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At least 379 records · Page 21

The Effects of Atmospheric Models on the Estimation of Infrasonic Source Functions at the Source Physics Experiment

We invert infrasound signals for an equivalent seismoacoustic source function using different atmospheric models to produce the necessary Green’s functions. The infrasound signals were produced by a series of underground chemical explosions as part of the Source Physics Experiment (SPE). In a previous study, we inverted the infrasound data using so-called predictive atmospheric models, which were based on historic, regional-scaled, publicly available weather observations interpolated onto a 3D grid. For the work presented here, we invert the same infrasound data, but using atmospheric models based on weather data collected in a time window that includes the approximate time of the explosion experiments, which we term postdictive models. We build two versions of the postdictive models for each SPE event: one that is based solely on the regional scaled observations, and one that is based on both regional scaled observations combined with on-site observations obtained by a weather sonde released at the time of the SPE. We then invert the observed data set three times, once for each atmospheric model type. We find that the estimated seismoacoustic source functions are relatively similar in waveform shape regardless of which atmospheric model that we used to construct the Green’s functions. However, we find that the amplitude of the estimated source functions is systematically dependent on the atmospheric model type: using the predictive atmospheric models to invert the data generally yields estimated source functions that are larger in amplitude than those estimated using the postdictive models.

54 ENVIRONMENTAL SCIENCES↗

Statistics of Green's functions on a disordered Cayley tree and the validity of forward scattering approximation

The accuracy of the forward scattering approximation for two-point Green's functions of the Anderson localization model on the Cayley tree is studied. A relationship between the moments of the Green's function and the largest eigenvalue of the linearized transfer-matrix equation is proved in the framework of the supersymmetric functional-integral method. The new large-disorder approximation for this eigenvalue is derived and its accuracy is established. Using this approximation the probability distribution of the two-point Green's function is found and compared with that in the forward scattering approximation (FSA). It is shown that FSA overestimates the role of resonances and thus the probability for the Green's function to be significantly larger than its typical value. The error of FSA increases with increasing the distance between points in a two-point Green's function.

71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗

Approximating and incorporating model uncertainty in an inversion for seismic source functions: Preliminary results

We present preliminary work on propagating model uncertainty into the estimation of the time domain source time functions of the seismic source. Our method is based on an estimated model covariance function, which we estimate from the data. The model covariance function is then used to construct a suite of surrogate Greens functions which we use in a Monte Carlo type inversion scheme. The result is a probability density function of the six independent source time functions, each of which corresponds to an individual component of the seismic moment tensor. We compare the results of our method with those obtained using a computationally expensive finite difference Monte Carlo method and find that our new method produces results that are deficient in low frequencies. The advantage of our new method, which we term the Karhunen-Loeve Monte Carlo (KLMC) method, is that is several orders of magnitude faster than our current method, which uses a finite difference scheme to produce the suite of forward models.

42 ENGINEERING↗

GaAs Neutron Response Functions and Radiation Damage Metrics

The radiation effects community needs clear, well-documented, neutron energy-dependent responses that can be used in assessing radiation-induced material damage to GaAs semiconductors and for correlating observed radiation-induced changes in the GaAs electronic properties with computed damage metrics. In support of the objective, this document provides: a) a clearly defined set of relevant neutron response functions for use in dosimetry applications; b) clear mathematical expressions for the defined response functions; and c) updated quantitative values for the energy- dependent response functions that reflect the best current nuclear data and modelling. This document recaps the legacy response functions. It then surveys the latest nuclear data and updates the recommended response function to support current GaAs damage studies. A detailed tabulation for six of the energy-dependent response functions is provided in an Appendix.

