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At least 91 records · Page 5

Ptychographic wavefront characterization for single-particle imaging at x-ray lasers

A well-characterized wavefront is important for many x-ray free-electron laser (XFEL) experiments, especially for single-particle imaging (SPI), where individual biomolecules randomly sample a nanometer region of highly focused femtosecond pulses. We demonstrate high-resolution multiple-plane wavefront imaging of an ensemble of XFEL pulses, focused by Kirkpatrick–Baez mirrors, based on mixed-state ptychography, an approach letting us infer and reduce experimental sources of instability. From the recovered wavefront profiles, we show that while local photon fluence correction is crucial and possible for SPI, a small diversity of phase tilts likely has no impact. Our detailed characterization will aid interpretation of data from past and future SPI experiments and provides a basis for further improvements to experimental design and reconstruction algorithms.

47 OTHER INSTRUMENTATION↗

Ecosystems and Networks Integrated with Genes and Molecular Assemblies (ENIGMA): Integrating Metabolomics into Environmental Systems Biology

Our research endeavors entail ambitious objectives to explore the communities of microorganisms and quantify their chemical input and output to determine specific biochemical activity. To achieve these scientific aims, we are creating advanced algorithms to scrutinize extensive experimental data produced through high-throughput technologies, enabling us to elucidate how biological functions are influenced by environmental factors on various scales, and how microbial systems alter their surroundings. By studying the metabolic interdependence of bacterial communities for their survival and reproductive prosperity, we can gain insights into their biochemical capabilities. To accomplish this, we employed cutting-edge mass spectrometry-based techniques and metabolic fingerprinting methods, which offer high chemical specificity and sensitivity. As our efforts progressed, the project evolved into ENIGMA, encompassing a broader range of technology development, including untargeted metabolomics and its implementation for system-level organism analysis.

54 ENVIRONMENTAL SCIENCES↗

Materials Characterization, Prediction, and Control Project: Characterization of 316L Stainless Steel after Solid Phase Processing using Ultrasonic NDE Method

The Pacific Northwest National Laboratory undertook the Materials Characterization, Prediction, and Control Laboratory Directed Research and Development Project to advance understanding of nuclear material processing and enable multifold acceleration in the development and qualification of new material systems produced via advanced manufacturing methods, such as solid phase processing, for use in national security and advanced energy applications (Smith 2021). A motivation of the Materials Characterization, Prediction, and Control Project was to demonstrate ultrasonic testing as a nondestructive evaluation method to complement traditional destructive methods for characterizing material microstructure with emphasis on grain size determination using a method that may have future applications for real-time inline process monitoring. The objective of the work described in this report is to establish the process and an analysis method for measuring grain sizes of polycrystalline metals with ultrafine grains using ultrasonic shear wave backscattering, building on prior studies on coarser-grained material. The work involves five tasks: Measured ultrasonic backscattering experimentally for a series of 316L stainless steel specimens with various grain sizes made by friction stir processing. Calculated ultrasonic backscattering coefficients from experimental data based on a physical measurement model. Measured ground truth grain sizes of the specimens from electron backscatter diffraction grain boundary images using a generalization of the ASTM E112 (ASTM 2021) intercept method. Built a curve of ultrasonic backscattering coefficients versus the ground truth intercept-based grain sizes to determine the correlation between mean grain sizes and ultrasonic measurements. Demonstrated the ability of using the correlation curve to deduce grain sizes with measured ultrasonic backscattering coefficients for a few 316L stainless steel specimens whose grain sizes were unknown beforehand but were targeted to be an extrapolation to larger grain sizes than used to formulate the correlation curves. Experimental procedures and computational algorithms are developed and validated for these tasks. This work establishes an ultrasonic technique for characterizing material microstructure with ultrafine grains that are often resulted by solid-phase processing. The technique is nondestructive, and it has the potential to be used for real time inline process monitoring. This work successfully demonstrates the viability of an ultrasonic nondestructive evaluation method for microstructural characterization of material having ultrafine grain structure (as small as 1?mm) and produced by an advanced manufacturing method. This includes a demonstration of the method to extrapolate to other conditions. While not demonstrated here, the method is expected to be viable for in-line, or near-inline, process monitoring in advanced manufacturing applications with suitable consideration for access of instrumentation to the material being manufactured.

