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DOE OSTI2022

First SELAP Algorithm Operational Experience of the New LLRF 3.0 RF Control System

The JLAB LLRF 3.0 system has been developed and is replacing the 30-year-old LLRF systems in the CEBAF accelerator. The LLRF system builds upon 25 years of design and operational RF control experience (digital and analog), and our recent collaboration in the design of the LCLSII LLRF system. The new system also incorporates a cavity control algorithm using a fully functional phase and amplitude locked Self Exciting Loop (SELAP). The first system (controlling 8 cavities) was installed and commissioned in August of 2021. Since then the new LLRF system has been operating with cavity gradients up to 20 MV/m, and electron beam currents up to 350 uA. This paper discusses the operational experience of the LLRF 3.0 SELAP algorithm along with other software and firmware tools like cavity and klystron characterization and quench detection.

Plawski, T. E.↗

DOE OSTI2024

Unraveling the impact of initial choices and in-loop interventions on learning dynamics in autonomous scanning probe microscopy

The current focus in Autonomous Experimentation (AE) is on developing robust workflows to conduct the AE effectively. This entails the need for well-defined approaches to guide the AE process, including strategies for hyperparameter tuning and high-level human interventions within the workflow loop. This paper presents a comprehensive analysis of the influence of initial experimental conditions and in-loop interventions on the learning dynamics of Deep Kernel Learning (DKL) within the realm of AE in scanning probe microscopy. We explore the concept of the “seed effect,” where the initial experiment setup has a substantial impact on the subsequent learning trajectory. Additionally, we introduce an approach of the seed point interventions in AE allowing the operator to influence the exploration process. Using a dataset from Piezoresponse Force Microscopy on PbTiO 3 thin films, we illustrate the impact of the “seed effect” and in-loop seed interventions on the effectiveness of DKL in predicting material properties. The study highlights the importance of initial choices and adaptive interventions in optimizing learning rates and enhancing the efficiency of automated material characterization. This work offers valuable insights into designing more robust and effective AE workflows in microscopy with potential applications across various characterization techniques.

47 OTHER INSTRUMENTATION↗

DOE OSTI2022

Enabling Modular Autonomous Feedback‐Loops in Materials Science through Hierarchical Experimental Laboratory Automation and Orchestration

Abstract Materials acceleration platforms (MAPs) operate on the paradigm of integrating combinatorial synthesis, high‐throughput characterization, automatic analysis, and machine learning. Within a MAP, one or multiple autonomous feedback loops may aim to optimize materials for certain functional properties or to generate new insights. The scope of a given experiment campaign is defined by the range of experiment and analysis actions that are integrated into the experiment framework. Herein, the authors present a method for integrating many actions within a hierarchical experimental laboratory automation and orchestration (HELAO) framework. They demonstrate the capability of orchestrating distributed research instruments that can incorporate data from experiments, simulations, and databases. HELAO interfaces laboratory hardware and software distributed across several computers and operating systems for executing experiments, data analysis, provenance tracking, and autonomous planning. Parallelization is an effective approach for accelerating knowledge generation provided that multiple instruments can be effectively coordinated, which the authors demonstrate with parallel electrochemistry experiments orchestrated by HELAO. Efficient implementation of autonomous research strategies requires device sharing, asynchronous multithreading, and full integration of data management in experimental orchestration, which to the best of the authors’ knowledge, is demonstrated for the first time herein.

36 MATERIALS SCIENCE↗

DOE OSTI2023

Cut site preference allows influenza A virus PA-X to discriminate between host and viral mRNAs

Many viruses block host gene expression to take over the infected cell. This process, termed host shutoff, is thought to promote viral replication by preventing antiviral responses and redirecting cellular resources to viral processes. Several viruses from divergent families accomplish host shutoff through RNA degradation by endoribonucleases. However, viruses also need to ensure expression of their own genes. The influenza A virus endoribonuclease PA-X solves this problem by sparing viral mRNAs and some host RNAs necessary for viral replication. Here, to understand how PA-X distinguishes between RNAs, we characterized PA-X cut sites transcriptome-wide using 5' rapid amplification of complementary DNA ends coupled to high-throughput sequencing. This analysis, along with RNA structure predictions and validation experiments using reporters, shows that PA-Xs from multiple influenza strains preferentially cleave RNAs at GCUG tetramers in hairpin loops. Importantly, GCUG tetramers are enriched in the human but not the influenza transcriptome. Moreover, optimal PA-X cut sites inserted in the influenza A virus genome are quickly selected against during viral replication in cells. This finding suggests that PA-X evolved these cleavage characteristics to preferentially target host over viral mRNAs in a manner reminiscent of cellular self versus non-self discrimination.

