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DOE OSTI2022

The Latent Dirichlet Allocation model applied to airborne LiDAR data: A case study on mapping forest degradation associated with fragmentation and fire in the Amazon region

1. LiDAR data are being increasingly used to provide a detailed characterization of the vertical profile of forests. This characterization enables the generation of new insights on the influence of environmental drivers and anthropogenic disturbances on forest structure as well as on how forest structure influences important ecosystem functions and services. Unfortunately, extracting information from LiDAR data in a way that enables the spatial visualization of forest structure, as well as its temporal changes, is challenging due to the high dimensionality of these data. 2. In this study, we show how the Latent Dirichlet Allocation model applied to LiDAR data (LidarLDA) can be used to identify forest structural types and how the relative abundance of these forest types changes throughout the landscape. The code to fit this model is made available through the open-source r package LidarLDA in github. We illustrate the use of LidarLDA both with simulated data and data from a large-scale fire experiment in the Brazilian Amazon region. 3. Using simulated data, we demonstrate that LidarLDA accurately identifies the number of forest types as well as their spatial distribution and absorptance probabilities. For the empirical data, we found that LidarLDA detects both landscape-level patterns in forest structure as well as the strong interacting effect of fire and forest fragmentation on forest structure based on the experimental fire plots. More specifically, LidarLDA reveals that proximity to forest edge exacerbates the impact of fires, and that burned forests remain structurally different from unburned areas for at least 7 years, even when burned only once. Importantly, LidarLDA generates insights on the 3D structure of forest that cannot be obtained using more standard approaches that just focus on top-of-the-canopy information (e.g. canopy height models based on LiDAR data). 4. By enabling the mapping of forest structure and its temporal changes, we believe that LidarLDA will be of broad utility to the ecological research community.

54 ENVIRONMENTAL SCIENCES↗

DOE OSTI2021

Combinations of Single Chain Variable Fragments From HIV Broadly Neutralizing Antibodies Demonstrate High Potency and Breadth

Broadly neutralizing antibodies (bNAbs) are currently being assessed in clinical trials for their ability to prevent HIV infection. Single chain variable fragments (scFv) of bNAbs have advantages over full antibodies as their smaller size permits improved diffusion into mucosal tissues and facilitates vector-driven gene expression. We have previously shown that scFv of bNAbs individually retain significant breadth and potency. Here we tested combinations of five scFv derived from bNAbs CAP256-VRC26.25 (V2-apex), PGT121 (N332-supersite), 3BNC117 (CD4bs), 8ANC195 (gp120-gp41 interface) and 10E8v4 (MPER). Either two or three scFv were combined in equimolar amounts and tested in the TZM-bl neutralization assay against a multiclade panel of 17 viruses. Experimental IC 50 and IC 80 data were compared to predicted neutralization titers based on single scFv titers using the Loewe additive and the Bliss-Hill model. Like full-sized antibodies, combinations of scFv showed significantly improved potency and breadth compared to single scFv. Combinations of two or three scFv generally followed an independent action model for breadth and potency with no significant synergy or antagonism observed overall although some exceptions were noted. The Loewe model underestimated potency for some dual and triple combinations while the Bliss-Hill model was better at predicting IC 80 titers of triple combinations. Given this, we used the Bliss-Hill model to predict the coverage of scFv against a 45-virus panel at concentrations that correlated with protection in the AMP trials. Using IC 80 titers and concentrations of 1μg/mL, there was 93% coverage for one dual scFv combination (3BNC117+10E8v4), and 96% coverage for two of the triple combinations (CAP256.25+3BNC117+10E8v4 and PGT121+3BNC117+10E8v4). Combinations of scFv, therefore, show significantly improved breadth and potency over individual scFv and given their size advantage, have potential for use in passive immunization.

60 APPLIED LIFE SCIENCES↗

DOE OSTI2023

Population Subdivision in the Gopher Frog (Rana capito) across the Fragmented Longleaf Pine-Wiregrass Savanna of the Southeastern USA

Delineating genetically distinct population segments of threatened species and quantifying population connectivity are important steps in developing effective conservation and management strategies aimed at preventing extinction. The gopher frog (Rana capito) is a xeric-adapted, pond-breeding species endemic to the Gulf and Atlantic coastal plains of the southeastern United States. This species has experienced extensive habitat loss and fragmentation in the formerly widespread longleaf pine-wiregrass savanna where it lives, resulting in individual abundance declines and population extinctions throughout its range. We used individual-based clustering methods along with Bayesian inference of historical migration based on almost 1500 multilocus microsatellite genotypes to examine genetic structure in this taxon. Clustering analyses identified panhandle and peninsular populations in Florida as distinct genetic clusters separated by the Aucilla River, consistent with the division between the Coastal Plain and peninsular mitochondrial lineages, respectively. Analysis of historical migration indicated an east–west population divergence event followed by immigration to the east. Together, our results indicate that the genetically distinct Coastal Plain and peninsular Florida lineages should be considered separately for conservation and management purposes.

