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Spatio-Temporal Data Analysis at Scale Using Models Based on Gaussian Processes

Gaussian processes are the most commonly used statistical model for spatial and spatio-temporal processes that vary continuously. They are broadly applicable in the physical sciences and engineering and are also frequently used to approximate the output of complex computer models, deterministic or stochastic. We undertook research related to theory, computation, and applications of Gaussian processes as well as some work on estimating extremes of distributions for which a Gaussian process assumption might be inappropriate. Our theoretical contributions include the development of new classes of spatial-temporal covariance functions with desirable properties and new results showing that certain covariance models lead to predictions with undesirable properties. To understand how Gaussian process models behave when applied to deterministic computer models, we derived what we believe to be the first significant results on the large sample properties of estimators of parameters of Gaussian processes when the actual process is a simple deterministic function. Finally, we investigated some theoretical issues related to maxima of observations with varying upper bounds and found that, depending on the circumstances, standard large sample results for maxima may or may not hold. Our computational innovations include methods for analyzing large spatial datasets when observations fall on a partially observed grid and methods for estimating parameters of a Gaussian process model from observations taken by a polar-orbiting satellite. In our application of Gaussian process models to deterministic computer experiments, we carried out some matrix computations that would have been infeasible using even extended precision arithmetic by focusing on special cases in which all elements of the matrices under study are rational and using exact arithmetic. The applications we studied include total column ozone as measured from a polar-orbiting satellite, sea surface temperatures over the Pacific Ocean, and annual temperature extremes at a site in New York City. In each of these applications, our theoretical and computational innovations were directly motivated by the challenges posed by analyzing these and similar types of data.

97 MATHEMATICS AND COMPUTING↗

Vibrational spectroscopy for imaging single microbial cells in complex biological samples

Here, vibrational spectroscopy is increasingly used for the rapid and non-destructive imaging of environmental and medical samples. Both Raman and Fourier-transform infrared (FT-IR) imaging have been applied to obtain detailed information on the chemical composition of biological materials, ranging from single microbial cells to tissues. Due to its compatibility with methods such as stable isotope labeling for the monitoring of cellular activities, vibrational spectroscopy also holds considerable power as a tool in microbial ecology. Chemical imaging of undisturbed biological systems (such as live cells in their native habitats) presents unique challenges due to the physical and chemical complexity of the samples, potential for spectral interference, and frequent need for real-time measurements. This Mini Review provides a critical synthesis of recent applications of Raman and FT-IR spectroscopy for characterizing complex biological samples, with a focus on developments in single-cell imaging. We also discuss how new spectroscopic methods could be used to overcome current limitations of singlecell analyses. Given the inherent complementarity of Raman and FT-IR spectroscopic methods, we discuss how combining these approaches could enable us to obtain new insights into biological activities either in situ or under conditions that simulate selected properties of the natural environment.

59 BASIC BIOLOGICAL SCIENCES↗

Influence of Hyperfine Coupling Strain on Two-Dimensional ESEEM Spectra from I = 1/2 Nuclei

HYSCORE, a variant of two-dimensional ESEEM spectroscopy, is currently one of the most effective tools in high-resolution solid-state EPR spectroscopy. Our systematic studies of hydrogen bonds with semiquinones in 15 N-labeled proteins have previously provided us with an extensive collection of 15 N HYSCORE spectra produced by N–H…O nitrogen donors. Examination of these spectra has indicated in several cases lineshape distortions not described by available theoretical models. We were able to explain all observed artificial phenomena in the 15 N spectra of semiquinones considering a single mechanism—strain of the isotropic hyperfine interaction. In this review article, we introduce the HYSCORE experiment and the theoretical background for spectra of I = 1/2 nuclei in orientation-disordered samples. We then present a description of the observed lineshape distortions and an explanation of the hyperfine strain’s influence on the experimental spectra. In the final part of the article, we discuss (i) similar lineshape distortions found in previously published spectra from 15 N, 29 Si, 31 P, and 57 Fe nuclei that can be explained using the approach applied for the analysis of the 15 N spectra of semiquinones, and (ii) a recently published analysis of 31P spectra with a different type of lineshape distortion based on a more sophisticated method, where the strength of anisotropic coupling is correlated with the sign and value of the isotropic constant in different conformations of a Cu(II) complex.