316 L Stainless Steel↗

Multimodal parameter spaces of a complex multi-channel neuron model

One of the most common types of models that helps us to understand neuron behavior is based on the Hodgkin–Huxley ion channel formulation (HH model). A major challenge with inferring parameters in HH models is non-uniqueness: many different sets of ion channel parameter values produce similar outputs for the same input stimulus. Such phenomena result in an objective function that exhibits multiple modes (i.e., multiple local minima). This non-uniqueness of local optimality poses challenges for parameter estimation with many algorithmic optimization techniques. HH models additionally have severe non-linearities resulting in further challenges for inferring parameters in an algorithmic fashion. To address these challenges with a tractable method in high-dimensional parameter spaces, we propose using a particular Markov chain Monte Carlo (MCMC) algorithm, which has the advantage of inferring parameters in a Bayesian framework. The Bayesian approach is designed to be suitable for multimodal solutions to inverse problems. We introduce and demonstrate the method using a three-channel HH model. We then focus on the inference of nine parameters in an eight-channel HH model, which we analyze in detail. We explore how the MCMC algorithm can uncover complex relationships between inferred parameters using five injected current levels. The MCMC method provides as a result a nine-dimensional posterior distribution, which we analyze visually with solution maps or landscapes of the possible parameter sets. The visualized solution maps show new complex structures of the multimodal posteriors, and they allow for selection of locally and globally optimal value sets, and they visually expose parameter sensitivities and regions of higher model robustness. We envision these solution maps as enabling experimentalists to improve the design of future experiments, increase scientific productivity and improve on model structure and ideation when the MCMC algorithm is applied to experimental data.

97 MATHEMATICS AND COMPUTING↗

Temperature dependence of magnetic anisotropy and magnetoelasticity from classical spin-lattice calculations

Here we present a classical molecular-spin dynamics (MSD) methodology that enables accurate computations of the temperature dependence of the magnetocrystalline anisotropy as well as magnetoelastic properties of magnetic materials. The nonmagnetic interactions are accounted for by a spectral neighbor analysis potential (SNAP) machine-learned interatomic potential, whereas the magnetoelastic contributions are accounted for using a combination of an extended Heisenberg Hamiltonian and a Néel pair interaction model, representing both the exchange interaction and spin-orbit-coupling effects, respectively. All magnetoelastic potential components are parameterized using a combination of first-principles and experimental data. Our framework is applied to the α phase of iron. Initial testing of our MSD model is done using a 0 K parametrization of the Néel interaction model. After this, we examine how individual Néel parameters impact the $B$ 1 and $B$ 2 magnetostrictive coefficients using a moment-independent δ sensitivity analysis. The results from this study are then used to initialize a genetic algorithm optimization which explores the Néel parameter phase space and tries to minimize the error in the B 1 and B 2 magnetostrictive coefficients in the range of 0–1200 K. Our results show that while both the 0 K and genetic algorithm optimized parametrization provide good experimental agreement for $B$ 1 and $B$ 2 , only the genetic algorithm optimized results can capture the second peak in the $B$ 1 magnetostrictive coefficient which occurs near approximately 800 K.

75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗

Simulation and Optimization of Volatile Fatty Acid Upgrading Strategies for Sustainable Transportation Fuel Production

