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DOE OSTI2022

A reliable workflow for improving nanoscale X-ray fluorescence tomographic analysis on nanoparticle-treated HeLa cells

Abstract Scanning X-ray fluorescence (XRF) tomography provides powerful characterization capabilities in evaluating elemental distribution and differentiating their inter- and intra-cellular interactions in a three-dimensional (3D) space. Scanning XRF tomography encounters practical challenges from the sample itself, where the range of rotation angles is limited by geometric constraints, involving sample substrates or nearby features either blocking or converging into the field of view. This study aims to develop a reliable and efficient workflow that can (1) expand the experimental window for nanoscale tomographic analysis of local areas of interest within a laterally extended specimen, and (2) bridge 3D analysis at micrometer and nanoscales on the same specimen. We demonstrate the workflow using a specimen of HeLa cells exposed to iron oxide core and titanium dioxide shell (Fe3O4/TiO2) nanocomposites. The workflow utilizes iterative and multiscale XRF data collection with intermediate sample processing by focused ion beam (FIB) sample preparation between measurements at different length scales. Initial assessment combined with precise sample manipulation via FIB allows direct removal of sample regions that are obstacles to both incident X-ray beam and outgoing XRF signals, which considerably improves the subsequent nanoscale tomography analysis. This multiscale analysis workflow has advanced bio-nanotechnology studies by providing deep insights into the interaction between nanocomposites and single cells at a subcellular level as well as statistical assessments from measuring a population of cells.

62 RADIOLOGY AND NUCLEAR MEDICINE↗

DOE OSTI2023

Crystal structure of MbnF: an NADPH-dependent flavin monooxygenase from Methylocystis strain SB2

Methanobactins (MBs) are ribosomally produced and post-translationally modified peptides (RiPPs) that are used by methanotrophs for copper acquisition. The signature post-translational modification of MBs is the formation of two heterocyclic groups, either an oxazolone, pyrazinedione or imidazolone group, with an associated thioamide from an X -Cys dipeptide. The precursor peptide (MbnA) for MB formation is found in a gene cluster of MB-associated genes. The exact biosynthetic pathway of MB formation is not yet fully understood, and there are still uncharacterized proteins in some MB gene clusters, particularly those that produce pyrazinedione or imidazolone rings. One such protein is MbnF, which is proposed to be a flavin monooxygenase (FMO) based on homology. To help to elucidate its possible function, MbnF from Methylocystis sp. strain SB2 was recombinantly produced in Escherichia coli and its X-ray crystal structure was resolved to 2.6 Å resolution. Based on its structural features, MbnF appears to be a type A FMO, most of which catalyze hydroxylation reactions. Preliminary functional characterization shows that MbnF preferentially oxidizes NADPH over NADH, supporting NAD(P)H-mediated flavin reduction, which is the initial step in the reaction cycle of several type A FMO enzymes. It is also shown that MbnF binds the precursor peptide for MB, with subsequent loss of the leader peptide sequence as well as the last three C-terminal amino acids, suggesting that MbnF might be needed for this process to occur. Finally, molecular-dynamics simulations revealed a channel in MbnF that is capable of accommodating the core MbnA fragment minus the three C-terminal amino acids.

59 BASIC BIOLOGICAL SCIENCES↗

DOE OSTI2023

TReactMech v4.217

TReactMech couples geomechanical processes (poroelasticity, failure, and inelastic strain) with multiphase nonisothermal flow (derived from TOUGH2) and reactive geochemical transport. At its core is the reactive-transport code TOUGHREACT v4.13. TReactMech is an efficient hybrid parallel simulator, solving the geomechanics using finite elements and MPI/PetSc, the multiphase flow using integrated finite difference and MPI/PETSc, and the reactive chemistry using OpenMP. The advantages of TReactMech are in its multiphase flow capabilities (e.g., supercritical CO2, supercritical water, air) and parallel geomechanics including full 3-D stress tensor, shear and tensile failure, coupled to porosity and permeability changes. It is backwardly compatible with TOUGH2 and TOUGHREACT v4.13, allowing for easier transitions between the codes. TReactMech can be used to simulate many natural and engineered subsurface systems, including geothermal reservoirs, borehole heat exchangers, geologic carbon sequestration, geologic storage of nuclear waste, groundwater resources, weathering, sediment diagenesis, seafloor hydrothermal circulation, hydrofracturing in unconventional reservoirs, and injection/production-induced surface deformation.

