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At least 127 records · Page 7

Near-canopy horizontal concentration heterogeneity of semivolatile oxygenated organic compounds and implications for 2-methyltetrols primary emissions

Semivolatile oxygenated organic compounds (SV-OVOCs) are important atmospheric species, in particular for the production and chemistry of atmospheric particulate matter and related impacts on air quality and climate. In this study, SV-OVOCs were collected in the horizontal plane of the roughness layer over the tropical forest in the central Amazon during the wet season of 2018. A sampler mounted to a copter-type, hovering unmanned aerial vehicle was used. Underlying the collection region, a plateau forest transitioned into a slope forest across several hundred meters. The concentrations of pinonic and pinic acids, which are monoterpene oxidation products, had no statistical difference over the two forests. By comparison, across the study period, differences in the concentration of 2-methyltetrols, which are products of isoprene oxidation, ranged from -70% to +480% over the two forests. The chemical lifetime of 2-methyltetrols in the atmosphere is sufficiently long that heterogeneity in the isoprene emission rate from the two forests followed by atmospheric oxidation does not explain the concentration heterogeneity of 2-methyltetrols. Standing waves and local meteorology also cannot account for the heterogeneity. Of the possibilities considered, the most plausible explanation is the direct emission from the forest of 2-methyltetrols produced through biological processes within the plants. Under this explanation, the rate of direct SV-OVOC emissions should be modulated by forest type and related environmental stressors. Direct emissions of SV-OVOCs should be more broadly considered for constraining and improving models of atmospheric composition, transport, and chemistry over tropical forests.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Exploring the impact of ions on oxygen K-edge X-ray absorption spectroscopy in NaCl solution using the GW-Bethe-Salpeter-equation approach

X-ray absorption spectroscopy (XAS) is a powerful experimental tool to probe the local structure in materials with the core hole excitations. Here, the oxygen K-edge XAS spectra of the NaCl solution and pure water are computed by using a recently developed GW-Bethe-Salpeter equation approach, based on configurations modeled by path-integral molecular dynamics with the deep-learning technique. The neural network is trained on ab initio data obtained with strongly constrained and appropriately normed density functional theory. The observed changes in the XAS features of the NaCl solution, compared to those of pure water, are in good agreement between experimental and theoretical results. We provided detailed explanations for these spectral changes that occur when NaCl is solvated in pure water. Specifically, the presence of solvating ion pairs leads to localization of electron-hole excitons. As a result, our theoretical XAS results support the theory that the effects of the solvating ions on the H-bond network are mainly confined within the first hydration shell of ions, however beyond the shell the arrangement of water molecules remains to be comparable to that observed in pure water.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Electron transfer in a crystalline cytochrome with four hemes

Diffusion of electrons over distances on the order of 100 μm has been observed in crystals of a small tetraheme cytochrome (STC) from Shewanella oneidensis [J. Huang et al . J. Am. Chem. Soc. 142, 10459–10467 (2020)]. Electron transfer between hemes in adjacent subunits of the crystal is slower and more strongly dependent on temperature than had been expected based on semiclassical electron-transfer theory. Here, in this work, we explore explanations for these findings by molecular-dynamics simulations of crystalline and monomeric STC. New procedures are developed for including time-dependent quantum mechanical energy differences in the gap between the energies of the reactant and product states and for evaluating fluctuations of the electronic-interaction matrix element that couples the two hemes. Rate constants for electron transfer are calculated from the time- and temperature-dependent energy gaps, coupling factors, and Franck–Condon-weighted densities of states using an expression with no freely adjustable parameters. Back reactions are considered, as are the effects of various protonation states of the carboxyl groups on the heme side chains. Interactions with water are found to dominate the fluctuations of the energy gap between the reactant and product states. The calculated rate constant for electron transfer from heme IV to heme Ib in a neighboring subunit at 300 K agrees well with the measured value. However, the calculated activation energy of the reaction in the crystal is considerably smaller than observed. We suggest two possible explanations for this discrepancy. The calculated rate constant for transfer from heme I to II within the same subunit of the crystal is about one-third that for monomeric STC in solution.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Tearing Stable Stationary ITER Baseline Operation in DIII-D

