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At least 109 records · Page 6

BayFlux: A Bayesian method to quantify metabolic Fluxes and their uncertainty at the genome scale

Metabolic fluxes, the number of metabolites traversing each biochemical reaction in a cell per unit time, are crucial for assessing and understanding cell function. 13 C Metabolic Flux Analysis ( 13 C MFA) is considered to be the gold standard for measuring metabolic fluxes. 13 C MFA typically works by leveraging extracellular exchange fluxes as well as data from 13 C labeling experiments to calculate the flux profile which best fit the data for a small, central carbon, metabolic model. However, the nonlinear nature of the 13 C MFA fitting procedure means that several flux profiles fit the experimental data within the experimental error, and traditional optimization methods offer only a partial or skewed picture, especially in “non-gaussian” situations where multiple very distinct flux regions fit the data equally well. Here, we present a method for flux space sampling through Bayesian inference (BayFlux), that identifies the full distribution of fluxes compatible with experimental data for a comprehensive genome-scale model. This Bayesian approach allows us to accurately quantify uncertainty in calculated fluxes. We also find that, surprisingly, the genome-scale model of metabolism produces narrower flux distributions (reduced uncertainty) than the small core metabolic models traditionally used in 13 C MFA. The different results for some reactions when using genome-scale models vs core metabolic models advise caution in assuming strong inferences from 13 C MFA since the results may depend significantly on the completeness of the model used. Based on BayFlux, we developed and evaluated novel methods (P- 13 C MOMA and P- 13 C ROOM) to predict the biological results of a gene knockout, that improve on the traditional MOMA and ROOM methods by quantifying prediction uncertainty.

59 BASIC BIOLOGICAL SCIENCES↗

Apodization Specific Fitting for Improved Resolution, Charge Measurement, and Data Analysis Speed in Charge Detection Mass Spectrometry

Short-time Fourier transforms with short segment lengths are typically used to analyze single ion charge detection mass spectrometry (CDMS) data either to overcome effects of frequency shifts that may occur during the trapping period or to more precisely determine the time at which an ion changes mass or charge, or enters an unstable orbit. The short segment lengths can lead to scalloping loss unless a large number of zero-fills are used, making computational time a significant factor in real-time analysis of data. Apodization specific fitting leads to a 9-fold reduction in computation time compared to zero-filling to a similar extent of accuracy. This makes possible real-time data analysis using a standard desktop computer. Rectangular apodization leads to higher resolution than the more commonly used Gaussian or Hann apodization and makes it possible to separate ions with similar frequencies, a significant advantage for experiments in which the masses of many individual ions are measured simultaneously. Equally important is a >20% increase in S/N obtained with rectangular apodization compared to Gaussian or Hann, which directly translates to a corresponding improvement in accuracy of both charge measurements and ion energy measurements that rely on the amplitudes of the fundamental and harmonic frequencies. Finally, combined with computing the fast Fourier transform in a lower-level language, this fitting procedure eliminates computational barriers and should enable real-time processing of CDMS data on a laptop computer.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Thermal expansion of 4H and 6H SiC from 5 K to 340 K

The first thermal expansion measurements of the 4H and 6H polytypes of SiC below room temperature are reported. The measurements were carried out on single-crystal specimens using high-resolution capacitive-based dilatometry. For both polytypes, the thermal expansion coefficient is below 2.4 × 10 -6 1/K near room temperature. No phase transitions are observed over the 5 K to 340 K temperature range of the measurements. The thermal expansion coefficient α of 4H SiC is slightly anisotropic for measurements parallel and perpendicular to the crystallographic c axis with α ∥ about 2.2 × 10 -7 1/K larger than α ⟂ near room temperature. For 6H SiC no discernible anisotropy is observed. The differences in anisotropy can be understood by considering the ratio of hexagonal to cubic bonds of each polytype. Narrow regions with negative thermal expansion that are within the limits of our resolution (~ 1 x 10 -8 ) are observed in the vicinity of 30 K for both specimens. In conclusion, tabulated data, polynomial fits, fit parameters, and comparison to data based on lattice-parameter measurements are provided.