30 DIRECT ENERGY CONVERSION↗

Surveillance for Western equine encephalitis St. Louis encephalitis and West Nile viruses using reverse transcription loop-mediated isothermal amplification

In this study, collection of mosquitoes and testing for vector-borne viruses is a key surveillance activity that directly influences the vector control efforts of public health agencies, including determining when and where to apply insecticides. Vector control districts in California routinely monitor for three human pathogenic viruses including West Nile virus (WNV), Western equine encephalitis virus (WEEV), and St. Louis encephalitis virus (SLEV). Reverse transcription quantitative polymerase chain reaction (RT-qPCR) offers highly sensitive and specific detection of these three viruses in a single multiplex reaction, but this technique requires costly, specialized equipment that is generally only available in centralized public health laboratories. We report the use of reverse transcription loop-mediated isothermal amplification (RT-LAMP) to detect WNV, WEEV, and SLEV RNA extracted from pooled mosquito samples collected in California, including novel primer sets for specific detection of WEEV and SLEV, targeting the nonstructural protein 4 (nsP4) gene of WEEV and the 3’ untranslated region (3’-UTR) of SLEV. Our WEEV and SLEV RT-LAMP primers allowed detection of <0.1 PFU/reaction of their respective targets in <30 minutes, and exhibited high specificity without cross reactivity when tested against a panel of alphaviruses and flaviviruses. Furthermore, the SLEV primers do not cross-react with WNV, despite both viruses being closely related members of the Japanese encephalitis virus complex. The SLEV and WEEV primers can also be combined in a single RT-LAMP reaction, with discrimination between amplicons by melt curve analysis. Although RT-qPCR is approximately one order of magnitude more sensitive than RT-LAMP for all three targets, the RT-LAMP technique is less instrumentally intensive than RT-qPCR and provides a more cost-effective method of vector-borne virus surveillance.

59 BASIC BIOLOGICAL SCIENCES↗

Advanced Experimental Technique for Radiation Damage Effects in Nuclear Waste Forms: Neutron Total Scattering Analysis

For the past 30 years, the development of durable materials for radionuclide immobilization has been driven by efforts to dispose of wastes generated by the nuclear fuel cycle [National Research Council, ‘Waste Forms Technology and Performance: Final Report’, the National Academies Press, Washington D.C., 2011]. Many materials have been developed, but there still exist large gaps in the knowledge of fundamental modes of waste form degradation in repository environments. An important aspect of waste form science is the behavior of the materials under intense irradiation from decaying actinides and fission products. This irradiation induces a wide range of defects and disorder, the details of which depend on the specific waste form material. At the present time, it is not fully explained how radiation effects will influence the performance of nuclear waste forms and their long-term retention of fission products and actinides under operational conditions. The complex defect behavior and radiation damage must be understood over a range of length scales, from the initial atomic-scale defect structure to the long-range observable material modification. This is particularly challenging and requires advanced characterization techniques. This contribution describes how pair distribution function (PDF) analysis obtained from neutron total scattering experiments can be applied in the research field of waste form science to uniquely characterize radiation effects in a wide range of materials, including crystalline complex oxides and waste glasses. Neutron scattering strength does not have an explicit Z-dependence; this allows access to many low-Z elements, such as oxygen, that cannot be accurately studied with X-rays. In many cases, this can permit a detailed analysis of both cation (often high-Z) and anion (often low-Z) defect behavior. In contrast to traditional crystallography, which relies on long-range order, PDF analysis probes the local defect structure, including changes in site occupation, coordination, and bond distance. This is particularly important when characterizing aperiodic waste glasses with no long-range order at all. In contrast to X-ray characterization which requires very little sample mass (~0.1 mg), neutron characterization (even at state-of-the-art spallation facilities) requires relatively large sample mass (~50 - 100 mg). In conclusion, obtaining this quantity is challenging for studies of irradiated materials, but by tailoring our experimental approach to use high-energy ions (GeV) with very high penetration depth, we are able to produce the required mass.

