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DOE OSTI2024

Qualitative and quantitative enhancement of parameter estimation for model-based diagnostics using automatic differentiation with an application to inertial fusion

Parameter estimation using observables is a fundamental concept in the experimental sciences. Mathematical models that represent the physical processes can enable reconstructions of the experimental observables and greatly assist in parameter estimation by turning it into an optimization problem which can be solved by gradient-free or gradient-based methods. In this work, the recent rise in flexible frameworks for developing differentiable scientific computing programs is leveraged in order to dramatically accelerate data analysis of a common experimental diagnostic relevant to laser–plasma and inertial fusion experiments, Thomson scattering. A differentiable Thomson-scattering data analysis tool is developed that uses reverse-mode automatic differentiation (AD) to calculate gradients. By switching from finite differencing to reverse-mode AD, three distinct outcomes are achieved. First, gradient descent is accelerated dramatically to the extent that it enables near real-time usage in laser–plasma experiments. Second, qualitatively novel quantities which require $\mathcal{O}(10^3)$ parameters can now be included in the analysis of data which enables unprecedented measurements of small-scale laser–plasma phenomena. Third, uncertainty estimation approaches that leverage the value of the Hessian become accurate and efficient because reverse-mode AD can be used for calculating the Hessian.

97 MATHEMATICS AND COMPUTING↗

DOE OSTI2025

Energy dependence of polarized 𝛾⁢𝛾 → 𝑒 + ⁢ 𝑒− in peripheral Au+Au collisions at $\sqrt{s_{NN}}$ = 54.4 and 200 GeV with the STAR experiment at RHIC

We report the differential yields at mid-rapidity of the Breit-Wheeler process (𝛾⁢𝛾 → 𝑒 + ⁢𝑒 − ) in peripheral Au+Aucollisions at $\sqrt{s_{NN}}$ = 54.4 and 200 GeV with the STAR experiment at the Relativistic Heavy Ion Collider (RHIC), as a function of energy $\sqrt{s_{NN}}$, 𝑒 + ⁢𝑒 − transverse momentum 𝑝 T , 𝑝$^{2}_{T}$, invariant mass 𝑀 𝑒⁢𝑒 , and azimuthal angle. In the invariant mass range of 0.4 < 𝑀 𝑒⁢𝑒 < 2.6GeV/𝑐 2 at low transverse momentum (𝑝 T < 0.15GeV/𝑐), the yields increase while the pair √⟨𝑝$^{2}_{T}$⟩ decreases with increasing $\sqrt{s_{NN}}$, a feature that is correctly predicted by the QED calculation. Here, the energy dependencies of the measured quantities are sensitive to the nuclear form factor, infrared divergence and photon polarization. The data are compiled and used to extract the charge radius of the Au nucleus.

73 NUCLEAR PHYSICS AND RADIATION PHYSICS↗

DOE OSTI2021

The J/ψ-007 Experiment: A Search for the LHCB Charm Pentaquarks in Hall C at Jefferson Lab

In the Jefferson Lab E12-16-007 (J/ψ- 007) experiment we measured the differential J/ψ photo-production cross section as a function of photon energy, Ey and Mandelstam variable t- the momentum transfer from the initial photon to the produced J/ψ- in the energy region where all the charm pentaquark states were discovered by the LHCb (Large Hadron Collider beauty) collaboration. The J/ψ-007 experiment was conducted in the experimental Hall C of the Thomas Jefferson National Accelerator Facility using a high-intensity real photon beam generated by a 10.6 GeV incident electron beam traversing a copper radiator upstream of a liquid hydrogen target. Two arm spectrometers of Hall C, HMS (High Momentum Spectrometer), and SHMS (Super High Momentum Spectrometer) were used to detect the e + e - dilepton J/ψ decay pairs in coincidence. The spectrometers' four momentum and angle settings scanned a photon beam energy range between 9.1 and 10.6 GeV and |t| up to 5 GeV 2 . An enhanced sensitivity to the s-channel resonant J/ψ photo-production was achieved by optimizing the spectrometer settings at a higher t region where the non-resonant standard t-channel J/ψ production cross section is strongly suppressed. No evidence for pentaquarks was observed and, the cross section upper limits for each LHCb pentaquark candidate were determined and are presented in this document.

