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DOE OSTI2013

A Quartet of PIF bHLH Factors Provides a Transcriptionally Centered Signaling Hub That Regulates Seedling Morphogenesis through Differential Expression-Patterning of Shared Target Genes in Arabidopsis

Dark-grown seedlings exhibit skotomorphogenic development. Genetic and molecular evidence indicates that a quartet of Arabidopsis Phytochrome (phy)-Interacting bHLH Factors (PIF1, 3, 4, and 5) are critically necessary to maintaining this developmental state and that light activation of phy induces a switch to photomorphogenic development by inducing rapid degradation of the PIFs. Here, using integrated ChIP–seq and RNA–seq analyses, we have identified genes that are direct targets of PIF3 transcriptional regulation, exerted by sequence-specific binding to G-box (CACGTG) or PBE-box (CACATG) motifs in the target promoters genome-wide. In addition, expression analysis of selected genes in this set, in all triple pif-mutant combinations, provides evidence that the PIF quartet members collaborate to generate an expression pattern that is the product of a mosaic of differential transcriptional responsiveness of individual genes to the different PIFs and of differential regulatory activity of individual PIFs toward the different genes. Together with prior evidence that all four PIFs can bind to G-boxes, the data suggest that this collective activity may be exerted via shared occupancy of binding sites in target promoters.

59 BASIC BIOLOGICAL SCIENCES↗

DOE OSTI2012

Structural and Mutational Analysis of Functional Differentiation between Synaptotagmins-1 and -7

Synaptotagmins are known to mediate diverse forms of Ca{sup 2+}-triggered exocytosis through their C{sub 2} domains, but the principles underlying functional differentiation among them are unclear. Synaptotagmin-1 functions as a Ca{sup 2+} sensor in neurotransmitter release at central nervous system synapses, but synaptotagmin-7 does not, and yet both isoforms act as Ca{sup 2+} sensors in chromaffin cells. To shed light into this apparent paradox, we have performed rescue experiments in neurons from synaptotagmin-1 knockout mice using a chimera that contains the synaptotagmin-1 sequence with its C{sub 2}B domain replaced by the synaptotagmin-7 C{sub 2}B domain (Syt1/7). Rescue was not achieved either with the WT Syt1/7 chimera or with nine mutants where residues that are distinct in synaptotagmin-7 were restored to those present in synaptotagmin-1. To investigate whether these results arise because of unique conformational features of the synaptotagmin-7 C{sub 2}B domain, we determined its crystal structure at 1.44 {angstrom} resolution. The synaptotagmin-7 C{sub 2}B domain structure is very similar to that of the synaptotagmin-1 C{sub 2}B domain and contains three Ca{sup 2+}-binding sites. Two of the Ca{sup 2+}-binding sites of the synaptotagmin-7 C{sub 2}B domain are also present in the synaptotagmin-1 C{sub 2}B domain and have analogous ligands to those determined for the latter by NMR spectroscopy, suggesting that a discrepancy observed in a crystal structure of the synaptotagmin-1 C{sub 2}B domain arose from crystal contacts. Overall, our results suggest that functional differentiation in synaptotagmins arises in part from subtle sequence changes that yield dramatic functional differences.

60 APPLIED LIFE SCIENCES↗

DOE OSTI2014

Impaired osteoblast differentiation in Annexin A2- and -A5-deficient cells

Annexins are a class of calcium-binding proteins with diverse functions in the regulation of lipid rafts inflammation,fibrinolysis, transcriptional programming and ion transport. Within bone, they are well-characterized as components of mineralizing matrix vesicles, although little else is known as to their function during osteogenesis. We generated annexin A2 (AnxA2)- or annexin A5 (AnxA5)-knockdown pre-osteoblasts, and asked whether proliferation or osteogenic differentiation was altered in knockdown cells, compared to vector controls. We report that DNA content, a marker of proliferation, was significantly reduced in both AnxA2 and AnxA5 knockdown cells. Alkaline phosphatase expression and staining activity were also suppressed in AnxA2- or AnxA5-knockdown after 14 days of culture. The pattern of osteogenic gene expression was altered in knockdown cells, with Col1a1 expressed more rapidly in knock-down cells, compared to controls. In contrast, Runx2, Ibsp, and Bglap all revealed decreased expression after 14 days of culture. Using a murine fracture model, we demonstrate that AnxA2 and AnxA5 are rapidly expressed within the fracture callus. These data demonstrate that AnxA2 and AnxA5 can influence bone formation via regulation of osteoprogenitor proliferation and differentiation in addition to their well-studied function in matrix vesicles.