36 MATERIALS SCIENCE↗

Measurements of three-flavor neutrino oscillations from a PISCES two-detector fit to the NOvA Experiment data

NOvA is a long-baseline neutrino oscillation experiment with two functionally identical detectors: a Near Detector (ND) at Fermilab, placed 1 km from the neutrino source, and a Far Detector (FD) located 810 km away from the ND in Minnesota. NOvA s primary physics goals are to measure the neutrino oscillation parameters $\theta_{23}$ and $\Delta m^2_{32}$ with high precision, determine the neutrino mass hierarchy, and constrain the value of $\delta_{CP}$, primarily via the study of muon neutrino to electron neutrino oscillation. Extracting values for oscillation parameters from fits to data usually relies on treating systematic uncertainties as nuisance parameters, a strategy that suffers from poor scalability as the number of uncertainties becomes larger. This work introduces PISCES (Parameter Inference with Systematic Covariance and Exact Statistics), a novel method that circumvents this scalability problem by encoding systematic uncertainties into a covariance matrix. PISCES utilizes a nested minimization in which optimal systematic pulls are first computed using the covariance matrix in an inner minimization step, then the oscillation parameters are profiled over in the outer minimization. PISCES also uses a Poisson Likelihood term, making it ideal for the inclusion of low-statistic samples in the fits. PISCES is a flexible framework that also supports complex fits, such as a joint Near and Far detector fit. In the standard NOvA analysis, oscillation parameters are extracted using an extrapolation technique in which the ND data indirectly constrain the FD prediction via a ratio method. PISCES, on the other hand, enables a simultaneous ND+FD fit, allowing the high-statistics ND data to directly constrain systematic uncertainties across all samples. This thesis presents the full PISCES joint ND+FD fit for the NOvA three-flavor analysis, details its implementation, and evaluates its performance through extensive robustness tests and fake data studies. It also provides a comparison between the PISCES joint ND+FD results and the standard NOvA extrapolation method using the full NOvA 10-year data set. The results demonstrate that PISCES can successfully fit NOvA data while incorporating the constraints from the ND detectors consistently, using physically motivated systematic uncertainties to account for data/MC discrepancies.

Rajaoalisoa, Miriama [Cincinnati U.]↗

Consistent lensing and clustering in a low- S 8 Universe with BOSS, DES Year 3, HSC Year 1, and KiDS-1000

ABSTRACT We evaluate the consistency between lensing and clustering based on measurements from Baryon Oscillation Spectroscopic Survey combined with galaxy–galaxy lensing from Dark Energy Survey (DES) Year 3, Hyper Suprime-Cam Subaru Strategic Program (HSC) Year 1, and Kilo-Degree Survey (KiDS)-1000. We find good agreement between these lensing data sets. We model the observations using the Dark Emulator and fit the data at two fixed cosmologies: Planck (S8 = 0.83), and a Lensing cosmology (S8 = 0.76). For a joint analysis limited to large scales, we find that both cosmologies provide an acceptable fit to the data. Full utilization of the higher signal-to-noise small-scale measurements is hindered by uncertainty in the impact of baryon feedback and assembly bias, which we account for with a reasoned theoretical error budget. We incorporate a systematic inconsistency parameter for each redshift bin, A, that decouples the lensing and clustering. With a wide range of scales, we find different results for the consistency between the two cosmologies. Limiting the analysis to the bins for which the impact of the lens sample selection is expected to be minimal, for the Lensing cosmology, the measurements are consistent with A = 1; A = 0.91 ± 0.04 (A = 0.97 ± 0.06) using DES+KiDS (HSC). For the Planck case, we find a discrepancy: A = 0.79 ± 0.03 (A = 0.84 ± 0.05) using DES+KiDS (HSC). We demonstrate that a kinematic Sunyaev–Zeldovich-based estimate for baryonic effects alleviates some of the discrepancy in the Planck cosmology. This analysis demonstrates the statistical power of small-scale measurements; however, caution is still warranted given modelling uncertainties and foreground sample selection effects.