59 BASIC BIOLOGICAL SCIENCES↗

DOE OSTI2022

Extracting the $\Lambda $ Polarizing Fragmentation Function from Belle e + e − Data within the TMD Formalism

Data from the Belle Collaboration for associated production (with a light unpolarized hadron) and single-inclusive production of transversely polarized Λ-hyperons in e + e − annihilation processes allowed to extract within a TMD approach, for the first time, the Λ polarizing fragmentation function. Recent theoretical developments on the computation of cross sections for single-inclusive hadron production in e + e − annihilation processes, within a Soft Collinear Effective Theory approach, combined with the CSS formalism for the double-hadron production case, can be used to perform a renewed analysis, adopting a full TMD factorization scheme. Preliminary results and a comparison between the two analyses are presented.

CSS evolution equations↗

DOE OSTI2024

Multi-scale modeling of fuel fragmentation and microstructural evolution

An overview of NEAMS program activities to model fuel fragmentation and microstructual evolution to a group of industry attendees at a meeting hosted by EPRI. Topics include atomistic methods to determine grain boundary strength, phase-field fracture modeling to determine critical pressure at grain boundaries, and coupled phase-field-cluster dynamics to model microstructural evolution.

11 NUCLEAR FUEL CYCLE AND FUEL MATERIALS↗

DOE OSTI2024

Antigen‐binding fragments with improved crystal lattice packing and enhanced conformational flexibility at the elbow region as crystallization chaperones

It has been shown previously that a set of three modifications—termed S1, Crystal Kappa, and elbow—act synergistically to improve the crystallizability of an antigen-binding fragment (Fab) framework. Here, we prepared a phage-displayed library and performed crystallization screenings to identify additional substitutions—located near the heavy-chain elbow region—which cooperate with the S1, Crystal Kappa, and elbow modifications to increase expression and improve crystallizability of the Fab framework even further. One substitution (K141Q) supports the signature Crystal Kappa-mediated Fab:Fab crystal lattice packing interaction. Another substitution (E172G) improves the compatibility of the elbow modification with the Fab framework by alleviating some of the strain incurred by the shortened and bulkier elbow linker region. A third substitution (F170W) generates a split-Fab conformation, resulting in a powerful crystal lattice packing interaction comprising the biological interaction interface between the variable heavy and light chain domains. In sum, we have used K141Q, E172G, and F170W substitutions—which complement the S1, Crystal Kappa, and elbow modifications—to generate a set of highly crystallizable Fab frameworks that can be used as chaperones to enable facile elucidation of Fab:antigen complex structures by x-ray crystallography.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

DOE OSTI2024

Flavor fragmentation function factorization

A definition of partonic jet flavor that is both theoretically well-defined and experimentally robust would have profound implications for measurements and predictions especially for heavy flavor applications. Recently, a definition of jet flavor was introduced as the net flavor flowing along the direction of the Winner-Take-All axis of a jet which is soft safe to all orders, but not collinear safe. Here, we exploit the lack of collinear safety and propose a factorization theorem of perturbative flavor fragmentation functions that resum collinear divergences and describe the evolution of flavor from the short distance of jet production to the long distance at which hadronization occurs. Collinear flavor evolution is governed by a small modification of the DGLAP equations. We present a detailed all-orders analysis and identify exact relations that must hold amongst the various anomalous dimensions by probability conservation and the existence of fixed points of the renormalization group flow. We explicitly validate the factorization theorem at one-loop order, and demonstrate its consistency at two loops in particular flavor channels. Starting at two-loops, constraints on phase space imposed by flavor measurements potentially allow for non-trivial soft contributions, but we demonstrate that they are scaleless and so explicitly vanish, ensuring that soft particles are summed inclusively and all divergences are exclusively collinear in nature. This factorization theorem opens the door to precision calculations with identified flavor in the infrared.