36 MATERIALS SCIENCE↗

Open library of g-functions for 34,321 configurations

Thermal response functions, known as g-functions, are commonly used in ground heat exchanger design tools and whole building energy simulation programs to simulate the ground heat exchanger performance. Calculation of g-functions can be quite computationally time-consuming, particularly as the number of boreholes gets large. However, once the g-function is computed, the actual simulation time can be quite short, particularly if a hybrid time-step (Cullin and Spitler 2011) approach is used. Because of this, pre-computed g-function libraries are commonly used in design tools and building simulation tools. This paper describes development of a new, publicly available library containing g-functions for 34,321 borehole field configurations; for each configuration, gfunctions are provided for 5 depths to allow interpolation between different borehole-to-height ratios. The available configurations include configurations in standard shapes: lines, rectangles, open rectangles, L-shapes, and U-shapes. It also includes new configurations: C-shapes, lopsided-U-shapes, and zoned rectangles, which are rectangular configurations with different interior and perimeter spacing of the boreholes.

Spitler, Jeffery↗

Influence functions for the Delaware Oil and Gas Basin Tower Network

This data consists of influence functions created for the Delaware tower network for the purpose of calculating methane enhancements in the region. Two different footprint models were used. The Lagrangian Particle Dispersion model (LPDM, Uliasz 1993) was run from March 2020-May 2023. The model uses in-house WRF simulations for the meteorological transport as described in Barkley et al., (2023). Nine hundred (900) particles were released during each hourly period and are traced back 72 hours backwards in time. A static binning height of 110 m AGL was used to calculate surface influence. After May 2023, the LPDM simulations were phased out and replaced with influence functions created using HYSPLIT under the STILT configuration (Lin et al., 2003). The STILT influence functions use HRRR for the meteorological transport (Dowell et al., 2022). Nine hundred (900) particles were released during each hourly period and are traced back 72 hours backwards in time. A binning height of half the boundary layer height was used to calculate surface influence. Footprints are currently available from Sept 2020-December 2024 and will be updated periodically as more are generated in time. No STILT influence functions were created for tower site Maljimar, which was decommissioned in March 2022. Lat/Lon grid information for the LPDM influence functions is contained in lpdm-lat-lon-grid.nc. STILT grid information is contained within the influence functions themselves. Tower coordinates and heights can be found in tower-info.csv

Barkley, Z. R.↗

Developing a media formulation to sustain ex vivo chloroplast function

Chloroplasts are critical organelles in plants and algae responsible for accumulating biomass through photosynthetic carbon fixation and cellular maintenance through metabolism in the cell. Chloroplasts are increasingly appreciated for their role in biomanufacturing, as they can produce many useful molecules, and a deeper understanding of chloroplast regulation and function would provide more insight for the biotechnological applications of these organelles. However, traditional genetic approaches to manipulate chloroplasts are slow, and generation of transgenic organisms to study their function can take weeks to months, significantly delaying the pace of research. To develop chloroplasts themselves as a quicker and more defined platform, we isolated chloroplasts from the green algae, Chlamydomonas reinhardtii, and examined their photosynthetic function after extraction. Combined with a metabolic modeling approach using flux-balance analysis, we identified key metabolic reactions essential to chloroplast function and leveraged this information into reagents that can be used in a “chloroplast media” capable of maintaining chloroplast photosynthetic function over time ex vivo compared to buffer alone. We envision this could serve as a model platform to enable more rapid design-build-test-learn cycles to study and improve chloroplast function in combination with genetic modifications and potentially as a starting point for the bottom-up design of a synthetic organelle-containing cell.

Chlamydomonas reinhardtii↗

Contrasting Community Assembly Forces Drive Microbial Structural and Potential Functional Responses to Precipitation in an Incipient Soil System