Underutilized wet waste is a promising feedstock for production of carbon-neutral or carbon-negative liquid transportation fuels. Arrested methanogenesis of wet wastes by microbes, which produces mixtures of C2-C8 carboxylic acids (volatile fatty acids, VFAs), is practiced industrially at a pilot scale and the VFA products can be catalytically upgraded to molecules suitable for use as transportation fuels (alcohols and alkanes) via sequential ketonization and hydrogenation, both steps of which have been demonstrated with high (>90%) yield at the lab scale. We present in this work a simulation-based decision-making framework which evaluates upgrading strategies of VFAs to alcohol- and hydrocarbon-based neat and blended diesel, jet, and gasoline fuels. The processes utilize sequential upgrading steps (ketonization and hydrogenation) accompanied by one distillation step (either separating VFAs before ketonization or alcohols after ketone hydrogenation) to form two liquid streams: a light alcohol stream best suited as a light-duty fuel and a heavy alcohol or hydrocarbon stream best suited as a diesel or jet fuel. Suitability of the liquid products as transportation fuels and maximum blending levels with petrofuels comes from simulation of critical fuel properties (boiling point, flash point, lower heating value, viscosity, melting point, water solubility, and cetane/octane number). Catalytic upgrading steps and fuel property mixing models used by the simulation are experimentally validated. We demonstrate the flexibility of the decision-making algorithm by evaluating processing scenarios for experimentally-observed VFA profiles with varied carbon chain length distributions. Processing scenarios are optimized for either maximum total renewable carbon utilization or production of heavy-duty (jet or diesel) fuels. We evaluate the economic viability and CO2 emissions of each proposed upgrading scenario using techno-economic and life cycle analyses. The decision-making framework developed in this work can also be used to down-select promising strategies for upgrading of other bio-based feedstocks to sustainable fuels and chemicals.

aviation fuel↗

Robust A-Optimal Experimental Design for Sensor Placement in Bayesian Linear Inverse Problems

Optimal design of experiments for Bayesian inverse problems has recently gained wide popularity and attracted much attention, especially in the computational science and Bayesian inversion communities. An optimal design maximizes a predefined utility function that is formulated in terms of the elements of an inverse problem, an example being optimal sensor placement for parameter identification. The state-of-the-art algorithmic approaches following this simple formulation generally overlook misspecification of the elements of the inverse problem, such as the prior or the measurement uncertainties. This work presents an efficient algorithmic approach for designing optimal experimental design schemes for Bayesian linear inverse problems such that the optimal design is robust to misspecification of elements of the inverse problem. Specifically, we consider a worst-case scenario approach for the uncertain or misspecified parameters, formulate robust objectives, and propose an algorithmic approach for optimizing such objectives. Furthermore, both relaxation and stochastic solution approaches are discussed with detailed analysis and insight into the interpretation of the problem and the proposed algorithmic approach. Extensive numerical experiments to validate and analyze the proposed approach are carried out for sensor placement in a parameter identification problem.

Bayesian inverse problems↗

Evidence of scaling advantage for the quantum approximate optimization algorithm on a classically intractable problem

The quantum approximate optimization algorithm (QAOA) is a leading candidate algorithm for solving optimization problems on quantum computers. However, the potential of QAOA to tackle classically intractable problems remains unclear. Here, we perform an extensive numerical investigation of QAOA on the low autocorrelation binary sequences (LABS) problem, which is classically intractable even for moderately sized instances. We perform noiseless simulations with up to 40 qubits and observe that the runtime of QAOA with fixed parameters scales better than branch-and-bound solvers, which are the state-of-the-art exact solvers for LABS. The combination of QAOA with quantum minimum finding gives the best empirical scaling of any algorithm for the LABS problem. We demonstrate experimental progress in executing QAOA for the LABS problem using an algorithm-specific error detection scheme on Quantinuum trapped-ion processors. Our results provide evidence for the utility of QAOA as an algorithmic component that enables quantum speedups.

97 MATHEMATICS AND COMPUTING↗

Rapid retrieval of first-order spatiotemporal distortions for ultrashort laser pulses

High-intensity, ultrashort laser sources are a foundational pillar for High-Energy-Density (HED) physics, and as the repetition-rates of these systems increase, diagnostics must be developed to match their data collection speed. Characterization of any spatiotemporal distortions in the laser pulse is necessary in order to standardize results across facilities. Here, we have previously developed a laser diagnostic called Spatially and Temporally Resolved Intensity and Phase Evaluation Device: Full Information from a Single Hologram, or STRIPED FISH, to measure the full spatiotemporal laser electric field on a single shot. In order to provide rapid feedback, we here adapt the STRIPED FISH retrieval algorithm, which typically has computation times of up to 30 minutes due to the high spatial resolution of the device and its retrieval of the complete four-dimensional pulse field, to distill the key electric field quantities into a handful of scalars for rapid assessment of the pulse's first order distortions. Here, our new, rapid non-iterative retrieval algorithm is validated with simulated and experimental data, and it provides, within seconds, the same first-order information as given by the full analysis. This algorithm is suitable for on-shot assessment of spatiotemporal distortions and can be adapted to assess high repetition-rate laser quality in HED experiments.

