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DOE OSTI2020

Models of SIV rebound after treatment interruption that involve multiple reactivation events

In order to assess the efficacy of novel HIV-1 treatments leading to a functional cure, the time to viral rebound is frequently used as a surrogate endpoint. The longer the time to viral rebound, the more efficacious the therapy. In support of such an approach, mathematical models serve as a connection between the size of the latent reservoir and the time to HIV-1 rebound after treatment interruption. The simplest of such models assumes that a single successful latent cell reactivation event leads to observable viremia after a period of exponential viral growth. Here we consider a generalization developed by Pinkevych et al. and Hill et al. of this simple model in which multiple reactivation events can occur, each contributing to the exponential growth of the viral load. We formalize and improve the previous derivation of the dynamics predicted by this model, and use the model to estimate relevant biological parameters from SIV rebound data. We confirm a previously described effect of very early antiretroviral therapy (ART) initiation on the rate of recrudescence and the viral load growth rate after treatment interruption. We find that every day ART initiation is delayed results in a 39% increase in the recrudescence rate (95% credible interval: [18%, 62%]), and a 11% decrease of the viral growth rate (95% credible interval: [4%, 20%]). We show that when viral rebound occurs early relative to the viral load doubling time, a model with multiple successful reactivation events fits the data better than a model with only a single successful reactivation event.

59 BASIC BIOLOGICAL SCIENCES↗

DOE OSTI2023

Antigen pressure from two founder viruses induces multiple insertions at a single antibody position to generate broadly neutralizing HIV antibodies

Vaccination strategies aimed at maturing broadly neutralizing antibodies (bnAbs) from naïve precursors are hindered by unusual features that characterize these Abs, including insertions and deletions (indels). Longitudinal studies of natural HIV infection cases shed light on the complex processes underlying bnAb development and have suggested a role for superinfection as a potential enhancer of neutralization breadth. Here we describe the development of a potent bnAb lineage that was elicited by two founder viruses to inform vaccine design. The V3-glycan targeting bnAb lineage (PC39-1) was isolated from subtype C-infected IAVI Protocol C elite neutralizer, donor PC39, and is defined by the presence of multiple independent insertions in CDRH1 that range from 1-11 amino acids in length. Memory B cell members of this lineage are predominantly atypical in phenotype yet also span the class-switched and antibody-secreting cell compartments. Development of neutralization breadth occurred concomitantly with extensive recombination between founder viruses before each virus separated into two distinct population “arms” that evolved independently to escape the PC39-1 lineage. Ab crystal structures show an extended CDRH1 that can help stabilize the CDRH3. Overall, these findings suggest that early exposure of the humoral system to multiple related Env molecules could promote the induction of bnAbs by focusing Ab responses to conserved epitopes.

59 BASIC BIOLOGICAL SCIENCES↗

DOE OSTI2014

The Insertion Green Monster (iGM) Method for Expression of Multiple Exogenous Genes in Yeast

Being a simple eukaryotic organism, Saccharomyces cerevisiae provides numerous advantages for expression and functional characterization of proteins from higher eukaryotes, including humans. However, studies of complex exogenous pathways using yeast as a host have been hampered by the lack of tools to engineer strains expressing a large number of genetic components. In addition to inserting multiple genes, it is often desirable to knock out or replace multiple endogenous genes that might interfere with the processes studied. Here, we describe the “insertion Green Monster” (iGM) set of expression vectors that enable precise insertion of many heterologous genes into the yeast genome in a rapid and reproducible manner and permit simultaneous replacement of selected yeast genes. As a proof of principle, we have used the iGM method to replace components of the yeast pathway for methionine sulfoxide reduction with genes encoding the human selenoprotein biosynthesis machinery and generated a single yeast strain carrying 11 exogenous components of the selenoprotein biosynthetic pathway in precisely engineered loci.

Saccharomyces cerevisiae↗

DOE OSTI2015

Proceedings of RIKEN BNL Research Center Workshop: Collectivity in Small Colliding Systems with High Multiplicity

The particle angular correlation measurements in small colliding systems, such as p+p, p+Pb, d+Au and 3 He+Au at RHIC and the LHC, have recently attracted significant interest. In particular, high-multiplicity events from such collisions exhibit a very similar pattern of longrapidity-range azimuthal correlations (the "ridge") as in Au+Au and Pb+Pb collisions. In AA collisions it is widely accepted that the ridge reflects various harmonic flow components arising from strong hydrodynamic response to fluctuating initial conditions. Hence, it is natural to ask whether the ridge observed in small colliding systems may also be interpreted as hydrodynamic flow plus fluctuating initial conditions. Although such a hydro-based interpretation can be made to work phenomenologically, it is unclear whether the hydrodynamic gradient expansion approach developed for A+A collisions is applicable in such small systems. Besides, there are alternative proposals in explaining the observation based on initial state effects (e.g. early gluon dynamics in a saturation picture). More recently, multi-particle cumulants measurements (as reported at QM14) have shown strong evidence for collectivity in high multiplicity p+Pb collisions, but the exact physical meaning of these measurements needs to be clarified. This Workshop specifically aimed to have focused discussions on these issues, and hopefully progress will be made in understanding them.