72 PHYSICS OF ELEMENTARY PARTICLES AND FIELDS↗

DOE OSTI2024

Multiplicity and event-scale dependent flow and jet fragmentation in pp collisions at $\sqrt{s}$ = 13 TeV and in p–Pb collisions at $\sqrt{s_{\textrm{NN}}}$ = 5.02 TeV

Long- and short-range correlations for pairs of charged particles are studied via two-particle angular correlations in pp collisions at $\sqrt{s}$ = 13 TeV and p–Pb collisions at $\sqrt{s_{\textrm{NN}}}$ = 5.02 TeV. The correlation functions are measured as a function of relative azimuthal angle Δφ and pseudorapidity separation Δη for pairs of primary charged particles within the pseudorapidity interval |η| < 0.9 and the transverse-momentum interval 1 < p T < 4 GeV/c. Flow coefficients are extracted for the long-range correlations (1.6 < |Δη| < 1.8) in various high-multiplicity event classes using the low-multiplicity template ft method. The method is used to subtract the enhanced yield of away-side jet fragments in high-multiplicity events. These results show decreasing flow signals toward lower multiplicity events. Furthermore, the flow coefficients for events with hard probes, such as jets or leading particles, do not exhibit any significant changes compared to those obtained from high-multiplicity events without any specific event selection criteria. The results are compared with hydrodynamic-model calculations, and it is found that a better understanding of the initial conditions is necessary to describe the results, particularly for low-multiplicity events.

72 PHYSICS OF ELEMENTARY PARTICLES AND FIELDS↗

DOE OSTI2026

Jet fragmentation function and groomed substructure of bottom quark jets in proton-proton collisions at 5.02 TeV

A measurement of the substructure of bottom quark jets (b jets) in proton-proton (pp) collisions is presented. The measurement uses data collected in pp collisions at $\sqrt{s}=5.02$ TeV, with a low number of simultaneous interactions per bunch crossing, recorded by the CMS experiment in 2017, corresponding to an integrated luminosity of 301 pb −1 . An algorithm to identify and cluster the charged decay daughters of b hadrons is developed for this analysis, which facilitates the exposure of the gluon radiation pattern of b jets using iterative Cambridge-Aachen declustering. The soft-drop-groomed jet radius, R g , and momentum balance, z g , of b quark jets are presented. These observables can be used to test perturbative quantum chromodynamics predictions that account for mass effects. Because the b hadron is partially reconstructed from its charged decay daughters, only charged particles are used for the jet substructure studies. In addition, a jet fragmentation function, z b,ch , is measured, which is defined as the distribution of the ratio of the transverse momentum (p T ) of the partially reconstructed b hadron with respect to the charged-particle component of the jet p T . The substructure variable distributions are unfolded to the charged-particle level. The b jet substructure is compared to the substructure of jets in an inclusive jet sample that is dominated by light-quark and gluon jets in order to assess the role of the b quark mass. A strong suppression of emissions at small R g values is observed for b jets when compared to inclusive jets, consistent with the dead-cone effect. The measurement is also compared with theoretical predictions from Monte Carlo event generators. This is the first substructure measurement of b jets that clusters together the b hadron decay daughters independent of the b hadron species and decay channel.

boosted jets↗

DOE OSTI2021

TMD fragmentation functions at N 3 LO

We compute the unpolarized quark and gluon transverse-momentum dependent fragmentation functions (TMDFFs) at next-to-next-to-next-to-leading order (N 3 LO) in perturbative QCD. The calculation is based on a relation between the TMDFF and the limit of the semi-inclusive deep inelastic scattering cross section where all final-state radiation becomes collinear to the detected hadron. The required cross section is obtained by analytically continuing our recent computation of the Drell-Yan and Higgs boson production cross section at N 3 LO expanded around the limit of all final-state radiation becoming collinear to one of the initial states. Our results agree with a recent independent calculation by Luo et al.

72 PHYSICS OF ELEMENTARY PARTICLES AND FIELDS↗

DOE OSTI2022

Higgs boson decay to charmonia via $\mathcal{c}$-quark fragmentation

We calculate the decay branching fractions of the Higgs boson to $J/ψ$ and $n_c$ via the charm-quark fragmentation mechanism for the color-singlet and color-octet states in the framework of non-relativistic QCD. The decay rates are governed by the charm-quark Yukawa coupling, unlike the decay H → $J/ψ$ +γ, which is dominated by the $γ^*- J/ψ$ mixing. We find that the decay branching fractions can be about 2 x 10 -5 for H →$c\bar c$ + $J/ψ$, and 6 x 10 -5 for H →$c\bar c$ + $n-c$. We comment on the perspective of searching for the Higgs boson to $J/ψ$ transition at the High-Luminosity LHC for testing the charm-quark Yukawa coupling.

