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At least 109 records · Page 6

Tandem repeats in giant archaeal Borg elements undergo rapid evolution and create new intrinsically disordered regions in proteins

Borgs are huge, linear extrachromosomal elements associated with anaerobic methane-oxidizing archaea. Striking features of Borg genomes are pervasive tandem direct repeat (TR) regions. Here, we present six new Borg genomes and investigate the characteristics of TRs in all ten complete Borg genomes. We find that TR regions are rapidly evolving, recently formed, arise independently, and are virtually absent in host Methanoperedens genomes. Flanking partial repeats and A-enriched character constrain the TR formation mechanism. TRs can be in intergenic regions, where they might serve as regulatory RNAs, or in open reading frames (ORFs). TRs in ORFs are under very strong selective pressure, leading to perfect amino acid TRs (aaTRs) that are commonly intrinsically disordered regions. Proteins with aaTRs are often extracellular or membrane proteins, and functionally similar or homologous proteins often have aaTRs composed of the same amino acids. We propose that Borg aaTR-proteins functionally diversify Methanoperedens and all TRs are crucial for specific Borg–host associations and possibly cospeciation.

59 BASIC BIOLOGICAL SCIENCES↗

System and method to facilitate a search for a hybrid-manufacturing process plan

One embodiment of the present disclosure provides a system and method for facilitating a search for a hybrid-manufacturing process plan for manufacturing an object. During operation, the system can obtain a set of partial order constraints constraining the order in which a set of at least two manufacturing actions, corresponding to addition or removal of predefined regions of space, appear in a process plan. The system can constrain, based on the set of partial order constraints, a search space. The search space can correspond to a tree in which the nodes represent the object's state and the edges represent available actions at each node. The system can then determine a set of optimized process plans represented by orderings of the actions, corresponding to paths on the search tree, that produce the desired final state in a cost-effective manner.

Crawford, Lara S.↗

Efficient proximal subproblem solvers for a nonsmooth trust-region method

In [R. J. Baraldi and D. P. Kouri, Mathematical Programming, (2022), pp. 1-40], we introduced an inexact trust-region algorithm for minimizing the sum of a smooth nonconvex and nonsmooth convex function. The principle expense of this method is in computing a trial iterate that satisfies the so-called fraction of Cauchy decrease condition—a bound that ensures the trial iterate produces sufficient decrease of the subproblem model. In this paper, we expound on various proximal trust-region subproblem solvers that generalize traditional trust-region methods for smooth unconstrained and convex-constrained problems. We introduce a simplified spectral proximal gradient solver, a truncated nonlinear conjugate gradient solver, and a dogleg method. Finally, we compare algorithm performance on examples from data science and PDE-constrained optimization.

97 MATHEMATICS AND COMPUTING↗

Clear Sky Tampa Bay: Tampa Bay Regional Policy Landscape Analysis (Florida Energy Resilience Policy Landscape) [Slides]

This deck focuses on policies and programs that may enable, constrain, or inform the deployment of solar and storage for resilience in the Tampa Bay Region. This deck also reviews planning approaches within the Tampa Bay Region to ensure that resources developed under the Clear Sky Tampa Bay project are consistent with established practice and relevant to regional practitioners.

14 SOLAR ENERGY↗

Robust Parameter Design on Dual Stochastic Response Models With Constrained Bayesian Optimization

In engineering system design, minimizing the variations of the quality measurements while guaranteeing their overall quality up to certain levels, namely the robust parameter design (RPD), is crucial. Recent works have dealt with the design of a system whose response-control variables relationship is a deterministic function with a complex shape and function evaluation is expensive. In this work, we propose a Bayesian optimization method for the RPD of stochastic functions. Dual stochastic response models are carefully designed for stochastic functions. The heterogeneous variance of the sample mean is addressed by the predictive mean of the log variance surrogate model in a two-step approach. We establish an acquisition function that favors exploration across the feasible and optimality-improvable regions to effectively and efficiently solve the stochastic constrained optimization problem. Further, the performance of our proposed method is demonstrated by the extensive numerical and case studies. Note to Practitioners-Many manufacturing processes involve undesirable variations, which create variations in the final products. For example, many emerging manufacturing processes, such as nanomanufacturing, involve complex physical and chemical dynamics and transformation, creating variations in the manufacturing output. In such processes, it is crucial to design the manufacturing processes or products so that they have minimum variations in their quality. Meanwhile, it is also important to maintain the overall quality of the designed processes or products. Furthermore, acquiring data from many advanced manufacturing processes is often very costly, especially in the designing stage. In this work, we propose a data-driven method that automatically finds the best setting of manufacturing processes or products with the minimum variations of quality and a given constraint on the average quality satisfied. Our proposed method is used before conducting every experiment; It analyzes the historical data from previous experiments and provides a setting to be used in the next experiment. Our proposed method efficiently utilizes the historical data, and thus finds the best robust setting by conducting only a small number of experiments.