We present a tearing stable, stationary and reproducible operating solution for DIII-D plasmas characterized by the ITER Baseline Scenario normalized parameter set and shape. In these plasmas low differential rotation (Δf1,2) between the core and edge is identified as the single root cause of the onset of the primary limiting instability, the 2,1 Neoclassical Tearing Mode (NTM), while a group of other examined parameters have a much weaker impact on the stability. Explanation is offered by drift kinetic simulations, which show a six-fold reduction in the NTM onset threshold due to diminished stabilizing ion polarization currents when the seed island drift frequency ceases in the local plasma frame. Based on the experimental observation and the explanation provided by the theory, a new method is developed to sustain Δf1,2 by modifying the edge neoclassical potential through neutral gas fueling. This method enables stationary ITER baseline operation free of disruptive 2,1 tearing modes.

70 PLASMA PHYSICS AND FUSION TECHNOLOGY↗

Connecting radio emission to AGN wind properties with broad absorption line quasars

ABSTRACT Broad absorption line quasars (BALQSOs) show strong signatures of powerful outflows, with the potential to alter the cosmic history of their host galaxies. These signatures are only seen in ∼10 per cent of optically selected quasars, although the fraction significantly increases in IR and radio selected samples. A proven physical explanation for this observed fraction has yet to be found, along with a determination of why this fraction increases at radio wavelengths. We present the largest sample of radio matched BALQSOs using the LOFAR Two-metre Sky Survey Data Release 2 and employ it to investigate radio properties of BALQSOs. Within the DR2 footprint, there are 3537 BALQSOs from Sloan Digital Sky Survey DR12 with continuum signal-to-noise ≥5. We find radio-detections for 1108 BALQSOs, with an important subpopulation of 120 LoBALs, an unprecedented sample size for radio matched BALQSOs given the sky coverage to date. BALQSOs are a radio-quiet population that show an increase of ×1.50 radio-detection fraction compared to non-BALQSOs. LoBALs show an increase of ×2.22 that of non-BALQSO quasars. We show that this detection fraction correlates with wind-strength, reddening, and C iv emission properties of BALQSOs and that these features may be connected, although no single property can fully explain the enhanced radio detection fraction. We create composite spectra for subclasses of BALQSOs based on wind strength and colour, finding differences in the absorption profiles of radio-detected and radio-undetected sources, particularly for LoBALs. Overall, we favour a wind-ISM interaction explanation for the increased radio-detection fraction of BALQSOs.

79 ASTRONOMY AND ASTROPHYSICS↗

New insight into knockout reactions from the two-proton halo nucleus 17 Ne

The unexplained disagreement in the dependence of spectroscopic factors (𝐶2⁢𝑆 exp ) on the binding energy obtained by nucleon knockout using different targets is still a puzzle that needs to be addressed. To find an explanation of this riddle through exclusive measurements using different targets. The exclusive measurements were performed by using a 17 Ne beam with an energy of 500 MeV/u incident on C and CH 2 targets. Through the standard theoretical approach, 𝐶 2⁢ 𝑆 exp were derived from the analysis of the experimental data on proton ejection from the proton halo in 17 Ne as well as from its core 15 O. For the C target, proton ejection from the proton halo gave 𝐶 2 ⁢𝑆 exp about 37% smaller than for the H target. But when protons are ejected from the core of 17 Ne, 𝐶 2 ⁢𝑆 exp are identical within statistical uncertainties. An explanation for the difference in 𝐶 2 ⁢𝑆 exp could be the removal of both halo protons, a more important reaction pathway for the C target. The 𝐶 2 ⁢𝑆 exp values obtained by analyzing the proton ejection from the core indicate that it is not affected by the interaction with the halo protons.

