the Mo atoms in Mo-doped iron oxide nanoparticles can be used to image dopant distributions in the nonresonant regime.
Hydrothermal liquefaction (HTL) of lignocellulosic biomass is plagued with low biocrude yields owing to the tendency of highly reactive oxygenated intermediates to condense to form biochars. By contrast, the high protein content in food waste is comprised of substantial nitrogen species, which are known to interact strongly with oxygenates through Maillard, amide, and peptide bond formation reactions. Co-feeding food waste and lignocellulose opens new reaction pathways for biocrude formation but is currently poorly understood. This work evaluated the molecular level interactions between food waste and lignocellulose model compounds and the corresponding effect on product yields and quality. Food waste–cellulose and food waste–xylan feedstock blends achieved maximum biocrude carbon yield improvements of 12.2% and 10.1%, respectively, relative to a simple linear model that interpolates between the yields of the pure feedstocks. Increases in biocrude yield were balanced by corresponding decreases in char yield, indicating synergistic interactions between the feeds during HTL. Biocrude volatility analysis revealed that increased biocrude yield preferentially benefitted the jet fuel fraction, which comprised up to 22.6% of the total carbon yield for food waste–cellulose blends. Biocrude and char were analyzed using GC–MS and FT-IR spectroscopy to investigate the source of synergistic trends and provide greater mechanistic understanding. Key cofeeding effects included the promotion of retro-aldol condensation reactions and trans-esterification of fatty acids, sequestering carbon in the biocrude phase via the inhibition of char formation while increasing biocrude volatility toward jet fuel-range compounds. These results indicate the potential for judicious selection of HTL cofeeds to increase both biocrude yield and selectivity to desired fuel precursors, including sustainable aviation fuel.
Efficient laser-driven plasma acceleration of ion beams requires precision control of the target–plasma profile, which is crucial to optimize the laser energy transfer. Along the laser propagation direction, this can be achieved by tailoring the temporal structure of the laser pulse. We show for the first time that frequency-doubling of a short pulse (hundreds-femtosecond range) petawatt-class mixed-glass laser system, which results in temporal intensity contrast enhancement, enables surface and volumetric laser–energy coupling, and the acceleration of proton beams from few-nanometer-thick foil targets. Experimentally, maximum ion energies and laser-to-proton energy conversion efficiencies were found to be both maximized at optimum laser and target conditions manifested when the normalized target density nearly equalizes the normalized laser vector potential, which is in agreement with theory and simulations. These signatures are recognized as a unique indication of the interaction between ultra-intense laser pulses with high temporal intensity contrast and ultra-thin nanometer-scale targets. Transverse modulations of accelerated proton beams in the form of bubble- and ring-like structures measured in the thinnest targets provide additional evidence of volumetric laser-driven particle acceleration regimes and transitional features in ultra-thin foil targets specific to laser–plasma interactions characterized by a high temporal intensity contrast. These results open avenues in the generation of high contrast laser pulses from short-pulse-femtosecond petawatt mixed-glass laser systems and demonstrate the feasibility of this technique for applications requiring high laser intensity contrast with high efficiency.
The structural origin of the memory effect is still elusive in glassy materials. Here, in this letter, the memory effect in a series of metallic glasses (MGs) is observed by two step annealing using differential scanning calorimetry (DSC) and molecular dynamics simulations. It demonstrates that the Kovacs peak can be reflected from not only the system potential energy but also the atomic dynamics, showing the memory effect could originate from the formation of more loose packing configurations around mobile atoms by structural rejuvenation in the second step of high temperature annealing. In contrast, the high-low temperature annealing protocol can only induce the monotonic relaxation. Therefore, our results pave a pathway to better understand the origin of memory effect in MGs and other glassy materials from their dynamics and local atomic structure.
Lithiation-assisted epitaxy offers a flexible and robust approach for synthesizing high-quality Li-containing materials and interfaces with precise control. Here, in this study, we use lithium tungstate (Li x WO 3+x/2 , where x = 0 to 2) as a model system to investigate the intertwined effects of Li out-diffusion-induced compositional changes and surface-diffusion-induced morphological changes. By systematically varying synthesis and processing conditions, we uncover their impact on lithium tungstate film formation. Comprehensive characterizations, including X-ray diffraction, atomic force microscopy, X-ray photoemission spectroscopy and time-of-flight secondary ion mass spectrometry, reveal that low-temperature growth (< 300 °C) followed by high-temperature annealing yields continuous lithium tungstate films with significantly reduced surface roughness. In contrast, high-temperature deposition (≥ 300 °C) accelerates surface diffusion and Li out-diffusion, leading to island formation. Furthermore, in situ scanning transmission electron microscopy demonstrates the beam sensitivity of Li 2 WO 4 and reveals a phase transition from Li 2 WO 4 to LiWO 3.5 under prolonged electron beam exposure. These findings deepen our understanding of how to control composition and morphology of Li-containing films, providing valuable insights for the design and integration of energy materials.