Sonnenthal, Eric↗

DOE OSTI2021

Land Surface Modeling 2.0 for agricultural climate change impact assessments

Focus Area: This white paper addresses DOE AI4ESP focus area #2 by providing a sketch blueprint for a next generation, hybrid AI/process-based global Land Surface Modeling (LSM) framework to improve projections of climate change impacts on the land surface system including agriculture and the hydrological cycle. Science Challenge: Climate change impacts on agriculture are highly uncertain: -50% to +150% global production changes for major grains under high-end climate change, for example. The core challenge in land surface system predictability is the large gap between the scale at which the relevant biological processes act and the scale at which the risks need to be assessed. Conventional empirical and process-based modeling approaches are insufficient. A new multi-scale modeling paradigm which employs AI/ML to learn from new streams of remote sensing data and targeted ’gene-to-global’ simulations is needed.

54 ENVIRONMENTAL SCIENCES↗

DOE OSTI2022

Structural, Criticality, and Radiation Dose Calculations to Support SNF Loading into a DOE Standard Canister

The DOE Standard Canister Demonstration Project includes the development of an internal support structure (ISS) for the 4.6-m-long and 45.7-cm-diameter canister. This study presents structural evaluations, criticality safety assessments, and dose rate calculations conducted within the scope of the ISS design process to support smooth canister loading operations and to ensure safe storage, transportation, and disposal of Peach Bottom 1 Core II (PB2) and Fort St. Vrain (FSV) SNF, currently stored at INL’s CPP-603 facility. The ISS includes a 316L stainless-steel basket that holds 12 PB2 SNF rods. The PB2 basket rests on top of six individual, 78.7-cm-long, 316L stainless-steel columns that are equally spaced and welded to the inner canister wall at the lower end of the shell. These columns represent the FSV basket and can hold one FSV SNF element. An A92014 T6 aluminum spacer disc is bolted to the bottom plate of the PB2 basket to vertically restrain the FSV SNF element after the PB2 basket is placed inside the canister above the FSV basket. The structural evaluations of the ISS followed applicable ASME BPVC.III.3 guidelines and included finite element (FE) analyses of the PB2 basket structure; analyses of welds and bolds; buckling analyses of selected components, and acceptability assessments of the expected basket deformations under loading operations. The criticality safety assessments used the Monte Carlo N-Particle (MCNP) software architecture Version 6.2, including ENDF/B-V continuous-energy cross-section libraries, considering intact SNF in a single storage overpack or two multistorage overpack configurations and intact or failed SNF configured for disposal. The dose rate computations are based on source terms taken from the DOE Spent Fuel Database. The isotopic composition was decay corrected for the year 2022 using the ORIGEN module in the SCALE suite. A 19-group photon spectrum and a 27-group neutron-source spectrum were generated and used in MCNP to calculate estimated dose-equivalent rates, both on DOE Standard Canister contact and at a radial distance of 1 m from the canister surface. The results of this study indicate a structurally sound system that can uphold its criticality safety functions throughout its intended operational phases. Furthermore, this study provides confidence that sufficient radiological protection is technically achievable.

