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Engineered Membrane Vesicle Production via oprF or oprI Deletion Has Distinct Phenotypic Effects in Pseudomonas putida -putative knockouts table

Table S1, putative gene knockout targets in P. putida KT2440 to enhance vesiculation; Table S2, protein sequence identity of OmpA from E. coli K12 to P. putida KT2440 genes; Table S3, strains utilized in this study and corresponding construction details; Table S4, oligonucleotides utilized in this study; Table S5, plasmids utilized in this study; Table S6, sequences for mNeonGreen, tags, and codon-optimized genes; Figure S1, particle count per gCDW for KT2440 and knockout strains corresponding to data presented in Figure 1B; Figure S2, OD600 measurements of extracted MVs from KT2440 and knockout strains; Figure S3, particle count per gCDW for WT, ΔPP_4669, and ΔPP_1502; Figure S4, particle count per gCDW for KT2440 and knockout strains corresponding to data presented in Figure 3C; Figure S5, sizes of MVs corresponding to particle counts in Figure S4; Figure S6, particle count per gCDW for KT2440 grown on 20 mM glucose alone or 20 mM glucose plus 12.5 mM p-coumarate and 12.5 mM ferulate; Figure S7 and Figure S8, principal component analysis of the cellular fractions; Figure S9, heatmap of outer membrane proteins with differential abundance; and Figure S10, mNeonGreen (mNG) fluorescence signal for the cellular fraction and the extracellular fraction

hypervesiculation↗

Spatially Resolved Raman Spectroscopic Investigation of Uranyl Fluoride: A Case Study in the Importance of Instrument Optimization

Raman spectroscopy is an emerging technique for rapid and nondestructive analysis of nuclear materials for forensic and nonproliferation applications as it is a powerful tool for distinguishing multiple chemical forms of materials with similar stoichiometries. Recent developments in spectroscopic software have enabled rapid data collection with high-speed Raman spectroscopic mapping capabilities. However, some uranium-rich materials are susceptible to degradation in humid air and/or laser-induced phase transformations. To mitigate environmental or measurement-related sample degradation of potential samples of interest, we have taken a systematic approach to define optimized data collection parameters for high-throughput measurements of uranyl fluoride (UO 2 F 2 ), which is an important intermediate material in the nuclear fuel cycle. First, we systematically describe the influence of optical magnification (5× to 100×), laser power, and exposure time on obtained signal for identical particles of UO 2 F 2 and find that at low laser power and exposure times, comparable signal is obtained regardless of optical magnification. Second, we ensure sample integrity during data collection, and third, collect spectroscopic maps that employ optimized parameters to reduce the time required to obtain spatially resolved spectroscopic information. Reductions of 90% and 99% in measurement times are discussed as they relate to differences in resolving spectroscopic features of particles in identical mapping areas. Finally, during this work, we found that additional data processing options were needed and thus developed a customized Python script for importing, processing, analyzing, and visualizing Raman spectroscopic map data.

46 INSTRUMENTATION RELATED TO NUCLEAR SCIENCE AND ↗

Review of multi-faceted morphologic signatures of actinide process materials for nuclear forensic science

Particle morphology is an emerging signature that has the potential to identify the processing history of unknown nuclear materials. Using readily available scanning electron microscopes (SEM), the morphology of nearly any solid material can be measured within hours. Coupled with robust image analysis and classification methods, the morphological features can be quantified and support identification of the processing history of unknown nuclear materials. The viability of this signature depends on developing databases of morphological features, coupled with a rapid data analysis and accurate classification process. With developed reference methods, datasets, and throughputs, morphological analysis can be applied within days to (i) interdicted bulk nuclear materials (gram to kilogram quantities), and (ii) trace amounts of nuclear materials detected on swipes or environmental samples. In conclusion, this review aims to develop validated and verified analytical strategies for morphological analysis relevant to nuclear forensics.