42 ENGINEERING↗

Near-Term Reliability and Resilience (NTRR) (Final Report)

The Near-Term Reliability and Resiliency (NTRR) was awarded in December 2020 as an inter-lab project to examine the reliability and resilience of the electricity grid and natural gas transportation availability. The project builds on studies conducted by The North American Electric Reliability Corporation (NERC), the U.S. Department of Energy (DOE), and other non-governmental research and operational focused on reliability and resilience analyses challenges. The research was conceived to address near-term scenarios (within 10 years), when many local and regional policy transitions could begin to impact grid reliability, resilience, and supporting infrastructure availability. To integrate the natural gas interdependency, the team began with the generating capacity and demand projections from the 2020 NERC Long-Term Reliability Assessment and the Bulk Electric System (BES) transmission topologies defined in the Western Electricity Coordinating Council (WECC) Anchor Data Set, Eastern Interconnection Reliability Assessment Group Multi-Regional Modeling Working Group (ERAG/MMWG) Data Set, the team calculated baseline regional power sector gas demands from present electricity delivery year through the end of delivery year 2030/31 by applying security constrained economic dispatch. This demand was compiled along with demand projections for regional residential, commercial, and industrial natural gas demands from the most recent Energy Information Administration (EIA) Annual Energy Outlook Reference Case into Deloitte’s MarketBuilder® North American Gas Model. Through the application of these demands, MarketBuilder® was projected the topology of natural gas flows in the natural gas pipeline network across the interconnected North American system along with regional natural gas prices that may be seen by market participants in future years Additionally, contingencies and sensitivities focused on the built models of the Eastern Interconnection (EI) and Western Interconnection (WI). They address challenges from the following with the outcomes being an identification of performance under the extreme conditions and an identification of potential grid weaknesses that should be addressed to mitigate the reduced performance and improve the resilience and reliability of the specific regions as well as the National Grid: • Weather events including extreme heat, extreme cold, high wind, no wind, wind and solar forecasting errors, and wildfires. • Gas availability, factoring in supply disruption (contractual and physical), seasonal availability constraints, and infrastructure limitations; and • Transmission availability and congestion.

03 NATURAL GAS↗

Toward Robust and Routine Determination of Mw for Small Earthquakes: Application to the 2020 Mw 5.7 Magna, Utah, Seismic Sequence

To better characterize seismic hazard, particularly, for induced seismicity, there is an increasing interest in methods to estimate moment magnitude (M w ) for small earthquakes. M w is generally preferred over other magnitude types, but, it is difficult to estimate M w for earthquakes with local magnitude (M L ) <3-3.5, using conventional moment tensor (MT) inversion. The 2020 M ww 5.7 Magna, Utah, seismic sequence provides an opportunity to illustrate and evaluate the value of spectral methods for this purpose. Starting with a high-quality seismic catalog of 2103 earthquakes (M L <5.6), we estimate M w using two independent spectral methods—one based on direct waves, yielding M w,direct , and the other based on coda waves, yielding M w,coda . For the direct-wave method, we present a non-parametric (NP) inversion scheme that solves for apparent geometrical spreading, G(R), and site effects (S), similar to other NP procedures that have been used to calibrate regional M L scales. The NP inversion is constrained using M ws derived from MTs for nine events in the Magna sequence. We recover statistically robust and physically reasonable G(R) and S and compute M w,direct for 635 Magna earthquakes down to M L 0.7. For the coda-wave method, we consider two separate calibration schemes involving previous MT solutions and compute M w,coda for 311 earthquakes down to M L 1.0. For 280 of the events that were processed with both methods—M w,direct and M w,coda —are strongly correlated (r = 0.98), with a mean difference of only 0.05. We compare M w,direct and M w,coda with M L and find reasonably good agreement for M L <3.6 with the theoretically predicted relationship of M w =(2/3)M L +C, in which C is a regional constant. Our results imply that seismic network operators can use spectral-based M w estimates to replace M L estimates for events with M L ≥1.0, and possibly smaller. The main requirement is the existence of a small number of MT solutions for calibration purposes.