6 ≤ A ≤ 19↗

Relaxation times for disoriented isospin condensates in high energy heavy ion collisions

Fluctuations between charged and neutral kaons measured by the ALICE Collaboration in Pb-Pb collisions at the CERN Large Hadron Collider (LHC) exceed conventional explanations. Previously it was shown that if the scalar condensate is accompanied by an electrically neutral isospin-1 field then the combination can produce large equilibrium fluctuations where ⟨$\overline{𝑢}$ ⁢𝑢⟩≠⟨ $\overline{𝑑}$𝑑⟩. Hadronizing strange and antistrange quarks might then strongly fluctuate between charged ($\overline{𝑢}$⁢𝑠 or $\overline{𝑠}$⁢𝑢) and neutral (𝑑⁢$\overline{𝑠}$⁢ or 𝑠⁢$\overline{𝑑}$) kaons. Here, we estimate the times for the condensates to achieve their equilibrium probability distributions within causal volumes in high energy heavy ion collisions. This is achieved by modeling the temperature dependence of the condensates, mesonic collective excitations, decay rates of the associated fields, and employing the Langevin and Fokker-Planck equations. Within this model, we find that the equilibration times are short compared with the expansion time, making disoriented isospin condensates a viable explanation for the anomalous fluctuations observed at the LHC.

Quark-gluon plasma↗

Demystifying Cyberattacks: Potential for Securing Energy Systems With Explainable AI : Preprint

Modernization of energy systems has led to in- creased interactions among multiple critical infrastructures and diverse stakeholders making the challenge of operational decision making more complex and at times beyond cognitive capabilities of human operators. The state-of-the-art machine learning and deep learning approaches show promise of supporting users with complex decision-making challenges, such as those occurring in our rapidly transforming cyber-physical energy systems. However, successful adoption of data-driven decision support technology for critical infrastructure will be dependent on the ability of these technologies to be trustworthy and contextually interpretable. In this paper, we investigate the feasibility of implementing XAI for interpretable detection of cyberattacks in the energy system. Leveraging a proof-of-concept simulation use case of detection of a data falsification attack on a photovoltaic system using XGBoost algorithm, we demonstrate how Local Interpretable Model-Agnostic Explanations (LIME), a flavor XAI approach, can help provide contextual and actionable interpretation of cyberattack detection.

artificial intelligence↗

Accumulation of collagen molecular unfolding is the mechanism of cyclic fatigue damage and failure in collagenous tissues

Overuse injuries to dense collagenous tissues are common, but their etiology is poorly understood. The predominant hypothesis that micro-damage accumulation exceeds the rate of biological repair is missing a mechanistic explanation. Here, we used collagen hybridizing peptides to measure collagen molecular damage during tendon cyclic fatigue loading and computational simulations to identify potential explanations for our findings. Our results revealed that triple-helical collagen denaturation accumulates with increasing cycles of fatigue loading, and damage is correlated with creep strain independent of the cyclic strain rate. Finite-element simulations demonstrated that biphasic fluid flow is a possible fascicle-level mechanism to explain the rate dependence of the number of cycles and time to failure. Molecular dynamics simulations demonstrated that triple-helical unfolding is rate dependent, revealing rate-dependent mechanisms at multiple length scales in the tissue. The accumulation of collagen molecular denaturation during cyclic loading provides a long-sought “micro-damage” mechanism for the development of overuse injuries.

59 BASIC BIOLOGICAL SCIENCES↗

Modeling Growth Kinetics, Interspecies Cell Fusion, and Metabolism of a Clostridium acetobutylicum / Clostridium ljungdahlii Syntrophic Coculture

ABSTRACT Clostridium acetobutylicum and Clostridium ljungdahlii grown in a syntrophic culture were recently shown to fuse membranes and exchange cytosolic contents, yielding hybrid cells with significant shifts in gene expression and growth phenotypes. Here, we introduce a dynamic genome-scale metabolic modeling framework to explore how cell fusion alters the growth phenotype and panel of metabolites produced by this binary community. Computational results indicate C. ljungdahlii persists in the coculture through proteome exchange during fusing events, which endow C. ljungdahlii cells with expanded substrate utilization, and access to additional reducing equivalents from C. acetobutylicum -evolved H 2 and through acquisition of C. acetobutylicum -native cofactor-reducing enzymes. Simulations predict maximum theoretical ethanol and isopropanol yields that are increased by 0.64 mmol and 0.39 mmol per mmol hexose sugar consumed, respectively, during exponential growth when cell fusion is active. This modeling effort provides a mechanistic explanation for the metabolic outcome of cellular fusion and altered homeostasis achieved in this syntrophic clostridial community. IMPORTANCE Widespread cell fusion and protein exchange between microbial organisms as observed in synthetic C. acetobutylicum / C. ljungdahlii culture is a novel observation that has not been explored in silico . The mechanisms responsible for the observed cell fusion events in this culture are still unknown. In this work, we develop a modeling framework that captures the observed culture composition and metabolic phenotype, use it to offer a mechanistic explanation for how the culture achieves homeostasis, and identify C. ljungdahlii as primary beneficiary of fusion events. The implications for the events described in this study are far reaching, with potential to reshape our understanding of microbial community behavior synthetically and in nature.