36 MATERIALS SCIENCE↗

Evaluating the ProtoDUNE-SP Detector Performance to Measure a 6 GeV/c Positive Kaon Inelastic Cross Section on Argon

The ProtoDUNE Single-Phase Liquid Argon Time Projection Chamber \\ (ProtoDUNE-SP LArTPC) is a prototype for the Deep Underground Neutrino Experiment (DUNE), a future long-baseline neutrino oscillation experiment. Based at the CERN Neutrino Platform, ProtoDUNE-SP LArTPC collected data from a charged test beam in the fall of 2018. It then took data of cosmic-ray muons from November 2018 to the summer of 2020. The main goals of the prototype were to measure parameters related to charged particle passage in argon and evaluate the performance of the detector to inform future DUNE Far Detector development. The test beam provided kaons, pions, muons, protons, and electrons to the detector. These particles represent common final state particles in neutrino interactions, therefore providing information to DUNE on modeling charged particles in argon for its neutrino physics program. In addition to neutrino physics, DUNE has proposed an analysis using the DUNE Far Detector module to set limits for proton decay through the decay channel $p\rightarrow K^++\bar{\nu}$. This measurement would require information on kaons in argon, providing ProtoDUNE-SP LArTPC another opportunity to aid DUNE. This thesis describes the calibration of ProtoDUNE-SP and its detector performance, which serves as a benchmark for the performance of the DUNE Far Detector modules. A specific calibration highlighted is the evaluation of the liquid argon purity in the detector. These measurements use cosmic-ray muons reconstructed in the detector that are calibrated and matched to data from scintillator strips external to the TPC, known as the Cosmic Ray Tagger (CRT). The thesis will discuss the algorithms to match the data between the ProtoDUNE-SP LArTPC and the CRT and discuss the liquid argon purity measurements using one of the algorithms. Data sets of calibrated tracks measured the liquid argon contamination as consistently below 100 ppt oxygen equivalent. After these discussions on the ProtoDUNE-SP LArTPC detector, the thesis will present an evaluation of the inclusive inelastic, sometimes referred to as a reactive, cross section on argon of kaons from the ProtoDUNE-SP test beam with an average momentum of 6 GeV/c.

46 INSTRUMENTATION RELATED TO NUCLEAR SCIENCE AND ↗

Results on low-mass weakly interacting massive particles from a 11 kg-day target exposure of DAMIC at SNOLAB

We present constraints on the existence of weakly interacting massive particles (WIMPs) from a 11 kg-day target exposure of the DAMIC experiment at the SNOLAB underground laboratory. The observed energy spectrum and spatial distribution of ionization events with electron-equivalent energies $>$200 eV$_{\rm ee}$ in the DAMIC CCDs are consistent with backgrounds from natural radioactivity. An excess of ionization events is observed above the analysis threshold of 50 eV$_{\rm ee}$. While the origin of this low-energy excess requires further investigation, our data exclude spin-independent WIMP-nucleon scattering cross sections $\sigma_{\chi-n}$ as low as $3\times 10^{-41}$ cm$^2$ for WIMPs with masses $m_{\chi}$ from 7 to 10 GeV$c^{-2}$ . These results are the strongest constraints from a silicon target on the existence of WIMPs with $m_{\chi}$$<$9 GeV$c^{-2}$ and are directly relevant to any dark matter interpretation of the excess of nuclear-recoil events observed by the CDMS silicon experiment in 2013.

72 PHYSICS OF ELEMENTARY PARTICLES AND FIELDS↗

The information content of jet quenching and machine learning assisted observable design

Jets produced in high-energy heavy-ion collisions are modified compared to those in proton-proton collisions due to their interaction with the deconfined, strongly-coupled quark-gluon plasma (QGP). In this work, we employ machine learning techniques to identify important features that distinguish jets produced in heavy-ion collisions from jets produced in proton-proton collisions. We formulate the problem using binary classification and focus on leveraging machine learning in ways that inform theoretical calculations of jet modification: (i) we quantify the information content in terms of Infrared Collinear (IRC)-safety and in terms of hard vs. soft emissions, (ii) we identify optimally discriminating observables that are in principle calculable in perturbative QCD, and (iii) we assess the information loss due to the heavy-ion underlying event and background subtraction algorithms. We illustrate our methodology using Monte Carlo event generators, where we find that important information about jet quenching is contained not only in hard splittings but also in soft emissions and IRC-unsafe physics inside the jet. This information appears to be significantly reduced by the presence of the underlying event. We discuss the implications of this for the prospect of using jet quenching to extract properties of the QGP. Since the training labels are exactly known, this methodology can be used directly on experimental data without reliance on modeling. We outline a proposal for how such an experimental analysis can be carried out, and how it can guide future measurements.