12 MANAGEMENT OF RADIOACTIVE AND NON-RADIOACTIVE W↗

DOE OSTI2020

Structural, Criticality, and Radiation Dose Calculations to support SNF Loading into a DOE Standard Canister

The DOE Standard Canister Demonstration Project includes the development of an internal support structure (ISS) for the 4.6-m long and 45.7-cm diameter canister. This study presents structural evaluations, criticality safety assessments, and dose rate calculations conducted within the scope of the ISS design process to support smooth canister loading operations and to ensure safe storage, transportation, and disposal of Peach Bottom 1 Core II (PB2) and Fort St. Vrain (FSV) SNF, currently stored at the CPP-603 facility of the INL. The ISS includes a 316L stainless steel basket that holds twelve PB2 SNF rods. Further, six individual, 78.7-cm long, 316L stainless steel columns are equally spaced and welded to the inner canister wall at the lower end of the shell. These columns represent the FSV basket and can hold one FSV SNF element. An A92014 T6 aluminum spacer disc is bolted to the bottom plate of the PB2 basket to vertically restrain the FSV SNF element after the PB2 basket is placed inside the canister on top of the FSV basket. The structural evaluations of the ISS followed applicable ASME BPVC.III.3 guidelines and included finite element (FE) analyses of the PB2 basket structure; analyses of welds and bolds; buckling analyses of selected components, and acceptability assessments of the expected basket deformations under loading operations. The criticality safety assessments used the Monte Carlo N-Particle (MCNP) software architecture version 6.2 including ENDF/B-V continuous energy cross-section libraries, considering intact SNF in a single storage overpack or two multi-storage overpack configurations, and intact or failed SNF configured for disposal. The dose rate computations are based on source terms taken from the DOE Spent Fuel Database. The isotopic composition was decay corrected for the year 2022 using the ORIGEN module in the SCALE suite. A 19-group photon spectrum and 27-group neutron-source spectra were generated and used in MCNP to calculate estimated dose-equivalent rates, both on DOE Standard Canister contact and at a radial distance of from the canister surface. The results of this study indicate a structurally sound system that can uphold its criticality safety functions throughout its intended operational phases. Further, they increase confidence that sufficient radiological protection is technically achievable.

12 MANAGEMENT OF RADIOACTIVE AND NON-RADIOACTIVE W↗

DOE OSTI2022

Prediction of strain, inter-layer interaction and critical current in CORC ® wires under axial strain by T-A modeling

Superconducting conductors on round core (CORC ® ) cables and wires can meet the needs of large high-field magnets, such as particle accelerators and compact nuclear fusion machines, due to their simple cabling process, high current-carrying capacity and reliable operation under high mechanical stresses. Many high-field magnets require CORC ® cables to carry a current of thousands of amperes in a background magnetic field exceeding 20 T. As a result, the large electromagnetic forces will deform the cable in the axial direction due to hoop stress and in the transverse direction by compressive stress. Therefore, it is essential to determine the irreversible deformation limit of the CORC ® cable under axial tensile load and optimize the cabling parameters to potentially extend this limit. Analytical and numerical methods are developed to assess the performance degradation of CORC ® wires under axial tensile load. The strain level, interlayer contact pressure and friction and their impact on the critical current are calculated by combining the mechanical response and the T-A method. Analyzing the results shows that the winding angle of the tape and the Poisson’s ratio of the inner core are key factors affecting the irreversible tensile strain limit of CORC ® wires. The smaller the winding angle and the higher the Poisson’s ratio of the inner core, the higher the irreversible tensile strain limit. For multi-layer CORC ® wires, the initial contact pressure caused by the cabling process must also be considered. The inter-layer interaction is coupled with the tape strain of each layer. The results of this research can serve as a basis for optimizing and designing CORC ® wires with extended irreversible strain limits.

75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗

DOE OSTI2020

Acid and heat stable enzymes for economical fuel production from biomass

CinderBio’s vision is to harness three billion years of biology to transform many industrial practices into sustainable processes with superior performance. Environments such as volcanic hot springs have evolved extremophilic microbes and enzymes that are naturally heat and acid stable. CinderBio was founded based on technologies developed at Lawrence Berkeley National Laboratory. Our core technologies are the molecular tools and know how to efficiently express extremophilic genes in an extremophilic host such that they retain their natural heat and acid stability. During this project, we tested our enzymes at the Advanced Biofuels and Bioproducts Process Development Unit (ABPDU), automated our fermentation and downstream processing, and built a comprehensive technoeconomic assessment (TEA) model for our manufacturing costs.

