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DOE OSTI2024

Filtering higher-order datasets

Many complex systems often contain interactions between more than two nodes, known as higher-order interactions, which can change the structure of these systems in significant ways. Researchers often assume that all interactions paint a consistent picture of a higher-order dataset's structure. In contrast, the connection patterns of individuals or entities in empirical systems are often stratified by interaction size. Ignoring this fact can aggregate connection patterns that exist only at certain scales of interaction. To isolate these scale-dependent patterns, we present an approach for analyzing higher-order datasets by filtering interactions by their size. We apply this framework to several empirical datasets from three domains to demonstrate that data practitioners can gain valuable information from this approach.

71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗

DOE OSTI2020

Determination of latent dimensionality in international trade flow

Currently, high-dimensional data is ubiquitous in data science, which necessitates the development of techniques to decompose and interpret such multidimensional (aka tensor) datasets. Finding a low dimensional representation of the data, that is, its inherent structure, is one of the approaches that can serve to understand the dynamics of low dimensional latent features hidden in the data. Moreover, decomposition methods with non-negative constraints are shown to extract more insightful factors. Nonnegative RESCAL is one such technique, particularly well suited to analyze self-relational data, such as dynamic networks found in international trade flows. Particularly, non-negative RESCAL computes a low dimensional tensor representation by finding the latent space containing multiple modalities. Furthermore, estimating the dimensionality of this latent space is crucial for extracting meaningful latent features. Here, to determine the dimensionality of the latent space with non-negative RESCAL, we propose a latent dimension determination method which is based on clustering of the solutions of multiple realizations of non-negative RESCAL decompositions. We demonstrate the performance of our model selection method on synthetic data. We then apply our method to decompose a network of international trade flows data from International Monetary Fund and shows that with a correct latent dimension determination, the resulting features are able to capture relevant empirical facts from economic literature.

97 MATHEMATICS AND COMPUTING↗

DOE OSTI2021

Propagation of priors for more accurate and efficient spectroscopic functional fits and their application to ferroelectric hysteresis

Multi-dimensional spectral-imaging is a mainstay of the scanning probe and electron microscopies, micro-Raman, and various forms of chemical imaging. In many cases, individual spectra can be fit to a specific functional form, with the model parameter maps, providing direct insight into material properties. Since spectra are often acquired across a spatial grid of points, spatially adjacent spectra are likely to be similar to one another; yet, this fact is almost never used when considering parameter estimation for functional fits. On datasets tried here, we show that by utilizing proximal information, whether it be in the spatial or spectral domains, it is possible to improve the reliability and increase the speed of such functional fits by ~2-3x, as compared to random priors. We explore and compare three distinct new methods: (1) spatially averaging neighborhood spectra, and propagating priors based on functional fits to the averaged case, (2) hierarchical clustering-based methods where spectra are grouped hierarchically based on response, with the priors propagated progressively down the hierarchy, and (3) regular clustering without hierarchical methods with priors propagated from fits to cluster means. Our results highlight that utilizing spatial and spectral neighborhood information is often critical for accurate parameter estimation in noisy environments, which we show for ferroelectric hysteresis loops acquired on a prototypical PbTiO3 thin film with piezoresponse spectroscopy. This method is general and applicable to any spatially measured spectra where functional forms are available. Examples include exploring the superconducting gap with tunneling spectroscopy, using the Dynes formula, or current-voltage curve fits in conductive atomic force microscopy mapping. Here we explore the problem for ferroelectric hysteresis, which, given its large parameter space, constitutes a more difficult task than, for example, fitting current-voltage curves with a Schottky emission formula.

42 ENGINEERING↗

DOE OSTI2025

Inverse model based error detection in beamline optics

Optics tuning in transfer lines and LINACs can be challenging due to the fact that multiple combinations of machine settings can lead to the same diagnostic output. Moreover, the lack of a periodic solution can limit the ability to infer optics in the same way as rings from BPM signals. Model based approaches are often used to assist with the optics tuning in combination with optimization or parameter estimation. Here we have developed a novel approach using machine learning inverse models trained on a known configuration to detect variations in quadrupole settings without explicitly including them in the model. This paper shows a comparison of neural network models and linear models on both a simulation based study and experimental studies conducted at the AGS to RHIC transfer line at Brookhaven National Lab.