annexin, bone, gene expression↗

DOE OSTI2016

Measurement of fiducial differential cross sections of gluon-fusion production of Higgs bosons decaying to W W ∗ → e ν μ ν with the ATLAS detector at s = 8 TeV

CERN-LHC. This paper describes a measurement of fiducial and differential cross sections of gluon-fusion Higgs boson production in the H->WW*->e nu mu nu channel, using 20.3 fb^{-1} of proton--proton collision data. The data were produced at a centre-of-mass energy of sqrt(s) = 8 TeV at the CERN Large Hadron Collider and recorded by the ATLAS detector in 2012. Cross sections are measured from the observed H->WW*->e nu mu nu signal yield in categories distinguished by the number of associated jets. The total cross section is measured in a fiducial region defined by the kinematic properties of the charged leptons and neutrinos. Differential cross sections are reported as a function of the number of jets, the Higgs boson transverse momentum, the dilepton rapidity, and the transverse momentum of the leading jet. The jet-veto efficiency, or fraction of events with no jets above a given transverse momentum threshold, is also reported. All measurements are compared to QCD predictions from Monte Carlo generators and fixed-order calculations, and are in agreement with the Standard Model predictions.

72 PHYSICS OF ELEMENTARY PARTICLES AND FIELDS↗

DOE OSTI2015

Measurement of differential J / ψ production cross-sections and forward-backward ratio in p+Pb collisions with the ATLAS detector

CERN-LHC. Measurements of differential cross-sections for J/psi production in p+Pb collisions at sqrt(s_NN) = 5.02 TeV at the LHC with the ATLAS detector are presented. The data set used corresponds to an integrated luminosity of 28.1 nb^-1. The J/psi mesons are reconstructed in the dimuon decay channel over the transverse momentum range 8< pT< 30 GeV and over the center-of-mass rapidity range -2.87< y* <1.94. Prompt J/psi are separated from J/psi resulting from b-hadron decays through an analysis of the distance between the J/psi decay vertex and the event primary vertex. The differential cross-section for production of nonprompt J/psi is compared to a FONLL calculation that does not include nuclear effects. Forward-backward production ratios are presented and compared to theoretical predictions. These results constrain the kinematic dependence of nuclear modifications of charmonium and b-quark production in p+Pb collisions.

72 PHYSICS OF ELEMENTARY PARTICLES AND FIELDS↗

DOE OSTI2017

Measurement of differential cross sections and W + / W − cross-section ratios for W boson production in association with jets at s = 8 TeV with the ATLAS detector

This paper presents a measurement of the W boson production cross section and the W+/W- cross-section ratio, both in association with jets, in proton-proton collisions at sqrt(s) = 8 TeV with the ATLAS experiment at the Large Hadron Collider. The measurement is performed in final states containing one electron and missing transverse momentum using data corresponding to an integrated luminosity of 20.2 fb^-1. Differential cross sections for events with at least one or two jets are presented for a range of observables, including jet transverse momenta and rapidities, the scalar sum of transverse momenta of the visible particles in the event, and the transverse momentum of the W boson. For a subset of the observables, the differential cross sections of positively and negatively charged W bosons are measured separately. In the cross-section ratio of W+/W- the dominant systematic uncertainties cancel out, improving the measurement precision by up to a factor of nine. The observables and ratios selected for this paper provide valuable input for the up quark, down quark, and gluon parton distribution functions of the proton.

72 PHYSICS OF ELEMENTARY PARTICLES AND FIELDS↗

DOE OSTI2019

Measurement of fiducial and differential W + W − production cross-sections at s = 13 TeV with the ATLAS detector

A measurement of fiducial and differential cross-sections for W+W- production in proton-proton collisions at sqrt(s)=13 TeV with the ATLAS experiment at the Large Hadron Collider using an integrated luminosity of 36.1fb-1 is presented. Events with one electron and one muon are selected, corresponding to the decay of the diboson system as WW->e nu mu nu. To suppress top-quark background, events containing jets with a transverse momentum exceeding 35 GeV are not included in the measurement phase space. The fiducial cross-section, six differential distributions and the cross-section as a function of the jet-veto transverse momentum threshold are measured and compared with several theoretical predictions. Constraints on anomalous weak boson self-interactions are also presented in the framework of a dimension-six effective field theory.