71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗

DOE OSTI2022

A fragmentation approach to jet flavor

An intuitive definition of the partonic flavor of a jet in quantum chromodynamics is often only well-defined in the deep ultraviolet, where the strong force becomes a free theory and a jet consists of a single parton. However, measurements are performed in the infrared, where a jet consists of numerous particles and requires an algorithmic procedure to define their phase space boundaries. To connect these two regimes, we introduce a novel and simple partonic jet flavor definition in the infrared. We define the jet flavor to be the net flavor of the partons that lie exactly along the direction of the Winner-Take-All recombination scheme axis of the jet, which is safe to all orders under emissions of soft particles, but is not collinear safe. Collinear divergences can be absorbed into a perturbative fragmentation function that describes the evolution of the jet flavor from the ultraviolet to the infrared. The evolution equations are linear and a small modification to traditional DGLAP and we solve them to leading-logarithmic accuracy. The evolution equations exhibit fixed points in the deep infrared, we demonstrate quantitative agreement with parton shower simulations, and we present various infrared and collinear safe observables that are sensitive to this flavor definition.

72 PHYSICS OF ELEMENTARY PARTICLES AND FIELDS↗

DOE OSTI2022

Transverse Λ polarization in e + e – processes within a TMD factorization approach and the polarizing fragmentation function

We perform a re-analysis of Belle data for the transverse Λ and Λ¯ polarization in e + e – annihilation processes within a transverse momentum dependent (TMD) factorization approach. We consider two data sets, one referring to the associated production of Λ’s with a light unpolarized hadron in an almost back-to-back configuration, and one for the inclusive Λ production, with the reconstruction of the thrust axis. We adopt the Collins-Soper-Sterman framework and employ the recent formulation on the factorization of single-inclusive hadron production. This extends a previous phenomenological study carried out in a more simplified TMD approach, leading to a new extraction of the polarizing fragmentation function (FF). While confirming several features of the previous analysis, here we include the proper QCD scale dependence of this TMD FF and carefully exploit the role of its nonperturbative component. Here, the compatibility, within a unique TMD factorization scheme, of double and single-inclusive hadron production is discussed in detail. Moreover, we consider another data set for inclusive Λ production, at much larger energies, from the OPAL Collaboration, in order to test the consistency of the entire approach. Finally, we elaborate on some fundamental issues like the role of SU(2) isospin symmetry and the heavy quark contributions.

72 PHYSICS OF ELEMENTARY PARTICLES AND FIELDS↗

DOE OSTI2025

Helium Release During Fracture and Granular Fragmentation of Rocks

Geogenic Helium-4 ( 4 He) in-situ increases locally in regions of large deformation generated naturally or anthropogenically. This gas release by deformation is a potential geochemical precursor signal for subsurface deformation. To evaluate the applicability of 4 He degassing for correlating deformation in different lithologies, we conducted high force crush tests, up to 97,800 N axial load, to assess the total 4 He released during fragmentation of the rocks. We observed that the highest 4 He released occurred in the sedimentary rocks and that release correlated strongly with lithologic age and U/Th content. Microstructural changes of the pre- and post-test rocks indicate that the degree of grain size reduction relates directly to the total 4 He released during crushing. The range of in-place 4 He was calculated based XRF measurements of uranium and thorium in each lithology, with the results indicating that the majority of the trapped 4 He was not released. However, the 4 He released by deformation depended upon how the each rock deformed during deformation and the degree of grain size reduction. We postulate that 4 He precursor signals can be used to understand subsurface deformation only if geomechanical and geochemical conditions for 4 He enrichment in a lithology are met.

Deformation signals↗

DOE OSTI2023

Multiphysics analysis of fuel fragmentation, relocation, and dispersal susceptibility–Part 1: Overview and code coupling strategies

The US nuclear energy industry is investigating strategies to increase the reactor operating cycle to 24 months, resulting in peak rod average burnups exceeding the current limit of 62 GWd/tU. This increase will in turn increase the probability of fuel fragmentation, relocation, and dispersal (FFRD) in the event of a loss-of-coolant accident (LOCA). This effort couples multiple codes to (1) evaluate full-core power histories for high-burnup fuel operated in a Westinghouse 4-loop pressurized water reactor, (2) model a postulated large-break LOCA, and (3) calculate the mass of fuel susceptible to FFRD. This paper, the first of three describing the work, focuses on code coupling strategies and FFRD susceptibility calculations. The other two companion papers focus on code-specific designs and analyses. Three codes were used in this work. VERA was used to calculate steady-state power histories, TRACE was used to model the transient thermal hydraulics, and BISON was used to model steady-state and transient fuel performance and cladding failure. Herein, several fuel pulverization models were used to calculate FFRD susceptibility in failed rods. Depending on the cladding failure/fuel pulverization model combination, the core-wide FFRD susceptibility during the postulated LOCA range from 0 to over 5,000 kg.