72 PHYSICS OF ELEMENTARY PARTICLES AND FIELDS↗

Large-x partons from Jefferson Lab to the LHC

This project addressed the longitudinal quark and gluon structure of hadrons, a key topic in the 2015 and 2023 NSAC long range plans for nuclear science. The research encompassed and combined theoretical studies with advanced Quantum Chromo Dynamics (QCD) analysis of experimental data, from Jefferson Lab to the Large Hadron Collider. The results have pushed the boundaries in both aspects, and capitalized on the results and methods developed in previous grant renewals.

72 PHYSICS OF ELEMENTARY PARTICLES AND FIELDS↗

Measurement of Rayleigh Scattering in Liquid Argon at Vacuum Ultraviolet Wavelengths

Liquid argon based detectors are limited in scintillation light analysis capabilities due to inconsistent measurements of fundamental constants essential for the reconstruction of scintillation events. This experiment measures the Rayleigh scattering length of vacuum ultraviolet light propagating in liquid argon in support of liquid argon experiments. Preliminary results are presented for the Rayleigh scattering length in a range of vacuum ultraviolet wavelengths. Current data collection and analysis methods in this measurement require further advancements to understand and eliminate anomalous phenomena in the data. Future measurements in this experiment aim to precisely measure the liquid argon ultraviolet light scattering length. Results will contribute to the development of new photon system analysis methods for liquid argon experiments.

72 PHYSICS OF ELEMENTARY PARTICLES AND FIELDS↗

QLBT: a linear Boltzmann transport model for heavy quarks in a quark-gluon plasma of quasi-particles

Abstract We develop a new heavy quark transport model, QLBT, to simulate the dynamical propagation of heavy quarks inside the quark-gluon plasma (QGP) created in relativistic heavy-ion collisions. Our QLBT model is based on the linear Boltzmann transport (LBT) model with the ideal QGP replaced by a collection of quasi-particles to account for the non-perturbative interactions among quarks and gluons of the hot QGP. The thermal masses of quasi-particles are fitted to the equation of state from lattice QCD simulations using the Bayesian statistical analysis method. Combining QLBT with our advanced hybrid fragmentation-coalescence hadronization approach, we calculate the nuclear modification factor $$R_\mathrm {AA}$$ R AA and the elliptic flow $$v_2$$ v 2 of D mesons at the Relativistic Heavy-Ion Collider and the Large Hadron Collider. By comparing our QLBT calculation to the experimental data on the D meson $$R_\mathrm {AA}$$ R AA and $$v_2$$ v 2 , we extract the heavy quark transport parameter $$\hat{q}$$ q ^ and diffusion coefficient $$D_\mathrm {s}$$ D s in the temperature range of $$1-4~T_\mathrm {c}$$ 1 - 4 T c , and compare them with the lattice QCD results and other phenomenological studies.

72 PHYSICS OF ELEMENTARY PARTICLES AND FIELDS↗

Strangeness enhancement at its extremes: multiple (multi-)strange hadron production in pp collisions at \(\sqrt{s}=5.02\) TeV

