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DOE OSTI2024

Efficient species identification for Pacific salmon genetic monitoring programs

Abstract Genetic monitoring of Pacific salmon in the Columbia River basin provides crucial information to fisheries managers that is otherwise challenging to obtain using traditional methods. Monitoring programs such as genetic stock identification (GSI) and parentage‐based tagging (PBT) involve genotyping tens of thousands of individuals annually. Although rare, these large sample collections inevitably include misidentified species, which exhibit low genotyping success on species‐specific Genotyping‐in‐Thousands by sequencing (GT‐seq) panels. For laboratories involved in large‐scale genotyping efforts, diagnosing non‐target species and reassigning them to the appropriate monitoring program can be costly and time‐consuming. To address this problem, we identified 19 primer pairs that exhibit consistent cross‐species amplification among salmonids and contain 51 species informative variants. These genetic markers reliably discriminate among 11 salmonid species and two subspecies of Cutthroat Trout and have been included in species‐specific GT‐seq panels for Chinook Salmon, Coho Salmon, Sockeye Salmon, and Rainbow Trout commonly used for Pacific salmon genetic monitoring. The majority of species‐informative amplicons (16) were newly identified from the four existing GT‐seq panels, thus demonstrating a low‐cost approach to species identification when using targeted sequencing methods. A species‐calling script was developed that is tailored for routine GT‐seq genotyping pipelines and automates the identification of non‐target species. Following extensive testing with empirical and simulated data, we demonstrated that the genetic markers and accompanying script accurately identified species and are robust to missing genotypic data and low‐frequency, shared polymorphisms among species. Finally, we used these tools to identify Coho Salmon incidentally caught in the Columbia River Chinook Salmon sport fishery and used PBT to determine their hatchery of origin. These molecular and computing resources provide a valuable tool for Pacific salmon conservation in the Columbia River basin and demonstrate a cost‐effective approach to species identification for genetic monitoring programs.

Robinson, Zachary L.↗

DOE OSTI2022

BETO 2021 Peer Review: Algae Biotechnology Partnership - Technology Area Session: Advanced Algae Systems

Development of advanced genetic and genomic tools for targeted algal metabolic engineering pursuits will be integral to achieving target biomass productivity and, ultimately, the BETO goal of cost-competitive biofuels derived from algal biomass by 2022. However, at present, broad-host-range tool development is currently hindered by strain-specific negative regulatory mechanisms. Indeed, the biological processes controlling algal transcription and translation are subject to complex host regulation, which often presents hurdles for targeted genetic engineering strategies. Advanced genetic approaches offer a means to rewire these regulatory systems and/or introduce novel functionality into algal biocatalysts. Synthetic systems biology approaches also present a means to construct novel genetic regulatory networks and rewire natural biological systems to establish an “orthogonal central dogma,” wherein non-native control elements are introduced into or evolved in host microbes for bypass of host control. To this end, the Algae Biotechnology Partnership aims to develop advanced genetic editing tools and synthetic and orthogonal genetic regulatory systems to enable universal metabolic engineering strategies in top-candidate deployment algal strains. Successful development will ultimately open the door for targeted strain-engineering strategies, aimed at maximizing algal outdoor biomass production, composition, and strain robustness.

biocatalysis↗

DOE OSTI2020

Axion dark matter detection by superconducting resonant frequency conversion

We propose an approach to search for axion dark matter with a specially designed superconducting radio frequency cavity, targeting axions with masses ma ≲ 10 -6 eV. Our approach exploits axion-induced transitions between nearly degenerate resonant modes of frequency ~ GHz. A scan over axion mass is achieved by varying the frequency splitting between the two modes. Compared to traditional approaches, this allows for parametrically enhanced signal power for axions lighter than a GHz. The projected sensitivity covers unexplored parameter space for QCD axion dark matter for 10 -8 eV ≲ ma ≲ 10 -6 eV and axion-like particle dark matter as light as ma~ 10 -14 eV.

