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At least 757 records · Page 42

Time-Gated Raman Spectroscopy (Intern Final Report)

Time-gated Raman spectroscopy is a powerful tool for rapid non-destructive analysis of chemical compounds, particularly when combined with other investigative methods. Time-gating the signal obtained from a sample during Raman spectroscopy allows for the removal of background emission and black body radiation, improving clarity and accuracy of scans. The main objectives of this project were to prove the lab’s time-gated Raman spectroscopy system works as proof of concept and to make select improvements to the in-house LabVIEW software used to run the time-gated system. This time-gated system will be added to the CTK’s TAP reactors in the future, but this is out of the scope of this internship project. This research is important, as understanding the mechanisms behind catalysts leads to designing better systems/materials and the perfection of catalysts, and energy-efficient chemical manufacturing is key when designing a greener future. The research for this project was done with samples at both ambient conditions in sample holders and at operando conditions (i.e., high temperature, unsteady-state) inside a small-volume chemical reactor. Numerous spectro-kinetic scans of the catalysts were obtained, but the advanced dynamics of these systems are still being interpreted. There is data that demonstrates that the time-gated system is correctly rejecting emission from samples, and one can observe real-time changes in the signal from the sample, due to coking or changes induced by redox chemistry. Chemical manufacturers and the planet are the main beneficiaries of catalysis research, as better catalysts will reduce carbon emissions.

36 MATERIALS SCIENCE↗

Iterative sampling of expensive simulations for faster deep surrogate training

Deep neural network (DNN) surrogates of expensive physics simulations are enabling a rapid change in the way that common experimental design and analysis tasks are approached. Surrogate models allow simulations to be performed in parallel and separately from downstream tasks, thereby enabling analyses that would be impossible with the simulation in-the-loop; surrogates based on DNNs can effectively emulate diverse non-scalar data of the types collected in fusion and laboratory-astrophysics experiments. The challenge is in training the surrogate model, for which large ensembles of physics simulations must be run, preferably without wasting computational effort on uninteresting simulations. Here, in this paper, we present an iterative sampling scheme that can preferentially propose simulations in interesting regions of parameter space without neglecting unexplored regions, allowing high-quality and wide-ranging surrogate models to be trained using 2–3 times fewer simulations compare to space-filling designs. Our approach uses an explicit importance function defined on the simulation output space, balanced against a measure of simulation density which serves as a proxy for surrogate accuracy. It is easy to implement and can be tuned to find interesting simulations early in the study, allowing surrogates to be trained quickly and refined as new simulations become available; this represents an important step towards the routine generation of deep surrogate models quickly enough to be truly relevant to experimental work.

70 PLASMA PHYSICS AND FUSION TECHNOLOGY↗

An introduction to the significance of sample size in particle analyses for nuclear forensics and radiological investigations

Particulate isotopic analysis in nuclear forensics has developed rapidly during the past two decades due to technical advances in determining the isotopic composition of individual particles. This paper introduces basic statistical concepts that can be applied by analysts to understand the importance of statistical adequacy when interpretating particle data. While these basic statistical methods provide a useful point-of-entry to particle data analysis, more sophisticated statistical and modeling approaches are needed to extract maximal information from such datasets in the future.

38 RADIATION CHEMISTRY, RADIOCHEMISTRY, AND NUCLEA↗

Automated detection of double nuclei galaxies using GOTHIC and the discovery of a large sample of dual AGN

We present a novel algorithm to detect double nuclei galaxies (DNG) called Gothic (Graph-bOosTed iterated HIll Climbing) – that detects whether a given image of a galaxy has two or more closely separated nuclei. Our aim is to test for the presence of dual/multiple active galactic nuclei (AGN) in galaxies that visually represent a DNG. Although galaxy mergers are common, the detection of dual AGN is rare. Their detection is very important as they help us understand the formation of supermassive black hole (SMBH) binaries, SMBH growth and AGN feedback effects in multiple nuclei systems. There is thus a need for an algorithm to do a systematic survey of existing imaging data for the discovery of DNGs and dual AGNs. We have tested Gothic on an established sample of DNGs with a 100 per cent detection rate and subsequently conducted a blind search of 1 million SDSS DR16 galaxies (with spectroscopic data available) lying in the redshift range of z = 0 to 0.75. From the list of candidate DNGs found, we have detected 159 dual AGNs, of which 2 are triple AGN systems. Our results show that dual AGNs are not common, and triple AGN even rarer. The colour (u–r) magnitude plots of the DNGs indicate that star formation is quenched as the nuclei come closer and as the AGN fraction increases. The quenching is especially prominent for dual/triple AGN galaxies that lie at the extreme end of the red sequence.