59 BASIC BIOLOGICAL SCIENCES↗

DOE OSTI2024

Precision-controlled ultrafast electron microscope platforms. A case study: Multiple-order coherent phonon dynamics in 1T-TaSe2 probed at 50 fs–10 fm scales

We report on the first detailed beam tests attesting the fundamental principle behind the development of high-current-efficiency ultrafast electron microscope systems where a radio frequency (RF) cavity is incorporated as a condenser lens in the beam delivery system. To allow for the experiment to be carried out with a sufficient resolution to probe the performance at the emittance floor, a new cascade loop RF controller system is developed to reduce the RF noise floor. Temporal resolution at 50 fs in full-width-at-half-maximum and detection sensitivity better than 1% are demonstrated on exfoliated 1T-TaSe2 system under a moderate repetition rate. To benchmark the performance, multi-terahertz edge-mode coherent phonon excitation is employed as the standard candle. The high temporal resolution and the significant visibility to very low dynamical contrast in diffraction signals via high-precision phase-space manipulation give strong support to the working principle for the new high-brightness femtosecond electron microscope systems.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

DOE OSTI2022

Mechanisms Engineering Test Loop (METL) Operations and Testing Report (FY2022)

This report documents the operations, testing, maintenance, and improvements that were performed at the Mechanisms Engineering Test Loop (METL) during FY2022. The METL facility had a very successful fourth year of operations and went through some new experiences such as taking the facility from its frozen state in October 2021 and thawing the facility and also recovering from an oxide plug in one of the cold trap lines. After the facility was fully thawed, the METL staff maintained the facility in a continuous molten state – either flowing sodium or a static flow condition. METL facility continued supporting the Gear Test Assembly (GTA) testing and hosted its first 28” test vessel experiment, called the Thermal Hydraulic Experimental Test Article (THETA) which was inserted into Test Vessel 4. Work to accommodate two additional experiments, a gripper test article (GrTA) and a flow sensor test article (F-STAr) continued as they are expected to make their debut in FY2023. In addition, the steam piping for the B308 scrubber unit was replaced with stainless steel piping and controls and new parts for the scrubber were purchased – such as a new pump, new storage tank, and new blower and motor. These components will ultimately replace the existing scrubber components when those 1970’s era require replacement.

42 ENGINEERING↗

DOE OSTI2024

Two-loop contributions of axion-like particles to electromagnetic and chromomagnetic form factors

Abstract Axions and axion-like particles emerge in many models for physics beyond the Standard Model. Thus, they have gained increasing research interest in both experimental and theoretical physics apart from their original proposition as a solution to the strong CP -problem. Among other aspects it has recently been shown that ALPs can potentially provide a solution to the long-lasting discrepancy between theory and experiment of the anomalous magnetic moment of the muon. Provided that the ALP has flavor-violating couplings to leptons, they can also mediate flavor-violating decays like $$\mu \rightarrow e\gamma $$ μ → e γ . Both processes are mediated through related form factors that we compute to two-loop order. We further show numerical implications of our calculations and how they might affect constraints on ALP couplings derived from experiments.