72 PHYSICS OF ELEMENTARY PARTICLES AND FIELDS↗

DOE OSTI2022

Single-stage gradient-based stellarator coil design: Optimization for near-axis quasi-symmetry

Here we present a new coil design paradigm for magnetic confinement in stellarators. Our approach directly optimizes coil shapes and coil currents to produce a vacuum quasi-symmetric magnetic field with a target rotational transform on the magnetic axis. This approach differs from the traditional two-stage approach in which first a magnetic configuration with desirable physics properties is found, and then coils to approximately realize this magnetic configuration are designed. The proposed single-stage approach allows us to find a compromise between confinement and engineering requirements, i.e., find easy-to-build coils with good confinement properties. Using forward and adjoint sensitivities, we derive derivatives of the physical quantities in the objective, which is constrained by a nonlinear periodic differential equation. In two numerical examples, we compare different gradient-based descent algorithms and find that incorporating approximate second-order derivative information through a quasi-Newton method is crucial for convergence. We also explore the optimization landscape in the neighborhood of a minimizer and find many directions in which the objective is mostly flat, indicating ample freedom to find simple and thus easy-to-build coils.

97 MATHEMATICS AND COMPUTING↗

DOE OSTI2026

Mark-18A Target Material Recovery Program: Initial Hot Startup

The Savannah River National Laboratory (SRNL) has been tasked by the National Nuclear Security Administration to recover highly valued isotopes from irradiated Mark-18A (Mk-18A) targets. The Savannah River Site (SRS) has sixty-five Mk-18A targets available for the recovery of the high valued materials. The Mk-18A targets were manufactured with Pu-242 then irradiated under high neutron flux in K-Reactor at the SRS from 1968 to 1978. The sixty-five Mk-18A targets are currently stored in the SRS L-Area Basin and will be removed one at a time and individually transported to SRNL. Upon receipt at SRNL, the Mk-18A target material will be removed from the confinement, dissolved, chemically separated, and calcined to a stable oxide. The flowsheet is designed to recover the plutonium as well as the trivalent actinides. The original targets were manufactured with varying quantities of Pu-242, ranging from 5.2 grams to 121.5 grams. Taking a graded approach to process start up, the lowest loaded target (FT-80-03) was selected as the first target to be received and processed at SRNL. As operational experience and knowledge is gained from processing targets, higher loaded targets will be selected for processing to increase the quantities of valuable isotopes recovered. Due to dose concerns, the receipt and processing of the Mk-18A targets is performed in the SRNL Shielded Cells Facility. The targets are stored in a double J-can confinement in the L-Area Basin. A specially designed cask was procured for transport of the targets from L-Area to SRNL. Once received at SRNL, the targets are loaded into the back of Cell 7 and resized as they enter the cell. The resized targets (1/4 length) are then processed one at a time through the following processes: caustic dissolution and filtration, acidic dissolution and filtration, elutable Reillex anion exchange, diglycolamide (DGA) resin extraction, and DGA calcination. This processing results in two product streams. The first is an aqueous plutonium solution which is removed from the shielded cells and taken to a glovebox for further purification and conversion to an oxide. The second is a calcined oxide product containing the Am and Cm as well as other lanthanide fission products which is removed from the shielded cells using a bagless transfer system. Both materials are packaged for shipment to Oak Ridge National Laboratory (ORNL). This paper will discuss the operating experience, lessons learned, and results from initial process hot startup.

Armstrong, Christopher [Savannah River National La↗

DOE OSTI2019

Memory embedded non-intrusive reduced order modeling of non-ergodic flows

Generating a digital twin of any complex system requires modeling and computational approaches that are efficient, accurate, and modular. Traditional reduced order modeling techniques are targeted at only the first two, but the novel nonintrusive approach we present in this study is an attempt at taking all three into account effectively compared to their traditional counterparts. Based on dimensionality reduction using proper orthogonal decomposition (POD), we introduce a long short-term memory neural network architecture together with a principal interval decomposition (PID) framework as an enabler to account for localized modal deformation. As an effective partitioning tool for breaking the Kolmogorov barrier, our PID framework, therefore, can be considered a key element in the accurate reduced order modeling of convective flows. Our applications for convection-dominated systems governed by Burgers, Navier-Stokes, and Boussinesq equations demonstrate that the proposed approach yields significantly more accurate predictions than the POD-Galerkin method and could be a key enabler toward near real-time predictions of unsteady flows.