79 ASTRONOMY AND ASTROPHYSICS↗

Mirror twin Higgs cosmology: constraints and a possible resolution to the H$_{0}$ and S$_{8}$ tensions

The mirror twin Higgs model (MTH) is a solution to the Higgs hierarchy problem that provides well-predicted cosmological signatures with only three extra parameters: the temperature of the twin sector, the abundance of twin baryons, and the vacuum expectation value (VEV) of twin electroweak symmetry breaking. These parameters specify the behavior of twin radiation and the acoustic oscillations of twin baryons, which lead to testable effects on the cosmic microwave background (CMB) and large-scale structure (LSS). While collider searches can only probe the twin VEV, through a fit to cosmological data we show that the existing CMB (Planck18 TTTEEE+lowE+lowT+lensing) and LSS (KV450) data already provide useful constraints on the remaining MTH parameters. Additionally, we show that the presence of twin radiation in this model can raise the Hubble constant H$_{0}$ while the scattering twin baryons can reduce the matter fluctuations S$_{8}$, which helps to relax the observed H$_{0}$ and S$_{8}$ tensions simultaneously. This scenario is different from the typical ΛCDM + ΔN$_{eff}$ model, in which extra radiation helps with the Hubble tension but worsens the S$_{8}$ tension. For instance, when including the SH0ES and 2013 Planck SZ data in the fit, we find that a universe with ≳ 20% of the dark matter comprised of twin baryons is preferred over ΛCDM by ~ 4σ. If the twin sector is indeed responsible for resolving the H$_{0}$ and S$_{8}$ tensions, future measurements from the Euclid satellite and CMB Stage 4 experiment will further measure the twin parameters to O(1 - 10%)-level precision. Our study demonstrates how models with hidden naturalness can potentially be probed using precision cosmological data.

72 PHYSICS OF ELEMENTARY PARTICLES AND FIELDS↗

Generating synthetic signaling networks for in silico modeling studies

Predictive models of signaling pathways have proven to be difficult to develop. Reasons include the uncertainty in the number of species, the complexity in species’ interactions, and the sparseness and uncertainty in experimental data. Traditional approaches to developing mechanistic models rely on collecting experimental data and fitting a single model to that data. This approach works for simple systems but has proven unreliable for complex systems such as biological signaling networks. For example, uncertainty and sparseness of the data often result in overfitted models that have little predictive value beyond recapitulating the experimental data itself. Thus, there is a need to develop new approaches to create predictive mechanistic models of complex systems. However, to determine the effectiveness of any new algorithm, a baseline model is needed to test its performance. To meet this need, we developed a method for generating artificial synthetic networks that are reasonably realistic and thus can be treated as ground truth models. These synthetic models can then be used to generate synthetic data for developing and testing algorithms designed to recover the underlying network topology and associated parameters. Here, we describe a simple approach for generating synthetic signaling networks that can be used for this purpose.

42 ENGINEERING↗

Elucidating the Discharge Behavior of Aqueous Zinc Sulfur Batteries in the Presence of Molybdenum(IV) Chalcogenide Catalyst: The Criticality of Interfacial Electrochemistry

The aqueous zinc-sulfur battery holds promise for significant capacity and energy density with low cost and safe operation based on environmentally benign materials. However, it suffers from the sluggish kinetics of the conversion reaction. Here, we highlight the efficacy of molybdenum(IV) sulfide (MoS 2 ) to reduce the overpotential of S-ZnS conversion in aqueous electrolytes and study the discharge products formed at the solid-solid and solid-liquid interfaces using experimental and theoretical approaches. Specifically, the MoS 2 -catalyzed electrochemical conversion reaction is characterized via ex situ X-ray diffraction (XRD), transmission electron microscopy (TEM) with energy dispersive spectroscopy (EDS), Raman spectroscopy, synchrotron-based Mo K-edge X-ray absorption spectroscopy (XAS), and in situ synchrotron-based X-ray computed tomography (XCT). Additionally, operando synchrotron-based S K-edge XAS and X-ray fluorescence (XRF) maps are collected to determine the spatial evolution of sulfur-based species at the electrode-electrolyte interface. Further, coupling the operando S K-edge XAS data with the simulated spectra and fitting the data suggested a possible ZnS 2 intermediate phase.