58 GEOSCIENCES↗

Mapping Permafrost Variability and Degradation Using Seismic Surface Waves, Electrical Resistivity, and Temperature Sensing: A Case Study in Arctic Alaska

Subsurface processes significantly influence surface dynamics in permafrost regions, necessitating utilizing diverse geophysical methods to reliably constrain permafrost characteristics. This research uses multiple geophysical techniques to explore the spatial variability of permafrost in undisturbed tundra and its degradation in disturbed tundra in Utqiagvik, Alaska. Here, we integrate multiple quantitative techniques, including multichannel analysis of surface waves (MASW), electrical resistivity tomography (ERT), and ground temperature sensing, to study heterogeneity in permafrost’s geophysical characteristics. MASW results reveal active layer shear wave velocities (V s ) between 240 and 370 m/s, and permafrost V s between 450 and 1,700 m/s, typically showing a low-high-low velocity pattern. Additionally, we find an inverse relationship between in situ V s and ground temperature measurements. The V s profiles along with electrical resistivity profiles reveal cryostructures such as cryopeg and ice-rich zones in the permafrost layer. The integrated results of MASW and ERT provide valuable information for characterizing permafrost heterogeneity and cryostructure. Corroboration of these geophysical observations with permafrost core samples’ stratigraphies and salinity measurements further validates these findings. This combination of geophysical and temperature sensing methods along with permafrost core sampling confirms a robust approach for assessing permafrost’s spatial variability in coastal environments. Our results also indicate that civil infrastructure systems such as gravel roads and pile foundations affect permafrost by thickening the active layer, lowering the V s , and reducing heterogeneity. We show how the resulting V s profiles can be used to estimate key parameters for designing buildings in permafrost regions and maintaining existing infrastructure in polar regions.

54 ENVIRONMENTAL SCIENCES↗

Modelling the nonlinear plasma response to externally applied three-dimensional fields with the Stepped Pressure Equilibrium Code

Small-amplitude, symmetry-breaking magnetic field perturbations, including resonant magnetic perturbations (RMPs) and error fields, can profoundly impact plasma properties in both tokamaks and stellarators. In this work, we perform the first comparison between the Stepped Pressure Equilibrium Code (SPEC) (a comparatively fast and efficient equilibrium code based on energy-minimisation principles) and M3D-C 1 (a high-fidelity albeit computationally expensive initial-value extended-magnetohydro-dynamic (MHD) code) to assess the conditions under which SPEC can be used to model the nonlinear, non-ideal plasma response to an externally applied (m = 2,n = 1) RMP field in an experimentally relevant geometry. We find that SPEC is able to capture the plasma response in the weakly nonlinear regime – meaning perturbation amplitudes below the threshold for break up of the separatrix and onset of secondary magnetic island formation – when around half of the total toroidal flux is enclosed in the volume containing the q = 2 resonant surface. Further, the observed dependence of SPEC solutions on input parameters, including toroidal flux and the number of volumes into which the plasma is partitioned, indicates that additional exploration of the underlying Multi-Region Relaxed MHD physics model is needed to constrain the choice of parameters. Nonetheless, this work suggests promising applications of SPEC to optimisation and fusion plasma design.