59 BASIC BIOLOGICAL SCIENCES↗

Genetic programming for understanding cognitive biases that generate polarization in social networks

Recent studies have applied agent-based models to infer human-interpretable explanations of individual-scale behaviors that generate macro-scale patterns in complex social systems. Genetic programming has proven to be an ideal explainable AI tool for this purpose, where primitives may be expressed in an interpretable fashion and assembled into agent rules. Evolutionary model discovery (EMD) is a tool that combines genetic programming and random forest feature importance analysis, to infer individual-scale, human-interpretable explanations from agent-based models. We deploy EMD to investigate the cognitive biases behind the emergence of ideological polarization within a population. An agent-based model is developed to simulate a social network, where agents are able to create or sever links with one another, and update an internal ideological stance based on their neighbors' stances. Agent rules govern these actions and constitute of cognitive biases. A set of 7 cognitive biases are included as genetic program primitives in the search for rules that generate hyper-polarization among the population of agents. We find that heterogeneity in cognitive biases is more likely to generate polarized social networks. Highly polarized social networks are likely to emerge when individuals with confirmation bias are exposed to those with either attentional bias, egocentric bias, or cognitive dissonance.

Gunaratne, Chathika↗

Evaluating the Trustworthiness of Explainable Artificial Intelligence (XAI) Methods Applied to Regression Predictions of Arctic Sea Ice Motion

Abstract Recent advances in explainable artificial intelligence (XAI) methods show promise for understanding predictions made by machine learning (ML) models. XAI explains how the input features are relevant or important for the model predictions. We train linear regression (LR) and convolutional neural network (CNN) models to make 1-day predictions of sea ice velocity in the Arctic from inputs of present-day wind velocity and previous-day ice velocity and concentration. We apply XAI methods to the CNN and compare explanations to variance explained by LR. We confirm the feasibility of using a novel XAI method [i.e., global layerwise relevance propagation (LRP)] to understand ML model predictions of sea ice motion by comparing it to established techniques. We investigate a suite of linear, perturbation-based, and propagation-based XAI methods in both local and global forms. Outputs from different explainability methods are generally consistent in showing that wind speed is the input feature with the highest contribution to ML predictions of ice motion, and we discuss inconsistencies in the spatial variability of the explanations. Additionally, we show that the CNN relies on both linear and nonlinear relationships between the inputs and uses nonlocal information to make predictions. LRP shows that wind speed over land is highly relevant for predicting ice motion offshore. This provides a framework to show how knowledge of environmental variables (i.e., wind) on land could be useful for predicting other properties (i.e., sea ice velocity) elsewhere. Significance Statement Explainable artificial intelligence (XAI) is useful for understanding predictions made by machine learning models. Our research establishes trustability in a novel implementation of an explainable AI method known as layerwise relevance propagation for Earth science applications. To do this, we provide a comparative evaluation of a suite of explainable AI methods applied to machine learning models that make 1-day predictions of Arctic sea ice velocity. We use explainable AI outputs to understand how the input features are used by the machine learning to predict ice motion. Additionally, we show that a convolutional neural network uses nonlinear and nonlocal information in making its predictions. We take advantage of the nonlocality to investigate the extent to which knowledge of wind on land is useful for predicting sea ice velocity elsewhere.

Hoffman, Lauren [Scripps Institution of Oceanograp↗

Why the Forcing from Carbon Dioxide Scales as the Logarithm of Its Concentration

Abstract The radiative forcing from carbon dioxide is approximately logarithmic in its concentration, producing about 4 W m −2 of global-mean forcing for each doubling. Although these are basic facts of climate science, competing explanations for them have been given in the literature. Here, the reasons for the logarithmic forcing of carbon dioxide are explored in detail and a simplified model for the forcing is constructed. An essential component is the particular distribution of absorption coefficients within the 15- μ m band of carbon dioxide. An alternative explanation, which does not depend on the spectrum of carbon dioxide but instead hinges on the tropospheric lapse rate, is shown to be neither necessary nor sufficient to explain the logarithmic forcing of carbon dioxide and to be generally inapplicable to well-mixed greenhouse gases in Earth’s atmosphere.