42 ENGINEERING↗

DOE OSTI2025

Modelling Tritium Production and Release at High-Energy Proton Accelerators

Tritium is a well-known byproduct of particle accelerator operations. To keep levels of tritium below regulatory limits, tritium production is actively monitored and managed at Fermilab. We plan to study tritium production in the targets, beamline components, and shielding elements of the Fermilab facilities such as NuMI, BNB, and MI-65. To facilitate the analysis, we construct a simple model and use three Monte Carlo radiation codes, FLUKA, MARS, and PHITS, to estimate the amount of tritium produced in these facilities. The analysis could also serve as an intercomparison between these code results related to tritium production. To assess the actual amounts of tritium that would be released from various materials, we employ a semi-empirical diffusion model. The results of this analysis are compared to experimental data whenever possible. This approach also helps to optimize proposed target materials with respect to the tritium production and release.

Georgobiani, Dali [Fermilab]↗

DOE OSTI2020

Investigating off-Hugoniot states using multi-layer ring-up targets

Abstract Laser compression has long been used as a method to study solids at high pressure. This is commonly achieved by sandwiching a sample between two diamond anvils and using a ramped laser pulse to slowly compress the sample, while keeping it cool enough to stay below the melt curve. We demonstrate a different approach, using a multilayer ‘ring-up’ target whereby laser-ablation pressure compresses Pb up to 150 GPa while keeping it solid, over two times as high in pressure than where it would shock melt on the Hugoniot. We find that the efficiency of this approach compares favourably with the commonly used diamond sandwich technique and could be important for new facilities located at XFELs and synchrotrons which often have higher repetition rate, lower energy lasers which limits the achievable pressures that can be reached.

75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗

DOE OSTI2023

Description of the multinucleon transfer mechanism for Ca 48 + Pu 244 and Kr 86 + Pt 198 reactions in a quantal transport approach

Multinucleon transfer (MNT) reactions involving heavy projectile and target combinations stand as a promising method for synthesizing new neutron-rich exotic nuclei, which may not be possible using hot or cold fusion reactions or fragmentation. Exploring the mechanisms behind MNT reactions is essential and it requires a comprehensive theoretical framework that can explain the physical observables in these reactions. This work aims to show that the quantal diffusion approach based on the stochastic mean-field (SMF) theory is capable of explaining the reaction dynamics observed in MNT reactions. Primary product mass distributions in 48 Ca + 244 Pu reaction at E c.m. = 203.2 MeV and 86 Kr + 198 Pt reaction at E c.m. = 324.2 MeV are calculated and compared with the available experimental data. In this work, we utilize the time-dependent Hartree-Fock (TDHF) calculations to analyze the mean-field reaction dynamics computationally in the reactions 48 Ca + 244 Pu and 86 Kr + 198 Pt for a broad range of initial angular momenta. Quantal transport description based on the SMF approach is used to calculate quantal diffusion coefficients and mass variances in 48 Ca + 244 Pu and 86 Kr + 198 Pt systems. The primary products arising from quasifission reactions are described by joint probability distribution in the SMF approach and those arising from fusion-fission are estimated by using the statistical deexcitation code gemini + +. Mean values of charge and mass numbers, scattering angles of the primary reaction products, and the total kinetic energies after the collision are calculated within the TDHF framework for a broad range of initial angular momenta. Throughout all the collisions, drift toward the mass symmetry and large mass dispersion associated with this drift are observed. Here, the calculated primary fragment and mass distributions using the SMF approach successfully explain experimental observations for the 48 Ca + 244 Pu and 86 Kr + 198 Pt systems. The primary mass distributions, mean values of binary products, and mass dispersions are determined and results are compared with the available experimental data. The observed agreement between the experimental data and SMF results highlights the effectiveness of the quantal diffusion mechanism based on the SMF approach, which does not include any adjustable parameters other than standard parameters of Skyrme energy density functional.