The probability to observe a specific number of strange and multi-strange hadrons (nS), denoted as P(nS), is measured by ALICE at midrapidity (|y| < 0.5) in $$\sqrt{s}=5.02$$ TeV proton-proton (pp) collisions, dividing events into several multiplicity-density classes. Exploiting, for the first time, a technique based on counting the number of strange-particle candidates event-by-event, this measurement allows one to extend the study of strangeness production beyond the mean of the distribution. This constitutes a new test bench for production mechanisms, probing events with a large imbalance between strange and non-strange content. The analysis of a large-statistics data sample makes it possible to extract P(nS) up to a maximum nS of 7 for $${\text{K}}_{\text{S}}^{0}$$, 5 for Λ and $$\overline{\Lambda }$$, 4 for Ξ− and $${\overline{\Xi } }^{+}$$, and 2 for Ω− and $${\overline{\Omega } }^{+}$$. From this, the probability of producing strange hadron multiplets per event is calculated, thereby enabling the extension of the study of strangeness enhancement to extreme situations where several strange quarks hadronize in a single event at midrapidity. Moreover, comparing hadron combinations with different u and d quark compositions and equal overall s quark content, the contribution to the enhancement pattern coming from non-strangeness related mechanisms is isolated. The results are compared with state-of-the-art phenomenological models implemented in commonly used Monte Carlo event generators, including PYTHIA 8 Monash 2013, PYTHIA 8 with QCD-based Color Reconnection and Rope Hadronization (QCD-CR + Ropes), and EPOS LHC, which incorporates both partonic interactions and hydrodynamic evolution. These comparisons show that the new approach dramatically enhances the sensitivity to the different underlying physics mechanisms modeled by each generator.

Abualrob, I J↗

Particle Response of Antenna-Coupled TES Arrays: Results from SPIDER and the Laboratory

Future mm-wave and sub-mm space missions will employ large arrays of multiplexed transition-edge-sensor (TES) bolometers. Such instruments must contend with the high flux of cosmic rays beyond our atmosphere that induce ‘glitches’ in bolometer data, which posed a challenge to data analysis from the Planck bolometers. Future instruments will face the additional challenges of shared substrate wafers and multiplexed readout wiring. Here, we explore the susceptibility of modern TES arrays to the cosmic ray environment of space using two data sets: the 2015 long-duration balloon flight of the SPIDER cosmic microwave background polarimeter, and a laboratory exposure of SPIDER flight hardware to radioactive sources. We find manageable glitch rates and short glitch durations, leading to minimal effect on SPIDER analysis. We constrain energy propagation within the substrate through a study of multi-detector coincidences and give a preliminary look at pulse shapes in laboratory data.

46 INSTRUMENTATION RELATED TO NUCLEAR SCIENCE AND ↗

Deformation and Fracture Behavior of Additively Manufactured 316L Stainless Steel

Tensile deformation and fracture behavior of an additively manufactured (AM) 316L stainless steel (SS) in the as-built, stress-relieved, and solution-annealed conditions was investigated using in situ tensile testing in a scanning electron microscope with an electron back scattering diffraction (SEM–EBSD) detector. Analyses were performed to discuss the characteristic deformation and fracture process of the fine-grained AM 316L SS with and without relaxation heat treatment. The as-built 316L showed the highest strength, and both post-build heat treatments lowered the strength of the alloy. Regardless of the post-build processing, the AM 316L SS showed overall higher strength but slightly lower ductility when compared to the wrought (WT) 316L SS. Analysis of EBSD data indicated that the characteristic microstructural features from AM, such as the complex and fine grain morphology, dislocation network, pores, and silicon-rich oxides, evolved and exerted various roles during the tensile deformation and fracture processes. Further, it was obvious that the interaction of dislocation slips with oxide particles and cavities (or pores) resulted in an accelerated cracking in AM 316L SS. Overall, however, their influence on mechanical behavior was limited, as the genuinely high ductility of 316L SS could help avoid any premature or brittle fracture.

36 MATERIALS SCIENCE↗

Improving microstructures segmentation via pretraining with synthetic data

Image analysis of material microstructures through microscopy is an integral capability in the field of materials science. The topological and chemical information obtained through microscopy allow us to draw vital connections between material microstructures, properties, and processing. While scanning electron microscopy (SEM) is able to yield a considerable wealth of information interpretable by the intuition of experts, there has been considerable interest in using machine learning, convolutional neural networks (CNNs) in particular, for such image analysis task. Training CNNs for an image analysis task requires a large annotated dataset. However, in many materials science applications, obtaining a large annotated dataset is cost and labor intensive. In this work, we study the use of synthetic data to enlarge the available annotated experimental data of uranium oxide. We utilize a modified Potts model to simulate uranium oxide particles with morphologies similar to those observed experimentally. We then leverage an image-to-image translation model to synthesize the simulated particles as if they are acquired with SEM. Through this process, we obtain pairs of particle images and their corresponding SEM representations, which corresponds to pairs of annotations and images. Unlike previous works, we leverage synthetic data for pretraining a CNN model prior, and finetune that model further with experimental data. We experimentally demonstrate that using synthetic data as incremental learning process benefits the overall performance compared to training a model on combined synthetic and experimental data.