72 PHYSICS OF ELEMENTARY PARTICLES AND FIELDS↗

DOE OSTI2025

Unified differentiable digital twin for the IOTA/FAST facility

As the design complexity of modern accelerators grows, there is more interest in using advanced simulations that have fast execution time or produce insights about accelerator state. One notable example of additional information are gradients of physical observables with respect to design parameters produced by differentiable simulations. The IOTA/FAST facility has recently begun a program to implement and experimentally validate a unified start-to-end differentiable digital twin to serve as a virtual accelerator test stand, allowing for rapid prototyping of new software and experiments with minimal beam time costs. In this contribution we will discuss our plans and progress. Specifically, we will cover the selection and benchmarking of both physics and ML codes, the development of generic interfaces between device models and surrogate or physics-based sections, and the export of the parameters through either a deterministic event loop or a fully asynchronous EPICS soft input/output controller. We will also discuss challenges in model calibration and uncertainty quantification, as well as future plans to support larger proton accelerators like PIPII and Booster.

Kuklev, Nikita [Fermilab]↗

DOE OSTI2023

DPFEHM: a differentiable subsurface physics simulator

The Earth’s subsurface is a key resource that provides energy via fossil fuels and geothermal sources, stores drinking water, and is used in the fight against climate change via carbon sequestration. Simulating the physical processes that occur in the Earth’s subsurface with computers enables better use of this resource. DPFEHM is a Julia package that includes computer models with a focus on the Earth’s subsurface, especially fluid flow, which is critical for the aforementioned applications. DPFEHM is able to solve the groundwater flow equations (single phase flow), Richards equation (air/water), the advection-dispersion equation, and the 2d wave equation. One of the key features of DPFEHM is that it supports automatic differentiation, so it can be integrated into machine learning workflows using frameworks such as Flux or PyTorch. The automatic differentiation capabilities give it the same performance as adjoint methods.

54 ENVIRONMENTAL SCIENCES↗

DOE OSTI2012

Derivative-based uncertainty quantification: automatic differentiation tools for SAS

Automatic differentiation, or more properly algorithmic differentiation (AD), is a technique for efficiently computing accurate derivatives for numerical models. It is based on augmenting the code with partial derivatives of elementary mathematical operations on important variables and retracing the calculation flow (in forward or reverse direction) to assemble derivatives by chain rule. The relative computational overhead associated with AD is bounded, independent of dimension, and is largely independent of the mathematical model.

Roderick, O.↗

DOE OSTI2016

Development of Techniques for Spent Fuel Assay – Differential Dieaway Final Report

This report summarizes the work done under a DNDO R&D funded project on the development of the differential dieaway method to measure plutonium in spent fuel. There are large amounts of plutonium that are contained in spent fuel assemblies, and currently there is no way to make quantitative non-destructive assay. This has led NA24 under the Next Generation Safeguards Initiative (NGSI) to establish a multi-year program to investigate, develop and implement measurement techniques for spent fuel. The techniques which are being experimentally tested by the existing NGSI project do not include any pulsed neutron active techniques. The present work covers the active neutron differential dieaway technique and has advanced the state of knowledge of this technique as well as produced a design for a practical active neutron interrogation instrument for spent fuel. Monte Carlo results from the NGSI effort show that much higher accuracy (1-2%) for the Pu content in spent fuel assemblies can be obtained with active neutron interrogation techniques than passive techniques, and this would allow their use for nuclear material accountancy independently of any information from the operator. The main purpose of this work was to develop an active neutron interrogation technique for spent nuclear fuel.

11 NUCLEAR FUEL CYCLE AND FUEL MATERIALS↗

DOE OSTI2016

Measurement of the $W+$ jets differential cross-sections in $p\bar{p}$ collisions at $\sqrt{s} = 1.96$ TeV using the CDF II Detector

In this thesis the measurements of differential cross sections for the production of the $W$-boson in association with jets in $p\bar{p}$ collisions at $\sqrt{s} = 1.96$ TeV are presented. The measurements are based on 9.0 fb$^{-1}$ of CDF Run II data (i.e., the full dataset). Only events in which the W-boson decays leptonically (i.e., W → ev and W → μv)and at least one jet is present are considered. The lepton candidates are required to have a transverse energy $E^{\ell}_T > 25$GeV and pseudorapidity in the range |n ℓ | < 1 whereas, the jets are reconstructed using the JETCLU algorithm with a radius of 0.4 requiring transverse energy $E^{jet}_T > 25$GeV and pseudorapidity in the range |η jet| < 2. The reconstructed W-boson transverse mass should be greater than 40GeV/c 2 . The differential cross sections as a function of the jet multiplicity ($N$ > or = to 1, 2, 3, 4) and the leading jet transverse energy, are measured separately for each decay channel and then combined. For a meaningful comparison with theory the measured cross-sections are unfolded to remove detector effects. The resulting particle-level cross-sections are compared to theoretical predictions.