73 NUCLEAR PHYSICS AND RADIATION PHYSICS↗

DOE OSTI2022

Duke Energy Carbon-Free Resource Integration Study

Duke Energy has partnered with the National Renewable Energy Laboratory (NREL) to evaluate pathways to achieving their carbon-free targets and to assess the operational impacts of the resulting system. This report details findings from Phase II of the Duke Low Carbon Resource Integration study, which consisted of three separate but interrelated analyses: (1) a resource assessment exploring the technical and economic potential and characteristics of wind and solar resources in the Carolinas; (2) capacity expansion modeling identifying the least-cost investment pathways for achieving 70% CO 2 emissions reductions in North Carolina by 2030 and a net-zero electricity system by 2050; and (3) detailed production cost modeling of power system operations at the higher shares of low- and zero-carbon emitting generation sources, informed by the capacity expansion modeling portion of the analysis. The analysis finds that Duke Energy can approach the 2030 and 2050 emissions target in North Carolina through investment in a combination of solar, wind, and storage along with maintaining its existing nuclear fleet. The average cost of CO 2 abatement in the Carolinas through 2021-2050 is on the order of $\$27-33$ per metric ton (range of $\$9-34$ per metric ton across key sensitivities).Duke Energy can expected increased interchange with neighbors to help balance higher levels of solar, although the ability to do this will depend on whether neighboring regions also move to integrate more carbon-free resources. As Duke Energy moves toward both the 2030 and 2050 targets, addressing energy needs during the winter peak period becomes particularly important, and the system relies on the availability of resources such as renewable or hydrogen combustion turbines, seasonal storage, or other similar technologies that are dispatchable but able to operate at low capacity factors.

29 ENERGY PLANNING, POLICY, AND ECONOMY↗

DOE OSTI2021

Artificial Reasoning System for Symptom-Based Conditional Failure Probability Estimation Using Bayesian Network

Advances in nuclear power technologies require enhanced capabilities for operator advice and autonomous control. One of the first tasks in the development of such capabilities is the formulation of symptom-based conditional failure probabilities for structures, systems, and components (SSCs) of interest, for which the primary goal is to aid plant personnel in deducing the probabilistic performance status of the monitored SSCs and in detecting impending faults/failure. The task of conditional failure probability estimation is a bidirectional inference problem and shall be logically tackled by the Bayesian network (BN) approach. As a knowledge-based artificial intelligence tool and a probabilistic graphical model, BN offers the capability of reasoning under uncertainty and graphical representation emulating the physical behavior of the target SSC. This paper provides a systematic overview of the BN technique and the software tools for handling implementation of BN models, along with the associated knowledge representation and reasoning paradigm. Both operational data and expert judgement can be readily incorporated into the knowledge base of a BN model. The challenges with data availability are highlighted, and the general approach to target SSC identification is presented. Our focus is upon failure-prone and risk-important balance of plant assets, especially cases having strong operator involvement. An exemplary case study on the failure of a motor-driven centrifugal pump is also conducted to demonstrate the usefulness and technical feasibility of the proposed artificial reasoning system using an expert system shell.

Zhao, Xingang↗

DOE OSTI2021

Plant Single-Cell Solutions for Energy and the Environment (Second Workshop Report)

Plants are important sources of energy and materials, and they collectively represent a critical component of Earth’s ecosystem. With increasing environmental stresses due to climate change and intensive agricultural practices, the need for resilient plants is greater than ever before. To secure plant resources for bioenergy, biomaterials, food, and ecosystem adaptation, a deeper understanding of the fundamental biology of plants at a cellular level is urgently needed. Plants contain a multitude of specialized cell types that compose tissues and organs. Pathogens often target specific cell types within plants, and the response of one cell to a particular stimulus is likely to be distinct from its neighbor because of underlying molecular and contextual differences. Understanding how these responses are distributed among cells, the main goal of single-cell approaches, will substantially enhance our ability to use targeted engineering for improving plant productivity and resilience. Furthermore, single-cell approaches are necessary to understand the interactions between plants and other ecosystem members such as fungi, bacteria, and archaea. Unlocking these gene-response mechanisms at a cellular level can improve our ability to adapt plants to environmental stresses, increasing their utility as feedstocks for biomaterials and bioenergy. Recent advances in high-throughput sequencing, mass spectrometry, microfluidics and miniaturization, artificial intelligence and machine learning, and bioinformatics have greatly improved our ability to detect and understand processes at a cellular level. In mammalian systems, single-cell transcriptomics has already led to many advances, such as newly identified cell types and cell-targeted treatment of diseases, and mass spectrometry-based single-cell proteomics has recently been demonstrated as a promising emerging technology. However, plant single-cell omics has lagged behind mammalian approaches due to the high cost of the technologies relative to available resources and to the innate biological features of plants, including the complexity of the cell wall and polyploidy. To better understand how single-cell methods could enable plant science, Lawrence Berkeley National Laboratory (Berkeley Lab) hosted a workshop on April 29, 2021, that brought together a diverse group of leaders in plant and/or single-cell biology. Attendees represented federal research programs and domestic and international academic institutions. During the workshop, three presenters described the current state of research in both experimental and computational approaches. While the focus of the workshop was on factors preventing plant biology researchers from fully adopting single-cell methodologies, workshop participants agreed that most barriers could be overcome with focused, strategic investment and coordinated efforts among institutions leading to significant scientific discoveries that would be difficult to obtain using more conventional technologies.

