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At least 1,009 records · Page 56

Learning From User Behavior: A Survey-Assist Algorithm for Longitudinal Mobility Data Collection

GPS-based travel surveys are widely used in mobility studies to gather crucial qualitative data, like purpose, transportation mode and replaced mode. However, survey response still poses a burden to users, especially in long-term mobility studies, leading to response fatigue. We explore a survey-assist strategy to ease this burden by a novel, user-level modeling approach that leverages past responses from each user to predict responses for new trips, without relying on external data sources like GIS data. We investigate three main algorithms for predicting responses: (i) clustering trips and extrapolating responses for similar trips, (ii) using random forest classification, and (iii) clustering that uses a hybrid algorithm to determine spatial structure, which is then fed as input to a classic random forest classifier. The clustering approach can flexibly predict responses for even complex qualitative survey questions; it achieved F-scores of 65%. The random forest pipeline uses architecture that restricts it to predicting three predetermined survey questions: trip purpose, mode, and replaced mode. However, it achieved F-scores of 78%. While the survey-assist approach has been implemented by several proprietary systems, to our knowledge, this is the first exploration in the academic literature. It follows that this is also the first rigorous evaluation of multiple algorithms that can implement the approach. The evaluation uses a large scale, publicly available, longitudinal dataset consisting of ~ 92k trips from 235 users over a period of roughly one and a half years. With this approach, travel surveys can be pre-filled with the predicted responses for each trip, thus streamlining the survey process for users. Combined with an active learning system that requests user input on low-confidence predictions, models can be updated and improved over time to better support the long-term collection of longitudinal qualitative data.

clustering↗

A New Capability of E4D For 3D Parallel Joint Inversion of DC Resistivity And Traveltime Data on Unstructured Mesh

A major challenge in interpreting geophysical data is how to derive consistent three-dimensional (3D) earth models of different physical properties from spatially and temporally limited measurements. Joint inversion with cross-gradient constraints is an approach to find such models by imposing structural similarities between different physical parameters. We have developed a parallel distributed-memory joint inversion code for direct-current (DC) resistivity and traveltime data using the cross-gradient constraint on unstructured mesh. The code utilizes existing E4D framework for parallel forward simulation, distributed storage and computation of the Jacobian matrix of forward operator, and parallel execution of matrix-vector multiplication during inversion. Besides, the joint inversion is solved by nonlinear conjugate gradient algorithm parallelized for DC resistivity and traveltime data. The joint inversion capability of E4D was tested using synthetic data from cross-borehole DC resistivity and traveltime data. The results indicate that the shape and size of the anomalies from the joint inversion are more reliable than those from separate inversions.

58 GEOSCIENCES↗

Performance Before and After Irradiation of Pixelated 3D Silicon Sensors for the HL-LHC CMS Tracker

The Large Hadron Collider (LHC) particle accelerator at European Center for Nuclear Research (CERN) will be shut down starting in 2026 to achieve the High Luminosity Large Hadron Collider (HL-LHC) upgrade. The upgrade will allow for higher fluences, in order to increase the probability of detecting increasingly rare particles, and to obtain higher precision measurements of known particles. To accommodate the new accelerator conditions, many aspects of the Compact Muon Solenoid (CMS) detector will be upgraded; of particular interest for this thesis are the silicon pixel detectors located in the inner tracker. These will be replaced and upgraded to accommodate the higher fluences of the HL-LHC upgrade, as well as to replace existing sensors which have sustained radiation damage. In order for the new sensors to operate under high luminosity conditions, they must be increasingly radiation hard, and in order to detect rare particles, they must be increasingly more precise. The performance of one Centro Nacional de Microelectronica (CNM) 3D silicon sensor before and after undergoing irradiation at fluences similar to those which will be observed at the HL-LHC was investigated to determine radiation hardness and precision. Data was collected at Fermi National Laboratory (Fermilab), in the Fermi National Laboratory Test Beam Facility (FTBF) silicon tracker telescope, which can be used to determine the number of particles, and tracks made by high energy protons passing through. The sensor was also irradiated at Fermilab in the Irradiation Test Area (ITA). Prior to data collection a tuning procedure is carried out to determine ideal bias voltage operating conditions, mask noisy and dead pixels, adjust to the ideal threshold, and map sensor gain. Data is then collected at the FTBF, where the sensor is installed in the center of the FTBF silicon telescope. Variables, including angle and bias voltage, are varied throughout data collection. Data is then processed using an alignment software to determine the exact telescope geometry, along with the tracks which were observed passing through the sensor and telescope. Sensor performance was found to be comparable before and after irradiation, with irradiated results showing slightly lower efficiencies and cluster sizes. Position resolution is comparable both before and after irradiation, and similar distributions of cluster shape are observed. After irradiation, the sensor shows increasing collected charge with bias, an indication of increased width of the depletion region. Peak charge pre-irradiation is higher than post-irradiation peak charge, indicating the irradiated results are not taken under fully-depleted conditions.

