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DOE OSTI2016

SIFT-based dense pixel tracking on 0.35 T cine-MR images acquired during image-guided radiation therapy with application to gating optimization

Purpose: To first demonstrate the viability of applying an image processing technique for tracking regions on low-contrast cine-MR images acquired during image-guided radiation therapy, and then outline a scheme that uses tracking data for optimizing gating results in a patient-specific manner. Methods: A first-generation MR-IGRT system—treating patients since January 2014—integrates a 0.35 T MR scanner into an annular gantry consisting of three independent Co-60 sources. Obtaining adequate frame rates for capturing relevant patient motion across large fields-of-view currently requires coarse in-plane spatial resolution. This study initially (1) investigate the feasibility of rapidly tracking dense pixel correspondences across single, sagittal plane images (with both moderate signal-to-noise and spatial resolution) using a matching objective for highly descriptive vectors called scale-invariant feature transform (SIFT) descriptors associated to all pixels that describe intensity gradients in local regions around each pixel. To more accurately track features, (2) harmonic analysis was then applied to all pixel trajectories within a region-of-interest across a short training period. In particular, the procedure adjusts the motion of outlying trajectories whose relative spectral power within a frequency bandwidth consistent with respiration (or another form of periodic motion) does not exceed a threshold value that is manually specified following the training period. To evaluate the tracking reliability after applying this correction, conventional metrics—including Dice similarity coefficients (DSCs), mean tracking errors (MTEs), and Hausdorff distances (HD)—were used to compare target segmentations obtained via tracking to manually delineated segmentations. Upon confirming the viability of this descriptor-based procedure for reliably tracking features, the study (3) outlines a scheme for optimizing gating parameters—including relative target position and a tolerable margin about this position—derived from a probability density function that is constructed using tracking results obtained just prior to treatment. Results: The feasibility of applying the matching objective for SIFT descriptors toward pixel-by-pixel tracking on cine-MR acquisitions was first retrospectively demonstrated for 19 treatments (spanning various sites). Both with and without motion correction based on harmonic analysis, sub-pixel MTEs were obtained. A mean DSC value spanning all patients of 0.916 ± 0.001 was obtained without motion correction, with DSC values exceeding 0.85 for all patients considered. While most patients show accurate tracking without motion correction, harmonic analysis does yield substantial gain in accuracy (defined using HDs) for three particularly challenging subjects. An application of tracking toward a gating optimization procedure was then demonstrated that should allow a physician to balance beam-on time and tissue sparing in a patient-specific manner by tuning several intuitive parameters. Conclusions: Tracking results show high fidelity in assessing intrafractional motion observed on cine-MR acquisitions. Incorporating harmonic analysis during a training period improves the robustness of the tracking for challenging targets. The concomitant gating optimization procedure should allow for physicians to quantitatively assess gating effectiveness quickly just prior to treatment in a patient-specific manner.

61 RADIATION PROTECTION AND DOSIMETRY↗

DOE OSTI2018

A Surveillance Infrastructure for Malaria Analytics: Provisioning Data Access and Preservation of Interoperability