We report solids irradiated by energetic photons can be eroded in two modes, depending on the radiation intensity. High average, low-peak power sources, e.g., synchrotron radiation and high-order harmonics, induce desorption of the material at a low etch rate. In contrast, high-peak-power radiation from extreme ultraviolet and x-ray lasers usually causes a massive removal of the material even by a single shot. In this contribution, an effective material erosion is reported in PMMA exposed to multiple accumulated pulses generated by the free-electron x-ray-laser Linac Coherent Light Source (LCLS, tuned at a photon energy of 830 eV in this study, operated in Menlo Park at Stanford, CA, USA) at a fluence below the single-pulse ablation threshold. The effect is caused by polymer-chain scissions initiated by single photons carrying enough energy to break the C—C bounds. High efficiency of the erosion is supposed to occur due to a correlation of the single-photon effects. The subthreshold damage exhibits a nonlinear dose dependence resulting from a competition between chain scissions and cross-linking processes. The cross-linking is proven by Raman spectroscopy of the irradiated polymer. Two theoretical models of the x-ray free-electron-laser-induced erosion are suggested, which provide an excellent agreement with the experimental results.
Here, we report the application of high-speed synchrotron X-ray phase contrast imaging (PCI) in real-time damage characterization for glass fiber reinforced composites (GFRCs) subjected to dynamic loading. Dynamic single-edge notched bending (DSENB) experiments on pre-notched S-2 GFRCs were performed on a modified Kolsky compression bar. During loading, the synchrotron X-ray beam penetrated through the composite specimen from the side to detect damage evolution inside the material. Entire dynamic events were recorded by a high-speed camera as image sequences.0° and 90° unidirectional and cross-ply composites were investigated. An optical imaging technique was also employed to capture similar dynamic events in comparison with the radiographic imaging. It is demonstrated that high-speed X-ray PCI had sufficient phase contrast to characterize a crack initiation at a 20-μm spatial resolution within 920 ns and track the crack geometry during propagation, thereby providing reliable data to quantify the dynamic damage resistance of GFRCs. Furthermore, being capable of recognizing microscopic damage-related features at a sub-10-μm resolution, high-speed X-ray PCI provided fundamental material failure mechanisms to reveal the essential of macroscale structural failure of composites. It can also track the damage evolution inside and between individual plies of laminated composites. However, current high-speed X-ray PCI technique only supports in-situ observation and the high timing and spatial resolutions are limited within a field of view of ~2.5 mm in square, preventing its application in the three-dimensional and larger-area damage detection for GFRC structures.
Antimony sesquiselenide has become an outstanding functional material for photovoltaics, energy storage and transformation, memory and photonic applications. Sb 2 Se 3 is one of the most successful emerging solar light absorbers and has also been identified as a highly promising ultralow-loss phase-change material (PCM) for next-generation coherent nanophotonic processors, photonic tensor cores, quantum and neuromorphic networks. Unlike benchmark telluride PCMs, Sb 2 Se 3 features a quasi-one-dimensional (1D) crystalline structure consisting of (Sb 4 Se 6 ) ∞ ribbons, lacks the typical PCM chemical bonding, and undergoes an extended semiconductor-metal transition above the melting point. Consequently, the origin of high optical contrast between crystalline (SET) and amorphous (RESET) logic states remains elusive and presents a significant challenge. Using high-energy X-ray diffraction and Raman spectroscopy over a wide temperature range, supported by first-principles simulations and complemented by thermal, optical and electrical measurements, as well as by 121 Sb-Mossbauer spectroscopy, the quasi-1D network of orthorhombic antimony sesquiselenide was found to undergo significant evolution in amorphous and supercooled Sb 2 Se 3 , leading to lower coordination, shorter interatomic distances and a higher p-electron density on antimony, indicating changes in chemical bonding. The observed novel Sb 2 Se 3 nanocrystalline polymorph, characterized by trigonal antimony coordination and more isolated Sb-Se ribbons, could help reduce multiple trapping defect states in the bandgap, which are typical of orthorhombic Sb 2 Se 3 , thereby enhancing the power-conversion efficiency of photovoltaic devices. Semimetallic and metallic liquid Sb 2 Se 3 exhibit a gradual transformation into a denser 2D and/or 3D network with higher antimony coordination. Localized electron states in the pseudogap are becoming extended, leading to an increase in electronic conductivity σ following the relationship σ ∝ N(E F ) 2 . Liquid Sb 2 Se 3 also appears to be strongly fragile, with a nonmonotonic change in viscosity and higher atomic mobility in the metallic liquid. Furthermore, these results explain extraordinary functionalities of Sb 2 Se 3 for photonic and energy applications.