72 PHYSICS OF ELEMENTARY PARTICLES AND FIELDS↗

DOE OSTI2021

Experimental and computational investigations of ethane and ethylene kinetics with copper oxide particles for Chemical Looping Combustion

In this work, reaction pathways for the oxidation of methane, ethane, and ethylene with CuO was obtained by ReaxFF Molecular Dynamics (MD) simulations between temperatures of 1000 K and 2000 K. Experiments in a fixed-bed flow reactor were preformed with methane, ethane, and ethylene at temperatures ranging from 500 K to 1000 K with time-dependent species measurements from an Electron-Ionization Molecular Beam Mass Spectrometer (MBMS), and species validation with Gas Chromatography (GC) for detection of complete and intermediate combustion products. The MBMS and GC allow for the detection of oxygenated species and larger species produced from radical reformation. The simulation and experiment agree on the production of such species as CH 3 CHO, CH 2 O, CO, and H 2 O, which allow for the creation of simple C1 and C2 reaction pathways, which can be used in kinetic models of C2 species and larger fuels such as biofuels, which inherently depend on C1 and C2 kinetics and reaction pathway. The simulation and experiment disagree on the formation of C 2 H 2 , CH 3 OH, and CO 2 with large amounts of C 2 H 2 being measured in the ethylene oxidation simulations and CH 3 OH being formed in methane oxidation simulations, while neither species were experimentally found. In the case of CO 2 large amounts of CO 2 are rapidly produced in experiments with C2 fuels at 800 K, while little-to-no CO 2 was observed in simulations. This is believed to be resulting from the extremely short timescale of the simulations, preventing total oxidation of the fuel. Here, the differences in products produced between simulation and experiment allow for the potential to modify the ReaxFF potential functions to more accurately model the experimental products of Cu–H–O–C reaction kinetics.

70 PLASMA PHYSICS AND FUSION TECHNOLOGY↗

DOE OSTI2023

Measurement of the muon anomalous precession frequency at the Muon g − 2 Experiment at Fermilab

The anomalous magnetic moment of the muon, $a_\mu = \frac{g-2}{2}$ is the fractional deviation of the muon $g$-factor from the value of 2. It emerges as the cumulative effect of the virtual particles participating in the muon interaction with a magnetic field via quantum loop corrections. Its value encodes all the possible interactions between the virtual particles and, for this reason, represents an important test of the Standard Model (SM). In particular, any deviation from the SM theoretical evaluation could be due to new physics contributions. The new Muon $g-2$ (E989) Experiment at Fermilab is currently operating to repeat and improve the previous E821 experiment at Brookhaven National Laboratory (BNL), aiming to reduce the experimental error by a factor of 4 to the final accuracy of 140 parts per billion (ppb). On April 7th, 2021, the E989 collaboration published the first result based on the first year of data taking (Run-1), measuring $a_\mu = 0.001~165~920~40(54)$ with a precision of 460 ppb. The measured value is consistent with the BNL measurement and strengthens the long-standing tension with the data-driven SM prediction to a combined discrepancy of 4.2$\sigma$. On the theory side, however, new efforts involving lattice-QCD techniques are starting to question the current consensus on the theoretical prediction, demanding new improvements on both the experimental and theoretical sides. The E989 collaboration is now finalizing the analysis of Run-2 and Run-3 data and a new publication is expected in the first half of 2023 with a combined statistical uncertainty of 200 ppb. The anomalous magnetic moment $a_\mu$ is measured as the ratio between the muon spin anomalous precession frequency, $\omega_a$, and the average magnetic field experienced by the muons as they circulate in the storage ring. This thesis presents a precession frequency analysis of the Run-1 data and an evaluation of the related systematic uncertainties. A new positron reconstruction developed for the analysis of the subsequent data-taking periods, aiming to reduce some of the major systematic uncertainties of the $\omega_a$ measurement, is presented. The author's involvement in the production of the Run-2/5 data and in the precise calibration of the detectors is discussed. Finally, the complete Run-1 $a_\mu$ result is presented.

43 PARTICLE ACCELERATORS↗

DOE OSTI2020

As-run thermal-hydraulic analysis of the EPRI-3 experiment

The EPRI-3 experiment was designed to irradiate various types of reactor internal component steels at a temperature of 288°C. The specimens were irradiated in an instrumented test train inside a pressurized water loop in the center lobe of the ATR during cycles 155B and 158B. Temperature was monitored using thermocouples placed at the top of the test train and melt wires placed within the test train. The purpose of this analysis is to calculate specimen temperature using measured data on reactor power and as-run calculations of heating rates of the test train. The experiment contains four thermocouples and several melt wires spanning the temperature range 239°C to 327°C. The accuracy of the model is assessed by comparing the measured and calculated in-pile tube inlet to outlet temperature difference, comparing the measured and calculated thermocouple temperatures, and comparing the calculated melt wire temperature to the temperature range indicated by examination of the melt wires.