Background: According to the World Health Organization, malaria surveillance is weakest in countries and regions with the highest malaria burden. A core obstacle is that the data required to perform malaria surveillance are fragmented in multiple data silos distributed across geographic regions. Furthermore, consistent integrated malaria data sources are few, and a low degree of interoperability exists between them. As a result, it is difficult to identify disease trends and to plan for effective interventions. Objective: We propose the Semantics, Interoperability, and Evolution for Malaria Analytics (SIEMA) platform for use in malaria surveillance based on semantic data federation. Using this approach, it is possible to access distributed data, extend and preserve interoperability between multiple dynamic distributed malaria sources, and facilitate detection of system changes that can interrupt mission-critical global surveillance activities. Methods: We used Semantic Automated Discovery and Integration (SADI) Semantic Web Services to enable data access and improve interoperability, and the graphical user interface-enabled semantic query engine HYDRA to implement the target queries typical of malaria programs. We implemented a custom algorithm to detect changes to community-developed terminologies, data sources, and services that are core to SIEMA. This algorithm reports to a dashboard. Valet SADI is used to mitigate the impact of changes by rebuilding affected services. Results: We developed a prototype surveillance and change management platform from a combination of third-party tools, community-developed terminologies, and custom algorithms. We illustrated a methodology and core infrastructure to facilitate interoperable access to distributed data sources using SADI Semantic Web services. This degree of access makes it possible to implement complex queries needed by our user community with minimal technical skill. We implemented a dashboard that reports on terminology changes that can render the services inactive, jeopardizing system interoperability. Using this information, end users can control and reactively rebuild services to preserve interoperability and minimize service downtime. Conclusions: We introduce a framework suitable for use in malaria surveillance that supports the creation of flexible surveillance queries across distributed data resources. The platform provides interoperable access to target data sources, is domain agnostic, and with updates to core terminological resources is readily transferable to other surveillance activities. A dashboard enables users to review changes to the infrastructure and invoke system updates. The platform significantly extends the range of functionalities offered by malaria information systems, beyond the state-of-the-art.

60 APPLIED LIFE SCIENCES↗

DOE OSTI2026

High-throughput validation of phase formability and simulation accuracy of Cantor alloys

High-throughput methods enable accelerated discovery of novel materials in complex systems such as high-entropy alloys, which exhibit intricate phase stability across vast compositional spaces. Computational approaches, including Density Functional Theory (DFT) and calculation of phase diagrams (CALPHAD), facilitate screening of phase formability as a function of composition and temperature. However, the integration of computational predictions with experimental validation remains challenging in high-throughput studies. In this work, we introduce a quantitative confidence metric to assess the agreement between predictions and experimental observations, providing a quantitative measure of the confidence of machine learning models trained on either DFT or CALPHAD input in accounting for experimental evidence. The experimental dataset was generated via high-throughput in-situ synchrotron X-ray diffraction on compositionally varied FeNiMnCr alloy libraries, heated from room temperature to ~1000 °C. Agreement between the observed and predicted phases was evaluated using either temperature-independent phase classification or a model that incorporates a temperature-dependent probability of phase formation. This integrated approach demonstrates where strong overall agreement between computation and experiment exists, while also identifying key discrepancies, particularly in FCC/BCC predictions at Mn-rich regions to inform future model refinement.

36 - MATERIALS SCIENCE↗

DOE OSTI2022

Fluid-Kinetic Coupling: Advanced Discretizations for Simulations on Emerging Heterogeneous Architectures (LDRD FY20-0643)