Atmospheric ice-nucleating particles (INPs) are an important subset of aerosol particles that are responsible for the heterogeneous formation of ice crystals. INPs modulate the arctic cloud phase (liquid vs. ice), resulting in implications for radiative feedbacks. The number of arctic INP studies investigating specific INP episodes or sources increased recently. However, existing studies are based on short-duration field data, and long-term datasets are lacking. Continuous, long-term measurements are key to determining the abundance and variability of ambient arctic INPs and constraining aerosol–cloud interactions, e.g., to verify and/or improve simulations of mixed-phase clouds. Here, we present a new long-duration INP dataset from the Arctic: 2 years of predominantly immersion-mode INP concentrations (n INP ) measured continuously at the National Oceanic and Atmospheric Administration's Barrow Atmospheric Baseline Observatory (BRW) on the North Slope of Alaska. A portable ice nucleation experiment chamber (PINE-03), which simulates adiabatic expansion cooling, was used to directly measure the ground-level INP abundance with an approximately 12 min time resolution from October 2021 to December 2023. We document PINE-03 n INP measurements as well as estimated ice nucleation active surface site density (n s ) over a wide range of heterogeneous freezing temperatures from −16 to −31 °C from which we introduce new season-specific parameterizations suitable for modeling mixed-phase clouds. Collocated aerosol and meteorological data were analyzed to assess the correlation between ambient n INP , air mass origin region, and meteorological variability. Our findings suggest (1) very high freezing efficiency of INPs across the measured temperatures (n s ≈ 2×10 8 –10 10 m −2 for −16 to −31 °C), which is a factor of 10–1000 times greater efficiency as compared to that found in the previous mid-latitude INP measurements in fall using the same instrument; (2) surprisingly high n INP (≥ 1 L −1 at −25 °C) for the examined temperatures throughout the year that were not measured by PINE-03 at other sites; and (3) high n INP in spring, possibly related to arctic haze episodes. Relatively low concentrations of aerosol surface area and contrasting high-INP concentrations at BRW relative to mid-latitude sites are the possible reasons for the observed high freezing efficiency.
The present finding illuminates the physics of the formation of interfaces of metal based hetero-structures near layer continuous limit as an approach to develop high-efficiency W/B 4 C multilayer (ML) optics with ML periodicity varying d = 1.86–1.23 nm at a fixed number of layer pairs N = 400. The microstructure of metal layers is tailored near the onset of grain growth to control the surface density of grains resulting in small average sizes of grains to sub-nanometers. This generates concurrently desirable atomically sharp interfaces, high optical contrast, and desirable stress properties over a large number of periods, which have evidence through the developed ML optics. We demonstrate significantly high reflectivities of ML optics measured in the energy range 10–20 keV, except for d = 1.23 nm due to quasi-continuous layers. The reflectivities at soft gamma-rays are predicted.
Optical nonreciprocity plays a key role in almost every optical system, directing light flow and protecting optical components from backscattered light. Controllable forms of on-chip nonreciprocity are needed for the robust operation of increasingly sophisticated photonic integrated circuits (PICs) in the context of classical and quantum computation, networking, communications, and sensing. However, it has been challenging to achieve wideband, low-loss optical nonreciprocity on-chip. In this paper, we demonstrate strong coupling and Rabi-like energy exchange between photonic bands, possessing a continuum of modes, to unlock nonreciprocity and frequency translation over wide optical bandwidths in silicon. Using a traveling-wave phonon field to drive indirect interband photonic transitions, we demonstrate band hybridization that enables an intriguing form of nonreciprocal dissipation engineering. Using the converted mode to create a nonreciprocal dissipation channel, we demonstrate a frequency-neutral, low-loss (less than 1 dB) isolator with high nonreciprocal contrast (more than 14 dB) and broad operating bandwidth (more than 59 GHz). Additionally, through the implementation of complete interband conversion, we demonstrate a high extinction (more than 55 dB) optical frequency translation operation with near-unity efficiency.