09 BIOMASS FUELS↗

DOE OSTI2026

Intelligent Experiments through Real-Time AI: Fast Data Processing and Autonomous Detector Control for High-Energy Nuclear Experiments

The aim of this project is to develop software and hardware for fast real-time data processing and autonomous detector control and calibration for the sPHENIX and the future EIC experiments. Below summarizes Georgia Tech team efforts in the past year: 1. We developed a real-time clustering algorithm and FPGA-based pipeline architecture for processing fired pixel data from ALPIDE sensors in sPHENIX experiments. Our Columnar Clustering Co-Design introduces a hardware-aware, stream-friendly approach that segments pixel data by column pairs using a Column Pair Clustering (CPC) strategy, followed by Cluster Stitching to merge adjacent subclusters. Implemented in Vitis HLS, the pipeline comprises five stages—read-in, subclustering, stitching, analysis, and write-out—connected by tagged HLS streams with custom end-of-event signaling for robust synchronization. We designed a pipelined dataflow model optimized for throughput, low latency, and minimal buffering, enabling scalable clustering across events of arbitrary size. Our system maintains spatial precision via center-of-mass and shape key extraction and efficiently handles edge cases such as fragmented or nested clusters. Compared against DBSCAN in both software and hardware, our approach demonstrates competitive performance under FPGA constraints. 2. We also conducted a comprehensive algorithm-to-hardware co-design of connected component analysis tailored for sPHENIX experiments, focusing on real-time, low-latency processing using FPGAs and High-Level Synthesis (HLS). Starting from a Python-based particle tracking pipeline, the team translated the core logic—graph traversal via DFS and Union-Find—into an HLS-compatible C++ model, replacing dynamic memory and recursion with static arrays and pipelined control flow. The final design includes a fully streamed and dataflow-compatible Union-Find kernel optimized across five iterations, incorporating loop pipelining, array partitioning, AXI/FIFO interface tuning, and function flattening. Experimental results show up to 14.8× speedup over the CPU baseline, reducing per-graph latency to 1.58 μs and demonstrating strong resource efficiency with only ~7k LUTs and zero BRAM usage. The design maintains functional correctness against the Python reference using a Python-based C-simulation framework and Mean Squared Error metrics. This work validates the potential of HLS-driven FPGA designs for edge-level HEP data acquisition, laying a scalable foundation for future integration with real-time detector pipelines and multi-graph processing systems.

73 NUCLEAR PHYSICS AND RADIATION PHYSICS↗

DOE OSTI2020

Programming Strategies for Irregular Algorithms on the Emu Chick

The Emu Chick prototype implements migratory memory-side processing in a novel hardware system. Rather than transferring large amounts of data across the system interconnect, the Emu Chick moves lightweight thread contexts to near-memory cores before the beginning of each remote memory read. Previous work has characterized the performance of the Chick prototype in terms of memory bandwidth and programming differences from more typical, non-migratory platforms, but there has not yet been an analysis of algorithms on this system. This work evaluates irregular algorithms that could benefit from the lightweight, memory-side processing of the Chick and demonstrates techniques and optimization strategies for achieving performance in sparse matrix-vector multiply operation (SpMV), breadth-first search (BFS), and graph alignment across up to eight distributed nodes encompassing 64 nodelets in the Chick system. We also define and justify relative metrics to compare prototype FPGA-based hardware with established ASIC architectures. The Chick currently supports up to 68x scaling for graph alignment, 80 MTEPS for BFS on balanced graphs, and 50% of measured STREAM bandwidth for SpMV.