Plasma physics simulations are vital for a host of Sandia mission concerns, for fundamental science, and for clean energy in the form of fusion power. Sandia's most mature plasma physics simulation capabilities come in the form of particle-in-cell (PIC) models and magnetohydrodynamics (MHD) models. MHD models for a plasma work well in denser plasma regimes when there is enough material that the plasma approximates a fluid. PIC models, on the other hand, work well in lower-density regimes, in which there is not too much to simulate; error in PIC scales as the square root of the number of particles, making high-accuracy simulations expensive. Real-world applications, however, almost always involve a transition region between the high-density regimes where MHD is appropriate, and the low-density regimes for PIC. In such a transition region, a direct discretization of Vlasov is appropriate. Such discretizations come with their own computational costs, however; the phase-space mesh for Vlasov can involve up to six dimensions (seven if time is included), and to apply appropriate homogeneous boundary conditions in velocity space requires meshing a substantial padding region to ensure that the distribution remains sufficiently close to zero at the velocity boundaries. Moreover, for collisional plasmas, the right-hand side of the Vlasov equation is a collision operator, which is non-local in velocity space, and which may dominate the cost of the Vlasov solver. The present LDRD project endeavors to develop modern, foundational tools for the development of continuum-kinetic Vlasov solvers, using the discontinuous Petrov-Galerkin (DPG) methodology, for discretization of Vlasov, and machine-learning (ML) models to enable efficient evaluation of collision operators. DPG affords several key advantages. First, it has a built-in, robust error indicator, allowing us to adapt the mesh in a very natural way, enabling a coarse velocity-space mesh near the homogeneous boundaries, and a fine mesh where the solution has fine features. Second, it is an inherently high-order, high-intensity method, requiring extra local computations to determine so-called optimal test functions, which makes it particularly suited to modern hardware in which floating-point throughput is increasing at a faster rate than memory bandwidth. Finally, DPG is a residual-minimizing method, which enables high-accuracy computation: in typical cases, the method delivers something very close to the $L^2$ projection of the exact solution. Meanwhile, the ML-based collision model we adopt affords a cost structure that scales as the square root of a standard direct evaluation. Moreover, we design our model to conserve mass, momentum, and energy by construction, and our approach to training is highly flexible, in that it can incorporate not only synthetic data from direct-simulation Monte Carlo (DSMC) codes, but also experimental data. We have developed two DPG formulations for Vlasov-Poisson: a time-marching, backward-Euler discretization and a space-time discretization. We have conducted a number of numerical experiments to verify the approach in a 1D1V setting. In this report, we detail these formulations and experiments. We also summarize some new theoretical results developed as part of this project (published as papers previously): some new analysis of DPG for the convection-reaction problem (of which the Vlasov equation is an instance), a new exponential integrator for DPG, and some numerical exploration of various DPG-based time-marching approaches to the heat equation. As part of this work, we have contributed extensively to the Camellia open-source library; we also describe the new capabilities and their usage. We have also developed a well-documented methodology for single-species collision operators, which we applied to argon and demonstrated with numerical experiments. We summarize those results here, as well as describing at a high level a design extending the methodology to multi-species operators. We have released a new open-source library, MLC, under a BSD license; we include a summary of its capabilities as well.

70 PLASMA PHYSICS AND FUSION TECHNOLOGY↗

DOE OSTI2025

Designing a Framework for Solving Multiobjective Simulation Optimization Problems

Multiobjective simulation optimization (MOSO) problems are optimization problems with multiple conflicting objectives, where evaluation of at least one of the objectives depends on a black-box numerical code or real-world experiment, which we refer to as a simulation. Whereas an extensive body of research is dedicated to developing new algorithms and methods for solving these and related problems, it is challenging and time-consuming to integrate these techniques into real-world production-ready solvers. This is partly because of the diversity and complexity of modern state-of-the-art MOSO algorithms and methods and partly because of the complexity and specificity of many real-world problems and their corresponding computing environments. The complexity of this problem is only compounded when introducing potentially complex and/or domain-specific surrogate-modeling techniques, problem formulations, design spaces, and data acquisition functions. Here, this paper carefully surveys the current state of the art in MOSO algorithms, techniques, and solvers, as well as problem types and computational environments where MOSO is commonly applied. We then present several key challenges in the design of a parallel multiobjective simulation optimization framework (ParMOO) and how they have been addressed. Finally, we provide two case studies demonstrating how customized ParMOO solvers can be quickly built and deployed to solve real-world MOSO problems.

engineering design optimization↗

DOE OSTI2021

AENET–LAMMPS and AENET–TINKER : Interfaces for accurate and efficient molecular dynamics simulations with machine learning potentials