70 PLASMA PHYSICS AND FUSION TECHNOLOGY↗

Rapid early gas accretion for the inner Galactic disc: A case for short accretion timescale

Recent observations of the Milky Way and galaxies at high redshifts suggest that galaxy discs were already in place soon after the Big Bang. While the gas infall history of the Milky Way in the inner disc has long been assumed to be characterised by a short accretion timescale, this has not been directly constrained using observations. Using data for the inner regions of the Milky Way recently produced by APOGEE and Gaia and of unprecedented quantity and quality, we aim to derive strong constraints on the infall history of the inner (< 6 kpc) Galaxy (with a focus on stars between 4 and 6 kpc, which we show is an appropriate proxy for the entire inner disc). We implemented gas infall into a chemical evolution model of the Galaxy disc, and used a Schmidt–Kennicutt law to connect the infall to the star formation. We explore a number of models, and two different formulations of the infall law. In one formulation, the infall is non-parametric, and in the other the infall has an explicitly exponential form. We fit the model parameters to the time–[Si/Fe] distribution of solar vicinity stars, and the metallicity and [Si/Fe] distribution function of stars with a galactocentric radius of between 4 and 6 kpc from APOGEE. Our results point to a fast, early gas accretion, and an upper limit on the accretion timescale of around 2 Gyr in the inner disc of the Milky Way. This suggests that at least half the baryons were in place within 2–3 Gyr of the Big Bang, and that half the stars of the inner disc formed within the first 5 Gyr, during the thick disc formation phase. This implies that the stellar mass of the inner disc is dominated by the thick disc, supporting our previous work, and that the gas accretion onto the inner disc was rapid and early.

79 ASTRONOMY AND ASTROPHYSICS↗

Long-term multi-wavelength study of 1ES 0647+250

The BL Lac object 1ES 0647+250 is one of the few distant γ-ray emitting blazars detected at very high energies (VHEs; &100 GeV) during a non-flaring state. It was detected with the MAGIC telescopes during a period of low activity in the years 2009-2011 as well as during three flaring activities in the years 2014, 2019, and 2020, with the highest VHE flux in the last epoch. An extensive multi-instrument data set was collected as part of several coordinated observing campaigns over these years. We aim to characterise the long-term multi-band flux variability of 1ES 0647+250, as well as its broadband spectral energy distribution (SED) during four distinct activity states selected in four different epochs, in order to constrain the physical parameters of the blazar emission region under certain assumptions. We evaluated the variability and correlation of the emission in the different energy bands with the fractional variability and the Z transformed discrete correlation function, as well as its spectral evolution in X-rays and γ rays. Owing to the controversy in the redshift measurements of 1ES 0647+250 reported in the literature, we also estimated its distance in an indirect manner through a comparison of the GeV and TeV spectra from simultaneous observations with Fermi-LAT and MAGIC during the strongest flaring activity detected to date. Moreover, we interpret the SEDs from the four distinct activity states within the framework of one-component and two-component leptonic models, proposing specific scenarios that are able to reproduce the available multi-instrument data. We find significant long-term variability, especially in X-rays and VHE γ rays. Furthermore, significant (3-4σ) correlations were found between the radio, optical, and high-energy (HE) γ-ray fluxes, with the radio emission delayed by about ~400 days with respect to the optical and γ-ray bands. The spectral analysis reveals a harder-when-brighter trend during the non-flaring state in the X-ray domain. However, no clear patterns were observed for either the enhanced states or the HE (30 MeV < E < 100 GeV) and VHE γ-ray emission of the source. The indirect estimation of the redshift yielded a value of z = 0.45 ± 0.05, which is compatible with some of the values reported in the literature. The SEDs related to the low-activity state and the three flaring states of 1ES 0647+250 can be described reasonably well with the both one-component and two-component leptonic scenarios. However, the long-term correlations indicate the need for an additional radio-producing region located about 3.6 pc downstream from the gamma-ray producing region.

79 ASTRONOMY AND ASTROPHYSICS↗

The cosmic web around the Coma cluster from constrained cosmological simulations

Galaxy clusters in the Universe occupy the important position of nodes of the cosmic web. They are connected among them by filaments, elongated structures composed of dark matter, galaxies, and gas. The connection of galaxy clusters to filaments is important, as it is related to the process of matter accretion onto the former. For this reason, investigating the connections to the cosmic web of massive clusters, especially well-known ones for which a lot of information is available, is a hot topic in astrophysics. In a previous work, we performed an analysis of the filament connections of the Coma cluster of galaxies, as detected from the observed galaxy distribution. In this work we resort to a numerical simulation whose initial conditions are constrained to reproduce the local Universe, including the region of the Coma cluster to interpret our observations in an evolutionary context. We detect the filaments connected to the simulated Coma cluster and perform an accurate comparison with the cosmic web configuration we detect in observations. We perform an analysis of the halos’ spatial and velocity distributions close to the filaments in the cluster outskirts. We conclude that, although not significantly larger than the average, the flux of accreting matter on the simulated Coma cluster is significantly more collimated close to the filaments with respect to the general isotropic accretion flux. This paper is the first example of such a result and the first installment in a series of publications which will explore the build-up of the Coma cluster system in connection to the filaments of the cosmic web as a function of redshift.