54 ENVIRONMENTAL SCIENCES↗

How Does Vertical Wind Shear Influence Updraft Characteristics and Hydrometeor Distributions in Supercell Thunderstorms?

Abstract Vertical wind shear is known to affect supercell thunderstorms by displacing updraft hydrometeor mass downshear, thereby facilitating the storms’ longevity. Shear also impacts the size of supercell updrafts, with stronger shear leading to wider, less dilute, and stronger updrafts with likely greater hydrometeor production. To more clearly define the role of shear across different vertical layers on hydrometeor concentrations and displacements relative to supercell updrafts, a suite of idealized numerical model simulations of supercells was conducted. Shear magnitudes were systematically varied across the 0–1, 1–6, and 6–12 km AGL layers, while the thermodynamic environment was held fixed. Simulations show that as shear magnitude increases, especially from 1 to 6 km, updrafts become wider and less dilute with an increase in hydrometeor loading, along with an increase in the low-level precipitation area/rate and total precipitation accumulation. Even with greater updraft hydrometeor loading amid stronger shear, updrafts are more intense in stronger shear simulations due to larger thermal buoyancy owing to wider, less dilute updraft cores. Furthermore, downshear hydrometeor displacements are larger in environments with stronger 1–6-km shear. In contrast, there is relatively less sensitivity of hydrometeor concentrations and displacements to variations in either 0–1- or 6–12-km shear. Results are consistent across free tropospheric relative humidity sensitivity simulations, which show an increase in updraft size and hydrometeor mass with increasing free tropospheric relative humidity owing to a reduction in entrainment-driven dilution for wider updrafts in moister environments. Significance Statement Rotating thunderstorms, known as supercells, are able to persist for multiple hours. One common explanation is that large changes in wind speed and/or direction with height, or shear, transport rain/hail away from supercell updrafts, supporting their maintenance. The strong shear within supercell environments, however, may also lead to greater rail/hail amounts, thereby leading to weaker storms due to this extra mass of water/ice within updrafts. Furthermore, the impact of shear across different height layers on supercell rain/hail characteristics has not been thoroughly investigated. In this study, computer simulations of supercells were conducted to determine that shear occurring between 1 and 6 km above ground level has a large impact on rain/hail distribution in supercells and that stronger shear in this layer leads to wider/stronger supercells with greater rain/hail accumulations at the surface. Additionally, some of the extra mass of water/ice is transported farther away from updrafts due to the stronger environmental storm-relative winds.

Meteorology & Atmospheric Sciences↗

Opposing Hysteresis Patterns in Flow and Outflow Macroscopic Fundamental Diagrams and Their Implications

Two key aggregated traffic models are the relationship between average network flow and density (known as the network or flow macroscopic fundamental diagram [flow-MFD]) and the relationship between trip completion and density (known as network exit function or the outflow-MFD [o-FMD]). The flow- and o-MFDs have been shown to be related by average network length and average trip distance under steady-state conditions. However, recent studies have demonstrated that these two relationships might have different patterns when traffic conditions are allowed to vary: the flow-MFD exhibits a clockwise hysteresis loop, while the o-MFD exhibits a counter-clockwise loop. One recent study attributes this behavior to the presence of bottlenecks within the network. The present paper demonstrates that this phenomenon may arise even without bottlenecks present and offers an alternative, but more general, explanation for these findings: a vehicle’s entire trip contributes to a network’s average flow, while only its end contributes to the trip completion rate. This lag can also be exaggerated by trips with different lengths, and it can lead to other patterns in the o-MFD such as figure-eight patterns. A simple arterial example is used to demonstrate this explanation and reveal the expected patterns, and they are also identified in real networks using empirical data. Then, simulations of a congestible ring network are used to unveil features that might increase or diminish the differences between the flow- and o-MFDs. Finally, more realistic simulations are used to confirm that these behaviors arise in real networks.