36 MATERIALS SCIENCE↗

Fiberboard Properties and Degradation Rates for Storage of 9975 Shipping Package in KAC (2020 Status Report)

Savannah River Site (SRS) stores plutonium materials within model 9975 shipping packages in the K-Area Complex (KAC). The 9975 shipping package consists of a 35 gallon stainless steel drum, Celotex fiberboard insulation, lead shield, and primary and secondary containment vessels. The 9975 shipping package design, performance, and analysis for safe transport of radioactive material are described in the Safety Analysis Report for Packaging (SARP). Celotex fiberboard provides three safety functions: thermal insulation to limit internal temperature during a fire, criticality control, and resistance to package crushing. The fiberboard material must retain its dimensions and density within certain ranges to provide the required impact resistance, criticality control, and fire resistance. The SRS Surveillance Program monitors material performance to establish a basis for service life and ensures the continued integrity of 9975 packages. Fiberboard samples, taken from multiple fiberboard assemblies fabricated from cane and softwood fiberboard, have been conditioning in elevated temperature environments since 2005. The samples are periodically examined to monitor thermal, mechanical, and physical properties, and assess degradation trends. Fiberboard properties of interest that are evaluated to demonstrate acceptable long-term performance include dimensional stability, density, compressive strength, thermal conductivity, and specific heat capacity. Duplicate samples from multiple package sources have been tested to identify the range of variability in fiberboard properties and degradation rates. Baseline and long-term testing of fiberboard material properties have been reported previously; reference 6 summarized experimental results of cane and softwood fiberboard through May 2019 and presented degradation models for the measured properties. This report presents the cumulative data collected through June 2020 and the corresponding updated aging models.

11 NUCLEAR FUEL CYCLE AND FUEL MATERIALS↗

High-throughput synthesis and corrosion behavior of sputter-deposited nanocrystalline Al x (CoCrFeNi) 100-x combinatorial high-entropy alloys

High-entropy alloys (HEAs) are inherently complex and potentially span a vast composition space, making their research and discovery challenging. In the present study, high-throughput synthesis of an Al x (CoCrFeNi) 100-x combinatorial material library covering x = 4.5–40 atomic percent Al is achieved, using magnetron cosputtering. The effects of Al on the microstructure and corrosion behavior are investigated. With the increased amount of Al, crystal-structures of thin films transform from face-centered cubic (FCC) to body-centered cubic (BCC). Both the FCC and BCC thin films demonstrate a uniform elemental distribution. Corrosion characteristics of combinatorial samples immersed in the 3.5 wt% (wt%) NaCl solution are evaluated via electrochemical tests. Complementary X-ray photoelectron spectroscopy analysis reveals the compositional variation of passivated films formed on the sample surface after immersion. The results show that the Al x (CoCrFeNi) 100-x HEA thin films possess outstanding corrosion-resistant properties, but the resistance diminishes with the increasing Al content. The decreased corrosion resistance is revealed to be directly related to the constituents of passivated films.