25 ENERGY STORAGE↗

Octet scalars shaping LHC distributions in 4-jet final states

We study properties of a hypothetical scalar particle, Θ, which is a color octet and an electroweak singlet. At hadron colliders, Θ is pair produced through its QCD coupling to gluons, so that its mass determines the cross section. It decays at tree level into $q\bar{q}$ through dimension-5 operators, and at one loop into gluons. Thus, the main LHC signature of Θ is a pair of dijets of equal invariant mass. The CMS search in this channel shows a 3.6σ excess over the QCD background for a dijet mass M jj ≈ 0.95 TeV, which can be due to Θ : its production cross section (65 fb for a real scalar) and the acceptance of the CMS event selection applied to pp → ΘΘ → ($q\bar{q}$) ($q\bar{q}$) yield a rate consistent with the excess. Furthermore, the shape of the dσ/dM jj signal is in agreement with the CMS result. Given the data-driven background fit performed by CMS, we find that a complex scalar (whose production rate is twice as large) fits better the data than a real scalar. Besides the pair of dijets, testable LHC signals include a trijet-dijet topology, a $t\bar{t}$ pair plus a dijet resonance, as well as final states involving a Higgs, W or Z boson plus jets.

Dobrescu, Bogdan A. [Fermi National Accelerator La↗

Fast Emulation of Expensive Simulations using Approximate Gaussian Processes [Slides]

Nuclear Computational Low-Energy Initiative (NUCLEI) collaboration uses Density Functional Theory (DFT) simulations to predict the structure and binding energies of nuclei over a wide range of proton (Z) and neutron (N) numbers. The DFT simulations utilize a particular parameterization of a Skyrme energy density functional called UNEDF1 which depends on 12 free parameters that must be fit to data (M Kortelainen et al 2014). Fitting involves comparing (e.g.) predicted binding energies of nuclei to experimentally measured values. We use only binding energies as observables, but DFT with UNEDF1 will predict structure (shape) observables as well. In this work, assessing the capability of approximate GP emulators to balance emulator accuracy with computational speed to facilitate improved UNEDF1 calibration. Sparse GPs are straightforward to train and accurate. Calibration is not straightforward with MCMC (using MH or HMC/NUTS). We produced reusable software for continuing and building on this work as well as accessing and using Darwin cluster compute resources

97 MATHEMATICS AND COMPUTING↗

A New Vehicle-to-Vehicle Communication Technology Based on Binary Light Code

The proliferation of Connected and Autonomous Vehicles (CAVs) has necessitated the development of efficient, reliable communication methods between vehicles and their surroundings. This study presents a novel methodology, the VECTOR system, that addresses this need by converting dynamic vehicle data into a binary code and displaying it on an LED panel. The system involves a three-step process of data collection, polynomial fitting of velocity data, and encoding the polynomial parameters into binary form using a Cyclic Redundancy Check (CRC). The study also explores the practical application of this system by conducting experiments with modified Lincoln MKZ hybrids, demonstrating the feasibility and efficiency of this approach. The paper presents both the methodology and results of these experiments, further expanding upon the potential applications and implications for CAV technology. By comparing the final accuracy, we find this approach can achieve 80% of the original velocity data.

Ma, Ke↗

A Parametric Reduced-Order Model for Inverter Short-Circuit Response in Protection Studies

This paper presents a reduced-order model (ROM) for grid-following (GFL) inverters that reproduces inverter fault current trajectories, including sub transients, transient, and steady-state phases, across a range of fault types, locations, and pre-fault operating points. . The proposed model is developed by: Constructing the positive- and negative-sequence current with parameterization fitted by large data training and fitting Validating using EMT simulation against EMT full model and demonstrating the ROM's capability to capture fault current magnitude, phase angle, and oscillatory transients. Building a standard EMT simulation platform library component for easy configuration and application.