72 PHYSICS OF ELEMENTARY PARTICLES AND FIELDS↗

Bayesian Monte Carlo Evaluation Framework for Imperfect Nuclear Data

Bayesian evaluation of resolved resonance region (RRR) nuclear data has historically been carried out using the generalized least squares (GLS) formalism, as implemented in, e.g., SAMMY. We have recently developed a prototype of Bayesian Monte Carlo (BMC) evaluation framework, implemented using a Markov Chain Monte Carlo (MCMC) method with a Metropolis-Hastings (MH) acceptance criterion. This was done in order to remove the approximations underlying the conventional GLS evaluations, namely, the linear approximation, and the approximation that all probability density functions (PDFs) are of the normal kind. Recent works by others have used similar stochastic approaches to quantify cross section uncertainties from ENDF evaluated co-variances, and/or, from integral benchmark data, but those have not been conceived as an evaluation framework like the one presented here.

97 MATHEMATICS AND COMPUTING↗

Ocean Energy for Ocean Worlds

Energy systems generating power from ocean waves, currents, tides, and thermal and salinity gradients are being developed to power oceanographic instrumentation and autonomous vehicles in Earth’s oceans. Exploration missions enabled or extended with in-situ energy harvesting on Earth may be similar to those on extra-terrestrial ocean worlds including mapping, biogeochemical sampling, acoustic monitoring, search for building blocks of life, and physical oceanographic characterization. With the addition of ocean energy available at the point of observation, data can be collected on larger spatial and temporal scales, enabling more comprehensive missions on other worlds. Power resource characteristics (e.g. current speed, variability) will similarly need to be assessed. Earth and extra-terrestrial ocean missions share vast technical challenges including high expense, need for advanced autonomy, ability to survive in the harshest environments, and limited communications or opportunities for intervention. Marine energy systems may be the only option for in-situ generation in certain scenarios (e.g., under a thick layer of ice) or advantageous over onboard energy storage options that may interfere with the natural environment (e.g., radioisotope thermoelectric generators). This work provides an overview of existing marine energy technology pertaining to ocean observations, highlights emerging research and development and new funding and program initiatives, explores similarities in mission requirements between terrestrial and extra-terrestrial applications, and suggests innovation pathways towards enabling high-value ocean world exploration powered by ocean energy.

Cavagnaro, Robert J.↗

Structural analyses of amorphous calcium carbonate before and after removing strontium ions from an aqueous solution

Amorphous calcium carbonate (ACC) is a precursor of crystalline calcium carbonate; hence, its structural information at the atomic level is very important for controlling the morphology of crystalline calcium carbonate. In this study, we attempted to elucidate the process of Sr extraction from aqueous solution by using ACC for the purpose of removal of radioactive Sr from the contaminated water leaked after the Fukushima Daiichi nuclear accident. Here, the pair distribution functions, g(r) obtained by X-ray and neutron diffraction (ND) measurements show that ACC has a structure partially similar to that of monohydrocalcite, suggesting that ACC is transferred to the crystalline calcium carbonate starting from its crystal nucleus. Rietveld analysis of the ND data showed that the ACC that removed Sr was crystallized to calcite. However, the Sr–O coordination analyzed using extended X-ray absorption fine structure (EXAFS) implies that the local environment of O around Sr is similar to that in crystalline calcium carbonate aragonite.