79 ASTRONOMY AND ASTROPHYSICS↗

The GMRT archive atomic gas survey – II. Mass modelling and dark matter halo properties across late-type spirals

Studying the kinematics and mass modelling of galaxies from H i 21 cm data provides valuable insights into the properties of both the baryonic components and the dark matter halo in nearby galaxies. Despite many observational studies, mass modelling of galaxies remains challenging due to different limitations. For example, most of the previous studies involving mass modelling are based on rotation curves derived from 2D velocity fields from H i or H α spectroscopic observation which are often affected by beam smearing and projection effect. However, kinematic modelling done by fitting the ‘Tilted ring model’ to 3D data cube is not affected by these issues. In this study, we present and compare 3D kinematic modelling of a pilot sample of 11 galaxies from the GMRT archive atomic gas survey (GARCIA) using two different publicly available pipelines. We model the observed H i rotation curve using 3.6-μm infrared data and SDSS r-band data for stellar contribution, H i surface density profile for gas, and Navarro–Frenk–White profile for dark matter halo; and employ the Markov chain Monte Carlo optimization method for parameter estimation. Further, to validate our analysis, we revisit important scaling relations, e.g. the M gas –M star relation, M star –M halo relation, M gas –M halo relation and Baryonic Tully–Fisher relation. Here, the scaling relations from our analysis are broadly consistent with that reported in the literature. A larger sample of galaxies from GARCIA in the near future will allow studying these scaling relations in greater details.

79 ASTRONOMY AND ASTROPHYSICS↗

Introduction to Metadata and Ontologies: Everything You Always Wanted to Know About Metadata and Ontologies (But Were Afraid to Ask)

Metadata are contextual data about your experimental data. Metadata are the who, what, when, where, and why of these data. Metadata puts these data into context. In microbiome research, metadata includes information about the sample: when it was collected, where it was collected from, what kind of sample it is, and what were the properties of the environment or experimental condition from which the sample was taken. Information about sample processing is also metadata: methods used to extract and purify molecules (e.g., DNA) from the sample, type of DNA sequencing or other ’omics analyses done, and where the raw experimental data are located. This documentation includes information on the following topics: What are metadata? What kinds of metadata are there? Why are metadata important? Why should metadata be standardized? Why should metadata be machine readable? What is an ontology? Why are ontologies important? What are some examples of ontologies? The documentation also includes further resources on metadata guides and tools and tips for formatting metadata for maximum utility.

59 BASIC BIOLOGICAL SCIENCES↗

Evaluation of the relative importance of preheat from hohlraum x rays and a radiative shock on a low-density foam

Indirectly driven shock-tube experiments were performed on the Omega Laser Facility to evaluate the relative importance of hohlraum x ray and radiative shock preheat sources on a low-density foam. X rays emitted from the hohlraum and a subsequent shock wave are channeled into a low-density foam sample, which contains a plastic preheat-witness disk placed downstream of the foam. Simultaneous radiographic measurements of the shock speed in the foam and the expansion rate of the witness disk due to preheat allow for the observation of effects from the hohlraum's low-energy and high-energy x-ray spectrum. Here we showed, from simulations, that low-energy x rays from the hohlraum are preferentially absorbed near the ablator surface (where the hohlraum and the shock tube meet), while higher-energy x rays largely pass through the ablator and foam and are volumetrically absorbed by the witness disk. Reproducing the experimentally measured shock speed and expansion of the witness disk simultaneously, we extracted the temperature evolution of preheated foam from the simulation and evaluated the relative importance of preheat sources on a low-density foam from hohlraum x-ray radiation and radiative shock. We found that radiation from the shock front was more effective at preheating the low-density foam than the high-energy x rays from the hohlraum. This shock-tube preheat experiment is important for understanding the results of the MARBLE experiments at the National Ignition Facility because initial conditions of foam-filled MARBLE capsules are sensitive to preheat.