36 MATERIALS SCIENCE↗

Site specific modification of the human plasma proteome by methylglyoxal

Increasing evidence identifies dicarbonyl stress from reactive glucose metabolites, such as methylglyoxal (MG), as a major pathogenic link between hyperglycemia and complications of diabetes. MG covalently modifies arginine residues, yet the site specificity of this modification has not been thoroughly investigated. Sites of MG adduction in the plasma proteome were identified using LC–MS/MS analysis in vitro following incubation of plasma proteins with MG. Treatment of plasma proteins with MG yielded 14 putative MG hotspots from five plasma proteins (albumin [nine hotspots], serotransferrin, haptoglobin [2 hotspots], hemopexin, and Ig lambda-2 chain C regions). The search results revealed two versions of MG-arginine modification, dihydroxyimidazolidine (R + 72) and hydroimidazolone (R + 54) adducts. One of the sites identified was R257 in human serum albumin, which is a critical residue located in drug binding site I. This site was validated as a target for MG modification by a fluorescent probe displacement assay, which revealed significant drug dissociation at 300 μM MG from a prodan–HSA complex (75 μM). Moreover, twelve human plasma samples (six male, six female, with two type 2 diabetic subjects from both genders) were analyzed using multiple reaction monitoring (MRM) tandem mass spectrometry and revealed the presence of the MG-modified albumin R257 peptide. These data provide insights into the nature of the site-specificity of MG modification of arginine, which may be useful for therapeutic treatments that aim to prevent MG-mediated adverse responses in patients. - Highlights: • Methylglyoxal (MG) selectively modifies arginine sites in human plasma proteome. • Dihydroxyimidazolidine and hydroimidazolone adducts on serum albumin identified • MG modification on albumin R257 associated with loss of drug site I binding capacity • MRM-tandem mass spectrometry enables sensitive detection of albumin MG-R257. • Site-specific MG modification may represent a useful monitor of effective therapy of T2DM.

60 APPLIED LIFE SCIENCES↗

Quantum Efficiency of Charge Transfer Competing against Nonexponential Processes: The Case of Electron Transfer from CdS Nanorods to Hydrogenase

Photoexcited charge transfer from semiconductor nanocrystals to charge acceptors is a key step for photon energy conversion in semiconductor nanocrystal-based light-harvesting systems. Charge transfer competes against relaxation processes within the nanocrystals, and this competition determines the quantum efficiency of charge transfer. The quantum efficiency is a critical design element in photochemistry, but in nanocrystal-acceptor systems its extraction from experimental data is complicated by sample heterogeneity and intrinsically nonexponential excited-state decay pathways. In this manuscript, we systematically explore these complexities using TA spectroscopy over a broad range of timescales to probe electron transfer from CdS nanorods to the redox enzyme hydrogenase. To analyze the experimental data, we build a model that quantifies the quantum efficiency of charge transfer in the presence of competing, potentially nonexponential, relaxation processes. Our approach can be applied to calculate the efficiency of charge or energy transfer in any donor-acceptor system that exhibits nonexponential donor decay and any ensemble distribution in the number of acceptors, provided that donor relaxation and charge transfer can be described as independent, parallel decay pathways. We apply this analysis to our experimental system and unveil the connections between particle morphology and quantum efficiency. Our model predicts a finite quantum efficiency even when the mean recombination time diverges, as it does in CdS nanostructures with spatially separated electron-hole pairs that recombine with power-law dynamics. We contrast our approach to the widely used expressions for the quantum efficiency based on average lifetimes, which for our system overestimate the quantum efficiency. Furthermore, the approach developed here is straightforward to implement and should be applicable to a wide range of systems.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

An Impedance Humidity Sensor Based on CVD Grown WSe 2 2D Films

2D materials-based planar devices have been sought after for gas and humidity sensor applications owing to their high sensitivity due to their ultrathin nature and increased surface area. Herein, 2D WSe 2 films-based planner devices were fabricated to evaluate their performance for potential application in humidity sensors. The structure and morphology of the WSe 2 sensing films were studied by Raman spectroscopy, photoluminescence, optical microscopy, and scanning electron microscopy (SEM) techniques. The relative humidity-dependent sensing performances of the 2D WSe 2 films were evaluated using current–voltage (I–V), relative impedance, and complex total impedance (electrochemical impedance spectroscopy, EIS) techniques. This sensor showed a very stable and repeatable performance investigated over the period of 18 months. The response and recovery times of the WSe 2 -based impedance sensors were found to be 40 and 30 s, respectively. The WSe 2 sensor exhibits a 2 ± 1% minimum hysteresis at a lower humidity level (50% RH) and around 8 ± 2% maximum hysteresis at relative humidity level (70% RH). This value of hysteresis is in the acceptable range during the initial investigation of any material to explore its potential for application in humidity sensors. The density functional theory (DFT) analysis was performed with the interaction from water molecules of the WSe 2 sample for a better understanding of the sensing mechanism of devices.