22 GENERAL STUDIES OF NUCLEAR REACTORS↗

DOE OSTI2022

Mechanism of tethered agonist-mediated signaling by polycystin-1

Mutations of polycystin-1 (PC1) are the major cause (85% of cases) of autosomal dominant polycystic kidney disease (ADPKD), which is the fourth leading cause of kidney failure. PC1 is thought to function as an atypical G protein-coupled receptor, yet the mechanism by which PC1 regulates G-protein signaling remains poorly understood. A significant portion of ADPKD mutations of PC1 encode a protein with defects in maturation or reduced function that may be amenable to functional rescue. In this work, we have combined complementary biochemical and cellular assay experiments and accelerated molecular simulations, which revealed an allosteric transduction pathway in activation of the PC1 C-terminal fragment. Our findings will facilitate future rational drug design efforts targeting the PC1 signaling function. Polycystin-1 (PC1) is an important unusual G protein-coupled receptor (GPCR) with 11 transmembrane domains, and its mutations account for 85% of cases of autosomal dominant polycystic kidney disease (ADPKD). PC1 shares multiple characteristics with Adhesion GPCRs. These include a GPCR proteolysis site that autocatalytically divides these proteins into extracellular, N-terminal, and membrane-embedded, C-terminal fragments (CTF), and a tethered agonist (TA) within the N-terminal stalk of the CTF that is suggested to activate signaling. However, the mechanism by which a TA can activate PC1 is not known. Here, we have combined functional cellular signaling experiments of PC1 CTF expression constructs encoding wild type, stalkless, and three different ADPKD stalk variants with all-atom Gaussian accelerated molecular dynamics (GaMD) simulations to investigate TA-mediated signaling activation. Correlations of residue motions and free-energy profiles calculated from the GaMD simulations correlated with the differential signaling abilities of wild type and stalk variants of PC1 CTF. They suggested an allosteric mechanism involving residue interactions connecting the stalk, Tetragonal Opening for Polycystins (TOP) domain, and putative pore loop in TA-mediated activation of PC1 CTF. Key interacting residues such as N3074–S3585 and R3848–E4078 predicted from the GaMD simulations were validated by mutagenesis experiments. Together, these complementary analyses have provided insights into a TA-mediated activation mechanism of PC1 CTF signaling, which will be important for future rational drug design targeting PC1.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

DOE OSTI2023

Release on the Virtual Test Bed of a Molten Salt Reactor Experiment SAM-Pronghorn Coupled Model using the Domain Overlapping Approach

The nuclear industry is taking leaps in innovations with companies seeking a sustainable energy future through advanced nuclear reactors. The Department of Energy (DOE)’s Nuclear Energy Advanced Modeling and Simulation (NEAMS) program seeks to substantiate and bolster the deployment of advanced reactors through flexible multifidelity, multiphysics simulations of advanced nuclear reactors. Applications like SAM for one-dimensional systems thermalhydraulics, and Pronghorn for multidimensional coarse mesh thermal-hydraulics, are geared to support innovations in industry by facilitating design, optimization, and licensing of advanced nuclear reactors. Coupling systems thermal-hydraulics and computational fluid dynamics codes can be difficult as the pressure coupling converges slowly; however, it is important to obtain the desired accuracy in each part of the primary loop. The authors of this model created an Overlapping-Domain Coupling (ODC) approach to coupling SAM and Pronghorn. Leveraging this coupling technique, a Molten Salt Reactor Experiment (MSRE) model was developed and released to the NEAMS/National Reactor Innovation Center (NRIC) Virtual Test Bed (VTB). The MSRE was chosen to be modeled because of the wealth of experimental data available and because of the strong physics coupling between the core and primary circuit. This paper contextualizes the history of the MSRE, describes the thermal hydraulics models used, and detail the implementation of multidimensional thermal-hydraulics and system codes based on the ODC method for the MSRE model. Finally, this paper presents how other modelers could apply the SAM Pronghorn ODC for other advanced reactor models.