79 ASTRONOMY AND ASTROPHYSICS↗

How can a diverse set of integral and semi-integral measurements inform identification of discrepant nuclear data?

Nuclear data are used for a variety of applications, including criticality safety, reactor performance, and material safeguards. Despite the breadth of use-cases, the effective neutron multiplication factor, keff, of ICSBEP critical assemblies are primarily used for nuclear data validation; these are sensitive to specific energy regions and nuclides and are unable to uniquely constrain nuclear data. As a consequence, general-purpose nuclear data libraries, such as ENDF/B-VIII.0, may have deficiencies that, while not apparent in criticality applications, negatively impact other applications, such as non-destructive analysis of special nuclear material and neutron diagnosed subcritical experiments. Recent work by the Experiments Underpinned by Computational Learning for Improvements in Nuclear Data (EUCLID) project developed a machine learning tool, RAFIEKI, which uses random forests and the SHAP metric to determine which nuclear data contribute most to predicted bias between measured and simulated responses (e.g. keff). This paper contrasts RAFIEKI analysis applied to keff only against RAFIEKI analysis with keff paired with either LLNL pulsed sphere measurements or subcritical benchmarks. Two examples show that a) including pulsed sphere measurements substantially increases 9Be nuclear data importance to bias between 2 and 15 MeV, and b) including subcritical benchmarks has the potential for disentangling compensating errors between 240Pu (n,el) and (n,il) cross-sections between 0.1 and 10 MeV. These results show that RAFIEKI analysis applied to response sets that include, but go beyond, keff can aid nuclear data evaluators in identifying issues in nuclear data.

73 NUCLEAR PHYSICS AND RADIATION PHYSICS↗

NuSTAR Bounds on Radiatively Decaying Particles from M82

Axions and other putative feebly interacting particles with a mass of tens to several hundreds of keVs can be produced in stellar cores with a Lorentz boost factor E a / m a ≲ 10 . Thus, starburst galaxies such as M82 are efficient factories of slow axions. Their decay a → γ γ would produce a large flux of x-ray photons, peaking around 100 keV and spread around the Galaxy by an angle that can be relatively large. We use observations of the Nuclear Spectroscopic Telescope Array mission to show that the absence of these features can constrain 30–500 keV axion masses into uncharted regions for axion-photon coupling of g a γ ∼ 10 − 10 – 10 − 12 GeV − 1 . Our argument can be applied to other heavy feebly interacting particles and astrophysical sources that are hot enough to produce them, yet cold enough to avoid large boost factors which slow down the decay. Published by the American Physical Society 2025

Candón, Francisco R. (ORCID:0009000231999278)↗

Potential Impacts of Assimilating All-sky Satellite Infrared Radiances on Convection-Permitting Analysis and Prediction of Tropical Convection

Geostationary infrared satellite observations are spatially dense [< 1/(20 km)2] and temporally frequent (< 1/hour). These suggest the possibility of using these observations to constrain sub-synoptic features over data sparse regions, such as tropical oceans. In this study, the potential impacts of assimilating water vapor channel brightness temperature (WV-BT) observations from the geostationary Meteorological Satellite 7 (Meteosat-7) on tropical convection analysis and prediction were systematically examined through a series of ensemble data assimilation experiments. WV-BT observations were assimilated hourly into convection-permitting ensembles using Penn State’s ensemble square root filter (EnSRF). Comparisons against independently observed Meteosat-7 window channel brightness temperature (Window-BT) show that the assimilation of WV-BT generally improved the intensities and locations of large-scale cloud patterns at spatial scales larger than 100 km. However, comparisons against independent soundings indicate that the EnSRF analysis produced a much stronger dry bias than the no data assimilation experiment. This strong dry bias is associated with the use of the simulated WV-BT from the prior mean during the EnSRF analysis step. A stochastic variant of the ensemble Kalman filter (NoMeanSF) is proposed. The NoMeanSF algorithm was able to assimilate the WV-BT without causing such a strong dry bias and the quality of the analyses’ horizontal cloud pattern is similar to EnSRF’s analyses. Finally, deterministic forecasts initiated from the NoMeanSF analyses possess better horizontal cloud patterns above 500 km than those of the EnSRF. These results suggest that it might be better to assimilate all-sky WV-BT through the NoMeanSF algorithm than EnSRF algorithm.