24 POWER TRANSMISSION AND DISTRIBUTION↗

An SU(5) × U(1)' SUSY GUT with a “vector-like chiral” fourth family to fit all low energy data, including the muon g – 2

An additional generation of quarks and leptons and their SUSY counterparts, which are vector-like under the Standard Model gauge group but are chiral with respect to the new U(1) 3–4 gauge symmetry, are added to the Minimal Supersymmetric Standard Model (MSSM). We show that this model is a GUT and unifies the three SM gauge couplings and also the additional U(1) 3–4 coupling at a GUT scale of ≈ 5 × 10 16 GeV and explains the experimentally observed deviation of the muon g – 2. We also fit the quark flavor changing processes consistent with the latest experimental data and look at the effect of the new particles on the W boson mass without obviously conflicting with the observed masses of particles, CKM matrix elements, neutrino mixing angles, their mass differences, and the lepton-flavor violating bounds. This model predicts sparticle masses less than 25 TeV, with a gluino mass ≈ 2.3 – 3 TeV consistent with constraints, and one of the neutralinos as the LSP with a mass of ≈ 480 – 580 GeV, which is a potential dark matter candidate. The model is string theory motivated and predicts the VL quarks, leptons, a massive Z' and two Dirac neutrinos at the TeV scale and the branching ratios of μ → eγ, τ → μγ and τ → 3μ with BR(μ → eγ) within reach of future experiments.

72 PHYSICS OF ELEMENTARY PARTICLES AND FIELDS↗

AI-Batt (Autonomous Identification of Battery Life Models) [SWR 21-36]

Autonomous Identification of Battery Life Models (AI-Batt) AI-Batt is a MATLAB code base for developing lifetime models for batteries from accelerated aging data. The code base provides many functions for processing, visualizing, and modeling battery aging data, making the data processing, exploration, and modeling workflow substantially faster. These tools are tailored for working with battery aging data sets, which usually consist of many separate time-series for each cell, with many test conditions and possible replicates at each condition, which makes it difficult to simply process or visualize the data set. Complex modeling tasks, such as cross-validation, sensitivity analysis, and uncertainty quantification have been implemented to enable thorough statistical investigation of model predictions. Additionally, several machine-learning algorithms are implemented to autonomously identify suitable models via symbolic regression. Data processing functions automatically cast data from the struct data type, which is commonly used to store experimental data, but is not an acceptable input for most algorithms, to the table data type, which can be easily used as input to any optimization algorithm. Also, the data can be separated into time-invariant and time-variant data tables, which is helpful for exploring the data set as well as developing separate models for time-variant and time-invariant aging mechanisms. For example, in aging tests with constant temperature, temperature is a time-invariant experimental condition. Visualization tools enable plotting of data, model fits, and model simulations possible with single-line function calls, empowering data exploration of complex data sets with both time-varying and time-invariant trends. Plots can be automatically generated for the whole data set, or separated by data group (groups of test replicates) or individual data series. Data points or data series can be automatically colored by the value of a variable with a variety of color maps, and model predictions can also be colored by the value of a fit statistic. Comparisons between data sets and the predictions/simulations of different models on the same data set can be easily plotted as well. Distributions of parameter values from bootstrap resampling can be plotted to visualize the reliability of parameter estimation, or determine any correlations between parameters. Modeling tools handle the complex task of creating and parsing symbolic equations for modeling battery lifetime. Equations are parsed to grab relevant data variables, parameter values, or specified sub-models for input into optimization, evaluation, or simulation functions. Models can be optimized locally (one set of parameters for each data series), bi-level (some parameters shared across the data set), or globally (single set of parameters for all data). Functions implementing symbolic regression algorithms help users to discover effective model equations, even in poorly sampled, high-dimensional data.