73 NUCLEAR PHYSICS AND RADIATION PHYSICS↗

DOE OSTI2015

Nanolipoprotein Particles (NLPs) as Versatile Vaccine Platforms for Co-delivery of Multiple Adjuvants with Subunit Antigens from Burkholderia spp. and F. tularensis - Annual Technical Report

The goal of this proposal is to demonstrate that co-localization of protein subunit antigens and adjuvants on nanolipoprotein particles (NLPs) can increase the protective efficacy of recombinant subunit antigens from Burkholderia spp. and Francisella tularensis against an aerosol challenge. NLPs are are biocompatible, high-density lipoprotein mimetics that are amenable to the incorporation of multiple, chemically-disparate adjuvant and antigen molecules. We hypothesize that the ability to co-localize optimized adjuvant formulations with subunit antigens within a single particle will enhance the stimulation and activation of key immune effector cells, increasing the protective efficacy of subunit antigen-based vaccines. While Burkholderia spp. and F. tularensis subunit antigens are the focus of this proposal, we anticipate that this approach is applicable to a wide range of DOD-relevant biothreat agents. The F344 rat aerosol challenge model for F. tularensis has been successfully established at Battelle under this contract, and Year 3 efficacy studies performed at Battelle demonstrated that an NLP vaccine formulation was able to enhance survival of female F344 rats relative to naïve animals. In addition, Year 3 focused on the incorporation of multiple Burkholderia antigens (both polysaccharides and proteins) onto adjuvanted NLPs, with immunological analysis poised to begin in the next quarter.

59 BASIC BIOLOGICAL SCIENCES↗

DOE OSTI2017

Multiple Ion Temperatures

We consider the implementation of multiple ion temperatures in an existing rad-hydro code. Particular issues which arise including splitting of the energy deposition terms including those involved in modeling shocks in the hydro; the calculation of thermonuclear burn rates in the presence of different ion temperatures; thermal diffusion with multiple temperatures including the difficulty associate with contact discontinuities; and the thermal coupling between different ions and between the individual ions and the electrons. A few simulations are performed to demonstrate the resulting improved modeling capability.

70 PLASMA PHYSICS AND FUSION TECHNOLOGY↗

DOE OSTI2015

Reducing Communication Costs for Sparse Matrix Multiplication within Algebraic Multigrid

We consider the sequence of sparse matrix-matrix multiplications performed during the setup phase of algebraic multigrid. In particular, we show that the most commonly used parallel algorithm is often not the most communication-efficient one for all of the matrix-matrix multiplications involved. By using an alternative algorithm, we show that the communication costs are reduced (in theory and practice), and we demonstrate the performance benefit for both model (structured) and more realistic unstructured problems on large-scale distributed-memory parallel systems. Our theoretical analysis shows that we can reduce communication by a factor of up to 5.4 for a model problem, and we observe in our empirical evaluation communication reductions of factors up to 4.7 for structured problems and 3.7 for unstructured problems. These reductions in communication translate to run-time speedups of up to factors of 2.3 and 2.5, respectively.

97 MATHEMATICS AND COMPUTING↗

DOE OSTI2017

Measurement of Reconstructed Charged Particle Multiplicities of Neutrino Interactions in MicroBooNE

We compare the observed charged particle multiplicity distributions in the MicroBooNE liquid argon time projection chamber from neutrino interactions in a restricted final state phase space to predictions of this distribution from several GENIE models. The measurement uses a data sample consisting of neutrino interactions with a final state muon candidate fully contained within the MicroBooNE detector. These data were collected in 2015-2016 with the Fermilab Booster Neutrino Beam (BNB), which has an average neutrino energy of 800 MeV, using an exposure corresponding to 5.0 × 10 19 protons-on-target. The analysis employs fully automatic event selection and charged particle track reconstruction and uses a data-driven technique to determine the contribution to each multiplicity bin from neutrino interactions and cosmic-induced backgrounds. The restricted phase space employed makes the measurement most sensitive to the higher-energy charged particles expected from primary neutrino-argon collisions and less sensitive to lower energy protons expected to be produced in final state interactions of collision products with the target argon nucleus.