43 PARTICLE ACCELERATORS↗

DOE OSTI2025

A model for selecting the best sustainable airport technology alternatives

Air transport is a continually expanding industry, a fact that has become even more evident with the recovery of the aviation industry post-COVID-19. This expansion amplified energy consumption at airports, which was already significantly high. Airport decision-makers are increasingly focusing on improving sustainability and addressing social, economic, and environmental criteria across airports worldwide. In this article, we propose a decision-making model for identifying a sustainable airport technology solution that minimizes the energy consumption of airport lighting while considering economic, emission, and life-cycle criteria. The proposed model combines data envelopment analysis and multi-criteria decision making techniques. We applied the model to the Dallas/Fort Worth International Airport (DFW) as a case study, considering eight lighting technology solutions, each with five luminous flux alternatives. Our model identified the best lighting technology solution for DFW outdoor and indoor environments based on the following criteria: luminous flux, capital costs, life-cycle costs, energy consumption, and emissions (CO2e, NOx, SO2, and PM2.5). The designed model is customizable to any airport and is applicable to a wide range of airport lighting technologies. In our analysis, Light-Emitting Diode lighting emerged as the most sustainable technology option. It ranked first in most cases due to its balance of high efficacy, long lifespan, low life-cycle cost, low capital cost, and lower emissions across all pollutants.

Tchivwila, Moise B↗

DOE OSTI2020

Bacterial Origin and Reductive Evolution of the CPR Group

The candidate phyla radiation (CPR) is a proposed subdivision within the bacterial domain comprising several candidate phyla. CPR organisms are united by small genome and physical sizes, lack several metabolic enzymes, and populate deep branches within the bacterial subtree of life. Here, these features raise intriguing questions regarding their origin and mode of evolution. In this study, we performed a comparative and phylogenomic analysis to investigate CPR origin and evolution. Unlike previous gene/protein sequence-based reports of CPR evolution, we used protein domain superfamilies classified by protein structure databases to resolve the evolutionary relationships of CPR with non-CPR bacteria, Archaea, Eukarya, and viruses. Across all supergroups, CPR shared maximum superfamilies with non-CPR bacteria and were placed as deep branching bacteria in most phylogenomic trees. CPR contributed 1.22% of new superfamilies to bacteria including the ribosomal protein L19e and encoded four core superfamilies that are likely involved in cell-to-cell interaction and establishing episymbiotic lifestyles. Although CPR and non-CPR bacterial proteomes gained common superfamilies over the course of evolution, CPR and Archaea had more common losses. These losses mostly involved metabolic superfamilies. In fact, phylogenies built from only metabolic protein superfamilies separated CPR and non-CPR bacteria. These findings indicate that CPR are bacterial organisms that have probably evolved in an Archaea-like manner via the early loss of metabolic functions. We also discovered that phylogenies built from metabolic and informational superfamilies gave contrasting views of the groupings among Archaea, Bacteria, and Eukarya, which add to the current debate on the evolutionary relationships among superkingdoms.

59 BASIC BIOLOGICAL SCIENCES↗

DOE OSTI2024

Heterogeneous mantle effects on the behavior of SmKS waves and outermost core imaging