Smith, Kandler↗

DESI 2024: Constraints on physics-focused aspects of dark energy using DESI DR1 BAO data

Baryon acoustic oscillation data from the first year of the Dark Energy Spectroscopic Instrument (DESI) provide near percent-level precision of cosmic distances in seven bins over the redshift range z=0.1–4.2. Here, this paper is the follow-up to the original DESI BAO cosmology paper [A. G. Adame et al. (DESI Collaboration), arXiv:2404.03002], which considered the conventional w 0 w a cold dark matter (CDM) model. We use the novel DESI data, together with other cosmic probes, to constrain the background expansion history using some well-motivated physical classes of dark energy. In particular, we explore three physics-focused behaviors of dark energy from the equation of state and energy density perspectives: the thawing class (matching many simple quintessence potentials), emergent class (where dark energy comes into being recently, as in phase transition models), and mirage class [where phenomenologically the distance to cosmic microwave background (CMB) last scattering is close to that from a cosmological constant Λ despite dark energy dynamics]. All three classes fit the data at least as well as Λ ⁢CDM, and indeed can improve on it by Δ⁢χ 2 ≈ –5 to –17 for the combination of DESI BAO with CMB and supernova data while having one more parameter. The mirage class does essentially as well as w 0 ⁢w a CDM and exhibits moderate to strong Bayesian evidence preference with respect to Λ⁢ CDM. These classes of dynamical behaviors highlight worthwhile avenues for further exploration into the nature of dark energy.

79 ASTRONOMY AND ASTROPHYSICS↗

Robustness of the Galactic Center excess morphology against masking

The Galactic Center excess (GCE) remains an enduring mystery, with leading explanations being annihilating dark matter or an unresolved population of millisecond pulsars. Analyzing the morphology of the GCE provides critical clues to identify its exact origin. We investigate the robustness of the inferred GCE morphology against the effects of masking, an important step in the analysis where the gamma-ray emission from point sources and the galactic disk are excluded. Using different masks constructed from Fermi point source catalogs and a wavelet method, we find that the GCE morphology, particularly its ellipticity and cuspiness, is relatively independent of the choice of mask for energies above 2–3 GeV. The GCE morphology systematically favors an approximately spherical shape, as expected for dark matter annihilation. Compared to various stellar bulge profiles, a spherical dark matter annihilation profile better fits the data across different masks and galactic diffuse emission backgrounds, except for the stellar bulge profile which provides a similar fit to the data. Modeling the GCE with two components, one from dark matter annihilation and one tracing the Coleman bulge, we find this two-component model outperforms any single component or combinations of dark matter annihilation and other stellar bulge profiles. Uncertainty remains about the exact fraction contributed by each component across different background models and masks. Furthermore, when the Coleman bulge dominates, its corresponding spectrum lacks characteristics typically associated with millisecond pulsars, suggesting that it mostly models the emission from other sources instead of the GCE that is still present and spherically symmetric.

72 PHYSICS OF ELEMENTARY PARTICLES AND FIELDS↗

Modification of conventional peak shapes to accurately represent spectral asymmetry: High-Resolution X-ray photoelectron spectra of [C 4 C 1 Pyrr][NTf 2 ] and [C 8 C 1 Im][NTf 2 ] ionic liquids

X-ray photoelectron spectroscopy (XPS) is one of the most widely used techniques for surface characterization. Analysis of XPS data is challenging and requires the analyst to fit the data with synthetic line shapes to reach physically meaningful interpretations. Experimental spectral envelopes, however, are complex and display asymmetric features that are often ignored or attributed to additional chemical components. The high-resolution XPS spectra of [C 4 C 1 Pyrr][NTf 2 ] and [C 8 C 1 Im][NTf 2 ] all exhibit a degree of asymmetry which is systematically observed at the higher binding energy side of photoemission envelopes. Here, we present the development of a refined fitting procedure for XPS spectra of these ionic liquid-based systems which include (a) Shirley background offset necessary to account for the insulator-like region and (b) spectral asymmetry in C 1s and N 1s regions. Further, Shirley and trapezoid components are applied to compensate for inelastic scattering taking place during electron transitions as high as 7.8 eV above the start of the fitting region in C 1s high-resolution spectrum. To demonstrate the fitness of this model, we present an analysis of a 2:1 mixture of [C 4 C 1 Pyrr][NTf 2 ]: [C 8 C 1 Im][NTf 2 ].

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