Duran, Burcu↗

DOE OSTI2025

Status of the PrimEx $\eta$ experiment at Jefferson Lab

The GlueX detector in the experimental Hall D at Jefferson Lab offers a unique opportunity to perform a measurement of the decay width of eta mesons through the Primakoff effect. The experiment complements the physics program at Jefferson Lab on measuring the decay width of light pseudoscalar mesons via the Primakoff process. The goal of the experiment is to measure differential cross sections of eta mesons at forward angles using a beam of tagged photons incident on a liquid 4He target, which will be used for the extraction of the decay width. This measurement is vital for understanding fundamental properties like the ratios of the light quark masses and the eta - eta' mixing angle, and will provide an important test of chiral symmetry breaking in QCD. Our experimental results will help reduce uncertainties on partial widths of all other eta decays. The experiment collected data during three physics runs between 2019 and 2022. We will give an overview of the PrimEx eta experiment and the current status of our data analyses. We will also discuss the feasibility of conducting future Primakoff measurements in light of the recent upgrade of the GlueX forward calorimeter and the potential accelerator energy upgrade to 22 GeV.

Somov, Alexander↗

DOE OSTI2023

Study of exclusive photoproduction of charmonium in ultra-peripheral lead-lead collisions

The cross-sections of exclusive (coherent) photoproduction J/ψ and ψ(2S) mesons in ultra-peripheral PbPb collisions at a nucleon-nucleon centre-of-mass energy of 5.02 TeV are measured using a data sample corresponding to an integrated luminosity of 228 ± 10 µb -1 , collected by the LHCb experiment in 2018. The differential cross-sections are measured separately as a function of transverse momentum and rapidity in the nucleus-nucleus centre-of-mass frame for J/ψ and ψ(2S) mesons. The integrated cross-sections are measured to be $σ^{coh}_{J/ψ}$ = 5.965 ± 0.059 ± 0.232 ± 0.262 mb and $σ^{coh}_{ψ(2S)}$ = 0.923 ± 0.086 ± 0.028 ± 0.040 mb, where the first listed uncertainty is statistical, the second systematic and the third due to the luminosity determination. The cross-section ratio is measured to be $σ^{coh}_{ψ(2S)}$/$σ^{coh}_{J/ψ}$ = 0.155 ± 0.014 ± 0.003, where the first uncertainty is statistical and the second is systematic. These results are compatible with theoretical predictions.

72 PHYSICS OF ELEMENTARY PARTICLES AND FIELDS↗

DOE OSTI2022

A Differentiable Hydrology Approach for Modeling With Time-Varying Parameters

In the analysis of observational data with mathematical models, it is often desirable to let one or more model parameters vary with time to account for changing environmental conditions or to offer more flexibility. A standard approach for dynamic models is to allow for the number of parameters to grow as a function of time, leading to a high-dimensional inference problem for long data records. We propose using Hamiltonian Monte Carlo, a gradient-based Markov chain Monte Carlo (MCMC) method, to perform Bayesian inference for time-varying parameters (TVP) in hydrology models. As derivatives of model error functions with regard to parameters are not available in closed form, we implemented the GR4J rainfall-runoff models in Theano/PyMC3, and Jax/NumPyro, allowing for the application of automatic differentiation techniques. A simulation experiment assessing the viability of these methods for recovering underlying temporal variation in parameters indicates that a discrete Gaussian random walk-based prior appears to be best suited across a range of scenarios while the continuous-time Gaussian process compares relatively poorly. In an analysis of 20 years of daily real-world streamflow records from the Model Parameter Estimation Experiment (MOPEX) hydrology data set with increasing data sparsity and at multiple temporal resolutions, we find that TVP inference with gradient-based MCMC is a flexible and reliable approach for analyzing hydrology models with dynamic parameter sets.