Seismic traveltime anomalies of waves that traverse the uppermost 100–200 km of the outer core have been interpreted as evidence of reduced seismic velocities (relative to radial reference models) just below the core–mantle boundary (CMB). These studies typically investigate differential traveltimes of SmKS waves, which propagate as P waves through the shallowest outer core and reflect from the underside of the CMB m times. The use of SmKS and S(m-1)KS differential traveltimes for core imaging are often assumed to suppress contributions from earthquake location errors and unknown and unmodelled seismic velocity heterogeneity in the mantle. The goal of this study is to understand the extent to which differential SmKS traveltimes are, in fact, affected by anomalous mantle structure, potentially including both velocity heterogeneity and anisotropy. Velocity variations affect not only a wave's traveltime, but also the path of a wave, which can be observed in deviations of the wave's incoming direction. Since radial velocity variations in the outer core will only minimally affect the wave path, in contrast to other potential effects, measuring the incoming direction of SmKS waves provides an additional diagnostic as to the origin of traveltime anomalies. Here we use arrays of seismometers to measure traveltime and direction anomalies of SmKS waves that sample the uppermost outer core. We form subarrays of EarthScope's regional Transportable Array stations, thus measuring local variations in traveltime and direction. We observe systematic lateral variations in both traveltime and incoming wave direction, which cannot be explained by changes to the radial seismic velocity profile of the outer core. Moreover, we find a correlation between incoming wave direction and traveltime anomaly, suggesting that observed traveltime anomalies may be caused, at least in part, by changes to the wave path and not solely by perturbations in outer core velocity. Modelling of 1-D ray and 3-D wave propagation in global 3-D tomographic models of mantle velocity anomalies match the trend of the observed traveltime anomalies. Overall, we demonstrate that observed SmKS traveltime anomalies may have a significant contribution from 3-D mantle structure, and not solely from outer core structure.

58 GEOSCIENCES↗

DOE OSTI2022

The avoidance of unwanted catch and cooperation: the case of the British Columbia groundfish trawl fishery

Abstract This paper focuses on a particularly successful avoidance of unwanted catch of protected, endangered, and threatened (PET) species in the form of ecologically important sponge and coral, to be found off Canada's Pacific coast. The fishery causing the unwanted catch—the British Columbia groundfish trawl fishery. A campaign to protect the sponge/coral led by environmental NGOs (ENGOs) resulted in the industry's access to the key California market being threatened. For reasons explained, the national resource manager's ability to take effective direct action had become severely compromised. The groundfish trawl fishing industry responded to the economic threat with a bottom up approach to the unwanted catch problem, by negotiating a habitat agreement with a consortium of ENGOs, with the blessing and full support of the national resource manager. The agreement, now in its tenth year of operation, has proved to be a remarkable success in avoidance of unwanted catch. The paper argues that the success rests fundamentally upon the fact that the fishers have been and are playing a stand alone stable cooperative game, which has led them in turn to play stable cooperative games with both the national resource manager and the ENGO consortium. The paper analyses the factors leading to the stand alone stable cooperative fisher game, doing so by necessity through the lens of game theory.

Grønbæk, L.↗

DOE OSTI2024

The Kinematics of Proal Chewing in Rats

Chewing kinematics are well-documented in several mammal species with fused mandibular symphyses, but relatively understudied in mammals with an unfused symphysis, despite the fact that more than half of extant Mammalia have an unfused mandibular symphysis. The Wistar brown rat (Rattus norvegicus) is widely used in human health research, including studies of mastication or neurological studies where mastication is the output behavior. These animals are known to have unfused mandibular symphyses and proal jaw (rostrocaudal) motion during occlusion, but the lack of high resolution, 3-dimensional analysis of rat chewing leaves the functional significance of symphyseal mobility unknown. We used biplanar fluoroscopy and the X-ray reconstruction of moving morphology workflow to quantify chewing kinematics in 3 brown rats, quantifying overall jaw kinematics, including motions about the temporomandibular joint and unfused mandibular symphysis. During occlusion, the teeth and the mandibular condyle translate almost exclusively anteriorly (proal) during occlusion, with little motion in any other degrees of freedom. At the symphysis, we observed minimal flexion throughout the chew cycle. Overall, there are fundamental differences in jaw kinematics between rats and other mammals and therefore rats are not an appropriate proxy for ancestral mammal jaw mechanics. Additionally, differences between humans and rat chewing kinematics must be considered when using rats as a clinical model for pathological feeding research.