70 PLASMA PHYSICS AND FUSION TECHNOLOGY↗

Evaluating Limits of Machine Learning-Assisted Raman Spectroscopy in Classification of Biological Samples

Machine learning (ML)-assisted Raman spectroscopy has become a powerful analytical tool for the classification and identification of analytes; however, technical challenges impacting its detection accuracy have not been thoroughly investigated. This study explores experimental factors affecting classification performance. Among the evaluated ML models, ML algorithms show minimal impact on classification accuracy. Instead, experimental factors, including spectral similarity between tested samples and data quality, dominate detection performance. Increases in spectral noise and spectral similarity significantly reduce classification accuracy. In well-controlled samples with low experimental noise, ML-assisted Raman spectroscopy can discriminate lipid mixtures with a composition difference of 1.85 mol %. To assess the effect of biological heterogeneity, we analyzed single-cell Raman spectra from Saccharomyces cerevisiae strains carrying single, double, or triple gene mutations. Intrinsic cell-to-cell variability introduced substantial spectral differences, severely reducing the accuracy of multiclass classification of these genetically similar strains at the single-cell level. Averaging Raman spectra across multiple cells improved classification accuracy by reducing this spectral variability. We also assess the effectiveness of transfer learning across different Raman spectrometers, specifically by applying an ML model trained on one instrument to another Raman spectrometer. Transfer learning can be improved with proper instrument calibration, highlighting the importance of instrument standardization. Overall, our results demonstrate that data quality and spectral similarity are the primary bottlenecks in ML-assisted Raman spectroscopy. Careful attention to sample preparation, data acquisition, measurement conditions, and instrument calibration is critical to achieving robust and reliable classification performance.

Fungi↗

Verification and validation of detonation-shock-dynamics relations for explosives described by general equation of state and chemical reaction models

Detonation shock dynamics is a powerful method to model the behaviour of High Explosives (HE). However in order to use this method, the underlying relationship between the local radius of curvature and the detonation speed must be known. Previous work has developed methods to calculate this effect using simple, single-step Arrhenius and polytropic gas, models for the chemical reaction and the equation of state, respectively. In recent years, more complex models for both reaction rates and equations of state have been developed which show better agreement with experimental data than these simple models, especially when considering condensed phase explosives.. This work presents the governing equations for solving these problems in a way that is generalised to use arbitrary equations of state as well as reaction models which may have more than a single step and multiple product species. This implementation is verified against exact solutions, demonstrating that the equations were implemented properly. The verified algorithm is then validated against experimental data and high fidelity simulations, showing that it is able to make accurate predictions in a regime where the underlying assumptions of the governing equations are valid. Importantly, this approach has many applications: from creating equivalent detonation shock dynamics models for existing reactive burn calibrations for HE; to developing new functional forms and calibrations of reactive burn models for condensed phase high explosives.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Sempervirens: A Fast Reconstruction Algorithm for Noisy and Incomplete Binary Matrix Representations of Trees

Applications such as reconstructing cell lineage trees (represented as phylogenetic trees) from single-cell sequencing data require reconstructing a {0,1}-matrix that has many errors and missing entries. We introduce Sempervirens, a very fast matrix reconstruction algorithm for noisy and incomplete matrix representations of phylogenetic trees. Sempervirens uses an iterative maximum-likelihood approach to determine the topology tree represented by the corrupted data. We show that Sempervirens is at least three orders of magnitude faster than other methods on thousand by thousand matrices, with the speed gap widening with larger matrices. We also show that Sempervirens matches state-of-the-art methods in reconstruction accuracy. The speed of Sempervirens enables it to be tractably applied to reconstructing much larger matrices than those that other methods can reconstruct. In addition to experimental results, we justify the algorithm with a mathematical treatment of its subprocedures.