X-ray phase contrast imaging (XPCI) provides enhanced image contrast beyond absorption-based x-ray imaging alone due to refraction and diffraction from gradients in the object material density. It is sensitive to small variations in density, such as internal voids, cracks, grains, defects, and material flow, as well as to stronger density variations such as from a shock wave. Beyond its initial use in biology and materials science, XPCI is now routinely used in inertial confinement fusion (ICF) and high energy density (HED) research, first to characterize ICF capsules and targets, and later applied in dynamic experiments, where coherent x-ray sources, ultrafast x-ray pulses, and high temporal and spatial resolution are required. In this Review article, XPCI image formation theory is presented, its diverse use in ICF and HED research is discussed, the unique requirements for ultrafast XPCI imaging are given, as well as current challenges and issues in its use.
This paper presents a scalable multigrid preconditioner targeting large-scale systems arising from discontinuous Petrov–Galerkin (DPG) discretizations of high-frequency wave operators. This work is built on previously developed multigrid preconditioning techniques of Petrides and Demkowicz (Comput. Math. Appl. 87 (2021) pp. 12–26) and extends the convergence results from $\mathscr{O}$(10 7 ) degrees of freedom (DOFs) to $\mathscr{O}$(10 9 ) DOFs using a new scalable parallel MPI/OpenMP implementation. Novel contributions of this paper include an alternative definition of coarse-grid systems based on restriction of fine-grid operators, yielding superior convergence results. In the uniform refinement setting, a detailed convergence study is provided, demonstrating h and p robust convergence and linear scaling with respect to the wave frequency. Finally, the paper concludes with numerical results on hp -adaptive simulations including a large-scale seismic modeling benchmark problem with high material contrast.
Understanding the effects of polymer brush architecture on particle interactions in solution is requisite to enable the development of functional materials based on self-assembled polymer-grafted nanoparticles (GNPs). Static and dynamic light scattering of polystyrene-grafted silica particle solutions in toluene reveals that the pair interaction potential, inferred from the second virial coefficient, A 2 , is strongly affected by the grafting density, σ, and degree of polymerization, N, of tethered chains. In the limit of intermediate σ (~0.3 to 0.6 nm -2 ) and high N, A 2 is positive and increases with N. This confirms the good solvent conditions and can be qualitatively rationalized on the basis of a pair interaction potential derived for grafted (brush) particles. In contrast, for high σ > 0.6 nm -2 and low N, A 2 displays an unexpected reversal to negative values, thus indicating poor solvent conditions. These findings are rationalized by means of a simple analysis based on a coarse-grained brush potential, which balances the attractive core-core interactions and the excluded volume interactions imparted by the polymer grafts. The results suggest that the steric crowding of polymer ligands in dense GNP systems may fundamentally alter the interactions between brush particles in solution and highlight the crucial role of architecture (internal microstructure) on the behavior of hybrid materials. The effect of grafting density also illustrates the opportunity to tailor the physical properties of hybrid materials by altering geometry (or architecture) rather than a variation of the chemical composition.
Strategies to control ongoing biological invasions are often developed by modelling the invasive species' population and aiming to reduce its abundance. However, if the ultimate objective is to protect and restore native species, focussing solely on the invader may not be optimal because it does not account for (i) species interactions that can cause the invader's impacts to depend nonlinearly on its abundance, (ii) collateral damages to native species incurred due to nonspecific removal methods or (iii) native-invader trait differences. Here, to identify an invader suppression strategy that maximizes average native population size, we applied optimal control theory to a two-species model of a native species threatened by an invasive competitor. We examined trade-offs between iterative physical removals that selectively target invaders and intensifiable chemical control that is nonselective but has higher efficacy. We found that while iterative removals were capable of supporting large native populations when applied continuously, cost could be prohibitively high. In contrast, when favourable native-invader trait differences enabled native species to re-establish more quickly than invaders, intensifiable methods could achieve substantial restoration benefits at lower cost by focussing removal effort into periodic, high-efficacy events. In a metapopulation, removals that rotated among spatial patches were optimal when the native species had higher dispersal, whereas synchronous removals were preferred when native recovery was initiated locally and the invader could disperse. For a case study in Hawaiian streams, we compared how effective two alternative methods of removing invasive live-bearing fishes (poeciliids) might be at restoring the endemic freshwater goby Sicyopterus stimpsoni. We found that rotenone (a piscicidal chemical) offered superior benefits when the control budget was small and efficacy was high, but that electrofishing (use of electricity to manually collect target fish) was better with larger budgets and in many lower-efficacy scenarios. Synthesis and applications. Our findings demonstrate that, by accounting for species interactions and collateral damage, invasive species control strategies can be optimized in light of species traits. Choices about the timing, locations and types of removal events present opportunities to increase the efficiency with which invasive species suppression benefits native species.