54 ENVIRONMENTAL SCIENCES↗

DOE OSTI2025

miss-SNF: a multimodal patient similarity network integration approach to handle completely missing data sources

Abstract Motivation Precision medicine leverages patient-specific multimodal data to improve prevention, diagnosis, prognosis, and treatment of diseases. Advancing precision medicine requires the non-trivial integration of complex, heterogeneous, and potentially high-dimensional data sources, such as multi-omics and clinical data. In the literature, several approaches have been proposed to manage missing data, but are usually limited to the recovery of subsets of features for a subset of patients. A largely overlooked problem is the integration of multiple sources of data when one or more of them are completely missing for a subset of patients, a relatively common condition in clinical practice. Results We propose miss-Similarity Network Fusion (miss-SNF), a novel general-purpose data integration approach designed to manage completely missing data in the context of patient similarity networks. miss-SNF integrates incomplete unimodal patient similarity networks by leveraging a non-linear message-passing strategy borrowed from the SNF algorithm. miss-SNF is able to recover missing patient similarities and is “task agnostic”, in the sense that can integrate partial data for both unsupervised and supervised prediction tasks. Experimental analyses on nine cancer datasets from The Cancer Genome Atlas (TCGA) demonstrate that miss-SNF achieves state-of-the-art results in recovering similarities and in identifying patients subgroups enriched in clinically relevant variables and having differential survival. Moreover, amputation experiments show that miss-SNF supervised prediction of cancer clinical outcomes and Alzheimer’s disease diagnosis with completely missing data achieves results comparable to those obtained when all the data are available. Availability and implementation miss-SNF code, implemented in R, is available at https://github.com/AnacletoLAB/missSNF.

Biochemistry & Molecular Biology↗

DOE OSTI2024

Reducing Operator Complexity of Galerkin Coarse-grid Operators with Machine Learning

Here, we propose a data-driven and machine-learning-based approach to compute non-Galerkin coarse-grid operators in multigrid (MG) methods, addressing the well-known issue of increasing operator complexity. Guided by the MG theory on spectrally equivalent coarse-grid operators, we have developed novel machine learning algorithms that utilize neural networks combined with smooth test vectors from multigrid eigenvalue problems. The proposed method demonstrates promise in reducing the complexity of coarse-grid operators while maintaining overall MG convergence for solving parametric partial differential equation problems. Numerical experiments on anisotropic rotated Laplacian and linear elasticity problems are provided to showcase the performance and comparison with existing methods for computing non-Galerkin coarse-grid operators.

97 MATHEMATICS AND COMPUTING↗

DOE OSTI2024

Unraveling the Pyrolytic Behavior and Kinetics of Single Polymers and Plastic-Rich Municipal Solid Waste Using Thermal Analysis

Pyrolysis is a highly promising thermochemical recycling technology for converting heterogenous plastic waste into sustainable fuels in a single step. Therefore, understanding the pyrolysis mechanism is essential for enabling rational reactor design and enhancing efficient recycling techniques. In this study, the thermal degradation behaviors and corresponding kinetics of pure polymers (PE, PP, and PET) and plastic-rich MSW were examined using simultaneous thermogravimetric analysis (TGA) and differential scanning calorimetry (DSC). Experiments were carried out in the temperature range of 30-800°C with variable heating rates from 5°C/min to 20°C/min in an ultra-high purity Argon atmosphere. Our results indicated that the plastic pyrolysis was an endothermic process, with varying decomposition temperature ranges depending on their structure and composition. Various iso-conversional model-free methods (Friedman, Flynn-Wall-Ozawa, Starink, and Kissinger-Akahira-Sunose) were utilized to determine the apparent activation energy of the plastic degradation, which increased in the following order: PET (214 kJ/mol), PP (218 kJ/mol), PE (245 kJ/mol), and MSW (249 kJ/mol). Finally, Criado’s master plots were employed to identify the best-fitting reaction model and the pre-exponential factor was subsequently determined.