Hein, Eric↗

DOE OSTI2024

Dopant Segregation in Single-Crystal Optical Fiber Grown via the Laser-Heated Pedestal Growth Technique

Single crystal (SC) optical fiber has promising potential to be used for optical fiber sensing applications in harsh conditions due to its robustness to high temperature, high radioactivity, and resistance to chemical corrosion as compared to optical sensors using silica fiber. However, SC fiber grown via the laser-heated pedestal growth (LHPG) technique innately does not have a core-cladding structure found in standard optical fiber, resulting in optical losses. In this work we investigate optimization of the growth parameters of a two LHPG process used to grow SC fiber with a graded index via introduction of dopants to the feedstock material. Feedstock material is fabricated with the first LHPG device, then sol-gel dip-coated to create outer films of dopant material. The dip-coated feedstock is used to grow SC fiber in which segregation of the dopant constituents occurs, resulting in a graded index of refraction across the fiber, and an effective core-cladding structure. Hardware and software improvements to both LHPG systems are presented and the growth parameters for short pieces of ~320-330 μm diameter YAG fiber has been established. Characterization techniques/procedures have also been established for future grown SC fiber. These improvements and preparations are anticipated to result in a significant increase in grown fiber quality with a similar growth rate to that previously established.

Lander, Gary↗

DOE OSTI2024

Dopant Segregation in Single-Crystal Optical Fiber Grown via the Laser-Heated Pedestal Growth Technique

Lander, Gary↗

DOE OSTI2026

Precision Polishing of Spheres Via In-Situ Process Monitoring and Machine-Learning-Based Optimization

Precision polishing for high surface finish is a vital step in the making of many high-tech components for optical and semiconductor modules as well as for wide ranging experimental samples for HED science that is at the core of LLNL’s mission. In particular, the fabrication of extremely smooth and round spheres comprised of low atomic number materials (low-Z such as high-density carbon or HDC, beryllium, hydrocarbon polymers, etc.) for Inertial Confinement Fusion (ICF) is entirely reliant on specialized polishing processes to achieve the surface smoothness.

36 MATERIALS SCIENCE↗

DOE OSTI2022

An additively-manufactured molten salt-to-supercritical carbon di-oxide primary heat exchanger for solar thermal power generation – Design and techno-economic performance

The design and techno-economic performance of a compact additively manufactured (AM) molten salt (MS)-to-supercritical carbon di-oxide (sCO2) primary heat exchanger (PHE) for solar thermal application is described. The PHE design consists of sCO2 flow through an array of microscale pin fins while the MS flows through mm-scale rectangular channels. Constraints imposed by AM using laser powder bed fusion method are considered in the design. Structural and fluid flow simulations are performed to arrive at a viable design of the core and headers. A simplified one-dimensional steady state model for the PHE is developed including the impact of surface roughness from the AM process. A process-based cost model is used to determine the tradeoff between thermofluidic design and manufacturing cost. A parametric study is performed using the thermo-fluidic and cost models to determine the set of geometrical and flow variables that result in high power density and low cost, while restricting the pressure drop on the sCO2 side to less than 2% of line pressure. Flow rates of MS and sCO2 were varied over heat capacity rate ratios ranging from 0.2 to 1. Results indicate that it is possible to design a low-pressure drop AM PHE with an effectiveness of 90% and a power density in excess of 10 MW/m3 (including headers). Fabrication of representative nickel superalloy specimens are shown to demonstrate that low-porosity parts with the requisite dimensional tolerance of PHE core can be generated.

14 SOLAR ENERGY↗

DOE OSTI2023

Mass transfer in catalytic depolymerization: External effectiveness factors and serendipitous processivity in stagnant and stirred melts

Several heterogeneous catalysts are being developed to recycle plastics. Most operate in viscous polymer melts, where external mass transfer effects could limit the supply of co-reactants to active sites. External mass transfer can also impede the diffusion of long chain products away from the catalyst after each cut. Product egress limitations could potentially confer unintentional processivity to catalyst operation, i.e. a tendency for the catalyst to repeatedly cut the same chain after an initial encounter. We formulate reaction–diffusion equations to quantify mass transfer effects on the co-reactant transport to the catalyst and the degree of serendipitous processivity. Results are developed for catalysts in stagnant or stirred melts, with simple expressions involving Damkohler, Peclet, and Sherwood numbers, i.e. dimensionless combinations of rate constants, catalyst particle size, polymer diffusivities, and shear rates (where applicable). In conclusion, we estimate the impact of these effects for a spherical core–shell catalyst.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