59 BASIC BIOLOGICAL SCIENCES↗

DOE OSTI2024

Geographical Insights into Suicide Mortality Through Spatial Machine Learning

Suicide mortality is a leading cause of death in the United States, with an upward trend that emphasizes its significance as a public health issue. Previous research has employed global models like ordinary least squares (OLS) regression and local models such as geographically weighted regression (GWR). While local models are useful for analyzing spatial variations in suicide mortality, they share limitations with traditional global models, particularly about their inability to handle multi-collinearity and non-linear relationships. Machine learning approaches, like random forests (RF), can address some of these limitations but often fail to account for spatial variability. This gap highlights the need for spatial ML models specifically designed to tackle suicide mortality. This research seeks to fill this void by using a geographically weighted random forest model (GWRF) to examine the associations between county-level suicide mortality in the U.S. from 2010 to 2020 and various social and environmental determinants of health. A key aspect of our methodology is disciplined feature selection, which reduces the pool of explanatory variables by about 90%. This refinement enhances the explanatory power of both global (R2 improved from 0.59 to 0.67) and local (R2 improved from 0.64 to 0.67) RF models while reducing their run times. An analysis of the importance scores for these selected features reveals that the drivers of suicide mortality vary by context. Thus, to effectively address regional disparities and inform targeted public health interventions, a holistic approach that incorporates multiple county-level characteristics is essential.

Lebakula, Viswadeep [ORNL] (ORCID:0000000152935914↗

DOE OSTI2021

Structural engineering of chimeric antigen receptors targeting HLA-restricted neoantigens

Chimeric antigen receptor (CAR) T cells have emerged as a promising class of therapeutic agents, generating remarkable responses in the clinic for a subset of human cancers. One major challenge precluding the wider implementation of CAR therapy is the paucity of tumor-specific antigens. Here, we describe the development of a CAR targeting the tumor-specific isocitrate dehydrogenase 2 (IDH2) with R140Q mutation presented on the cell surface in complex with a common human leukocyte antigen allele, HLA-B*07:02. Engineering of the hinge domain of the CAR, as well as crystal structure-guided optimization of the IDH2 R140Q- HLA-B*07:02-targeting moiety, enhances the sensitivity and specificity of CARs to enable targeting of this HLA-restricted neoantigen. This approach thus holds promise for the development and optimization of immunotherapies specific to other cancer driver mutations that are difficult to target by conventional means.

99 GENERAL AND MISCELLANEOUS↗

DOE OSTI2020

Integration of phage and yeast display platforms: A reliable and cost effective approach for binning of peptides as displayed on-phage

Hundreds of target specific peptides are routinely discovered by peptide display platforms. However, due to the high cost of peptide synthesis only a limited number of peptides are chemically made for further analysis. Here we describe an accurate and cost effective method to bin peptides on-phage based on binding region(s), without any requirement for peptide or protein synthesis. This approach, which integrates phage and yeast display platforms, requires display of target and its alanine variants on yeast. Flow cytometry was used to detect binding of peptides on-phage to the target on yeast. Once hits were identified, they were synthesized to confirm their binding region(s) by HDX (Hydrogen deuterium exchange) and crystallography. Moreover, we have successfully shown that this approach can be implemented as part of a panning process to deplete non-functional peptides. This technique can be applied to any target that can be successfully displayed on yeast; it narrows down the number of peptides requiring synthesis; and its utilization during selection results in enrichment of peptide population against defined binding regions on the target.