59 BASIC BIOLOGICAL SCIENCES↗

DOE OSTI2022

An agent-based blackboard system for multi-objective optimization

In the field of multi-objective optimization, there are a multitude of algorithms from which to choose. Each algorithm has strengths and weaknesses associated with the mechanics for finding the Pareto front. Recently, researchers have begun to examine how multi-agent environments can be used to help solve multi-objective optimization problems. In this work, we propose a multi-objective optimization algorithm based on a multi-agent blackboard system (MABS). The MABS framework allows for multiple agents to read and write pertinent optimization problem data to a central blackboard agent. Agents can stochastically search the design space, use previously discovered solutions to explore local optima, or update and prune the Pareto front. A centralized blackboard framework allows the optimization problem to be solved in a cohesive manner and permits stopping, restarting, or updating the optimization problem. The MABS framework is tested against three alternative optimization algorithms across a suite of engineering design problems and typically outperforms the other algorithms in discovering the Pareto front. A parallelizability study is performed where we find that the MABS is able to evaluate a set number of designs, which require an evaluation time ranging from 0 to 300 seconds, quicker than a traditional optimization algorithm: this fact becomes more apparent the longer it takes to evaluate a design. To provide context for the benefits provided by MABS, a real-world nuclear engineering design problem is examined. MABS is used to examine the placement of experiments in a nuclear reactor, where we are able to evaluate hundreds of configurations for experimental placement while maintaining a strict set of safety constraints.

22 GENERAL STUDIES OF NUCLEAR REACTORS↗

DOE OSTI2023

Computer-aided, resistance gene-guided genome mining for proteasome and HMG-CoA reductase inhibitors

Secondary metabolites (SMs) are biologically active small molecules, many of which are medically valuable. Fungal genomes contain vast numbers of SM biosynthetic gene clusters (BGCs) with unknown products, suggesting that huge numbers of valuable SMs remain to be discovered. It is challenging, however, to identify SM BGCs, among the millions present in fungi, that produce useful compounds. One solution is resistance gene-guided genome mining, which takes advantage of the fact that some BGCs contain a gene encoding a resistant version of the protein targeted by the compound produced by the BGC. The bioinformatic signature of such BGCs is that they contain an allele of an essential gene with no SM biosynthetic function, and there is a second allele elsewhere in the genome. We have developed a computer-assisted approach to resistance gene-guided genome mining that allows users to query large databases for BGCs that putatively make compounds that have targets of therapeutic interest. Working with the MycoCosm genome database, we have applied this approach to look for SM BGCs that target the proteasome β6 subunit, the target of the proteasome inhibitor fellutamide B, or HMG-CoA reductase, the target of cholesterol reducing therapeutics such as lovastatin. Our approach proved effective, finding known fellutamide and lovastatin BGCs as well as fellutamide- and lovastatin-related BGCs with variations in the SM genes that suggest they may produce structural variants of fellutamides and lovastatin. Gratifyingly, we also found BGCs that are not closely related to lovastatin BGCs but putatively produce novel HMG-CoA reductase inhibitors.

59 BASIC BIOLOGICAL SCIENCES↗

DOE OSTI2020

Electron tomography imaging methods with diffraction contrast for materials research

Transmission electron microscopy (TEM) and scanning transmission electron microscopy (STEM) enable the visualization of three-dimensional (3D) microstructures ranging from atomic to micrometer scales using 3D reconstruction techniques based on computed tomography algorithms. This 3D microscopy method is called electron tomography (ET) and has been utilized in the fields of materials science and engineering for more than two decades. Although atomic resolution is one of the current topics in ET research, the development and deployment of intermediate-resolution (non-atomic-resolution) ET imaging methods have garnered considerable attention from researchers. This research trend is probably not irrelevant due to the fact that the spatial resolution and functionality of 3D imaging methods of scanning electron microscopy (SEM) and X-ray microscopy have come to overlap with those of ET. In other words, there may be multiple ways to carry out 3D visualization using different microscopy methods for nanometer-scale objects in materials. From the above standpoint, this review paper aims to (i) describe the current status and issues of intermediate-resolution ET with regard to enhancing the effectiveness of TEM/STEM imaging and (ii) discuss promising applications of state-of-the-art intermediate-resolution ET for materials research with a particular focus on diffraction contrast ET for crystalline microstructures (superlattice domains and dislocations) including a demonstration of in situ dislocation tomography.