DOE OSTI2024

TRISO PARTICLE FUEL POLISHING PROCESS COMPARISON

The investigation of the TRISO coated particles is important in terms of verification the quality of the nuclear fuel samples before placing them in the reactor core. To determine the degree of damage to the coated particles, the samples must be properly polished in order to uncover the inner layers. The poster presents a comparison of two polishing methods. Mechanical polishing method, which is used frequently for sample preparations generates additional mechanical damages in the studied fuel particle, thus directly affecting the experimental results. Due to that, a novel way to polish the samples is presented - an ionic polishing method. Based on the obtained results, it was concluded that the ion polishing method is better because the level of interference with the structures of the individual layers of the tested samples is much lower than with the mechanical method.

11 NUCLEAR FUEL CYCLE AND FUEL MATERIALS↗

DOE OSTI2024

Detecting fractures and monitoring hydraulic fracturing processes at the first EGS Collab testbed using borehole DAS ambient noise

Enhanced geothermal systems (EGS) require cost-effective monitoring of fracture networks. We validate the capability of using borehole distributed acoustic sensing (DAS) ambient noise for fracture monitoring using core photos and core logs. The EGS Collab project has conducted 10 m scale field experiments of hydraulic fracture stimulation using 50–60 m deep experimental wells at the Sanford Underground Research Facility (SURF) in Lead, South Dakota. The first EGS Collab testbed is located at 1616.67 m (4850 ft) depth at SURF and consists of one injection well, one production well, and six monitoring wells. All wells are drilled subhorizontally from an access tunnel called a drift. The project uses a single continuous fiber-optic cable installed sequentially in the six monitoring wells to record DAS data for monitoring hydraulic fracturing during stimulation. We analyze 60 s time records of the borehole DAS ambient noise data and compute the noise root-mean-square (rms) amplitude on each channel (points along the fiber cable) to obtain DAS ambient noise rms amplitude depth profiles along the monitoring wellbore. Our noise rms amplitude profiles indicate amplitude peaks at distinct depths. We compare the DAS noise rms amplitude profiles with borehole core photos and core logs and find that the DAS noise rms amplitude peaks correspond to the locations of fractures or lithologic changes indicated in the core photos or core logs. We then compute the hourly DAS noise rms amplitude profiles in two monitoring wells during three stimulation cycles in 72 h and find that the DAS noise rms amplitude profiles vary with time, indicating the fracture opening/growth or closing during the hydraulic stimulation. Our results demonstrate that borehole DAS passive ambient noise can be used to detect fractures and monitor fracturing processes in EGS reservoirs.

58 GEOSCIENCES↗

DOE OSTI2022

Cooperative multivalent receptor binding promotes exposure of the SARS-CoV-2 fusion machinery core

The molecular events that permit the spike glycoprotein of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) to bind and enter cells are important to understand for both fundamental and therapeutic reasons. Spike proteins consist of S1 and S2 domains, which recognize angiotensin-converting enzyme 2 (ACE2) receptors and contain the viral fusion machinery, respectively. Ostensibly, the binding of spike trimers to ACE2 receptors promotes dissociation of the S1 domains and exposure of the fusion machinery, although the molecular details of this process have yet to be observed. We report the development of bottom-up coarse-grained (CG) models consistent with cryo-electron tomography data, and the use of CG molecular dynamics simulations to investigate viral binding and S2 core exposure. We show that spike trimers cooperatively bind to multiple ACE2 dimers at virion-cell interfaces in a manner distinct from binding between soluble proteins, which processively induces S1 dissociation. We also simulate possible variant behavior using perturbed CG models, and find that ACE2-induced S1 dissociation is primarily sensitive to conformational state populations and the extent of S1/S2 cleavage, rather than ACE2 binding affinity. These simulations reveal an important concerted interaction between spike trimers and ACE2 dimers that primes the virus for membrane fusion and entry.

59 BASIC BIOLOGICAL SCIENCES↗