Machine-learning potentials (MLPs) trained on data from quantum-mechanics based first-principles methods can approach the accuracy of the reference method at a fraction of the computational cost. To facilitate efficient MLP-based molecular dynamics and Monte Carlo simulations, an integration of the MLPs with sampling software is needed. Here, we develop two interfaces that link the atomic energy network (ænet) MLP package with the popular sampling packages TINKER and LAMMPS. The three packages, ænet, TINKER, and LAMMPS, are free and open-source software that enable, in combination, accurate simulations of large and complex systems with low computational cost that scales linearly with the number of atoms. Scaling tests show that the parallel efficiency of the ænet–TINKER interface is nearly optimal but is limited to shared-memory systems. The ænet–LAMMPS interface achieves excellent parallel efficiency on highly parallel distributed memory systems and benefits from the highly optimized neighbor list implemented in LAMMPS. We demonstrate the utility of the two MLP interfaces for two relevant example applications: the investigation of diffusion phenomena in liquid water and the equilibration of nanostructured amorphous battery materials.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

DOE OSTI2017

Probabilistic Risk Assessment of CO2 Trapping Mechanisms in a Sandstone CO2-EOR Field in Northern Texas, USA

This study employs a polynomial chaos expansion (PCE) technique to develop the reduced order models (ROMs) integrated with the Monte Carlo simulations to quantify uncertainties of CO 2 storage associated with enhanced oil recovery (EOR) in a commercial-scale CO 2 -EOR field. The Morrow B sandstone at the Farnsworth Unit (FWU) EOR field in northern Texas was selected as a case study. A 3-D reservoir model, including simulation of a five-spot injection/production well pattern, was constructed based on the data from well logs and cores, and an updated seismic interpretation in the FWU. Porosity and permeability were considered as sources of uncertainty. The 1000-realization heterogeneous random fields of porosity and permeability were generated based on the variogram analysis on the core measurements of the FWU. Three model outputs of interest include the amount of CO 2 trapped by three trapping mechanisms, i.e. hydrodynamic trapping, oil dissolution trapping, and aqueous dissolution trapping. The total of 25 runs were conducted with the simulations of a 20-year CO 2 -EOR period, and a 20-year monitoring period to develop the ROMs between uncertain model input parameters (i.e., porosity and permeability in this study) and model outputs at the end of simulation for each grid cell using PCE approach. The high coefficient of determination (R 2 ) and small normalized root mean square error (NRMSE) between the simulated (using reservoir modeling) and predicted (using ROMs) CO 2 storage indicate that the ROMs are acceptable and reliable to be used for the predictions. Given the 1000 Monte Carlo samplings of the model input parameters, cumulative distribution functions (CDFs) and uncertainty bounds (10 th and 90 th percentiles) of model outputs were estimated based on ROMs. At the end of simulation, the most injected CO 2 at the FWU was stored by hydrodynamic trapping (between 121,400 and 166,860 tonnes), followed by oil dissolution trapping (between 55,303 and 76,816 tonnes), and aqueous dissolution trapping (between 1979 and 2751 tonnes).

58 GEOSCIENCES↗

DOE OSTI2020

Optimization of Energy Flow through Synthetic Metabolic Modules and Regulatory Networks in a Model Photosynthetic Eukaryotic Microbe

Photosynthetic organisms have recently gained considerable attention for a role in development of renewable energy sources. Genome-enabled systems biology methods, coupled with functional and synthetic genomics, present opportunities to develop sustainable and economical applications such as fuel production within the next 10 to 15 years. However, optimization of light-driven metabolism for biomass or biofuel production will require a detailed systems biology understanding of photosynthetic processes and cellular metabolism. Genome-scale metabolic models (GEMs) are at the core of systems analysis of cellular processes and form a common organizational framework for analyses of data resulting from functional genomics experimental work and computational studies. Therefore, there is a clear demand for high quality photosynthetic model organisms and the appropriate computational tools that enable systems analysis of light-driven metabolism. Through research conducted we expanded the currently available repertoire of photosynthetic GEMs to include the commercially valuable model diatom Phaeoctylum tricornutum. Diatoms have a peculiar and distinct evolutionary footprint and represent a major eukaryotic lineage that is taxonomically and functionally distinct from green and red algae and vascular plants. Therefore, the true potential for light-driven metabolism aimed at biofuel production remains poorly understood at a systems level for a large subset of the global diversity of photosynthetic organisms. The metabolic capabilities of P. tricornutum were comparatively modeled with those from other photosynthetic groups in order to elucidate the occurrence of metabolic traits within and between phototrophs. Additionally, this research resulted in significant extension of the COnstraints Based Reconstruction and Analysis (COBRA) Toolbox to accommodate the crucial need for infrastructure required for ‘omics data integration and analysis in the context of genome-scale models. Therefore, the proposed research achieved two important goals. First, within the broad scope of photosynthetic organisms, we functionally compared and, as a result, identified cellular processes that require optimization in order to enable deployment as biofuel feedstock. Second, the proposed research resulted in development of key computational infrastructure, which can be further extended to other biological systems, that is currently lacking but necessary for multiple ‘omics data integration.