Bashir, Muhammad Aamir↗

DOE OSTI2024

Cross-Section Measurements of Lambda(1405) Photoproduction from CLAS G12 Data

The nature of the Λ(1405) state remains an unsolved puzzle despite being predicted in 1959 and experimentally confirmed soon thereafter in 1961. It has an unusual line shape that deviates from a Breit-Wigner form, typically associated with resonances. Theoretical explanations of this first, excited Λ hyperon range from it being a three-quark state (uds) to being a dynamically generated, quasi-bound KN¯ molecule to consisting of a two-pole (two resonances) structure. None of these descriptions of Λ(1405) are universally accepted. Thus, there is a need for additional data on this notoriously cryptic state to help guide theoretical models. Measurements such as cross sections can assist to elucidate our understanding of resonances and how they’re produced. In this analysis, data from the CLAS g12 experiment were studied and differential cross-section measurements for Λ(1405) photoproduction were extracted. The results contained within this work are in relatively good agreement with prior photoproduction measurements (CLAS g11). Moreover, the energy range over which the existing measurements extend is expanded to higher values with these new results. These higher energy cross-section measurements should prove to be beneficial for subsequent analyses of Λ(1405).

Reed, Trevor↗

DOE OSTI2021

Mathematical analysis of laboratory microbial experiments demonstrating deterministic chaotic dynamics

Presented is a system of four ordinary differential equations and a mathematical analysis of microbiological experiments in a four-component chemostat—nutrient n, rods r, cocci c, and predators p. The analysis is consistent with the conclusion that previous experiments produced features of deterministic chaotic and classical dynamics depending on dilution rate. The surrogate model incorporates as much experimental detail as possible, but necessarily contains unmeasured parameters. The objective is to understand better the differences between model simulations and experimental results in complex microbial populations. The key methodology for simulation of chaotic dynamics, consistent with the measured dilution rate and microbial volume averages, was to cause the preference of p for r vs. c to vary with the r and c concentrations, to make r more competitive for nutrient than c, and to recycle some dying p biomass, leading to a modified version of the Monod kinetics model. Our mathematical model demonstrated that the occurrence of chaotic dynamics requires a predator, p, preference for r versus c to increase significantly with increases in r and c populations. Also included is a discussion of several generalizations of the existing model and a possible involvement of the minimum energy dissipation principle. This principle appears fundamental to thermodynamic systems including living systems. Several new experiments are suggested.

59 BASIC BIOLOGICAL SCIENCES↗

DOE OSTI2023

How machine learning can extend electroanalytical measurements beyond analytical interpretation

Electroanalytical measurements are routinely used to estimate material properties exhibiting current and voltage signatures. Analysis of such measurements relies on analytical expressions of material properties to describe the experiments. The need for analytical expressions limits the experiments that can be used to measure properties as well as the properties that can be estimated from a given experiment. Such analytical relations are essentially solutions of the physics-based differential equations (with properties as coefficients) describing the material behavior under certain specific conditions. In recent years, a new machine learning-based approach has been gaining popularity wherein the differential equations are numerically solved to interpret the electroanalytical experiments in terms of corresponding material properties. Since the physics-based differential equations are solved, one can additionally estimate underlying fields, e.g., concentration profile, using such an approach. To exemplify the characteristics of such a machine learning assisted interpretation of electroanalytical measurements, we use data from the Hebb–Wagner test on a magnesium spinel intercalation host. In conclusion, as compared to the traditional analytical expression-based interpretation, the emerging approach decreases experimental efforts to characterize relevant material properties as well as provides field information that was previously inaccessible.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

DOE OSTI2024

Development of a new CEDAR for kaon identification at the NA62 experiment at CERN

The NA62 experiment at CERN utilises a differential Cherenkov counter with achromatic ring focus (CEDAR) for tagging kaons within an unseparated monochromatic beam of charged hadrons. The CEDAR-H detector was developed to minimise the amount of material in the path of the beam by using hydrogen gas as the radiator medium. The detector was shown to satisfy the kaon tagging requirements in a test-beam before installation and commissioning at the experiment. The CEDAR-H performance was measured using NA62 data collected in 2023.