algorithms↗

Modeling Approach for the Aluminum-clad Dry Storage Pilot using HFIR Fuel

To confirm that the dry storage of aluminum-clad research reactor spent nuclear fuel (ASNF) will remain within the safety envelope after applied drying schemes and that the resulting evolution of the gas space composition, temperature, and pressure conditions are understood, a dry storage pilot project is being established. The pilot will incorporate an instrumented lid for discrete interval or for on-demand gas composition and temperature monitoring of two DOE Standard Canisters (DSCs) loaded with three High Flux Isotope Reactor (HFIR) inner cores per DSC. Each DSC would be subjected to a separate alternative candidate drying scheme. Canisters will undergo 1 to 5 years of monitoring, including internal temperature and gas sampling to track pressure and composition changes. This report outlines the approach for modeling the ASNF-in-canister behavior in terms of evolving gas space conditions for the ASNF dry storage pilot using HFIR fuel. The ASNF has an adherent surface oxyhydroxide layer comprised of boehmite/bayerite that generates hydrogen when subjected to irradiation. Three-dimensional multi-physics computational fluid dynamics simulations will be executed to compute the thermal field within the DSC and provide inputs to a chemical model employed to compute pressure buildup as hydrogen is generated in the system. Implemented in Cantera, the chemical model solves gas phase and aluminum oxyhydroxide surface-mediated radiolysis reactions. Gas phase reactions are sourced from Wittman and Hanson (2015), whereas surface-mediated reactions are incorporated by fitting experimental data using an optimization algorithm (Abboud, 2023). Water radiolysis reactions from Wren and Ball (2001) are adopted with modifications as described in Abboud (2023c). Understanding the effect of the hydrogen buildup over time is important for long-term storage safety considerations. Modeling results will include the canister pressure, temperature, and composition evolution from the initial helium backfill with the addition of radiolytically-evolved chemical species (e.g., hydrogen and oxygen). The specific HFIR cores for the pilot program have not yet been selected, and the overall design is still in development. The CFD-chemical model used for this work will be based on prior models with necessary updates to allow for improved accuracy and efficiency. The experimental data obtained from the HFIR demonstration will be used to improve and validate the computational models to predict the ASNF-in-canister behavior.

12 MANAGEMENT OF RADIOACTIVE AND NON-RADIOACTIVE W↗

Optimal Protocols in Quantum Annealing and Quantum Approximate Optimization Algorithm Problems

Quantum annealing (QA) and the quantum approximate optimization algorithm (QAOA) are two special cases of the following control problem: apply a combination of two Hamiltonians to minimize the energy of a quantum state. Which is more effective has remained unclear. Here we analytically apply the framework of optimal control theory to show that generically, given a fixed amount of time, the optimal procedure has the pulsed (or “bang-bang”) structure of QAOA at the beginning and end but can have a smooth annealing structure in between. This is in contrast to previous works which have suggested that bang-bang (i.e., QAOA) protocols are ideal. To support this theoretical work, we carry out simulations of various transverse field Ising models, demonstrating that bang-anneal-bang protocols are more common. Futher, the general features identified here provide guideposts for the nascent experimental implementations of quantum optimization algorithms.

71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗

PYK-SubstitutionOME: an integrated database containing allosteric coupling, ligand affinity and mutational, structural, pathological, bioinformatic and computational information about pyruvate kinase isozymes

Interpreting changes in patient genomes, understanding how viruses evolve and engineering novel protein function all depend on accurately predicting the functional outcomes that arise from amino acid substitutions. To that end, the development of first-generation prediction algorithms was guided by historic experimental datasets. However, these datasets were heavily biased toward substitutions at positions that have not changed much throughout evolution (i.e. conserved). Although newer datasets include substitutions at positions that span a range of evolutionary conservation scores, these data are largely derived from assays that agglomerate multiple aspects of function. To facilitate predictions from the foundational chemical properties of proteins, large substitution databases with biochemical characterizations of function are needed. We report here a database derived from mutational, biochemical, bioinformatic, structural, pathological and computational studies of a highly studied protein family—pyruvate kinase (PYK). A centerpiece of this database is the biochemical characterization—including quantitative evaluation of allosteric regulation—of the changes that accompany substitutions at positions that sample the full conservation range observed in the PYK family. We have used these data to facilitate critical advances in the foundational studies of allosteric regulation and protein evolution and as rigorous benchmarks for testing protein predictions. We trust that the collected dataset will be useful for the broader scientific community in the further development of prediction algorithms.