70 PLASMA PHYSICS AND FUSION TECHNOLOGY↗

Oxygen isotope ratios in zircon and garnet: A record of assimilation and fractional crystallization in the Dinkey Dome peraluminous granite, Sierra Nevada, California

Abstract The 119 Ma Dinkey Dome pluton in the central Sierra Nevada Batholith is a peraluminous granite and contains magmatic garnet and zircon that are complexly zoned with respect to oxygen isotope ratios. Intracrystalline SIMS analysis tests the relative importance of magmatic differentiation processes vs. partial melting of metasedimentary rocks. Whereas δ18O values of bulk zircon concentrates are uniform across the entire pluton (7.7‰ VSMOW), zircon crystals are zoned in δ18O by up to 1.8‰, and when compared to late garnet, show evidence of changing magma chemistry during multiple interactions of the magma with wall rock during crustal transit. The evolution from an early high-δ18O magma [δ18O(WR) = 9.8‰] toward lower values is shown by high-δ18O zircon cores (7.8‰) and lower δ 18O rims (6.8‰). Garnets from the northwest side of the pluton show a final increase in δ18O with rims reaching 8.1‰. In situ REE measurements show zircon is magmatic and grew before garnets. Additionally, δ18O in garnets from the western side of the pluton are consistently higher (avg = 7.3‰) relative to the west (avg = 5.9‰). These δ18O variations in zircon and garnet record different stages of assimilation and fractional crystallization whereby an initially high-δ18O magma partially melted low-δ18O wallrock and was subsequently contaminated near the current level of emplacement by higher δ18O melts. Collectively, the comparison of δ18O zoning in garnet and zircon shows how a peraluminous pluton can be constructed from multiple batches of variably contaminated melts, especially in early stages of arc magmatism where magmas encounter significant heterogeneity of wall-rock assemblages. Collectively, peraluminous magmas in the Sierran arc are limited to small <100 km2 plutons that are intimately associated with metasedimentary wall rocks and often surrounded by later and larger metaluminous tonalite and granodiorite plutons. The general associations suggest that early-stage arc magmas sample crustal heterogeneities in small melt batches, but that with progressive invigoration of the arc, such compositions are more effectively blended with mantle melts in source regions. Thus, peraluminous magmas provide important details of the nascent Sierran arc and pre-batholithic crustal structure.

Geochemistry & Geophysics↗

Assessing microbial residues in soil as a potential carbon sink and moderator of carbon use efficiency

Abstract A longstanding assumption of glucose tracing experiments is that all glucose is microbially utilized during short incubations of ≤2 days to become microbial biomass or carbon dioxide. Carbon use efficiency (CUE) estimates have consequently ignored the formation of residues (non-living microbial products) although such materials could represent an important sink of glucose that is prone to stabilization as soil organic matter. We examined the dynamics of microbial residue formation from a short tracer experiment with frequent samplings over 72 h, and conducted a meta-analysis of previously published glucose tracing studies to assess the generality of these experimental results. Both our experiment and meta-analysis indicated 30–34% of amended glucose-C ( 13 C or 14 C) was in the form of residues within the first 6 h of substrate addition. We expand the conventional efficiency calculation to include residues in both the numerator and denominator of efficiency, thereby deriving a novel metric of the potential persistence of glucose-C in soil as living microbial biomass plus residues (‘carbon stabilization efficiency’). This new metric indicates nearly 40% of amended glucose-C persists in soil 180 days after amendment, the majority as non-biomass residues. Starting microbial biomass and clay content emerge as critical factors that positively promote such long term stabilization of labile C. Rapid residue production supports the conclusion that non-growth maintenance activity can illicit high demands for C in soil, perhaps equaling that directed towards growth, and that residues may have an underestimated role in the cycling and sequestration potential of C in soil.