59 BASIC BIOLOGICAL SCIENCES↗

DOE OSTI2018

Functional characterization of three GH10 xylanases

Decreased availability of fossil fuels has driven an increased demand for sustainable energy sources such as biofuels. One area of bioenergy research involves development of biocatalysts able to efficiently degrade biomass “waste”‐products, such as substrates derived from corn stover, rather than easily‐fermentable biomass used for food, such as starch from corn kernels. Xylanases are of interest for their ability to hydrolyze hemicellulosic sugars found in plant cell walls, allowing utilization of waste‐derived biomass. In this study, three xylanases of glycoside hydrolase family 10 (GH10) are functionally characterized and optimized for temperature and pH, as well as kinetically analyzed for xylose monomer and oligomer production. These enzymes, GH10‐4, GH10‐9, and GH10‐15, demonstrate activity upon substrates xylan and arabinoxylan. For GH10‐4, optima are 50°C at pH 8 on xylan and 45°C at pH 8 on arabinoxylan. For GH10‐9, optima are 70°C at pH 5 on xylan and 70°C at pH 5 on arabinoxylan. For GH10‐15, optima are 50°C at pH 8 on xylan and 45°C at pH 5 on arabinoxylan. Kinetic analysis reveals GH10‐4 produces xylose (X1), xylobiose (X2), xylotriose (X3), xylotetraose (X4), and xylopentaose (X5) from xylan, while GH10‐9 and GH10‐15 produce X1, X2, and X3. From arabinoxylan, GH10‐4 produces X1, X2, X3, X4, while GH10‐9 and GH10‐15 produce X1, X2, X3. Conclusive kinetic data may suggest applicability of these enzymes for industrial use within biocatalysts and contribute further insight to the functionality of enzymes within GH10. Support or Funding Information The authors are grateful for financial support by the Integrated Biological Sciences Summer Research Program (IBS‐SRP, NSF) at the University of Wisconsin‐Madison and the Great Lakes Bioenergy Research Center (GLBRC) of the U.S. Department of Energy. Presentation travel support is provided by the Ronald E. McNair Scholars Program of Winthrop University. The authors also thank Lai Bergeman, Craig Bingman, Bob Smith, Emily Beebe, Kirk Vander Meulen, Amber Smith, David Wassarman, and John Greenler for professional support.

Park, Jesslyn↗

DOE OSTI2024

Proton Quenching in Rare-Earth Inorganic Scintillators: GAGG:Ce and YSO:Ce

Scintillator detectors are an integral component of radiation detection systems for a variety of applications such as medical imaging, accelerator diagnostics, and space science. Typically, a scintillator detector’s response is characterized using gamma sources to understand the detection response to different types of radiation, including charged particle detection. However, there exists a nonlinearity of the amount of light produced from an incident gamma ray of specific energy and the light produced from an incident charged particle of the same energy. This important effect, known as quenching, must be accounted for to interpret energies from charged particles incident on detectors. In this article, we present results of quenching parameterization for two types of cerium-doped inorganic scintillators, Y2SiO5:Ce (YSO:Ce) and Gd3Al2Ga3O12:Ce (GAGG:Ce). We measured the light output from incident proton energies from 1 to 25 MeV using a 3-MV tandem accelerator and two reactions: Au(p,p)Au and 3He(d,p)⁴He. Using gamma-ray sources to calibrate the detectors, we compared the measured electron-equivalent energy versus the incident energy expected. Using an adaptation of the Birks semi-empirical formula, we extracted the Birks parameter (kB) to understand quenching. For one of the GAGG:Ce samples, the kB parameter of 0.0072 [g cm-2 MeV-1] is comparable to a similar study where the value of kB was 0.0065 [g cm-2 MeV-1]. For YSO:Ce, no other kB values were found in the literature. Three different types of GAGG:Ce were used to collect measurements of kB as a function of dopant concentration.