36 MATERIALS SCIENCE↗

An investigation into the potential for wind turbines to cause barotrauma in bats

The high rates of bat mortality caused by operating wind turbines is a concern for wind energy and wildlife stakeholders. One theory that explains the mortality is that bats are not only killed by impact trauma, but also by barotrauma that results from exposure to the pressure variations caused by rotating turbine blades. To date, no published research has calculated the pressure changes that bats may be exposed to when flying near wind turbines and then used these data to estimate the likelihood that turbines cause barotrauma in bats. To address this shortcoming, we performed computational fluid dynamics simulations of a wind turbine and analytical calculations of blade-tip vortices to estimate the characteristics of the sudden pressure changes bats may experience when flying near a utility-scale wind turbine. Because there are no data available that characterize the pressure changes that cause barotrauma in bats, we compared our results to changes in pressure levels that cause barotrauma and mortality in other mammals of similar size. This comparison shows that the magnitude of the low-pressures bats experience when flying near wind turbines is approximately 8 times smaller than the pressure that causes mortality in rats, the smallest mammal for which data are available. The magnitude of the high-pressures that bats may experience are approximately 80 times smaller than the exposure level that causes 50% mortality in mice, which have a body mass similar to several bat species that are killed by wind turbines. Further, our results show that for a bat to experience the largest possible magnitude of low- and high-pressures, they must take very specific and improbable flight paths that skim the surface of the blades. Even a small change in the flight path results in the bat being hit by the blade or experiencing a much smaller pressure change. Accordingly, if bats have a physiological response to rapid low- and high-pressure exposure that is similar to other mammals, we conclude that it is unlikely that barotrauma is responsible for a significant number of turbine-related bat fatalities, and that impact trauma is the likely cause of the majority of wind-turbine-related bat fatalities.

17 WIND ENERGY↗

cTULIP: application of a human-based RNA-seq primary tumor classification tool for cross-species primary tumor classification in canine

The domestic dog, Canis familiaris, is quickly gaining traction as an advantageous model for use in the study of cancer, one of the leading causes of death worldwide. Naturally occurring canine cancers share clinical, histological, and molecular characteristics with the corresponding human diseases. In this study, we take a deep-learning approach to test how similar the gene expression profile of canine glioma and bladder cancer (BLCA) tumors are to the corresponding human tumors. We likewise develop a tool for identifying misclassified or outlier samples in large canine oncological datasets, analogous to that which was developed for human datasets. We test a number of machine learning algorithms and found that a convolutional neural network outperformed logistic regression and random forest approaches. We use a recently developed RNA-seq-based convolutional neural network, TULIP, to test the robustness of a human-data-trained primary tumor classification tool on cross-species primary tumor prediction. Our study ultimately highlights the molecular similarities between canine and human BLCA and glioma tumors, showing that protein-coding one-to-one homologs shared between humans and canines, are sufficient to distinguish between BLCA and gliomas. The results of this study indicate that using protein-coding one-to-one homologs as the features in the input layer of TULIP performs good primary tumor prediction in both humans and canines. Furthermore, our analysis shows that our selected features also contain the majority of features with known clinical relevance in BLCA and gliomas. Our success in using a human-data-trained model for cross-species primary tumor prediction also sheds light on the conservation of oncological pathways in humans and canines, further underscoring the importance of the canine model system in the study of human disease.

60 APPLIED LIFE SCIENCES↗

The impact of new d(p,γ)3 rates on Big Bang Nucleosynthesis

We consider the effect on Big Bang Nucleosynthesis (BBN) of new measurements of the d(p,γ) 3 He cross section by the LUNA Collaboration. These have an important effect on the primordial abundance of D/H which is also sensitive to the baryon density at the time of BBN. We have re-evaluated the thermal rate for this reaction, using a world average of cross section data, which we describe with model-independent polynomials; our results are in good agreement with a similar analysis by LUNA. We then perform a full likelihood analysis combining BBN and Planck cosmic microwave background (CMB) likelihood chains using the new rate combined with previous measurements and compare with the results using previous rates. Concordance between BBN and CMB measurements of the anisotropy spectrum using the old rates was excellent. The predicted deuterium abundance at the Planck value of the baryon density was (D/H) BBN+CMB old = (2.57 ± 0.13) × 10 –5 which can be compared with the value determined from quasar absorption systems (D/H) obs = (2.55 ± 0.03) × 10 –5 . Using the new rates we find (D/H) BBN+CMB = (2.51 ± 0.11) × 10 –5 . We thus find consistency among BBN theory, deuterium and 4He observations, and the CMB, when using reaction rates fit in our data-driven approach. We also find that the new reaction data tightens the constraints on the number of relativistic degrees of freedom during BBN, giving the effective number of light neutrino species N ν = 2.880 ± 0.144 in good agreement with the Standard Model of particle physics. Lastly, we note that the observed deuterium abundance continues to be more precise than the BBN+CMB prediction, whose error budget is now dominated by d(d,n) 3 He and d(d,p) 3 H.