46 INSTRUMENTATION RELATED TO NUCLEAR SCIENCE AND ↗

DOE OSTI2020

Transient voltage-reversal in transformers with multiple secondary coils

By using a transformer with multiple secondary coils, a single unipolar power source can drive multiple loads that have different steady-state operating-voltage requirements. We show that, during initial turn-on, a transient voltage that is opposite in sign to the operating voltage can be induced in one or more of the secondary coils. This is because the surging currents in the coils during turn-on produce a strong inductive interaction between all the coils. In a particular secondary coil, the voltage induced by a neighboring secondary can be larger, and opposite in sign to, the voltage directly induced by the primary coil. The effect is transient because, when the secondary circuits reach their steady-state operating currents, they no longer couple inductively to each other. We also show that, during the turn-on period, the voltage induced in a secondary coil can be significantly larger than its steady-state voltage. These transient effects are controlled by the values of the "coil-coupling" parameters, which are functions of the transformer geometry and of the magnetic permeability and electrical resistivity of the materials used. The results are derived from the circuit equations, and verified using PSpice simulations.

24 POWER TRANSMISSION AND DISTRIBUTION↗

DOE OSTI2020

Subcritical Multiplication Ex-Core Calculations with Shift

This report details the development and testing of Virtual Environment for Reactor Applications (VERA) as applied to full core subcritical multiplication ex-core calculations with Shift. The limiting factor in being able to run these detector calculations with Monte Carlo is the amount of computational memory used by a fully-loaded full core problem. The main development features added to VERA in this effort were enabling source biasing and separable weight windows and integrating multithreading in Shift. With these capabilities, a subcritical multiplication detector response calculation on a full core Watts Bar Nuclear Plant Unit 1 (WBN1) ex-core model was successfully run on a moderately sized computing cluster.

22 GENERAL STUDIES OF NUCLEAR REACTORS↗

DOE OSTI2020

Navigation and Meteorological Data from Multiple Sensors on Airborne Platform (NAVMET-AIR) Value-Added Product Report

The Navigation and Meteorological Data from Multiple Sensors on Airborne Platform (NAVMET-AIR) value-added product encompasses the aafnaviwg data set in the ARM Data Center (ADC), known as the IWG file, named for the Inter-Agency Working Group for Airborne Data and Telemetry Systems (IWGADTS). Its purpose is to produce a suite of tools to promote standardization of instrument interface, data format, and data processing. This data set’s contents are navigational and meteorological state variables at 1 Hz. It also contains higher-order data flags created by ARM Aerial Facility (AAF) scientists to aid analysis such as periods when the aircraft is flying level, operating in maneuvers, or flying through cloud. Due to the nature of research flights, the payload of the aircraft consists of many duplicate and overlapping instruments to ensure, in case of instrument failure, there is a backup to record the data. Measurements from multiple instruments are consolidated into a single file. Each variable of this data set is carefully chosen from the onboard instrumentation and quality checked by AAF scientists to create this wholistic and most accurate data set for airborne research. This document is intended to be a hub towards the individual “read me” files produced for each campaign. For reference about what instrument was used for calculations on specific days, the read me files are located in the ARM IOP archive at the addresses listed, or access the IOP (intensive operational period) database at https://www.archive.arm.gov/.

54 ENVIRONMENTAL SCIENCES↗

DOE OSTI2021

Combining information from multiple cosmological surveys: inference and modeling challenges

The tightest and most robust cosmological results of the next decade will be achieved by bringing together multiple surveys of the Universe. This endeavor has to happen across multiple layers of the data processing and analysis, e.g., enhancements are expected from combining Euclid, Rubin, and Roman (as well as other surveys) not only at the level of joint processing and catalog combination, but also during the post-catalog parts of the analysis such as the cosmological inference process. While every experiment builds their own analysis and inference framework and creates their own set of simulations, cross-survey work that homogenizes these efforts, exchanges information from numerical simulations, and coordinates details in the modeling of astrophysical and observational systematics of the corresponding datasets is crucial.