46 INSTRUMENTATION RELATED TO NUCLEAR SCIENCE AND ↗

DOE OSTI2025

Spatial Signatures of Electron Correlation in Least-Squares Tensor Hypercontraction

Least Squares Tensor Hypercontraction (LS-THC) has received some attention in recent years as an approach to reduce the significant computational costs of wavefunc- tion based methods in quantum chemistry. However, previous work has demonstrated that the LS-THC factorization performs disproportionately worse in the description of wavefunction components (e.g. cluster amplitudes T 2 ) than Hamiltonian compo- nents (e.g. electron repulsion integrals (pq|rs)). This work develops novel theoretical methods to study the source of these errors in the context of the real-space T 2 kernel, and reports, for the first time, the existence of a “correlation feature” in the errors of the LS-THC representation of the “exchange-like” correlation energy EX and T 2 that is remarkably consistent across ten molecular species, three correlated wavefunctions, and four basis sets. This correlation feature portends the existence of a “pair-point kernel” missing in the usual LS-THC representation of the wavefunction, which critically depends upon pairs of grid points situated close to atoms and with inter-pair distances between one and two Bohr radii. These findings point the way for future LS-THC developments to address these shortcomings.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

DOE OSTI2026

Reconstruction and Dissolution of Copper Catalysts during Electrocatalytic Nitrate Reduction

Copper-based electrocatalysts are widely explored for electrochemical nitrate remediation, yet their stability under operating conditions remains poorly understood. While nanoscale and subnanoscale Cu motifs are known to restructure during the nitrate reduction reaction (NO 3 RR), how these transformations translate into irreversible material loss remains unclear. Here, we quantify Cu dissolution during NO 3 RR as a function of catalyst architecture and electrolyte chemistry using two model systems: single-atom Cu (Cu 1 ) and Cu nanoparticles (Cu NP ). Time-resolved leaching measurements, integrated with in situ X-ray absorption spectroscopy (XAS), reveal measurable Cu loss for both catalysts during NO 3 RR. Dissolution is concentrated at the initiation of electrolysis, coinciding with rapid restructuring, and depends strongly on morphology, with Cu NP consistently exhibiting greater Cu loss than Cu 1 . In situ XAS reveals that Cu 1 forms transient metallic clusters under reduction that largely redisperse upon returning to open-circuit voltage, whereas Cu NP undergoes reduction of an oxidized surface layer accompanied by sustained Cu loss during electrolysis. Notably, the presence of nitrate significantly intensifies restructuring and Cu loss, highlighting the critical role of electrolyte composition. Furthermore, these findings establish a direct link between electrochemical restructuring and Cu dissolution, unveiling electrolyte-dependent interactions as key determinants of catalyst durability in electrochemical nitrate conversion.