Microbial communities in incipient soil systems serve as the only biotic force shaping landscape evolution. However, the underlying ecological forces shaping microbial community structure and function are inadequately understood. We used amplicon sequencing to determine microbial taxonomic assembly and metagenome sequencing to evaluate microbial functional assembly in incipient basaltic soil subjected to precipitation. Community composition was stratified with soil depth in the pre-precipitation samples, with surficial communities maintaining their distinct structure and diversity after precipitation, while the deeper soil samples appeared to become more uniform. The structural community assembly remained deterministic in pre- and post-precipitation periods, with homogenous selection being dominant. Metagenome analysis revealed that carbon and nitrogen functional potential was assembled stochastically. Sub-populations putatively involved in the nitrogen cycle and carbon fixation experienced counteracting assembly pressures at the deepest depths, suggesting the communities may functionally assemble to respond to short-term environmental fluctuations and impact the landscape-scale response to perturbations. We propose that contrasting assembly forces impact microbial structure and potential function in an incipient landscape; in situ landscape characteristics (here homogenous parent material) drive community structure assembly, while short-term environmental fluctuations (here precipitation) shape environmental variations that are random in the soil depth profile and drive stochastic sub-population functional dynamics.

16S amplicon sequencing↗

SineKAN: Kolmogorov-Arnold Networks using sinusoidal activation functions

Recent work has established an alternative to traditional multi-layer perceptron neural networks in the form of Kolmogorov-Arnold Networks (KAN). The general KAN framework uses learnable activation functions on the edges of the computational graph followed by summation on nodes. The learnable edge activation functions in the original implementation are basis spline functions (B-Spline). Here, we present a model in which learnable grids of B-Spline activation functions are replaced by grids of re-weighted sine functions (SineKAN). We evaluate numerical performance of our model on a benchmark vision task. We show that our model can perform better than or comparable to B-Spline KAN models and an alternative KAN implementation based on periodic cosine and sine functions representing a Fourier Series. Further, we show that SineKAN has numerical accuracy that could scale comparably to dense neural networks (DNNs). Compared to the two baseline KAN models, SineKAN achieves a substantial speed increase at all hidden layer sizes, batch sizes, and depths. Current advantage of DNNs due to hardware and software optimizations are discussed along with theoretical scaling. Additionally, properties of SineKAN compared to other KAN implementations and current limitations are also discussed.

Reinhardt, Eric↗

Citric Acid Functionalized Natural Fibers to Enhance Thermal Stability and Moisture Resistance in Polylactic Acid Composites

Cellulosic fibers can impart many unique benefits into composite applications, such as reduced weight or structural reinforcement; however, these materials also increase hygroscopicity and decrease thermal stability, restricting broader applications. The present work adapted an experimental process for functionalizing the cellulose surface using citric acid (CA) for three fibers: a 100% cellulose bleached soft Kraft pulp (e.g., creafill) and two natural fibers with similar composition but different fiber morphology, flax fiber and banana fiber. The process uses CA with a sodium hypophosphite (SHP) catalyst to chemically functionalize fiber surfaces, and the reaction mechanism was investigated through Fourier Transform Infrared Spectroscopy (FTIR), which suggested a grafting mechanism rather than a surface-based crosslinking between neighboring sites. Functionalized fibers were compounded into polylactic acid (PLA) at 20 wt.% to better understand how this functionalization might impact critical performance properties like thermal stability, crystallization, thermal mechanical properties, and water uptake of these composites. The study demonstrated varying levels of efficacy for the functionalization of cellulosic fibers with CA/SHP and the fiber with the most open microstructure, e.g., banana fiber, exhibited the largest change in its properties with a 38% reduction in water uptake compared to untreated banana fiber composites. Parallel evaluation of the functionalization process for different fibers demonstrates the importance of fiber morphology on surface modification and can enable their use in composites by demonstrating the efficacy of this potentially low-cost, low-toxicity method for reducing hygroscopicity and improving thermal stability.