36 MATERIALS SCIENCE↗

Self-interacting neutrinos, the Hubble parameter tension, and the cosmic microwave background

Here, we perform a comprehensive study of cosmological constraints on nonstandard neutrino self-interactions using cosmic microwave background and baryon acoustic oscillation data. We consider different scenarios for neutrino self-interactions distinguished by the fraction of neutrino states allowed to participate in self-interactions and how the relativistic energy density, N eff , is allowed to vary. Specifically, we study cases in which all neutrino states self-interact and N eff varies; two species free-stream, which we show alleviates tension with laboratory constraints, while the energy in the additional interacting states varies; and a variable fraction of neutrinos self-interact with either the total N eff fixed to the Standard Model value or allowed to vary. In no case do we find compelling evidence for new neutrino interactions or nonstandard values of N eff . In several cases, we find additional modes with neutrino decoupling occurring at lower redshifts z dec ~ 10 3–4 . We do a careful analysis to examine whether new neutrino self-interactions solve or alleviate the so-called H 0 tension and find that, when all Planck 2018 CMB temperature and polarization data are included, none of these examples eases the tension more than allowing a variable N eff comprised of free-streaming particles. Although we focus on neutrino interactions, these constraints are applicable to any light relic particle.

72 PHYSICS OF ELEMENTARY PARTICLES AND FIELDS↗

Riverine Plastic Pollution: Sampling and Analysis Methods

Riverine plastic pollution has been found in all major U.S. rivers, but the exact amount of plastic being released to the oceans has not been quantified. Field studies conducted in U.S. rivers have used a range of sampling and analysis techniques and rarely measured the mass of the plastic collected. Measurements of riverine plastic pollution are needed to calibrate and validate models used to estimate the U.S. riverine plastic emissions to the oceans. This report surveys measurement methods used to quantify riverine pollution and current estimates of U.S. riverine plastic pollution from measurements and models. Measurement methods include field sampling and laboratory analysis. Field sampling methods are described for large (macro) and small (micro) plastic particles. Laboratory analysis methods are described for macro and microplastic with an emphasis on the detailed characterization processes of microplastics. Waterborne leachate analysis is also briefly described. Three models are described that estimate plastic pollution based on mismanaged plastic waste in the river catchment basins. The models were validated and calibrated with global data sources. The data sources were predominantly outside of the U.S., where the magnitude and composition of plastic pollution is different than what is found in U.S. rivers. Comprehensive measurements of riverine plastics are needed not only to characterize the riverine plastic pollution, but also parameterize and validate models of plastic fate and transport. This report also describes five key U.S. rivers that span a range of sizes and environmental conditions that could be sampled to obtain data to support characterization and model development of plastic pollution from rivers to oceans. Sampling and analysis protocol recommendations are made to ensure the highest quality of data are collected in the five rivers.

54 ENVIRONMENTAL SCIENCES↗

Improving Fission Products at CARIBU: Near Field Detection (Q2/FY24 Quarterly Progress Report)

We continue to make progress in the analysis of 111 Ag decay data to determine gamma-ray intensities with the aim of improving these intensities to below 1% precision. The correctness of detection efficiencies is integral to obtaining accurate and precise results. While Geant4 provides us with efficiencies for detection of a coincidence event of a beta-particle with a 96, 245, or 342 gamma-ray, as outlined in Figure 1, it is important that we validate these results with the efficiencies obtained from the experimental decay data.