72 PHYSICS OF ELEMENTARY PARTICLES AND FIELDS↗

DOE OSTI2017

High Temperature Heat Exchanger Design and Fabrication for Systems with Large Pressure Differentials

The project’s main purpose was to design, build and test a compact heat exchanger for supercritical carbon dioxide (sCO 2 ) power cycle recuperators. The compact recuperator is required to operate at high temperature and high pressure differentials, 169 bar (~2,500 psi), between streams of sCO 2 . Additional project tasks included building a hot air-to-sCO 2 Heater heat exchanger (HX) and design, build and operate a test loop to characterize the recuperator and heater heat exchangers. A novel counter-current microtube recuperator was built to meet the high temperature high differential pressure criteria and tested. The compact HX design also incorporated a number of features that optimize material use, improved reliability and reduced cost. The air-to-sCO 2 Heater HX utilized a cross flow, counter-current, micro-tubular design. This compact HX design was incorporated into the test loop and exceeded design expectations. The test loop design to characterize the prototype Brayton power cycle HXs was assembled, commissioned and operated during the program. Both the prototype recuperator and Heater HXs were characterized. Measured results for the recuperator confirmed the predictions of the heat transfer models developed during the project. Heater HX data analysis is ongoing.

20 FOSSIL-FUELED POWER PLANTS↗

DOE OSTI2017

The Differential Cross Section and Λ Recoil Polarization from γδ -> Κ0(ρ)

Presented is the analysis of the differential cross section and Λ recoil polarization from the reaction γδ -> Κ0(ρ). This work measured these observables over beam energies from 0.90 GeV to 3.0 GeV. These measurements are the first in this channel to cover such a wide range of energies. The data were taken using the CEBAF Large Acceptance Spectrometer (CLAS) at Jefferson Laboratory (JLAB) along with a tagged photon beam. This analysis was completed by identifying events of interest that decayed into the final state topology of π-π+,π-&rho'(ρ). Through conservation of energy and momentum, the Κ0, Λ and missing mass of the spectator proton were reconstructed. Utilizing the same analysis techniques, the observables were measured on two different experiments with good agreement. Photoproduction of strange mesons from the neutron are difficult to measure, consequently there are only a few measurements of this kind. Despite that, these reactions supply essential complementary data to those on the proton. The differential cross sections and the recoil polarization extracted, span the region where new nucleon resonances have been found from studies of the reaction γρ -> Κ+Λ. Comparisons between the Κ+Λ and Κ0Λ cross section demonstrate that possible interference terms near 1900 MeV are less pronounced in the latter. This unexpected result inspired a partial wave analyses (PWA) to be fitted to the data. The fit solution shows that this measurement fostered an improvement on the knowledge of observed resonance parameters, necessary to understanding these excited states. The study of nucleon resonances is a key motivating factor since the resonance masses can be calculated from the theory of the strong nuclear force, called quantum chromodynamics, or QCD.

72 PHYSICS OF ELEMENTARY PARTICLES AND FIELDS↗

DOE OSTI2022

Mitigate: An Adaptive Network Data Anonymization Tool Using Condensation-Based Differential Privacy