22 GENERAL STUDIES OF NUCLEAR REACTORS↗

DOE OSTI2024

Light dilaton in rare meson decays and extraction of its CP property

Abstract The dilatonϕis a pseudo-Nambu-Goldstone boson associated with the spontaneous breaking of scale invariance in a nearly conformal theory, and couples to the trace of the stress-energy tensor. We analyze experimental constraints on a light dilaton with mass in the MeV–GeV range from rare meson decays. New model-independent inclusive bounds for theb→sϕtransition largely exclude the parameter space of a light dilaton that could explain the muong− 2 anomaly. Despite similarities between a dilaton and a Higgs-portal scalar, the dilaton-photon coupling is enhanced compared to the Higgs-portal scalar due to contributions from loops of the conformal sector. Consequently, the shortened lifetime of the dilaton relaxes bounds fromK→π+ invisible searches at the NA62 experiment and constraints from the Big Bang Nucleosynthesis. We utilize this fact to search for the dilaton signature at a lepton collider such as the ongoing Belle II experiment. Further, we demonstrate how to extract the CP property of the dilaton using the variation of the differential cross-section ofe + e − →e + e − ϕwith the azimuthal angle between the outgoing leptons.

Physics↗

DOE OSTI2020

Cas9 interrogates DNA in discrete steps modulated by mismatches and supercoiling

The CRISPR-Cas9 nuclease has been widely repurposed as a molecular and cell biology tool for its ability to programmably target and cleave DNA. Cas9 recognizes its target site by unwinding the DNA double helix and hybridizing a 20-nucleotide section of its associated guide RNA to one DNA strand, forming an R-loop structure. A dynamic and mechanical description of R-loop formation is needed to understand the biophysics of target searching and develop rational approaches for mitigating off-target activity while accounting for the influence of torsional strain in the genome. Here we investigate the dynamics of Cas9 R-loop formation and collapse using rotor bead tracking (RBT), a single-molecule technique that can simultaneously monitor DNA unwinding with base-pair resolution and binding of fluorescently labeled macromolecules in real time. By measuring changes in torque upon unwinding of the double helix, we find that R-loop formation and collapse proceed via a transient discrete intermediate, consistent with DNA:RNA hybridization within an initial seed region. Using systematic measurements of target and off-target sequences under controlled mechanical perturbations, we characterize position-dependent effects of sequence mismatches and show how DNA supercoiling modulates the energy landscape of R-loop formation and dictates access to states competent for stable binding and cleavage. Consistent with this energy landscape model, in bulk experiments we observe promiscuous cleavage under physiological negative supercoiling. The detailed description of DNA interrogation presented here suggests strategies for improving the specificity and kinetics of Cas9 as a genome engineering tool and may inspire expanded applications that exploit sensitivity to DNA supercoiling.

59 BASIC BIOLOGICAL SCIENCES↗

DOE OSTI2021

Structural basis for differential recognition of phosphohistidine-containing peptides by 1-pHis and 3-pHis monoclonal antibodies

In 2015, monoclonal antibodies (mAbs) that selectively recognize the 1-pHis or 3-pHis isoforms of phosphohistidine were developed by immunizing rabbits with degenerate Ala/Gly peptides containing the nonhydrolyzable phosphohistidine (pHis) analog- phosphotriazolylalanine (pTza). Here, we report structures of five rabbit mAbs bound to cognate pTza peptides: SC1-1 and SC50-3 that recognize 1-pHis, and their 3-pHis–specific counterparts, SC39-4, SC44-8, and SC56-2. These cocrystal structures provide insights into the binding modes of the pTza phosphate group that are distinct for the 1- and 3-pHis mAbs with the selectivity arising from specific contacts with the phosphate group and triazolyl ring. The mode of phosphate recognition in the 3-pHis mAbs recapitulates the Walker A motif, as present in kinases. The complementarity-determining regions (CDRs) of four of the Fabs interact with the peptide backbone rather than peptide side chains, thus conferring sequence independence, whereas SC44-8 shows a proclivity for binding a GpHAGA motif mediated by a sterically complementary CDRL3 loop. Specific hydrogen bonding with the triazolyl ring precludes recognition of pTyr and other phosphoamino acids by these mAbs. Kinetic binding experiments reveal that the affinity of pHis mAbs for pHis and pTza peptides is submicromolar. Bound pHis mAbs also shield the pHis peptides from rapid dephosphorylation. The epitope–paratope interactions illustrate how these anti-pHis antibodies are useful for a wide range of research techniques and this structural information can be utilized to improve the specificity and affinity of these antibodies toward a variety of pHis substrates to understand the role of histidine phosphorylation in healthy and diseased states.