79 ASTRONOMY AND ASTROPHYSICS↗

DOE OSTI2022

Multiple Stream Low-Cost Recycling Method

The global composite industry generates large quantities of waste and which mostly end as landfill due to lack of meaningful end-use applications for the multiple waste streams. In a recent report by the Electric Power Research Institute (EPRI), waste generated by the wind industry could reach 370,000 tons a year of composite wind energy blades being decommissioned and scrapped. Wind energy is just one major industry utilizing composite materials. The waste generated by industry includes End-of-Life (EoL) materials and manufacturing process scrap. GreenTex Solutions has developed a unique and innovative technology to recycle the composite waste streams in a range of forms made from production waste and EoL materials. This includes manufacturing waste materials such as dry chopped fiber tow, loose fibers, shredded fibers from reinforcement fabrics, cured/semi-cured prepregs, and it also includes fully-cured composite structure waste (such as edge trims from cured parts) from manufacturing aircraft, automobiles, wind blades, boats, and composite cylinders (tanks). Current recycling methods involve recovering the structural fiber by removing the matrix resin through methods such as pyrolysis. The resulting fibers are used in injection molding or wet laid nonwoven mats and other usable forms. The GreenTex technology bypasses these intermediate steps to create the lowest possible recycling processing costs and the lowest embodied energy/CO2 emissions. The end-product from the GreenTex technology is a finished industrial composite part/application versus intermediate fibers or fabrics. The GreenTex manufacturing process enables cross-industry reuse of recycled feedstock by taking waste from multiple industries (wind energy, aerospace, marine, etc.) and recycles the waste into a product used in other industries. The initial target market application is structural flooring for intermodal shipping containers and truck bodies. One of the team’s key partners is Wabash National which produced 29,000 truck bodies in 2019. The current flooring system is comprised of solid oak “butcher board” laminated panels. Additionally, Mediterranean Shipping Containers (MSC) transports over 1.8 million twenty-foot equivalent units per year in intermodal shipping containers. The current container floor is laminated hardwood that is harvested from the rain forests of Central and South America. The project is to develop a flooring system made from recycled composites that can be qualified for both companies (Wabash and MSC). Initial prototypes validated that the recycled composites panels are lighter and thinner with much higher mechanical strength. These results suggest a typical truck trailer would have 20% lower tare weight. The GreenTex technology is not limited to flooring and is widely applicable to other transportation elements such as walls, roof elements, cab areas and related structural components. Under this project different composite waste streams were evaluated and then combined to develop a formulation that would meet the targeted performance criteria for a flooring system. Wet compression molding was used to fabricate plaques at different tonnage using various composite waste streams. The plaques were tested for flexure and impact.

36 MATERIALS SCIENCE↗

DOE OSTI2022

(U) SENSMG: First-Order Sensitivities of Neutron Reaction Rates, Reaction-Rate Ratios, Leakage, k eff , α , and Subcritical Multiplication Using PARTISN

SENSMG is a tool for computing first-order sensitivities of neutron reaction rates, reaction-rate ratios, leakage, k eff , α, and subcritical multiplication using the PARTISN multigroup discrete-ordinates code. SENSMG computes sensitivities to all of the transport cross sections and data (total, fission, a nu, chi, and all scattering moments), two edit cross sections (absorption and capture), and the density for every nuclide and energy group. It also computes sensitivities to the mass density for every material and derivatives with respect to all interface locations and outer boundaries. It computes sensitivities to user specified reactions whose cross sections are available in a user-supplied NJOY output file. The tool can be used for one-dimensional spherical and slab (r) and two-dimensional cylindrical (r-z) geometries. The tool can be used for fixed-source and eigenvalue problems. For most responses, the tool implements Generalized Perturbation Theory (GPT) as discussed by Williams and Stacey. The tool is thus limited to computing sensitivities only for GPT-allowable responses. For subcritical multiplication, the tool implements sensitivities derived by O’Brien and Clark. SENSMG has a similar role as the old SWANLAKE (Ref. 8), FORSS (Ref. 9), and SENSIT (Ref. 10) codes. It has capabilities similar to those of SUSD3D (Refs. 11 and 12), which also uses PARTISN. Section II of this report describes the theory behind adjoint-based sensitivities, gives the equations that SENSMG solves, and defines the sensitivities that are output. Section III describes the user interface, including the input file and command line options. Section IV describes the output. Section V gives some notes about the coding that may be of interest. Section VI presents some sample problems and discusses verification, which is ongoing. Section VII lists needs and ideas for future work. Appendix A lists most of the input files whose results are presented in Sec. VI. Appendix B provides some useful details on one of the cross-section libraries that SENSMG supports.