46 INSTRUMENTATION RELATED TO NUCLEAR SCIENCE AND ↗

DOE OSTI2022

Relationships between fault characteristics and seismic responses in a large lab-scale tri-axial injection test conducted on a faulted Castlegate Sandstone

Here to investigate mechanisms causing microseismicity (M w < 2) at a CO 2 injection site, a large-scale triaxial block experiment was carried out on a faulted (saw-cut) cubic-meter of Castlegate Sandstone. The experiment consisted of injection tests at varying differential stresses, while monitoring and recording pore pressure and acoustic emissions (AEs). During the experiment, ~33,000 AEs and ~14 mm of horizontal displacement/slip, like a strike-slip fault movement, occurred. To understand the AE responses and ascertain fault characteristics near the located AEs, we modeled the topography of the fault surface, fault aperture, and fault-gouge thickness using pre- and post-experiment laser scans of the fault surface on each half of the block. Additionally, we characterized surface roughness parallel and perpendicular to slip. Models show crushing and flattening of the fault surfaces can be linked to the spatiotemporal distribution of AEs within 50 mm of the fault surface. Approximately 65% of AEs were in areas with small aperture (≤300 μm); thicker fault gouge was observed in adjacent areas with wider aperture and shows a two-fold reduction in grain size relative to unaltered Castlegate Sandstone. This work provides a conceptual understanding on fault surface evolution, which can be applied towards modeling of seismic slip.

58 GEOSCIENCES↗

DOE OSTI2025

A Tale from the Trenches: Applying Metamorphic and Differential Testing to Bioinformatics Software

Metamorphic and differential testing have been proposed as best practices for testing software that is difficult to test, such as for programs in scientific domains. An assumption is that these approaches can be easily customized and applied to almost any domain. However, scientific software is often data-driven, and metamorphic relations may require significant domain knowledge to develop. In addition, tools are often written for ad-hoc experimentation by the scientists and often embed many assumptions about the importance and representation of different natural phenomena. In this paper, we present our experience applying both metamorphic and differential testing to a set of four computational biology tools that predict the growth of an organism. While our original goal was to evaluate these techniques to improve our system-level testing, we encountered multiple roadblocks along the way. Although we did find faults (some confirmed by developers), we also uncovered a set of challenges, including the considerable manual effort required for (a) defining domain-specific tests, (b) validating correctness, and (c) distinguishing between issues stemming from poor data and those arising from incorrect software.

Marsh, Alexis L [Iowa State University/Ames Labora↗

DOE OSTI2020

Weak neutral current axial form factor using $ \left(\overline{\nu}\right)\nu $-nucleon scattering and lattice QCD inputs