73 NUCLEAR PHYSICS AND RADIATION PHYSICS↗

Experimental Report: Multi-Instrument Comparison of AAF Size Distribution Instruments

Aerosols are particles suspended in the atmosphere, ranging in size from nanometers to micrometers. Their size distribution affects key atmospheric processes, including nucleation, coagulation, scavenging, activation, and radiative properties (Seinfeld and Pandis 2016). Aerosol size distribution is a critical parameter in atmospheric science, influencing processes such as cloud formation and radiative forcing. Accurate representation of aerosol size distributions is essential for understanding their impact on climate, air quality, and human health. However, aerosol size and composition vary significantly across time and space due to meteorological conditions and natural or anthropogenic sources. (Wu and Boor 2021). Various instruments are used to measure aerosol size distributions, each with distinct principles, advantages, and limitations. This report begins with an in-depth overview of aerosol size-distribution comparison studies, focusing on the passive cavity aerosol spectrometer probe (PCASP), portable optical particle spectrometer (POPS), ultra-high-sensitivity aerosol spectrometer (UHSAS), aerodynamic particle sizer (APS), and scanning mobility particle sizer (SMPS). All of these instruments are used by the U.S. Department of Energy Atmospheric Radiation Measurement (ARM) Aerial Facility (AAF), which commissioned this comparison and report. The report evaluates the strengths and weaknesses of these instruments, highlights their applications, and discusses efforts to merge data from multiple instruments for comprehensive analysis.

54 ENVIRONMENTAL SCIENCES↗

Measurement of Neutron Multiplicity in Charged Current Neutrino Interactions on Oxygen

The Accelerator Neutrino Neutron Interaction Experiment (ANNIE) is a 26-ton gadolinium-doped water Cherenkov detector located 100~meters downstream in the Booster Neutrino Beam (BNB) at the Fermi National Accelerator Laboratory (Fermilab). Its primary goals are to (1) measure the neutron yield from $\nu_\mu$ interactions as a function of momentum transfer $Q^2$ so that neutrino-nucleus interaction models can be better constrained, and (2) demonstrate the power of novel, fast-timing detectors with the first deployment of Large Area Picosecond PhotoDetectors (LAPPDs). Current knowledge of neutrino-nucleus interactions fall short in modeling the topologies of such interactions, leading to inaccurate reconstruction of event kinematics such as particle energy, direction, and vertex. As a consequence, the accuracy of cross section measurements is impacted, which is necessary for precise physics measurements. Neutrons are an indication of inelasticity and affect the determination of the energy of the parent neutrino. Quantifying the neutron yield is a step towards reducing the associated uncertainties, and thus improving our understanding of these complex interactions and benefiting the next generation of long-baseline neutrino experiments. ANNIE will make use of LAPPDs to measure neutron multiplicity of CC-0$\pi$ $\nu_\mu$ interactions on oxygen, making it the first experiment to deploy an array of these photodetectors. Because the LAPPD is a novel photodetection technology, much customization is required to integrate it into existing electronics. The first half of this thesis covers the significant progress made towards the first deployment of the LAPPD system. From its test stand at Fermilab, the LAPPD system was systematically tested and put together until deployment readiness was achieved. I present my contributions to the design, fabrication, and testing of the waterproof housing and cables, and the commissioning of the LVHV board that powers the LAPPD and its readout electronics. These efforts brought the LAPPD system significantly closer to deployment, and eventually first data. The second half of this thesis presents the vertex and energy reconstruction algorithms developed to analysis the beam data with PMT-only information. While much progress has been made towards the deployment of LAPPDs, with several in the detector tank, efforts to integrate the LAPPD datastream are in progress. Thus, I developed a ring edge detection technique using PMT data to fit the muon vertex and determine its energy. The analysis in this thesis finds average neutron yields of $\Bar{n}_{data} = 0.452 \pm 0.039 (\text{stat}) \pm 0.27 (\text{sys})$ for a selection of muon neutrino candidates in the fiducial volume of ANNIE and corrected with an averaged neutron detection efficiency. An equivalent analysis for simulated beam data results in an average neutron yield of $\Bar{n}_{MC} = 0.582 \pm 0.018 (\text{stat}) \pm 0.25 (\text{sys})$. Future work includes application of efficiency corrections at a positional level, quantification of all systematic uncertainties, and neutron multiplicity measurements with other event topologies.

43 PARTICLE ACCELERATORS↗