72 PHYSICS OF ELEMENTARY PARTICLES AND FIELDS↗

Bi-fidelity modeling of uncertain and partially unknown systems using DeepONets

Recent advances in modeling large-scale, complex physical systems have shifted research focuses towards data-driven techniques. However, generating datasets by simulating complex systems can require significant computational resources. Similarly, acquiring experimental datasets can prove difficult. For these systems, often computationally inexpensive, but in general inaccurate models, known as the low-fidelity models, are available. Here in this paper, we propose a bi-fidelity modeling approach for complex physical systems, where we model the discrepancy between the true system's response and a low-fidelity response in the presence of a small training dataset from the true system's response using a deep operator network, a neural network architecture suitable for approximating nonlinear operators. We apply the approach to systems that have parametric uncertainty and are partially unknown. Three numerical examples are used to show the efficacy of the proposed approach to model uncertain and partially unknown physical systems.

MATHEMATICS AND COMPUTING↗

Computation of conventional and alternative jet fuel sensitivity to lean blowout

Large Eddy Simulations (LES) are performed to compute the sensitivity of a conventional (A-2) and an alternate bio-jet (C-1) fuel to Lean Blowout (LBO). A realistic aviation gas turbine engine combustor configuration is considered. Reliable experimental LBO data and OH* chemiluminescence data for the conventional and alternate jet fuel in the combustor configuration have recently become available. The present work utilizes a highly automated, on-the-fly meshing strategy, along with adaptive mesh refinement, to demonstrate the feasibility of capturing the realistic combustion processes. A Lagrangian framework, with initial conditions specified using measurements of spray statistics, is used to model the fuel spray. Newly developed compact reaction mechanisms based on fuel surrogates are validated for the A-2 and the C-1 fuels. The compact reaction mechanisms are implemented using a detailed finite rate chemistry solver. Spray statistics computed by the present LES simulations compare well with available measurements at stable flame conditions near the lean blowout limit. The computed shape of the stable flame as represented by line integrated OH concentrations compares well with the experimental OH* chemiluminescence data. Lean blowout is reached by gradually decreasing the fuel flow rate in the computations, similar to that in the experiments. The results of the LES simulations effectively capture the fuel composition effects and estimate the sensitivity of the LBO limits to the fuel type. The computed trends in LBO limits agree within engineering accuracy with the experimental results for conventional and alternative aviation fuels. The methodology for predicting the fuel composition effects on the lean blowout limits in a fully resolved realistic, complex combustor is established for the first time.

Adaptive mesh refinement↗

The incongruity of validating quantitative proteomics using western blots

Similar to the age-old reviewer request for quantitative PCR validation of RNA sequencing data, nearly every researcher using proteomics technologies has, at one time or another, been asked by a reviewer to provide “western blot validation” of their mass spectrometry-based protein abundance data. We believe this request demonstrates a lack of awareness amongst the plant biology community about the extraordinary improvements in cost, sensitivity and reliability the field of mass spectrometry-based proteomics has made in recent years. Here, in this study, as a group of experts in different domains of quantitative plant proteomics, we explain why “western blot validation” of quantitative proteomics data is both unnecessary and invalid. Furthermore, we invite our colleagues in the plant science community to update their perception of quantitative mass spectrometry as a sensitive and reliable method of protein identification and quantitation.