59 BASIC BIOLOGICAL SCIENCES↗

DOE OSTI2022

A 20 Gbps PAM4 data transmitter ASIC for particle physics experiments

We present the design and test results of a novel data transmitter ASIC operating up to 20.48 Gbps with 4-level Pulse-Amplitude-Modulation (PAM4) for particle physics experiments. This ASIC, named GBS20, is fabricated in a 65 nm CMOS technology. Two serializers share a 5.12 GHz Phase Locked Loop (PLL) clock. The outputs from the serializers are combined into a PAM4 signal that directly drives a Vertical-Cavity-Surface-Emitting-Laser (VCSEL). The input data channels, each at 1.28 Gbps, are scrambled with an internal 2$^{7}$-1 Pseudo-Random Binary Sequence (PRBS), which also serves as a frame aligner. GBS20 is tested to work at 10.24 and 20.48 Gbps with a VCSEL-based Transmitter-Optical-Subassembly (TOSA). The power consumption of GBS20 is below 238 mW and reduced to 164 mW in the low-power mode.

46 INSTRUMENTATION RELATED TO NUCLEAR SCIENCE AND ↗

DOE OSTI2024

Code Validation of SAM Using Forced and Natural Circulation Data from NACIE-UP Benchmark

Heavy liquid metals (HLMs) are promising candidates as coolants of Generation IV fast reactors due to their thermophysical properties. In the last decade, experimental work has been proposed as part of research and development efforts to develop such systems. In this context, researchers from the Brasimone Research Center have conducted many experiments using the Natural Circulation Experiment Upgrade (NACIE-UP) facility to study the thermofluid dynamic behavior of HLMs in rod bundle configurations with or without wire wrappers. This facility consists of a rectangular loop operated with lead-bismuth eutectic. Sensors across the loop monitor relevant parameters, i.e. temperatures, heat transfer, and flow conditions. Here, in the present work, we carefully select published data from NACIE-UP to validate the System Analysis Module (SAM), a modern system analysis code developed at Argonne National Laboratory. We developed one SAM model using specifications of the facility geometry and materials existing in relevant papers and reports. On top of that, these references provided the boundary conditions for simulating natural circulation and forced convection experiments in either steady or transient conditions. The SAM model simulates five test cases with diverse operating conditions. Ultimately, the code is proven to predict temperatures and mass flow rates that closely match the experiments. The discrepancies between numerical predictions and diverse transients are limited to a few degrees Celsius, showcasing that SAM is well suited for analyzing nuclear systems relying on HLM coolants.

advanced reactors↗

DOE OSTI2020

As-run thermal-hydraulics analysis of the EPRI-2 experiment

The EPRI-2 experiment was designed to irradiate various types of reactor pressure vessel steels at a temperature of 288°C (PLN-3934). The specimens were irradiated in a non-instrumented test train inside a pressurized water loop in the center lobe of the ATR during PALM cycle 153B. Temperature was indicated by post-irradiation examination of melt wires placed within the test train. The purpose of this analysis is to calculate specimen temperature using measured data on reactor power and as-run calculations of heating rates of the test train. The experiment contains several melt wires spanning the temperature range 239°C to 327°C. The accuracy of the model is assessed by comparing the measured and calculated in-pile tube inlet to outlet temperature difference, and comparing the calculated specimen temperature to the temperature range indicated by examination of the melt wires.

22 GENERAL STUDIES OF NUCLEAR REACTORS↗