Geyer, Kevin (ORCID:0000000252182745)↗

Automatic detection of cataclysmic variables from SDSS images

Abstract Investigating rare and new objects have always been an important direction in astronomy. Cataclysmic variables (CVs) are ideal and natural celestial bodies for studying the accretion process of semi-detached binaries with accretion processes. However, the sample size of CVs must increase because a lager gap exists between the observational and the theoretical expanding CVs. Astronomy has entered the big data era and can provide massive images containing CV candidates. CVs as a type of faint celestial objects, are highly challenging to be identified directly from images using automatic manners. Deep learning has rapidly developed in intelligent image processing and has been widely applied in some astronomical fields with excellent detection results. YOLOX, as the latest YOLO framework, is advantageous in detecting small and dark targets. This work proposes an improved YOLOX-based framework according to the characteristics of CVs and Sloan Digital Sky Survey (SDSS) photometric images to train and verify the model to realise CV detection. We use the Convolutional Block Attention Module to increase the number of output features with the feature extraction network and adjust the feature fusion network to obtain fused features. Accordingly, the loss function is modified. Experimental results demonstrate that the improved model produces satisfactory results, with average accuracy (mean average Precision at 0.5) of 92.0%, Precision of 92.9%, Recall of 94.3%, and $F1-score$ of 93.6% on the test set. The proposed method can efficiently achieve the identification of CVs in test samples and search for CV candidates in unlabeled images. The image data vastly outnumber the spectra in the SDSS-released data. With supplementary follow-up observations or spectra, the proposed model can help astronomers in seeking and detecting CVs in a new manner to ensure that a more extensive CV catalog can be built. The proposed model may also be applied to the detection of other kinds of celestial objects.

Astronomy & Astrophysics↗

Automating data analysis for hydrogen/deuterium exchange mass spectrometry using data-independent acquisition methodology

We present a hydrogen/deuterium exchange workflow coupled to tandem mass spectrometry (HX-MS 2 ) that supports the acquisition of peptide fragment ions alongside their peptide precursors. The approach enables true auto-curation of HX data by mining a rich set of deuterated fragments, generated by collisional-induced dissociation (CID), to simultaneously confirm the peptide ID and authenticate MS 1 -based deuteration calculations. The high redundancy provided by the fragments supports a confidence assessment of deuterium calculations using a combinatorial strategy. The approach requires data-independent acquisition (DIA) methods that are available on most MS platforms, making the switch to HX-MS 2 straightforward. Importantly, we find that HX-DIA enables a proteomics-grade approach and wide-spread applications. Considerable time is saved through auto-curation and complex samples can now be characterized and at higher throughput. We illustrate these advantages in a drug binding analysis of the ultra-large protein kinase DNA-PKcs, isolated directly from mammalian cells.

59 BASIC BIOLOGICAL SCIENCES↗

BEYONDPLANCK XI. Bayesian CMB analysis with sample-based end-to-end error propagation

We present posterior sample-based cosmic microwave background (CMB) constraints from Planck LFI and WMAP observations as derived through global end-to-end Bayesian processing within the BeyondPlanck framework. We first use these samples to study correlations between CMB, foreground, and instrumental parameters, and we identify a particularly strong degeneracy between CMB temperature fluctuations and free-free emission on intermediate angular scales (400 ≲ ℓ ≲ 600), which is mitigated through model reduction, masking, and resampling. We compare our posterior-based CMB results with previous Planck products, and find generally good agreement, although with notably higher noise due to our exclusion of HFI data. We find a best-fit CMB dipole amplitude of 3362.7 ± 1.4 µK, in excellent agreement with previous Planck results. The quoted dipole uncertainty is derived directly from the sampled posterior distribution, and does not involve any ad hoc contributions for Planck instrumental systematic effects. Similarly, we find a temperature quadrupole amplitude of ${σ}_{2}^{TT}$ = 229 ± 97 µK 2 , which is in good agreement with previous results in terms of the amplitude, but the uncertainty is an order of magnitude larger than the naive diagonal Fisher uncertainty. Relatedly, we find lower evidence for a possible alignment between the quadrupole and octopole than previously reported due to a much larger scatter in the individual quadrupole coefficients, caused both by marginalizing over a more complete set of systematic effects, but also by our more conservative analysis mask required to mitigate the free-free degeneracy. For higher multipoles, we find that the angular temperature power spectrum is generally in good agreement with both Planck and WMAP. At the same time, we note that this is the first time the sample-based asymptotically exact Blackwell-Rao estimator has been successfully established for multipoles up to ℓ ≤ 600, and it now accounts for the majority of the cosmologically important information. Overall, this analysis demonstrates the unique capabilities of the Bayesian approach with respect to end-to-end systematic uncertainty propagation, and we believe it can and should play an important role in the analysis of future CMB experiments. Cosmological parameter constraints are presented in a companion paper.