36 MATERIALS SCIENCE↗

DOE OSTI2023

Determining Stress in Metallic Conducting Layers of Microelectronics Devices Using High Resolution Electron Backscatter Diffraction and Finite Element Analysis

Delayed failure due to stress voiding is a concern with some aging microelectronics, as these voids can grow large enough to cause an open circuit. Local measurements of stress in the metallic layers are crucial to understanding and predicting this failure, but such measurements are complicated by the fact that exposing the aluminum conducting lines will relieve most of their stress. In this study, we instead mechanically thin the device substrate and measure distortions on the thinned surface using high resolution electron backscatter diffraction (HREBSD). These measurements are then related to the stresses in the metallic layers through elastic simulations. This study found that in legacy components that had no obvious voids, the stresses were comparable to the theoretical stresses at the time of manufacture (≈300 MPa). Distortion fields in the substrate were also determined around known voids, which may be directly compared to stress voiding models. In conclusion, the technique presented here for stress determination, HREBSD coupled with finite element analysis to infer subsurface stresses, is a valuable tool for assessing failure in layered microelectronics devices.

HREBSD↗

DOE OSTI2020

The stellar mass Fundamental Plane: the virial relation and a very thin plane for slow rotators

ABSTRACT Early-type galaxies – slow and fast rotating ellipticals (E-SRs and E-FRs) and S0s/lenticulars – define a Fundamental Plane (FP) in the space of half-light radius Re, enclosed surface brightness Ie, and velocity dispersion σe. Since Ie and σe are distance-independent measurements, the thickness of the FP is often expressed in terms of the accuracy with which Ie and σe can be used to estimate sizes Re. We show that: (1) The thickness of the FP depends strongly on morphology. If the sample only includes E-SRs, then the observed scatter in Re is $\sim 16{{\ \rm per\ cent}}$, of which only $\sim 9{{\ \rm per\ cent}}$ is intrinsic. Removing galaxies with M* < 1011 M⊙ further reduces the observed scatter to $\sim 13{{\ \rm per\ cent}}$ ($\sim 4{{\ \rm per\ cent}}$ intrinsic). The observed scatter increases to $\sim 25{{\ \rm per\ cent}}$ usually quoted in the literature if E-FRs and S0s are added. If the FP is defined using the eigenvectors of the covariance matrix of the observables, then the E-SRs again define an exceptionally thin FP, with intrinsic scatter of only 5 per cent orthogonal to the plane. (2) The structure within the FP is most easily understood as arising from the fact that Ie and σe are nearly independent, whereas the Re−Ie and Re−σe correlations are nearly equal and opposite. (3) If the coefficients of the FP differ from those associated with the virial theorem the plane is said to be ‘tilted’. If we multiply Ie by the global stellar mass-to-light ratio M*/L and we account for non-homology across the population by using Sérsic photometry, then the resulting stellar mass FP is less tilted. Accounting self-consistently for M*/L gradients will change the tilt. The tilt we currently see suggests that the efficiency of turning baryons into stars increases and/or the dark matter fraction decreases as stellar surface brightness increases.

Bernardi, M.↗

DOE OSTI2020

Concentrations of dark haloes emerge from their merger histories

ABSTRACT The concentration parameter is a key characteristic of a dark matter halo that conveniently connects the halo’s present-day structure with its assembly history. Using ‘Dark Sky’, a suite of cosmological N-body simulations, we investigate how halo concentration evolves with time and emerges from the mass assembly history. We also explore the origin of the scatter in the relation between concentration and assembly history. We show that the evolution of halo concentration has two primary modes: (1) smooth increase due to pseudo-evolution; and (2) intense responses to physical merger events. Merger events induce lasting and substantial changes in halo structures, and we observe a universal response in the concentration parameter. We argue that merger events are a major contributor to the uncertainty in halo concentration at fixed halo mass and formation time. In fact, even haloes that are typically classified as having quiescent formation histories experience multiple minor mergers. These minor mergers drive small deviations from pseudo-evolution, which cause fluctuations in the concentration parameters and result in effectively irreducible scatter in the relation between concentration and assembly history. Hence, caution should be taken when using present-day halo concentration parameter as a proxy for the halo assembly history, especially if the recent merger history is unknown.