59 BASIC BIOLOGICAL SCIENCES↗

DOE OSTI2024

Direct Mapping of Polyclonal Epitopes in Serum by HDX-MS

Elucidating the interactions that drive antigen recognition is central to understanding antibody-mediated protection and is vital for the rational design of immunogens. Often, structural knowledge of epitopes targeted by antibodies is derived from isolated studies of monoclonal antibodies, for which numerous structural techniques exist. In contrast, there are very few approaches capable of mapping the full scope of antigen surfaces targeted by polyclonal sera through the course of a natural antibody response. Here, in this study, we develop an approach using immobilized antigen coupled to hydrogen/deuterium exchange with mass spectrometry (HDX-MS) to probe epitope targeting in the context of the fully native serum environment. Using the well-characterized Staphylococcal enterotoxin B (SEB) as a model system, we show that complex combinations of epitopes can be detected and subtle differences across different anti-sera can be discerned. This work reveals new insight into how neutralizing antibodies and antisera target SEB, and more importantly, establishes a novel method for directly mapping the epitope landscape of polyclonal sera.

antigens↗

DOE OSTI2026

Extension of Solvent-Assisted Linker Exchange to Supported Metal–Organic Framework Thin Films

Solvent-assisted linker exchange (SALE) is a common postsynthetic approach used to accommodate metal–organic frameworks (MOFs) for targeted applications. As this technique is relatively untested in immobilized MOF structures, we repeated the generalized SALE approach with ZIF-8 deposited directly onto solid substrates and assessed the results with a variety of techniques, including time-of-flight secondary-ion mass spectrometry (ToF-SIMS). Our methods confirm that the supported films maintain their key structural properties while allowing for linker substitution with foreign species. Alongside experiments, we used computational modeling to quantify the relative energetics of SALE reactions with a variety of linkers. These techniques together reveal that SALE is translatable to immobilized MOFs. Additionally, we recognize how various aspects of the postsynthetic approach can bear consequences for the material’s final micro- and macroscopic properties. Furthermore, the results uncover basic yet critical details needed to inform future efforts to engineer MOF films with functional properties.

Ligands↗

DOE OSTI2023

A Germline-Targeting Chimpanzee SIV Envelope Glycoprotein Elicits a New Class of V2-Apex Directed Cross-Neutralizing Antibodies

HIV-1 and its SIV precursors share a broadly neutralizing antibody (bNAb) epitope in variable loop 2 (V2) at the envelope glycoprotein (Env) trimer apex. Here, we tested the immunogenicity of germ line-targeting versions of a chimpanzee SIV (SIVcpz) Env in human V2-apex bNAb heavy-chain precursor-expressing knock-in mice and as chimeric simian-chimpanzee immunodeficiency viruses (SCIVs) in rhesus macaques (RMs). Trimer immunization of knock-in mice induced V2-directed NAbs, indicating activation of V2-apex bNAb precursor-expressing mouse B cells. SCIV infection of RMs elicited high-titer viremia, potent autologous tier 2 neutralizing antibodies, and rapid sequence escape in the canonical V2-apex epitope. Six of seven animals also developed low-titer heterologous plasma breadth that mapped to the V2-apex. Antibody cloning from two of these animals identified multiple expanded lineages with long heavy chain third complementarity determining regions that cross-neutralized as many as 7 of 19 primary HIV-1 strains, but with low potency. Negative stain electron microscopy (NSEM) of members of the two most cross-reactive lineages confirmed V2 targeting but identified an angle of approach distinct from prototypical V2-apex bNAbs, with antibody binding either requiring or inducing an occluded-open trimer. Probing with conformation-sensitive, nonneutralizing antibodies revealed that SCIV-expressed, but not wild-type SIVcpz Envs, as well as a subset of primary HIV-1 Envs, preferentially adopted a more open trimeric state. These results reveal the existence of a cryptic V2 epitope that is exposed in occluded-open SIVcpz and HIV-1 Env trimers and elicits cross-neutralizing responses of limited breadth and potency.

59 BASIC BIOLOGICAL SCIENCES↗