79 ASTRONOMY AND ASTROPHYSICS↗

The role of radio loudness in Eigenvector 1 and the Baldwin Effect of [O iii ] λ5007

ABSTRACT The radio emission is an important observable of quasars, but its relationship to Eigenvector 1 and the [O iii] λ5007 Baldwin Effect is not fully understood. We explore these issues based on a sample of 1800 quasars taken from the Sloan Digital Sky Survey Data Release 7. We employ a new approach of selecting subsamples in the plane of fundamental physical parameters of the black hole mass and Eddington ratio, so as to reduce variables and complexity in analyses. Based on these subsamples, we investigate the relationship between radio loudness R and Eigenvector 1 and find that radio loudness is correlated with [O iii] λ5007 emission, but has no clear relationship with optical Fe ii emission, which indicates that the radio power is probably not a driver of Eigenvector 1 but merely a secondary process. In addition, we also investigate the impact of radio loudness on the Baldwin Effect of [O iii] λ5007. We find that when the radio loudness is not strong (log R < 2), the Baldwin Effect of [O iii] λ5007 is clear, while in the samples of extreme radio loudness (log R ≥ 2), the Baldwin Effect of [O iii] λ5007 becomes weaker or even disappears. We suggest that both radio loudness and luminosity influence the relative strength of [O iii].

79 ASTRONOMY AND ASTROPHYSICS↗

Electronic and magnetic structures that hinder the superconducting state in the collapsed phase of $\mathrm{SrCr_2}$ $\mathrm{As_2}$

The lack of superconductivity in the family of materials $AB_2$ $\mathrm{As_2}$ ($A$ = $\mathrm{Sr, Ba}$ and $B$ = $\mathrm{Cr, Mn}$) under doping or pressure is an intriguing issue, considering the resemblance of these materials to their cousin materials and superconductors $\mathrm{(Ba, Sr) Fe_2}$ $\mathrm{As_2}$. In this context, the suppression of magnetism together with the presence of electron and hole pockets in the Brillouin zone seem to be fundamental ingredients to explain superconductivity. In this paper, we report a tetragonal to collapsed-tetragonal phase transition in $\mathrm{SrCr_2}$ $\mathrm{As_2}$ under high pressure with the appearance of hole and electron pockets in the Brillouin zone. In this collapsed-tetragonal phase, a residual local magnetic moment in the Cr-ion site and a finite global magnetic energy are derived. Importantly, this scenario would suggest why superconductivity is prevented in this compound. Our observations were obtained from the analysis of synchrotron x-ray diffraction measurements of polycrystalline samples of $\mathrm{SrCr_2}$ $\mathrm{As_2}$, and using first-principles simulations, under pressures $P$ in the range $\mathrm{1.4}$ $\mathrm{GPa}$ < $P$ < $\mathrm{20 GPa}$ at room temperature.

75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗

Operando XPS in reactive plasmas: The importance of the wall reactions

In this article, advancements in differential pumping and electron optics over the past few decades have enabled x-ray photoelectron spectroscopy (XPS) measurements at (near-)ambient pressures, bridging the pressure gap for characterizing realistic sample chemistries. Recently, we have demonstrated the capabilities of an ambient pressure XPS setup for in situ plasma environment measurements, allowing plasma-surface interactions to be studied in operando rather than using the traditional before-and-after analysis approach. This new “plasma-XPS” technique facilitates the identification of reaction intermediates critical for understanding plasma-assisted surface processes relevant to semiconductor nanomanufacturing, such as physical vapor deposition, etching, atomic layer deposition, and many other plasma applications. In this paper, we apply the plasma-XPS approach to monitor real-time surface chemical changes on a model Ag(111) single crystal exposed to oxidizing and reducing plasmas. We correlate surface-sensitive data with concurrent gas-phase XPS measurements and residual gas mass-spectrum analysis of species generated during plasma exposure, highlighting the significant role of plasma-induced chamber wall reactions. Ultimately, we demonstrate that plasma-XPS provides comprehensive insights into both surface and gas-phase chemistry, establishing it as a versatile and dynamic characterization tool with broad applications in microelectronics research. Finally, we outline potential enhancements and future metrology directions to advance plasma-XPS investigations further.