72 PHYSICS OF ELEMENTARY PARTICLES AND FIELDS↗

DOE OSTI2022

Multiplication of Freestanding Compound Semiconductor Membranes from a Single Wafer by Alternating Growth with 2D Materials

Single-crystal compound semiconductors, such as III-N and III-V, are important building blocks for functional devices due to their high electron mobilities, wide range of bandgaps, and excellent optoelectronic properties. However, current methods to produce their freestanding membranes for heterointegration suffer from slow processes or poor material quality. Here, we demonstrate an approach to grow and harvest multiple wafer-scale single-crystal membranes with high throughput by introducing weak van der Waals interfaces between epitaxial layers. This is achieved by directly growing two-dimensional (2D) materials on compound semiconductors in their native deposition systems, which enables alternating growth of 2D material and compound semiconductor epitaxial layers in a single run. Each epilayer in the multi-stack structure is then sequentially harvested by mechanical exfoliation, producing multiple freestanding single-crystal membranes with extremely high throughput from a single wafer, primed for integration in mixed-dimensional heterostructures.

Han, Ne Myo↗

DOE OSTI2022

Multiplication of Freestanding Compound Semiconductor Membranes from a Single Wafer by Alternating Growth with 2D Materials

Han, Ne Myo↗

DOE OSTI2023

Characterization of Impure Plutonium Oxide Neutron Calibration Standards through Evaluation by Neutron Multiplicity Equations

Plutonium oxide calibration standards STD4C, STD6C and STD8C have been historically used, and are currently the only MT52 standards in use, for calibration and measurement control program of Passive/Active Neutron Coincidence Counter known as PAN1 at PF-4. In this paper, previously measured high-statistics data are used in conjunction with neutron multiplicity equations to determine multiplication M and α parameter of these standards as the explicit knowledge of these parameters may allow quantification of precision and bias of accountability measurements of different material types and matrices of items.

11 NUCLEAR FUEL CYCLE AND FUEL MATERIALS↗

DOE OSTI2024

Geophysical Signatures of Crack Network Coalescence in Rocks at Multiple Length Scales

The main goal of the research project was to identify the geophysical signatures of fracture growth in natural rocks by utilizing novel geophysical techniques. The research objectives were to (a) investigate the potential for geophysical methods to determine when cracks initiate, the types and locations of propagated cracks, and the coalescence of networks of cracks in natural rocks at multiple scales, (b) determine how damage at the microscale evolved into damage at the macroscale and then link the microscopic and macroscopic observations, (c) quantify crack coalescence in rocks under realistic stress conditions using coupled mechanical-geophysical-optical visualization, and (d) identify the precursors in geophysical signals to crack coalescence. The following research thrusts were explored to achieve the research objectives: (1) uniaxial compression testing of rock specimens with and without a set of pre‐existing flaws and (2) triaxial compression testing of natural rock specimens. These thrusts allowed for exploring fracturing in rocks under realistic in situ environments and at multiple scales. This project provided educational opportunities for nine graduate and undergraduate students and resulted in 27 peer-reviewed publications. This first research thrust focused on investigating the micromechanics of fractures in rocks through uniaxial compression testing combined with advanced geophysical and imaging techniques, specifically acoustic emission (AE) monitoring, ultrasonic imaging, and 2-dimensional Digital Image Correlation (2D-DIC). By examining damage processes under time-independent and time-dependent loading conditions, insights into damage localization, crack initiation, and fracturing mechanisms were gained. It was observed that the AE signals and the strain-based measurements directly reflect the state of damage in the rock specimen and could be used to identify the cracking levels, such as the crack initiation (CI) and crack damage (CD), and the mode of deformation. A novel calibration apparatus was developed to enhance the accuracy of AE sensors, allowing for the estimation of key parameters such as magnitude, source dimension, stress drop, and radiated seismic energy associated with the fractures. The findings highlighted significant variations in the temporal evolution of AE source parameters during the primary, secondary, and tertiary stages of creep, identifying tensile cracking as the primary deformation mode. The second research thrust focused on enhancing the understanding of fracturing processes in natural rocks through triaxial compression testing, real-time AE monitoring, and ultrasonic monitoring. We investigated the impact of various factors such as fracture propagation regimes, injection parameters, rock types, and pre-existing conditions on the hydraulic fracture (HF) behavior using scaled true-triaxially loaded specimens of Barre granite and Lyons sandstone. Custom sensor housing facilitated concurrent active and passive monitoring to analyze hydro-mechanical responses and microseismicity associated with different HF scenarios. A coupled investigation of passive microseismicity and active signal attributes permitted a detailed comprehension of the various HF processes (aseismic deformation, fracture initiation and propagation, fluid permeation, and leak-off) and their dependence on the specific rock type. The findings of this research demonstrated the effectiveness of AE monitoring techniques in providing valuable insights into the impact of various factors on the behavior and dynamics of HF processes. The advancements in monitoring techniques, offering a more thorough and precise approach, represent a significant step towards optimizing HF practices and ensuring sustainable resource extraction.

58 GEOSCIENCES↗