59 BASIC BIOLOGICAL SCIENCES↗

Toward autonomous laboratories: Convergence of artificial intelligence and experimental automation

The ever-increasing demand for novel materials with superior properties inspires retrofitting traditional research paradigms in the era of artificial intelligence and automation. An autonomous experimental platform (AEP) has emerged as an exciting research frontier that achieves full autonomy via integrating data-driven algorithms such as machine learning (ML) with experimental automation in the material development loop from synthesis, characterization, and analysis, to decision making. In this review, we started with a primer to describe how to develop data-driven algorithms for solving material problems. Then, we systematically summarized recent progress on automated material synthesis, ML-enabled data analysis, and decision-making. Finally, we discussed the challenges and opportunities in an endeavor to develop the next-generation AEP for ultimately realizing an autonomous or self-driving laboratory. In conclusion, this review will provide insights for researchers aiming to learn the frontier of ML in materials science and deploy AEP in their labs for accelerating material development.

36 MATERIALS SCIENCE↗

MRT 7365: Power flow physics and key physics phenomena

The Z accelerator at Sandia National Laboratories conducts z-pinch experiments at 26 MA in support of DOE missions in stockpile stewardship, dynamic materials, fusion, and other basic sciences. Increasing the current delivered to the z-pinch would extend our reach in each of these disciplines. To achieve increases in current and accelerator efficiency, a fraction of Z’s shots are set aside for research into transmission-line power flow. These shots, with supporting simulations and theory, are incorporated into this Advanced Diagnostics milestone report. The efficiency of Z is reduced as some portion of the total current is shunted across the transmission-line gaps prior to the load. This is referred to as “current loss”. Electrode plasmas have long been implicated in this process, so the bulk of dedicated power-flow experiments are designed to measure the plasma environment. The experimental analyses are enhanced by simulations conducted using realistic hardware and Z voltage pulses. In the same way that diagnostics are continually being improved for sensitivity and resolution, the modeling capability is continually being improved to provide faster and more realistic simulations. The specifics of the experimental hardware, diagnostics, simulations, and algorithm developments are provided in this report. The combined analysis of simulation and data confirms that electrode plasmas have the most detrimental impact on current delivery. Experiments over the last three years have tested the theoretical current-loss mechanisms of enhanced ion current, plasma gap closure, and Hall-related current. These mechanisms are not mutually exclusive and may be coincident in the final feed as well as in upstream transmission lines. The final-feed geometries tested here, however, observe lower-density plasmas without dominant ion currents which is consistent with a Hall-related current. The picture of plasma formation and transport formed from experiment and simulation is informing hardware designs being fielded on Z now and being proposed for the Next-Generation Pulsed Power (NGPP) facility. In this picture, the strong magnetic fields that heat the electrodes above particle emission thresholds also confine the charged particles near the surface. Some portion of the plasmas thus formed is transported into the transmission-line gap under the force of the electric field, with aid from plasma instabilities. The gap plasmas are then transported towards the load by a cross-field drift, where they accumulate and contribute to a likely Hall-related cross-gap current. The achievements in experimental execution, model validation, and physical analysis presented in this report set the stage for continued progress in power flow and load diagnostics on Z. The planned shot schedule for Z and Mykonos will provide data for extrapolation to higher current to ensure the predicted performance and efficiency of a NGPP facility.

43 PARTICLE ACCELERATORS↗

Efficient Hybrid Attack Graph Generation for Cyber-Physical System Resilience Experimentation (Final Project Report)

HAGEN project has developed theory, algorithms, and capabilities to assist cyber physical system modelers and operators to perform system and device-level vulnerability assessment, risk assessment, impact assessment, and mitigation planning. The project generates hybrid attack graphs for Cyber-Physical System (CPS) resilience experimentation at desired scale and speed. The project will produce composite attack datasets, algorithms, and demonstrable prototypical tools, and a library of high-impact attack sequences for a given CPS of interest. This report provided overall summary of research and development performed between FY22-24.

45 MILITARY TECHNOLOGY, WEAPONRY, AND NATIONAL DEF↗