citric acid↗

Pre-Bleaching Coral Microbiome Is Enriched in Beneficial Taxa and Functions

Coral reef health is tightly connected to the coral holobiont, which is the association between the coral animal and a diverse microbiome functioning as a unit. The coral holobiont depends on key services such as nitrogen and sulfur cycling mediated by the associated bacteria. However, these microbial services may be impaired in response to environmental changes, such as thermal stress. A perturbed microbiome may lead to coral bleaching and disease outbreaks, which have caused an unprecedented loss in coral cover worldwide, particularly correlated to a warming ocean. The response mechanisms of the coral holobiont under high temperatures are not completely understood, but the associated microbial community is a potential source of acquired heat-tolerance. Here we investigate the effects of increased temperature on the taxonomic and functional profiles of coral surface mucous layer (SML) microbiomes in relationship to coral–algal physiology. We used shotgun metagenomics in an experimental setting to understand the dynamics of microbial taxa and genes in the SML microbiome of the coral Pseudodiploria strigosa under heat treatment. The metagenomes of corals exposed to heat showed high similarity at the level of bacterial genera and functional genes related to nitrogen and sulfur metabolism and stress response. The coral SML microbiome responded to heat with an increase in the relative abundance of taxa with probiotic potential, and functional genes for nitrogen and sulfur acquisition. Coral–algal physiology significantly explained the variation in the microbiome at taxonomic and functional levels. These consistent and specific microbial taxa and gene functions that significantly increased in proportional abundance in corals exposed to heat are potentially beneficial to coral health and thermal resistance.

59 BASIC BIOLOGICAL SCIENCES↗

Natively Periodic Fast Multipole Method: Approximating the Optimal Green’s Function

The fast multipole method (FMM) obeys periodic boundary conditions "natively" if it uses a periodic Green's function for computing the multipole expansion in the interaction zone of each FMM oct-tree node. One can define the "optimal" Green's function for such a method that results in the numerical solution that converges to the equivalent particle-mesh (PM) solution in the limit of sufficiently high order of multipoles. A discrete functional equation for the optimal Green's function can be derived, but is not practically useful as methods for its solution are not known. Instead, this paper presents an approximation for the optimal Green's function that is accurate to better than 10 -3 in ${L}_{\mathrm{MAX}}$ norm and 10 -4 in L 2 norm for practically useful multipole counts. Such an approximately optimal Green's function offers a practical way for implementing the FMM with periodic boundary conditions natively, without the need to compute lattice sums or to rely on hybrid FMM-PM approaches.

46 INSTRUMENTATION RELATED TO NUCLEAR SCIENCE AND ↗

Measuring the Conditional Luminosity and Stellar Mass Functions of Galaxies by Combining the Dark Energy Spectroscopic Instrument Legacy Imaging Surveys Data Release 9, Survey Validation 3, and Year 1 Data

In this investigation, we leverage the combination of the Dark Energy Spectroscopic Instrument (DESI) Legacy Imaging Surveys Data Release 9, Survey Validation 3, and Year 1 data sets to estimate the conditional luminosity functions and conditional stellar mass functions (CLFs and CSMFs) of galaxies across various halo mass bins and redshift ranges. To support our analysis, we utilize a realistic DESI mock galaxy redshift survey (MGRS) generated from a high-resolution Jiutian simulation. An extended halo-based group finder is applied to both MGRS catalogs and DESI observation. By comparing the r- and z-band luminosity functions (LFs) and stellar mass functions (SMFs) derived using both photometric and spectroscopic data, we quantified the impact of photometric redshift (photo-z) errors on the galaxy LFs and SMFs, especially in the low-redshift bin at the low-luminosity/mass end. By conducting prior evaluations of the group finder using MGRS, we successfully obtain a set of CLF and CSMF measurements from observational data. We find that at low redshift, the faint-end slopes of CLFs and CSMFs below ~10 9 h –2 L ⊙ (or h –2 M ⊙ ) evince a compelling concordance with the subhalo mass functions. After correcting the cosmic variance effect of our local Universe following Chen et al., the faint-end slopes of the LFs/SMFs turn out to also be in good agreement with the slope of the halo mass function.