2D- WSe2↗

High-quality Acinetobacter genomes recovered from combat wounds via metagenomic sequencing resemble cultured isolate genomes

The ability to accurately characterize wound pathogens is critical to informing clinical decisions for wound infections with complex treatment requirements. Acinetobacter baumannii is an impactful nosocomial pathogen in combat wounds and civilian hospital-acquired infections. An informed understanding of the phylogenetics and epidemiology of A. baumannii infections in military and civilian environments could guide approaches that improve antibiotic treatment regimens for both military and civilian patients. Whole-genome data for bacterial strains can be difficult to obtain due to challenges in culturing isolates from preserved military specimens. Metagenomic sequencing and assembly create opportunities for genomic analysis of pathogens directly from clinical specimens. The ability to perform comparative analyses between metagenome-derived genomes and culture-derived genomes would support a range of comparative bacterial genomic studies. Wound tissue biopsy and effluent samples from combat injuries were subjected to metagenomic sequencing and assembly. In total, 42 microbial metagenome-assembled genomes (MAGs) were obtained directly from metagenomic sequence data, 36 of which were designated “high” quality. Thirty of these genomes corresponded to Acinetobacter, with 29 mapping specifically to A. baumannii. Other observed genera included Bordetella, Citrobacter, Escherichia, and Pseudomonas. Single-copy and multi-copy orthologs were identified across Acinetobacter MAGs and publicly available isolate genomes derived from military and civilian sources. Both MAG and military isolate genomes were annotated with antimicrobial resistance data, and MAG genomes were statistically comparable to genomes obtained from isolates. Our results highlight the potential of de novo metagenome assembly for enabling high-resolution characterization directly from clinical specimens, thereby improving diagnostic precision, guiding antimicrobial stewardship, and enhancing understanding of pathogen evolution across diverse healthcare and battlefield environments.

Acinetobacter baumannii↗

Quarterly Research Performance Progress Report (Q8)