Mehta, Devang↗

Systematic characterization of gene function in the photosynthetic alga Chlamydomonas reinhardtii

Most genes in photosynthetic organisms remain functionally uncharacterized. Here, using a barcoded mutant library of the model eukaryotic alga Chlamydomonas reinhardtii, we determined the phenotypes of more than 58,000 mutants under more than 121 different environmental growth conditions and chemical treatments. A total of 59% of genes are represented by at least one mutant that showed a phenotype, providing clues to the functions of thousands of genes. Mutant phenotypic profiles place uncharacterized genes into functional pathways such as DNA repair, photosynthesis, the CO 2 -concentrating mechanism and ciliogenesis. We illustrate the value of this resource by validating phenotypes and gene functions, including three new components of an actin cytoskeleton defense pathway. The data also inform phenotype discovery in land plants; mutants in Arabidopsis thaliana genes exhibit phenotypes similar to those we observed in their Chlamydomonas homologs. We anticipate that this resource will guide the functional characterization of genes across the tree of life.

59 BASIC BIOLOGICAL SCIENCES↗

Internal gravity waves in massive stars: II. Frequency analysis across stellar mass

Stars that are over 1.6 solar masses are generally known to possess convective cores and radiative envelopes, which allows for the propagation of outwardly travelling internal gravity waves (IGWs). Here, we study the generation and propagation of IGWs in such stars using two-dimensional, fully non-linear hydrodynamical simulations with realistic stellar reference states from the one-dimensional stellar evolution code, Modules for Stellar Astrophysics. Compared to previous similar works, this study utilises radius-dependent thermal diffusivity profiles for five different stellar masses at the middle of the main sequence: 3 M ⊙ , 5 M ⊙ , 7 M ⊙ , 10 M ⊙ , and 13 M ⊙ . From the simulations, we find that the surface perturbations are larger for higher masses, but no noticeable trends are observed for the frequency slopes with different stellar masses. The slopes are also similar to the results from previous works. We compared our simulation results with stellar photometric data from a recent survey and we found that for frequency intervals above 8 μHz, there is a good agreement between the temperature frequency slopes from the simulations and the surface brightness variations of these observed stars. This indicates that the brightness variations are caused by core-generated IGWs.

79 ASTRONOMY AND ASTROPHYSICS↗

OrbNet Denali: A machine learning potential for biological and organic chemistry with semi-empirical cost and DFT accuracy

We present OrbNet Denali, a machine learning model for an electronic structure that is designed as a drop-in replacement for groundstate density functional theory (DFT) energy calculations. The model is a message-passing graph neural network that uses symmetryadapted atomic orbital features from a low-cost quantum calculation to predict the energy of a molecule. OrbNet Denali is trained on a vast dataset of 2.3 × 10 6 DFT calculations on molecules and geometries. This dataset covers the most common elements in biochemistry and organic chemistry (H, Li, B, C, N, O, F, Na, Mg, Si, P, S, Cl, K, Ca, Br, and I) and charged molecules. OrbNet Denali is demonstrated on several well-established benchmark datasets, and we find that it provides accuracy that is on par with modern DFT methods while offering a speedup of up to three orders of magnitude. For the GMTKN55 benchmark set, OrbNet Denali achieves WTMAD-1 and WTMAD-2 scores of 7.19 and 9.84, on par with modern DFT functionals. For several GMTKN55 subsets, which contain chemical problems that are not present in the training set, OrbNet Denali produces a mean absolute error comparable to those of DFT methods. For the Hutchison conformer benchmark set, OrbNet Denali has a median correlation coefficient of R 2 = 0.90 compared to the reference DLPNO-CCSD(T) calculation and R 2 = 0.97 compared to the method used to generate the training data (ωB97X-D3/def2- TZVP), exceeding the performance of any other method with a similar cost. Similarly, the model reaches chemical accuracy for noncovalent interactions in the S66x10 dataset. For torsional profiles, OrbNet Denali reproduces the torsion profiles of ωB97X-D3/def2-TZVP with an average mean absolute error of 0.12 kcal/mol for the potential energy surfaces of the diverse fragments in the TorsionNet500 dataset.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Interpretation of Lyman opacity measurements in JET with the ITER-like wall using a particle balance approach