42 ENGINEERING↗

Chemical classification program synthesis using generative artificial intelligence

Accurately classifying chemical structures is essential for cheminformatics and bioinformatics, including tasks such as identifying bioactive compounds of interest, screening molecules for toxicity to humans, finding non-organic compounds with desirable material properties, or organizing large chemical libraries for drug discovery or environmental monitoring. However, manual classification is labor-intensive and difficult to scale to large chemical databases. Existing automated approaches either rely on manually constructed classification rules, or are deep learning methods that lack explainability. This work presents an approach that uses generative artificial intelligence to automatically write chemical classifier programs for classes in the Chemical Entities of Biological Interest (ChEBI) database. These programs can be used for efficient deterministic run-time classification of SMILES structures, with natural language explanations. The programs themselves constitute an explainable computable ontological model of chemical class nomenclature, which we call the ChEBI Chemical Class Program Ontology (C3PO). We validated our approach against the ChEBI database, and compared our results against deep learning models and a naive SMARTS pattern based classifier. C3PO outperforms the naive classifier, but does not reach the performance of state of the art deep learning methods. However, C3PO has a number of strengths that complement deep learning methods, including explainability and reduced data dependence. C3PO can be used alongside deep learning classifiers to provide an explanation of the classification, where both methods agree. The programs can be used as part of the ontology development process, and iteratively refined by expert human curators.

Artificial Intelligence↗

SoyFACE Fumigation Data Files

This data set is related to the SoyFACE experiments, which are open-air agricultural climate change experiments that have been conducted since 2001. The fumigation experiments take place at the SoyFACE farm and facility in Champaign County, Illinois during the growing season of each year, typically between June and October. - The "SoyFACE Plot Information 2001 to 2021" file contains information about each year of the SoyFACE experiments, including the fumigation treatment type (CO2, O3, or a combination treatment), the crop species, the plots (also referred to as 'rings' and labeled with numbers between 2 and 31) used in each experiment, important experiment dates, and the target concentration levels or 'setpoints' for CO2 and O3 in each experiment. - This data set includes files with minute readings of the fumigation levels ( "SoyFACE 1-Minute Fumigation Data Files" folder) from the SoyFACE experiments. The "Soyface 1-Minute Fumigation Data Files" folder contains sub-folders for each year of the experiments, each of which contains sub-folders for each ring used in that year's experiments. This data set also includes hourly data files for the fumigation experiments ( "SoyFACE Hourly Fumigation Data Files" folder) created from the 1-minute files, and hourly ambient/weather data files for each year of the experiments ( "Hourly Weather and Ambient Data Files" folder). The ambient CO2 and O3 data are collected at SoyFACE, and the weather data are collected from the SURFRAD and WARM weather stations located near the SoyFACE farm. - The "Fumigation Target Percentages" file shows how much of the time the CO2 and O3 fumigation levels are within a 10 or 20 percent margin of the target levels when the fumigation system is turned on. - The "Matlab Files" folder contains custom code (Aspray, E.K.) that was used to clean the "SoyFACE 1-Minute Fumigation Data" files and to generate the "SoyFACE Hourly Fumigation Data" and "Fumigation Target Percentages" files. Code information can be found in the "SoyFACE Hourly Fumigation Data Explanation" file. - Finally, the " * Explanation" files contain information about the column names, units of measurement, and other pertinent information for each data file. * NOTE: We have identified some files in the “SoyFACE 1-Minute Fumigation Data Files” folder in our SoyFACE data set submission that were not downloaded properly - the files were present in the folder, but the actual files were empty. V3 ensures that there are no longer any empty files in the data set.

agricultural↗

Understanding oxidation of Fe-Cr-Al alloys through explainable artificial intelligence

Abstract The oxidation resistance of FeCrAl based on alloying composition and oxidizing conditions is predicted using a combinatorial experimental and artificial intelligence approach. A neural network (NN) classification model was trained on the experimental FeCrAl dataset produced at GE Research. Furthermore, using the SHapley Additive exPlanations (SHAP) explainable artificial intelligence (XAI) tool, we explore how the NN can showcase further material insights that are unavailable directly from a black-box model. We report that high Al and Cr content forms protective oxide layer, while Mo in FeCrAl creates thick unprotective oxide scale that is vulnerable to spallation due to thermal expansion. Graphical abstract

Materials Science↗