As part of Task 1, we have started by testing our modeling capabilities by reproducing isothermal DFIT simulations presented in the literature. Once satisfied with the results we have started by targeting the modeling of the DFITs at conducted at well 58-32. We have a identified a specific test (cycle 4 in zone 2) as the most interesting to be model with GEOS hydraulic fracturing module. Thus, we have first produced results with an isothermal model and adjusted model parameters to get a satisfying match with field pressure data. The, we have added thermal effects and compared the modeling results with and without thermal effects to estimate how thermal effects may influence test interpretation. Models seem to suggest that, for small volumes of fluid, thermal effects are moderate. In Task 2, we have adapted GEOS phase-field formulation to be able to simulate near-wellbore hydraulic fracture nucleation and propagation. We have devised a novel formulation that, compared to other existing ones, incorporates rock strengths. We have submitted a journal publication about our work. We are currently employing this phase-field formulation to model the experiments taking place at U Pitt and help us understand the effect of various parameters. In Task 3, we have built a model of the region surround well 16A and have started modeling stage 3 stimulation because of its simpler planar geometry. After calibrating simulation parameters using known analytical solutions, we have simulated the stage 3 stimulation using our isothermal hydraulic fracturing module, varying the permeability field, the stress conditions including different physics to get a better understanding of the numerical challenges and of the effects of varying these parameters on the simulation results. In Task 4 laboratory experimentation, a set of specialized drilling and injection tools has been customized and constructed to accommodate an inclined well with an orientation of up to 30 degrees relative to material anisotropy or principal stress axes. These inclined samples have also undergone thermal stress and hydraulic fracturing at a temperature of 190 degrees Celsius. Furthermore, both vertical and deviated sampling testing setups enable an extended analysis of post-peak pressure behaviors, facilitating post-test pressure analyses such as the G-function, step rate, and fracture reopening measurements. Thus, the key components of in-situ stress estimation can be extracted and validated through our experiment, providing a solid foundation for validating existing in-situ stress estimation theories or proposing new ones. Simultaneously, we are integrating computer vision techniques with traditional experimental fracture observation methods such as multi-overcore/slicing and water-penetration fracture observation. This combination will prove beneficial in populating the hydraulic fracture patterns database, generated under challenging EGS conditions. This approach aims to deepen our understanding of the complexities in EGS reservoirs and pave the way for future data-driven investigations. Additionally, PITT has also equipped the ELE International compression machine, which is now prepared for conducting indirect tensile and fracture toughness tests. These tests will aid in characterizing how rock fabrics influence the resulting fracture patterns. Additionally, we have completed the required personnel training and gained access to Scanning Electron Microscopy (SEM) and Energy Dispersive Spectroscopy (EDS) for conducting more detailed characterization and analysis of rock fabrics, as well as the examination of thermal and hydraulically induced fracture patterns. Thus, the PITT team has effectively demonstrated the capabilities of our experimental apparatuses in exploring the thermal effects, well deviation angles, material anisotropy, and operational choices (such as circulation rate, injection fluid viscosity, and injection rate) and their impact on pressure responses and fracture trajectories under the Utah FORGE conditions.

15 GEOTHERMAL ENERGY↗

Accelerating the identification of novel secondary metabolites in bioenergy plant root exudates using MicroED

Small molecule metabolites drive inter- and intraspecies communication and dependencies in diverse biological systems, yet a large proportion of these important chemical compounds remain uncharacterized in plants and microbes. Approximately 90% of the metabolites in root exudate profiles are unknown compounds, despite the importance of root exudate composition in plant-microbe interactions. We need advanced analytical capabilities that will support rapid discovery and structural elucidation of metabolites from biological samples that may be limited in quantity and high in complexity. To fill this gap, this project aimed to develop an integrated workflow involving metabolite extraction, separation, and crystallization from plant root exudates followed by characterization using nuclear magnetic resonance (NMR) spectroscopy, mass spectrometry, and microcrystal electron diffraction (MicroED). Using crude root exudates from sorghum, this project successfully developed higher throughput exudate fractionation strategies to obtain pure compounds for crystallization and identified crystals in multiple fractions that diffracted. Additional efforts to increase the throughput of high-quality crystal generation for MicroED, such as crystallization screening and crystallization chaperone exploration, will be needed to further advance root exudate metabolite identification. The overall optimized sample preparation process can then be integrated with the existing data collection and data analysis pipelines for MicroED at PNNL to facilitate more rapid natural product discovery.

59 BASIC BIOLOGICAL SCIENCES↗

Analyzing Relationships Between Economic and Neighborhood-Related Social Determinants of Health and Intensive Care Unit Length of Stay for Critically Ill Children With Medical Complexity Presenting With Severe Sepsis