36 MATERIALS SCIENCE↗

DOE OSTI2020

MoorDyn V2: New Capabilities in Mooring System Components and Load Cases

MoorDyn, an open-source mooring dynamics model, is being expanded with capabilities for additional mooring system features and load cases. As floating wind turbine technology matures, mooring systems are becoming more sophisticated and more complex scenarios need to be considered in the design process. Mooring systems may have synthetic line materials, ballast/buoyancy bodies along the lines, or interconnections between platforms. Failure modes may involve multiple cascading line failures that depend on mooring system dynamics. Features recently added to MoorDyn aim to address these emerging needs. MoorDyn’s linear elasticity model has been supplemented to support user-defined stress-strain curves, which can be adjusted to represent synthetic mooring materials. Rigid six-degree-of-freedom bodies in the mooring system can now be modeled using two new model objects. “Rod” objects provide an option for rigid cylindrical bodies. They use the existing Morison equation-based hydrodynamics model and can be connected to mooring lines at either end. “Body” objects provide a generic six-degree-of-freedom rigid-body representation based on a lumped-parameter model of translational and rotational properties. Rod objects can be added to Body objects and mooring lines can be attached at any location, allowing a wide variety of submerged structures to be integrated into the mooring system. Lastly, a means of dynamically simulating mooring line failures has been implemented. These new features, currently in the C++ version of MoorDyn, are described and then demonstrated on a two-turbine shared-mooring array. A qualitative view of the results suggests the new features are functioning as expected.

49 EE - Wind and Water Power Program - Wind (EE-4W↗

DOE OSTI2024

Binary pseudo-random array standards for calibration of 3D optical surface profilers used for metrology with significantly curved x-ray optics

High-accuracy metrology is vitally important in manufacturing ultra-high-quality free-form mirrors designed to manipulate X-ray light with nanometer-scale wavelengths. The current capabilities and possibility for improvements in X-ray mirror manufacturing are limited by inherent imperfections of the integrated metrology tools. In the case of Fizeau interferometry, metrology tools are currently calibrated with super-polished flat test-standard/reference mirrors. This is acceptable for measuring slightly curved X-ray optics. However, for even moderately curved aspherical X-ray mirrors the flat-reference calibration is not sufficiently accurate and stitching Fizeau interferometer-based surface metrology is used to mitigate the problem. But still, the retrace and aberration errors, as well as the limited spatial resolution, described with the instrument transfer function (ITF), can be transferred into the optical surface topography of X-ray mirrors obtained in stitching metrology. For ITF calibration, we have developed an original technique, based on test standards structured as two-dimensional (2D) highly-randomized (HR) binary pseudo-random arrays (BPRAs). The technique employs the unique properties of the HR BPRA patterns in the spatial frequency domain., i.e. the inherent 2D power spectral density of the HR BPRA pattern has a deterministic white-noise-like character that allows direct determination of the ITF with uniform sensitivity over the entire spatial frequency range and field-of-view of an instrument. Here, we explore technological, metrological, and analytical aspects essential for calibration of the retrace and aberration errors of Fizeau interferometers using different types of tilted test samples, including a super-polished reference mirror for the re-trace calibration and the uniformly redundant array (URA) BPRA standards for the geometrical distortion (aberration) calibration. While the first method was previously demonstrated by researchers at DIAMOND Light Source, a method based on the URA BPRA is described and demonstrated here for the first time. We outline the design and fabrication process used in fabrication of URA BPRA test standards, and present the results of application of the URA BPRA standards demonstrating the high efficacy of our approach to geometrical distortion calibration of Fizeau interferometers. We also discuss the possible sources of unexpected peculiarities of the systematic errors, including an astigmatic character of the retrace error, observed with Fizeau interferometers at the Advanced Light Source X-Ray Optics Laboratory.

Munechika, Keiko↗

DOE OSTI2020

MoorDyn V2: New Capabilities in Mooring System Components and Load Cases: Preprint

49 EE - Wind and Water Power Program - Wind (EE-4W↗

DOE OSTI2024

Integrating viruses into soil food web biogeochemistry

The soil microbiome is recognized as an essential component of healthy soils. Viruses are also diverse and abundant in soils, but their roles in soil systems remain unclear. Here we argue for the consideration of viruses in soil microbial food webs and describe the impact of viruses on soil biogeochemistry. The soil food web is an intricate series of trophic levels that span from autotrophic microorganisms to plants and animals. Each soil system encompasses contrasting and dynamic physicochemical conditions, with labyrinthine habitats composed of particles. Conditions are prone to shifts in space and time, and this variability can obstruct or facilitate interactions of microorganisms and viruses. Because viruses can infect all domains of life, they must be considered as key regulators of soil food web dynamics and biogeochemical cycling. Finally, we highlight future research avenues that will enable a more robust understanding of the roles of viruses in soil function and health.