Chan, Man-Yau↗

Optimization-based algorithms for nonlinear mechanics and frictional contact

An optimization-based strategy for solving nonlinear mechanics problems is proposed. In contrast to typical nonlinear equation solver algorithms that aim to find zeros in the residual force function, we minimize an energy (or energy-like) function to encourage solutions which are locally stable equilibria. These smooth and potentially non-convex objective functions are minimized using a preconditioned conjugate-gradient trust-region algorithm. Contact is formulated as an inequality constrained minimization problem, and is solved with an augmented Lagrangian algorithm. Friction is included in the approach via a regularized quasi-potential energy, and other dissipative behavior is included through the use of variational constitutive updates. Finally, to accelerate convergence rates for the Lagrange multipliers, we propose a novel multiplier update algorithm utilizing the Fischer-Burmeister function, and demonstrate super-linear solver convergence for some applications.

42 ENGINEERING↗

Wolf-Rayet Galaxies in SDSS-IV MaNGA. II. Metallicity Dependence of the High-mass Slope of the Stellar Initial Mass Function

As hosts of living high-mass stars, Wolf-Rayet (WR) regions or WR galaxies are ideal objects for constraining the high-mass end of the stellar initial mass function (IMF). We construct a large sample of 910 WR galaxies/regions that cover a wide range of stellar metallicity (from Z ~ 0.001 to 0.03) by combining three catalogs of WR galaxies/regions previously selected from the SDSS and SDSS-IV/MaNGA surveys. We measure the equivalent widths of the WR blue bump at ~4650 Å for each spectrum. They are compared with predictions from stellar evolutionary models Starburst99 and BPASS, with different IMF assumptions (high-mass slope α of the IMF ranging from 1.0 to 3.3). Both singular evolution and binary evolution are considered. We also use a Bayesian inference code to perform full spectral fitting to WR spectra with stellar population spectra from BPASS as fitting templates. We then make a model selection among different α assumptions based on Bayesian evidence. These analyses have consistently led to a positive correlation of the IMF high-mass slope α with stellar metallicity Z, i.e., with a steeper IMF (more bottom-heavy) at higher metallicities. Specifically, an IMF with α = 1.00 is preferred at the lowest metallicity (Z ~ 0.001), and an Salpeter or even steeper IMF is preferred at the highest metallicity (Z ~ 0.03). These conclusions hold even when binary population models are adopted.

79 ASTRONOMY AND ASTROPHYSICS↗

Modeling Electron Acceleration and Transport in the Early Impulsive Phase of the 2017 September 10th Solar Flare

The X8.2-class limb flare on 2017 September 10 is among the best studied solar flare events owing to its great similarity to the standard flare model and the broad coverage by multiple spacecraft and ground-based observations. These multiwavelength observations indicate that electron acceleration and transport are efficient in the reconnection and flare looptop regions. However, there lacks a comprehensive model for explaining and interpreting the multi-faceted observations. In this work, we model the electron acceleration and transport in the early impulsive phase of this flare. We solve the Parker transport equation that includes the primary acceleration mechanism during magnetic reconnection in the large-scale flare region modeled by MHD simulations. We find that electrons are accelerated up to several MeV and fill a large volume of the reconnection region, similar to the observations shown in microwaves. The electron spatial distribution and spectral shape in the looptop region agree well with those derived from the microwave and hard X-ray emissions before magnetic islands grow large and dominate the acceleration. Future emission modelings using the electron maps will enable direct comparison with microwave and hard X-ray observations. These results shed new light on the electron acceleration and transport in a broad region of solar flares within a data-constrained realistic flare geometry.

79 ASTRONOMY AND ASTROPHYSICS↗