Objectives: Of the Social Determinants of Health (SDoH), we evaluated socioeconomic and neighborhood-related factors which may affect children with medical complexity (CMC) admitted to a Pediatric Intensive Care Unit (PICU) in Shelby County, Tennessee with severe sepsis and their association with PICU length of stay (LOS). We hypothesized that census tract-level socioeconomic and neighborhood factors were associated with prolonged PICU LOS in CMC admitted with severe sepsis in the underserved community. Methods: This single-center retrospective observational study included CMC living in Shelby County, Tennessee admitted to the ICU with severe sepsis over an 18-month period. Severe sepsis CMC patients were identified using an existing algorithm incorporated into the electronic medical record at a freestanding children's hospital. SDoH information was collected and analyzed using patient records and publicly available census-tract level data, with ICU length of stay as the primary outcome. Results: 83 encounters representing 73 patients were included in the analysis. The median PICU LOS was 9.04 days (IQR 3.99–20.35). The population was 53% male with a median age of 4.1 years (IQR 1.96–12.02). There were 57 Black/African American patients (68.7%) and 85.5% had public insurance. Based on census tract-level data, about half (49.4%) of the CMC severe sepsis population lived in census tracts classified as suffering from high social vulnerability. There were no statistically significant relationships between any socioeconomic and neighborhood level factors and PICU LOS. Conclusion: Pediatric CMC severe sepsis patients admitted to the PICU do not have prolonged lengths of ICU stay related to socioeconomic and neighborhood-level SDoH at our center. A larger sample with the use of individual-level screening would need to be evaluated for associations between social determinants of health and PICU outcomes of these patients.

60 APPLIED LIFE SCIENCES↗

Atomic-Scale Structural Mapping of Active Sites in Monolayer PGM-Free Catalysts by Low-Voltage 4D-STEM

Two-dimensional (2D) materials have attracted a large amount of attention in both basic and applied fields, and scanning transmission electron microscopy (STEM) is often uniquely well-suited for characterizing the atomic-scale structure of these materials [1-4]. As a result, STEM is poised to significantly impact progress on platinum group metal (PGM)-free catalysts, which are currently under intense development to enable low-cost, commercially viable hydrogen fuel cells [5]. While recent advancements have resulted in fuel cell performance comparable to Pt catalysts by some measures [6], cell durability remains a significant challenge, limiting practical applications [7]. Catalytically active sites in PGM-free materials are proposed to be FeN4 complexes embedded in a graphene lattice (Fig. 1b) within layered or other larger materials, but this is still under debate largely due to the range of potential actives sites predicted by computational methods and lack of methods for directly validating these models [5]. Fundamental insights into the atomic structure and resulting degradation pathways of proposed active sites are therefore needed to fully understand and control cell performance and durability [6].2D materials typically make ideal samples for STEM, but those within PGM-free catalysts present additional challenges since these materials are often defect-rich, with a high density of edges, dopant atoms, etc., which significantly increase susceptibility to beam damage at standard operating voltages. This makes analysis of potential FeN4 active sites particularly challenging, since a large proportion of Fe exists at edge sites where beam-induced atomic displacements can prohibit high-resolution structural characterization [6]. Conventional dark-field imaging compounds this problem by producing less signal for a given dose and being less sensitive to light elements than dose-efficient phase contrast imaging techniques such as those enabled by four-dimensional (4D)-STEM [8-10] (Fig. 1a). Consequently, active site structural analysis is often left to methods such as low-resolution imaging combined with quantum chemical calculations [6], which hinders accurate determination of reaction and degradation mechanisms.Here, we demonstrate direct atomic-scale structural mapping of FeN4 sites by performing low-voltage 4D-STEM on a model PGM-free catalyst system with many exposed monolayer regions. To accomplish this, we pair a 30 keV aberration-corrected probe with a fast pixelated detector that has optimal performance at low beam voltages [11]. This enables us to simultaneously image light and heavy elements with high signal-to-noise by center-of-mass analysis (Fig. 1c) while minimizing beam-induced atomic displacements at sensitive sites. The monolayer nature of these materials additionally allows for experimental validation by direct comparison with multislice simulations [12] of model structures (Fig. 1d-e). This work demonstrates how low-voltage 4D-STEM will provide new insights into the atomic-scale structure and degradation mechanisms of active sites in PGM-free catalysts, facilitating the development of low-cost hydrogen fuel cells and other energy conversion technologies in the future [13].