We present a determination of the neutral current weak axial charge $G$ $^{Z}_{A}$(0) = –0.654(3) stat (5) sys using the strange quark axial charge $G$ $^{s}_{A}$(0) calculated with lattice QCD. We then perform a phenomenological analysis, where we combine the strange quark electromagnetic form factor from lattice QCD with (anti)neutrino-nucleon scattering differential cross section from MiniBooNE experiments in a momentum transfer region 0.24 ≲ Q 2 ≲ 0.71 GeV 2 to determine the neutral current weak axial form factor $G$ $^{Z}_{A}$(Q 2 ) in the range of 0 ≲ Q 2 ≤ 1 GeV 2 . This yields a phenomenological value of $G$ $^{Z}_{A}$(0) = –0.687(89)stat(40)sys. The value of $G$ $^{Z}_{A}$(0) constrained by the lattice QCD calculation of $G$ $^{s}_{A}$(0), when compared to its phenomenological determination, provides a significant improvement in precision and accuracy and can be used to provide a constraint on the fit to $G$ $^{Z}_{A}$(Q 2 ) for Q 2 > 0. This constrained fit leads to an unambiguous determination of (anti)neutrino-nucleon neutral current elastic scattering differential cross section near Q 2 = 0 and can play an important role in numerically isolating nuclear effects in this region. We show a consistent description of $G$ $^{Z}_{A}$(Q 2 ) obtained from the (anti)neutrino-nucleon scattering cross section data requires a nonzero contribution of the strange quark electromagnetic form factor. We demonstrate the robustness of our analysis by providing a post-diction of the BNL E734 experimental data.

72 PHYSICS OF ELEMENTARY PARTICLES AND FIELDS↗

DOE OSTI2024

Identifying a novel pathway for extracellular electron uptake in Methanosarcina barkeri using shotgun

The overarching goal of this project was to identify the genetic and/or enzymatic basis for extracellular electron uptake in Methanosarcina barkeri—an organism we previously characterized to be capable of this process using poised potential electrodes and a range of electrochemical techniques. In our first aim, we will utilized proteomic techniques that labels extracellular proteins with free amine groups with biotin and perform a selective purification of these proteins from the rest of the proteome. These were identified using mass spectrometry, providing us insight into the identity of the cell surface proteins, including redox active proteins present during extracellular electron uptake. We will also used an isobaric tagging technique (iTRAQ labeling) of proteomes from different experiment conditions to look at differential proteins expression and better understand the total pathway involved in extracellular electron uptake coupled to methanogenesis. In our final aim, we will investigated the electrochemical nature of electron uptake in co-cultures, compared to our pure culture data sets. We predict the process of electron uptake from electrodes replicates what goes on in nature when these organisms for co-cultures with electrogenic microbes such as Geobacter, and to test this hypothesis we have begun to probe co-cultures electrochemically during direct interspecies electron transfer. Our final aim took much longer than expected due to challenges replicating co-cultures between Geobacter metallireducens and Methanosarcina barkeri. We found the major problem with this work was the inability of the M. barkeri strain we used (and we tried strains from three different labs) to successfully grow on acetate in the absence of hydrogen. As such, we began to use the strain Methanosarcina acetivorans—another close relative that specializes on acetate growth. We are currently in the process of comparing electrochemical observations of this microorganism between pure and co-culture experiments.

59 BASIC BIOLOGICAL SCIENCES↗

DOE OSTI2024

Measurement of prompt D + and ${D}_s^{+}$ production in p Pb collisions at $\sqrt{s_{NN}}$ = 5.02 TeV

The production of prompt D + and $D^+_s$ mesons is studied in proton-lead collisions at a centre-of-mass energy of $\sqrt{^{S}NN}$ = 5.02 TeV. The data sample corresponding to an integrated luminosity of (1.58 ± 0.02)nb –1 is collected by the LHCb experiment at the LHC. The differential production cross-sections are measured using D + and $D^+_s$ candidates with transverse momentum in the range of 0 < p T < 14 GeV/c and rapidities in the ranges of 1.5 < y* < 4.0 and –5.0 < y* < –2.5 in the nucleon-nucleon centre-of-mass system. For both particles, the nuclear modification factor and the forward-backward production ratio are determined. These results are compared with theoretical models that include initial-state nuclear effects. In addition, measurements of the cross-section ratios between D + , $D^+_s$ and D 0 mesons are presented, providing a baseline for studying the charm hadronization in lead-lead collisions at LHC energies.

72 PHYSICS OF ELEMENTARY PARTICLES AND FIELDS↗