Modern network devices collect a large amount of data that can be analyzed to identify bottlenecks, anomalies, cyber-attacks, etc. Therefore, there is often a need to analyze such collections of network data quite often by an external expert or by the research community. However, these collections of data contain sensitive, proprietary information. In order for the network data to be shared, it must first be anonymized. The overall objective of this project is to develop an innovative privacy management tool to anonymize network data and achieve sufficient privacy, acceptable data utility, and efficient data analysis at the same time. No existing anonymization methods can achieve all of these at the same time. The core of this technology is a differential private clustering algorithm that provides strong privacy protection, preserves data properties important for subsequent analysis, and allows the party receiving the anonymized data to conduct analysis directly on anonymized data without the need of decryption or any extra processing. The research carried out was to design, implement and verify a solution to this problem by completing the following tasks: 1) developing the core technology; 2) developing a context based method that automatically recommends fields that must be anonymized; 3) conducted experiments showing superior results using our approach compared to existing tools, and 4) developed an intuitive but basic user interface. The research that was conducted generated novel algorithmic techniques that utilize state-of-the-art methods such as condensation, differential privacy preservation, clustering, automated tuning based on contextual awareness, and recommendation techniques to specify columns to users for anonymization leading to optimal privacy that allows research analysis on the dataset. Experiments were conducted to evaluate the efficacy of these novel algorithmic techniques by performing analysis on original non-anonymized datasets, then conducting analysis on the same yet anonymized datasets and comparing the results of the analyses. Overall, the anonymized analysis results were within 1% of the original results, verifying that the generated technology not only guarantees a high level of privacy but also enables research analysis as if it were conducted on the original dataset. Potential applications of this technology include anonymization of any type of structured network datasets that contain sensitive identifiers, such as IP addresses, that can be used in multiple applications. For example, to create an AI or machine learning model for cyber security, e.g., to detect attacks, or for performance analysis, e.g., identify bottlenecks or predict performance. In addition, a market analysis that was conducted for potential applications of this technology identified a broader range of applications of our anonymization technology beyond the network sector that includes healthcare, banking, insurance, securities, finance (FISB), data brokering, cloud services, ad sales, and government.

97 MATHEMATICS AND COMPUTING↗

DOE OSTI2023

High Energy Quasi - Differential Neutron Emission Measurements of 181 Ta and 19 F [Slides]

This presentation begins with the motivation for performing 181 Ta and 19 F high energy quasi-differential and neutron emission measurements. It then provides a discussion of significant pulse digitization upgrade. The Quasi-Differential methodology and importance for validating nuclear data are provided. Preliminary results from 181 Ta and 19 F are displayed. The presentation concludes with a discussion and future studies.

73 NUCLEAR PHYSICS AND RADIATION PHYSICS↗

DOE OSTI2022

Methodology of the Extraction of Multi-Differential Cross Sections of Charged-Current $\nu_\mu$-Argon Interactions in MicroBooNE Using Wire-Cell $\nu_\mu$CC Selection

Neutrino physics experiments rely on accurate nuclear-interaction models that are in part guided by experimental observations. Multi-differential cross section measurements are particularly valuable for exploring the underlying physics described in these models, making them a significant step forward in the field. This note presents methodology in preparation to unfold neutrino flux-averaged double and triple-differential cross sections of the inclusive muon neutrino charged-current interaction on Argon. This work builds upon the existing framework and methodology presented in recent energy dependent cross section measurements at MicroBooNE using the Wire-Cell tomographic event reconstruction. The signal definition, choice of binning, and handling of estimated detector uncertainties are discussed, and the MicroBooNE simulation model is validated over the multi-dimensional phase space of muon momentum, muon polar angle, and visible hadronic energy.

72 PHYSICS OF ELEMENTARY PARTICLES AND FIELDS↗

DOE OSTI2022

Measurement of Triple-Differential Inclusive Muon Neutrino Charged-Current Cross Sections on Argon with the MicroBooNE Detector

We report the first measurement of the differential cross section $d^2σ(E_ν)/dcos(θ_µ)dP_µ$for inclusive muon neutrino charged-current scattering on argon. This measurement utilizes data from6.5×10 20 protons on target of exposure collected using the MicroBooNE liquid argon time projection chamber located on-axis in the Fermilab Booster Neutrino Beam with a mean neutrino energy of approximately 0.8 GeV. In this note, the mapping from reconstructed kinematics to truth quantities, particularly from reconstructed to true neutrino energy, is validated by comparing the distribution of reconstructed hadronic energy in data to that of the model prediction in different muon scattering angle bins after conditional constraint from the muon momentum distribution in data. The success of this validation gives confidence that the missing energy in the MicroBooNE detector is well-modeled within its uncertainties in simulation, enabling the unfolding to an energy-dependent triple-differential measurement over muon momentum, muon scattering angle, and neutrino energy. The unfolded measurement covers an extensive phase space, providing a wealth of information useful for future LArTPC experiments measuring neutrino oscillations. Comparisons with model predictions show the best agreement with Neut 5.4.0.1 at low energy, and with NuWro 19.02.01 at higher energies, particularly at forward muon scattering angles.

72 PHYSICS OF ELEMENTARY PARTICLES AND FIELDS↗