Zachman, Michael↗

Introducing Molecular Hypernetworks for Discovery in Multidimensional Metabolomics Data

Orthogonal separations of data from high-resolution mass spectrometry can provide insight into sample composition and address challenges of complete annotation of molecules in untargeted metabolomics. “Molecular networks” (MNs), as used in the Global Natural Products Social Molecular Networking platform, are a prominent strategy for exploring and visualizing molecular relationships and improving annotation. MNs are mathematical graphs showing the relationships between measured multidimensional data features. MNs also show promise for using network science algorithms to automatically identify targets for annotation candidates and to dereplicate features associated with a single molecular identity. Here, this paper introduces “molecular hypernetworks” (MHNs) as more complex MN models able to natively represent multiway relationships among observations. Compared to MNs, MHNs can more parsimoniously represent the inherent complexity present among groups of observations, initially supporting improved exploratory data analysis and visualization. MHNs also promise to increase confidence in annotation propagation, for both human and analytical processing. We first illustrate MHNs with simple examples, and build them from liquid chromatography- and ion mobility spectrometry-separated MS data. We then describe a method to construct MHNs directly from existing MNs as their “clique reconstructions”, demonstrating their utility by comparing examples of previously published graph-based MNs to their respective MHNs.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Multi-time series RNA-seq analysis of Enterobacter lignolyticus SCF1 during growth in lignin-amended medium

The production of lignocellulosic-derived biofuels is a highly promising source of alternative energy, but it has been constrained by the lack of a microbial platform capable to efficiently degrade this recalcitrant material and cope with by-products that can be toxic to cells. Species that naturally grow in environments where carbon is mainly available as lignin are promising for finding new ways of removing the lignin that protects cellulose for improved conversion of lignin to fuel precursors. Enterobacter lignolyticus SCF1 is a facultative anaerobic Gammaproteobacteria isolated from tropical rain forest soil collected in El Yunque forest, Puerto Rico under anoxic growth conditions with lignin as sole carbon source. Whole transcriptome analysis of SCF1 during E.lignolyticus SCF1 lignin degradation was conducted on cells grown in the presence (0.1%, w/w) and the absence of lignin, where samples were taken at three different times during growth, beginning of exponential phase, midexponential phase and beginning of stationary phase. Lignin-amended cultures achieved twice the cell biomass as unamended cultures over three days, and in this time degraded 60% of lignin. Transcripts in early exponential phase reflected this accelerated growth. A complement of laccases, aryl-alcohol dehydrogenases, and peroxidases were most up-regulated in lignin amended conditions in mid-exponential and early stationary phases compared to unamended growth. The association of hydrogen production by way of the formate hydrogenlyase complex with lignin degradation suggests a possible value added to lignin degradation in the future.

Orellana, Roberto (ORCID:0000000306333458)↗

Detection Identification and Quantification of Keto-Hydroperoxides in Low-Temperature Oxidation.

Keto-hydroperoxides are reactive partially oxidized intermediates that play a central role in chain-branching reactions during the low-temperature oxidation of hydrocarbons. In this Perspective, we outline how these short lived species can be detected, identified, and quantified using integrated experimental and theoretical approaches. The procedures are based on direct molecular-beam sampling from reactive environments, followed by mass spectrometry with single-photon ionization, identification of fragmentation patterns, and theoretical calculations of ionization thresholds, fragment appearance energies, and photoionization cross sections. Using the oxidation of neo-pentane and tetrahydrofuran as examples, the individual steps of the experimental approaches are described in depth together with a detailed description of the theoretical efforts. For neo-pentane, the experimental data are consistent with the calculated ionization and fragment appearance energies of the keto-hydroperoxide, thus adding confidence to the analysis routines and the employed levels of theory. For tetrahydrofuran, multiple keto-hydroperoxide isomers are possible due to the presence of nonequivalent O 2 addition sites. Despite this additional complexity, the experimental data allow for the identification of two to four keto-hydroperoxides. Mole fraction profiles of the keto-hydroperoxides, which are quantified using calculated photoionization cross sections, are provided together with estimated uncertainties as function of the temperature of the reactive mixture and can serve as validation targets for chemically detailed mechanisms.

Hansen, Nils↗