Wang, Kuan↗

DOE OSTI2020

Optimizing LSST observing strategy for weak lensing systematics

ABSTRACT The Legacy Survey of Space and Time (LSST) survey will provide unprecedented statistical power for measurements of dark energy. Consequently, controlling systematic uncertainties is becoming more important than ever. The LSST observing strategy will affect the statistical uncertainty and systematics control for many science cases; here, we focus on weak lensing (WL) systematics. The fact that the LSST observing strategy involves hundreds of visits to the same sky area provides new opportunities for systematics mitigation. We explore these opportunities by testing how different dithering strategies (pointing offsets and rotational angle of the camera in different exposures) affect additive WL shear systematics on a baseline operational simulation, using the ρ-statistics formalism. Some dithering strategies improve systematics control at the end of the survey by a factor of up to ∼3–4 better than others. We find that a random translational dithering strategy, applied with random rotational dithering at every filter change, is the most effective of those strategies tested in this work at averaging down systematics. Adopting this dithering algorithm, we explore the effect of varying the area of the survey footprint, exposure time, number of exposures in a visit, and exposure to the Galactic plane. We find that any change that increases the average number of exposures (in filters relevant to WL) reduces the additive shear systematics. Some ways to achieve this increase may not be favorable for the WL statistical constraining power or for other probes, and we explore the relative trade-offs between these options given constraints on the overall survey parameters.

79 ASTRONOMY AND ASTROPHYSICS↗

DOE OSTI2020

The weak imprint of environment on the stellar populations of galaxies

ABSTRACT We investigate the environmental dependence of the stellar populations of galaxies in Sloan Digital Sky Survey Data Release 7 (SDSS DR7). Echoing earlier works, we find that satellites are both more metal-rich (<0.1 dex) and older (<2 Gyr) than centrals of the same stellar mass. However, after separating star-forming, green valley, and passive galaxies, we find that the true environmental dependence of both stellar metallicity (<0.03 dex) and age (<0.5 Gyr) is in fact much weaker. We show that the strong environmental effects found when galaxies are not differentiated result from a combination of selection effects brought about by the environmental dependence of the quenched fraction of galaxies, and thus we strongly advocate for the separation of star-forming, green valley, and passive galaxies when the environmental dependence of galaxy properties are investigated. We also study further environmental trends separately for both central and satellite galaxies. We find that star-forming galaxies show no environmental effects, neither for centrals nor for satellites. In contrast, the stellar metallicities of passive and green valley satellites increase weakly (<0.05 and <0.08 dex, respectively) with increasing halo mass, increasing local overdensity and decreasing projected distance from their central; this effect is interpreted in terms of moderate environmental starvation (‘strangulation’) contributing to the quenching of satellite galaxies. Finally, we find a unique feature in the stellar mass–stellar metallicity relation for passive centrals, where galaxies in more massive haloes have larger stellar mass (∼0.1 dex) at constant stellar metallicity; this effect is interpreted in terms of dry merging of passive central galaxies and/or progenitor bias.

Trussler, James↗

DOE OSTI2020

Can assembly bias explain the lensing amplitude of the BOSS CMASS sample in a Planck cosmology?

ABSTRACT In this paper, we investigate whether galaxy assembly bias can reconcile the 20–40 ${{\ \rm per\ cent}}$ disagreement between the observed galaxy projected clustering signal and the galaxy–galaxy lensing signal in the Baryon Oscillation Spectroscopic Survey CMASS galaxy sample. We use the suite of abacuscosmos lambda cold dark matter simulations at Planck best-fitting cosmology and two flexible implementations of extended halo occupation distribution (HOD) models that incorporate galaxy assembly bias to build forward models and produce joint fits of the observed galaxy clustering signal and the galaxy–galaxy lensing signal. We find that our models using the standard HODs without any assembly bias generalizations continue to show a 20–40 ${{\ \rm per\ cent}}$ overprediction of the observed galaxy–galaxy lensing signal. We find that our implementations of galaxy assembly bias do not reconcile the two measurements at Planck best-fitting cosmology. In fact, despite incorporating galaxy assembly bias, the satellite distribution parameter, and the satellite velocity bias parameter into our extended HOD model, our fits still strongly suggest a $\sim \! 34{{\ \rm per\ cent}}$ discrepancy between the observed projected clustering and galaxy–galaxy lensing measurements. It remains to be seen whether a combination of other galaxy assembly bias models, alternative cosmological parameters, or baryonic effects can explain the amplitude difference between the two signals.

79 ASTRONOMY AND ASTROPHYSICS↗