36 MATERIALS SCIENCE↗

Campylobacter jejuni resistance to human milk involves the acyl carrier protein AcpP

Campylobacter jejuni is a common foodborne pathogen worldwide that is associated with high rates of morbidity and mortality among infants in low- to middle-income countries (LMICs). Human milk provides infants with an important source of nutrients and contains antimicrobial components for protection against infection. However, recent studies, including our own, have found significantly higher levels of Campylobacter in diarrheal stool samples collected from breastfed infants compared to non-breastfed infants in LMICs. We hypothesized that C. jejuni has unique strategies to resist the antimicrobial properties of human milk. Transcriptional profiling found human milk exposure induces genes associated with ribosomal function, iron acquisition, and amino acid utilization in C. jejuni strains 81–176 and 11168. However, unidentified proteinaceous components of human milk prevent bacterial growth. Evolving both C. jejuni isolates to survive in human milk resulted in mutations in genes encoding the acyl carrier protein (AcpP) and the major outer membrane porin (PorA). Introduction of the PorA/AcpP amino acid changes into the parental backgrounds followed by electron microscopy showed distinct membrane architectures, and the AcpP changes not only significantly improved growth in human milk, but also yielded cells surrounded with outer membrane vesicles. Analyses of the phospholipid and lipooligosaccharide (LOS) compositions suggest an imbalance in acyl chain distributions. For strain 11168, these changes protect both evolved and 11168ΔacpP G33R strains from bacteriophage infection and polymyxin killing. Taken together, this study provides insights into how C. jejuni may evolve to resist the bactericidal activity of human milk and flourish in the hostile environment of the gastrointestinal tract.

60 APPLIED LIFE SCIENCES↗

BiomeProbe [Abstract]

We propose the development and application of a microtiter plate-based chemical probe assay that can facilitate the rapid quantification of fecal microbiome-associated enzyme functional activities (“gut pharmacomicrobiomics”). Our initial proof-of-concept project with FedImpact is to show that one or more glucuronidase probes can be used for sensitive and reproducible characterization of fecal microbe glucuronidase activities. Glucuronidase enzymes are important for contributing to enterohepatic recycling of therapeutic drug compounds, resulting in impaired or prolonged drug activity. Importantly, the assay to be developed will permit facile ‘swapping’ of chemical probes to characterize different and multiple enzyme activities. Similarly, the assay is naïve to the biological sample to be analyzed.

59 BASIC BIOLOGICAL SCIENCES↗

Shock-reshock of zirconium to explore the effect of microstructure on the alpha-omega phase transformation

Phase transformations play an important role in the mechanical behavior of materials subjected to extreme loading conditions. A series of shock-reshock experiments were fielded to determine whether the phase transitions in materials are significantly enhanced or inhibited by preexisting microstructural features. Polycrystalline zirconium samples were shock loaded using gas-gun plate impact and soft recovered to examine microstructure using electron backscatter diffraction (EBSD). Drive conditions were varied to study the (hcp) alpha to (hexagonal) omega solidsolid phase transformation. Recovered samples were then subjected to a second shock loading event to determine the change in material behavior as a function of pre-shock microstructure. Crystallography of phase fragments in the final microstructure showed that prior twinning (formed during the shock to a peak stress below the transition threshold) appeared to suppress omega formation/retention after reshock. Conversely, when a material was initially shocked into the omega phase field, retained-omega was not found to have a large impact on subsequent omega formation during reshock. This suggests that nucleation and growth of omega phase are important processes, and the relative activity of nucleation vs. growth processes is modified by a pre-existing substructure. Additionally, orientation relationships reveal a reverse transformation pathway (omega to alpha) dominates the final microstructure, suggesting significant grain growth in the omega phase field is possible even for dynamic timescales.

36 MATERIALS SCIENCE↗