79 ASTRONOMY AND ASTROPHYSICS↗

CAZyme domain architectures suggest fine-scale functional differentiation among anaerobic fungi and bacteria during lignocellulose conversion to volatile fatty acids

Anaerobic fermentation with microbial communities (microbiomes) is an emerging platform for conversion of lignocellulosic biomass to biofuels and bioproducts. The process relies on diverse anaerobic microbes that interact to deconstruct and convert lignocellulosic biomass into a range of products, such as volatile fatty acids (VFAs), which can be achieved by arresting methanogenesis during fermentation. However, defining the distinct functional roles played by various fungi and bacteria during anaerobic biodegradation remains poorly understood. Here, we performed parallel enrichment experiments from cow faeces, goat faeces, and anaerobic digester sludge, selecting for fungal or bacterial dominated communities that convert sorghum biomass into VFAs. Subsequently we reconstructed metabolic networks across these enrichments based on recovered bacterial metagenome-assembled genomes (MAGs) and fungal isolate genomes and profiled their metabolic activity using metatranscriptomics to identify potential functional niches. Our findings implicate diverse bacteria affiliated with the Bacteroidales and Lachnospiraceae in the direct conversion of lignocellulosic biomass to propionate and butyrate, respectively, whereas Neocallimastix-dominated fungal enrichments converted lignocellulose to lactate, acetate and formate. Analysis of carbohydrate-active enzymes (CAZymes) revealed fine-scale differences between microbes that expressed unique multi-functional enzymes linking two or more CAZymes together with distinct carbohydrate binding motifs, implicating lignocellulose structure as a key driver of selection and niche differentiation. Most of these multi-functional enzymes localized complementary degradation functions together, likely conferring synergistic degradation effects within and between microbiome members. We anticipate that these findings will help inform efforts to develop synthetic microbiomes with tailored functionality for low-cost conversion of lignocellulosic biomass to fuels and bio-based chemicals.

Lawson, Christopher E [University of Toronto;]↗

Mapping the functional landscape of the receptor binding domain of T7 bacteriophage by deep mutational scanning

The interaction between a bacteriophage and its host is mediated by the phage's receptor binding protein (RBP). Despite its fundamental role in governing phage activity and host range, molecular rules of RBP function remain a mystery. Here, we systematically dissect the functional role of every residue in the tip domain of T7 phage RBP (1660 variants) by developing a high-throughput, locus-specific, phage engineering method. This rich dataset allowed us to cross compare functional profiles across hosts to precisely identify regions of functional importance, many of which were previously unknown. Substitution patterns showed host-specific differences in position and physicochemical properties of mutations, revealing molecular adaptation to individual hosts. We discovered gain-of-function variants against resistant hosts and host-constricting variants that eliminated certain hosts. To demonstrate therapeutic utility, we engineered highly active T7 variants against a urinary tract pathogen. Our approach presents a generalized framework for characterizing sequence–function relationships in many phage–bacterial systems.

59 BASIC BIOLOGICAL SCIENCES↗

The discrete Green's function paradigm for two-way coupled Euler-Lagrange simulation

We outline a methodology for the simulation of particle-laden flows whereby the dispersed and fluid phases are two-way coupled. The drag force which couples fluid and particle momentum depends on the undisturbed fluid velocity at the particle location, and this latter quantity requires modelling. We demonstrate that the undisturbed fluid velocity, in the low particle Reynolds number limit, can be related exactly to the discrete Green's function of the discrete Stokes equations. The method is general in that it can be extended to other partial differential equations which may be associated with particle-laden flows, such as the thermal energy equation or Maxwell's equations. In this work, we demonstrate the method of discrete Green's functions by obtaining these functions for the Navier-Stokes equations at low particle Reynolds number in a two-plane channel geometry. We perform verification at low and finite particle Reynolds number for the case of a point-particle settling under gravity parallel to a plane wall, for different wall normal separations. In comparing to other point-particle schemes the discrete Green's function approach is the most robust at low particle Reynolds number, accurate at all wall-normal separations and is the most accurate in the near wall region at finite Reynolds number. We discuss how the accuracy away from the wall at finite Reynolds number could be improved by appealing to Oseen-like discrete Green's functions. Finally we demonstrate that the discrete Green's function approach can have important implications on statistics of particle-laden turbulent channel flow.