11 NUCLEAR FUEL CYCLE AND FUEL MATERIALS↗

DOE OSTI2023

Multiphysics analysis of fuel fragmentation, relocation, and dispersal susceptibility–Part 3: Thermal hydraulic evaluation of large break LOCA under high-burnup conditions

Increasing the peak rod average burnup of pressurized water reactor (PWR) fuel beyond 62 GWd/tU may increase fuel fragmentation, relocation, and dispersal (FFRD) susceptibility during a large break loss of coolant accident (LBLOCA). TRACE thermal hydraulic (TH) LBLOCA analyses were performed for a realistic 24-month high-burnup PWR equilibrium cycle, to inform subsequent transient BISON high-burnup FFRD susceptibility evaluations. Realistic LBLOCA systems behavior was first established by configuring to and comparing with the BEMUSE OECD LBLOCA benchmark. Fuel and operating conditions were then applied from high-burnup VERA depletion calculations. LBLOCA simulations were performed for 281 selected high-burnup rods, for which transient TH boundary conditions were collected for later use in BISON. The TRACE results indicated that rod linear heat rate (rather than burnup) is the main predictor of peak cladding temperature (PCT) during the event. PCT typically occurred at a local burnup lower than the rod-average burnup, especially for twice-burned fuel.

11 NUCLEAR FUEL CYCLE AND FUEL MATERIALS↗

DOE OSTI2023

Multiphysics analysis of fuel Fragmentation, Relocation, and dispersal Susceptibility–Part 2: High-Burnup Steady-State operating and fuel performance conditions

The US nuclear industry is pursuing increased cycle lengths and increasing the peak rod-averaged burnup in an effort to increase the economic viability of the US nuclear fleet. Increasing burnup will afford economic viability by enabling utilities to optimize core designs to reduce the number of fresh fuel assemblies per cycle and allow nuclear power plants to operate for a longer period of time. Longer operating periods will also decrease the number of outages experienced by a nuclear power plants and, therefore, offer utilities significant operational savings. However, extending the peak rod-averaged burnup beyond 62 GWd/tU results in operating fuel rods to higher burnup under higher power conditions. This operating regime is expected to result in higher fuel temperatures, fission gas release (FGR), and rod internal pressures (RIPs) that may challenge historical safety basis and affect high-burnup (HBU) experimental testing. In particular, these conditions directly affect fuel fragmentation, relocation, and dispersal (FFRD) susceptibility, so understanding the pretransient operating conditions is critical for developing test plans that evaluate the FFRD and develop strategies to mitigate it. This paper evaluates the operating conditions and fuel performance of HBU (greater than62 GWd/tU rod average) fuel. Additionally, it investigates fuel performance sensitivities and discusses the effect on fuel performance. Here, this work used two codes. Virtual Environment for Reactor Applications (VERA) was used to calculate steady-state power histories, identify HBU operating conditions using 10 different realistic HBU core designs, and down-select rods to a representative subset of fuel rods for subsequent BISON evaluation. The BISON fuel performance code was used to investigate steady-state HBU operating conditions and assess uncertainties associated with FGR and its effect on fuel temperatures and RIPs. The VERA and BISON results will provide direct input for HBU experimental testing and support subsequent TRACE and BISON transient fuel performance analyses.

11 NUCLEAR FUEL CYCLE AND FUEL MATERIALS↗

DOE OSTI2020

Microscopic analysis of copper current collectors and mechanisms of fragmentation under compressive forces

Extensive fragmentation of copper current collectors was observed after spherical indentation on prismatic and large-format pouch Li-ion cells by 3D X-ray computed tomography (XCT). Microscopic analysis including scanning electron microscopy (SEM), scanning transmission electron microscopy (STEM) and x-ray photoelectron microscopy (XPS) was carried out on copper current collectors from used commercial cells and pristine anodes. The copper-graphite cross-section images showed rough interface areas affected by reactions and diffusion in the used cell. Electron probe micro-analyzer (EPMA) element mapping showed the interface area was rich in oxygen and phosphorus. A detectable amount of phosphorus was also uniformly distributed inside the current collector. The same oxygen and phosphorus distributions were confirmed by STEM/EDS analysis. XPS depth profiles on multiple elements revealed the interface area of the aged anode was rich in Li, F, P, O and C and diffused at least 50 nm into the copper. In comparison, the pristine anode showed a very smooth C/Cu interface. No other elements were detected. For commercial cells, the reactions in the interface area and diffusion of multiple elements into the lattice and grain boundaries were responsible for the embrittlement of the copper current collectors. Finally, permanent cell capacity loss was observed in electrochemical performance of the indented cells.

36 MATERIALS SCIENCE↗