Recent measurements of the Ly β /D α ratio in the JET ITER-like wall (ILW) divertor show comparatively more pronounced Ly β reabsorption relative to previous results in JET with the carbon wall (JET-C). At the outer horizontal target ion current rollover point a Ly β reabsorption rate of 60% is measured, increasing to 80% in more pronounced detachment, implying a Ly α reabsorption rate of 90%–98%. The radially resolved Ly β /D α measurements are used to constrain Lyman opacity corrections to atomic rate coefficients using the population escape factor technique in order to capture the local changes to the excited state population structure in the high Lyman opacity regions at and outboard of the outer strike point. To check the self-consistency of the Lyman opacity measurements, a detailed spectroscopic interpretation of the outer divertor particle balance is presented, in which the impact of opacity corrections to the Ly α inverse photon efficiency coefficients is assessed. A five-fold deficit in the estimated D + source rate obtained with optically thin plasma assumptions is reconciled once the opacity corrections are factored into the Ly α photon rate to ionization rate conversion. The experiment results are reproduced in EDGE2D-EIRENE density scan simulations in which an imposed ad hoc Lyman reabsorption rate is recovered spectroscopically using synthetic measurements, and a similar shortfall in the D + source rate estimates is reconciled using Lyman opacity corrected atomic data. The model limitations prevent a more detailed self-consistent analysis of the Lyman opacity impact on divertor parameters and detachment evolution, and hence motivate renewed efforts to re-establish routine exploitation of the photon transport modelling capabilities in the EIRENE code package. Lyman opacity corrections to atomic data coefficients are necessary for spectroscopic interpretation of the JET-ILW divertor plasma, with significant influence on the divertor plasma also a likely consequence of the presence of strong Ly α reabsorption. Finally, a scan of auxiliary heating powers spanning L-mode and H-mode conditions reveals a strong correlation of the measured Ly β opacity with the outer target temperature, suggesting new possibilities for using Lyman opacity measurements in establishing detachment scalings.

70 PLASMA PHYSICS AND FUSION TECHNOLOGY↗

The smallest fluid on earth

High energy heavy ion collisions create quark gluon plasmas that behave like almost perfect fluids. Very similar features to those that led to this insight have also been observed in experimental data from collisions of small systems, involving protons or other light nuclei. Here we describe recent developments aimed at understanding whether, and if so how, systems that produce relatively few particles (orders of magnitude less than in typical heavy ion collisions) and are only one to a few times the size of a proton, can behave like fluids. This involves a deeper understanding of fluid dynamics and its applicability, improvements of our understanding of the initial geometry of the collisions by considering fluctuations of the proton shape, as well as advancements in the calculation of initial state effects within an effective theory of quantum chromodynamics, which can affect the observables that are used to study fluid behavior. We further address open questions and discuss future directions.

73 NUCLEAR PHYSICS AND RADIATION PHYSICS↗

Jet-hadron correlations with respect to the event plane in $\sqrt{s_{NN}}$ = 200 GeV Au + Au collisions in STAR

Angular distributions of charged particles relative to jet axes are studied in $\sqrt{s_{NN}}$ = 200 GeV Au+Au collisions as a function of the jet orientation with respect to the event plane. This differential study tests the expected path-length dependence of energy loss experienced by a hard-scattered parton as it traverses the hot and dense medium formed in heavy-ion collisions. A second-order event plane is used in the analysis as an experimental estimate of the reaction plane formed by the collision impact parameter and the beam direction. Charged-particle jets with 15 < 𝑝 T,jet < 20 and 20 < 𝑝 T,jet < 40 ⁢GeV/𝑐 were reconstructed with the anti-𝑘 T algorithm with radius parameter setting of 𝑅 = 0.4 in the 20–50% centrality bin to maximize the initial-state eccentricity of the interaction region. The reaction plane fit method is implemented to remove the flow-modulated background with better precision than prior methods. Yields and widths of jet-associated charged-hadron distributions are extracted in three angular bins between the jet axis and the event plane. The event-plane (EP) dependence is further quantified by ratios of the associated yields in different EP bins. No dependence on orientation of the jet axis with respect to the event plane is seen within the uncertainties in the kinematic regime studied. This finding is consistent with a similar experimental observation by ALICE in $\sqrt{s_{NN}}$ = 2.76 TeV Pb-Pb collision data.

73 NUCLEAR PHYSICS AND RADIATION PHYSICS↗