42 ENGINEERING↗

Enabling Marine Energy Integration for Ocean Observing: Functional Requirements

Marine renewable energy (i.e., wave, tidal or ocean current, thermal gradient, and salinity gradient) or MRE can revolutionize ocean observing capabilities. Five use cases representing a range of ocean observing platforms were developed based on end-user feedback. Drawing from these use cases, common needs or functional requirements were developed to help guide the integration of MRE power delivery for ocean observation structures and functions. The functional requirements were determined from descriptions of the use cases, specifications of hardware that are used or closely associated with existing ocean observation platforms, and direct feedback from ocean observation sensor/platform developers and users. Twenty types of functional requirements were identified, including those associated with power and energy use; physical system requirements; temperature and depth; electrical, acoustic, and motion interference; and reliability. Each set of functional requirements is illustrated as features of the use cases. By defining functional requirements for MRE technology integration in ocean observing platforms, and focusing on end-user requirements, barriers to developing MRE-driven ocean observation missions can be reduced.

Cavagnaro, Robert J.↗

Functionalized Magnetic Nanoparticles for Technetium Sequestration from Groundwater

Technetium 99 (Tc) is among the most common environmental contaminants at DOE sites and one of the most common risk drivers in low- and high-level waste disposal sites. The majority of Tc is generated from anthropogenic sources, such as nuclear power plants, global weapons, nuclear storage facilities and medical applications. Through these sources, Tc contamination has been unintentionally introduced in to the environment. The most common chemical form of Tc is Tc(VII)O{sub 4}{sup -}. Due to its high solubility and mobility, Tc can enter the food chain and cause adverse health effects to humans. Currently, ion exchange resins and reduction processes are the most common approaches for Tc immobilization. Although these techniques have shown to be effective, they also possess major drawbacks, such as high cost, low adsorption capacity, and complex creation and maintenance. Therefore, development of more efficient and simple technologies for the remediation of Tc-contaminated systems are needed. Functionalized magnetic nanoparticles have been used to remove organic and inorganic contaminants from water resources. These nanoparticles have attracted extensive attention as an adsorbent material due to their large surface area, high efficiency, low-cost, easy functionalization and separation with a magnet. This study seek to develop functionalized magnetic iron oxide nanoparticles for the efficient removal of Tc and other heavy metal contaminants from water resources under ambient conditions. Objectives: Synthesize magnetic iron oxide nanoparticles and functionalize their surface with Cetyltrimethylammonium Bromide (CTAB) and tetraethyl-orthosilicate (TEOS). Characterize the synthesized nanoparticles using scanning electron microscopy (SEM) coupled with energy dispersive X-ray spectroscopy (EDS), Dynamic Light Scattering (DLS) and Zeta PALS. Perform adsorption studies to evaluate their adsorption behavior and capacity for (a) Technetium using Rhenium (ReO{sub 4}{sup -}) as a surrogate and (b) heavy metals, e.g. Cu{sup 2+}. Conclusions: Magnetic iron oxide nanoparticles were successfully functionalized with CTAB and TEOS. The functionalization of the iron oxide nanoparticles affects their surface charge and their hydrodynamic diameter. The addition of CTAB or TEOS decreased the hydrodynamic diameter of the nanoparticles due to repulsive and steric forces. The SEM micrographs show spherical nanoparticles of different sizes. The EDX analysis shows the presence of iron and oxygen from the iron oxide crystalline structure, and the different constituents of the CTAB and TEOS molecules. Proof-of-concept shows the successful adsorption of rhenium (ReO{sub 4}{sup -}) and copper Cu{sup 2+}) onto CTAB-Fe{sub 2}O{sub 3} and TEOS-Fe{sub 2}O{sub 3} respectively.

12 MANAGEMENT OF RADIOACTIVE AND NON-RADIOACTIVE W↗