59 BASIC BIOLOGICAL SCIENCES↗

DOE OSTI2026

The landscape of regulatory element evolution in a C4 perennial grass

Gene regulatory evolution is a well-known source of phenotypic diversity and adaptive evolution. Although cis-regulatory elements (CREs) play a vital role in gene expression evolution, the molecular evolution of CREs remains mostly unknown due to the difficulty in identifying and characterizing these functional elements. Comparative genomic analyses of noncoding DNA can be leveraged to identify conserved noncoding sequences (CNS), many of which may harbor functional CREs conserved by purifying selection. However, purely computational inference of CREs from putative CNS can be erroneous due to the complex genomic architecture in plants. One promising experimental approach to identify CREs is by profiling accessible chromatin regions (ACRs) that are often associated with the location of CREs. In this study, we use comparative genomics along with the profiling of ACRs to study the molecular evolution of putative functional noncoding regulatory regions in Panicoid grasses. We identified sets of CNS that varied in relationship to the degree of evolutionary divergence among the studied taxa, including identifying core-Panicoid-CNS. We augmented this analysis by profiling ACRs in Panicum hallii ecotypes using ATAC-seq. ACRs had low SNP density at the summit, harbored a high frequency of core-Panicoid-CNS, and were enriched with expression QTL. These data help to annotate the P. hallii genome for putative functional elements and suggest that a large proportion of these ACRs are evolving under purifying selection. Turnover in CNS and ACR between ecotypes of P. hallii identifies a small set of putatively divergent CREs that may underlie differences in gene regulation between genotypes from inland and coastal habitats. In summary, we profiled ACRs in Panicoid grasses and integrated this data with our putative CNS prediction framework, which provides unique insight into patterns of polymorphism and divergence in CREs in C4 perennial grasses.

59 BASIC BIOLOGICAL SCIENCES↗

DOE OSTI2022

Machine learning-assisted ultrafast flash sintering of high-performance and flexible silver–selenide thermoelectric devices

Flexible thermoelectric generators (TEGs) have shown immense potential for serving as a power source for wearable electronics and the Internet of Things. A key challenge preventing large-scale application of TEGs lies in the lack of a high-throughput processing method, which can sinter thermoelectric (TE) materials rapidly while maintaining their high thermoelectric properties. Herein, we integrate high-throughput experimentation and Bayesian optimization (BO) to accelerate the discovery of the optimum sintering conditions of silver–selenide TE films using an ultrafast intense pulsed light (flash) sintering technique. Due to the nature of the high-dimensional optimization problem of flash sintering processes, a Gaussian process regression (GPR) machine learning model is established to rapidly recommend the optimum flash sintering variables based on Bayesian expected improvement. For the first time, an ultrahigh-power factor flexible TE film (a power factor of 2205 μW m -1 K -2 with a zT of 1.1 at 300 K) is demonstrated with a sintering time less than 1.0 second, which is several orders of magnitude shorter than that of conventional thermal sintering techniques. Further, the films also show excellent flexibility with 92% retention of the power factor (PF) after 10 3 bending cycles with a 5 mm bending radius. In addition, a wearable thermoelectric generator based on the flash-sintered films generates a very competitive power density of 0.5 mW cm -2 at a temperature difference of 10 K. This work not only shows the tremendous potential of high-performance and flexible silver–selenide TEGs but also demonstrates a machine learning-assisted flash sintering strategy that could be used for ultrafast, high-throughput and scalable processing of functional materials for a broad range of energy and electronic applications.

25 ENERGY STORAGE↗