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DOE OSTI2021

The Baghdad Atlas: A relational database of inelastic neutron-scattering (n,n ' γ) data

A relational database has been developed based on the original (n,n'γ) work carried out by A. M. Demidov et al., at the Nuclear Research Institute in Baghdad, Iraq (Demidov et al., 1978) for 105 independent measurements comprising 76 elemental samples of natural composition and 29 isotopically-enriched samples. The information from this Atlas includes: γ-ray energies and relative intensities; nuclide and level data corresponding to the residual nucleus and meta data associated with the target sample that allows for the extraction of the flux-weighted (n,n'γ) cross sections for a given transition relative to a defined value. The optimized angular-distribution-corrected fast-neutron flux-weighted partial γ-ray cross section for the production of the 846.8-keV 21+→0gs+γ-ray transition in 56Fe, determined to be $\langle$σγ$\rangle$=143(29) mb, is used for this purpose. However, different values for the adopted cross section can be readily implemented to accommodate user preference based on revised determinations of this quantity. The Atlas (n,n'γ) data has been compiled into a series of CSV-style ASCII data sets and a suite of Python scripts have been developed to build and install the database locally. The database can then be accessed directly through the SQLite engine, or using alternative methods such as the Jupyter Notebook Python-browser interface. Several examples exploiting different interaction methodologies are distributed with the complete software package.

73 NUCLEAR PHYSICS AND RADIATION PHYSICS↗

DOE OSTI2023

A reference-area-free strain mapping method using precession electron diffraction data

Here, in this work, we developed a method using precession electron diffraction data to map the residual elastic strain at the nano-scale. The diffraction pattern of each pixel was first collected and denoised. Template matching was then applied using the center spot as the mask to identify the positions of the diffraction disks. Statistics of distances between the selected diffracted disks enable the user to make an informed decision on the reference and to generate strain maps. Strain mapping on an unstrained single crystal sapphire shows the standard deviation of strain measurement is 0.5%. With this method, we were able to successfully measure and map the residual elastic strain in VO 2 on sapphire and martensite in a Ni 50.3 Ti 29.7 Hf 20 shape memory alloy. This approach does not require the user to select a “strain-free area” as a reference and can work on datasets even with the crystals oriented away from zone axes. This method is expected to provide a robust and more accessible alternative means of studying the residual strain of various material systems that complements the existing algorithms for strain mapping.

46 INSTRUMENTATION RELATED TO NUCLEAR SCIENCE AND ↗

DOE OSTI2025

Modeling the Behavior of Complex Aqueous Electrolytes Using Machine Learning Interatomic Potentials: The Case of Sodium Sulfate

Understanding the structure and thermodynamics of solvated ions is essential for advancing applications in electrochemistry, water treatment, and energy storage. While ab initio molecular dynamics methods are highly accurate, they are limited by short accessible time and length scales whereas classical force fields struggle with accuracy. Herein, we explore the structure and thermodynamics of complex monovalent-divalent ion pairs using Na 2 SO 4 (aq) as a case study by applying a machine learning interatomic potential (MLIP) trained on density functional theory (DFT) data. Our MLIP-based approach reproduces key bulk properties such as density and radial distribution functions of water. We provide the hydration structure of the sodium and sulfate ions in the 0.1–2 M concentration range and the one-dimensional and two-dimensional potentials of mean force for the sodium–sulfate ion pairing at the low concentration limit (0.1 M), which are inaccessible to DFT. At low concentrations, the sulfate ion is strongly solvated, leading to the stabilization of solvent-separated ion pairs over contact ion pairs. Minimum energy pathway analysis revealed that coordinating two sodium ions with a sulfate ion is a multistep process whereby the sodium ions coordinate to the sulfate ion sequentially. Finally, we demonstrate that MLIPs allow the study of solvated ions beyond simple monovalent pairs with DFT-level accuracy in their low concentration limit (0.1 M) via statistically converged properties from ns-long simulations.

anions↗

DOE OSTI2022

Manipulating Two-Photon Absorption of Molecules through Efficient Optimization of Entangled Light

We report how the unique temporal and spectral features of pulsed entangled photons from a parametric downconversion source can be utilized for manipulating electronic excitations through the optimization of their spectral phase. A new comprehensive optimization protocol based on Bayesian optimization has been developed in this work to selectively excite electronic states accessible by two-photon absorption. Using our optimization method, the entangled two-photon absorption probability for a thiophene dendrimer can be enhanced by up to a factor of 20, while classical light turns out to be nonoptimizable. Moreover, the optimization involving photon entanglement enables selective excitation that would not be possible otherwise. In addition to optimization, we have explored entangled two-photon absorption in the small entanglement time limit showing that entangled light can excite molecular electronic states that are vanishingly small for classical light. As a result, we demonstrate these opportunities with an application to a thiophene dendrimer.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

DOE OSTI2025

Machine Learning-Accelerated First-Principles Molecular Dynamics Reveals C–C Coupling Mechanisms toward Ethylene on Cu(100)

Here, the Cu(100) termination has been identified as the most effective facet for converting CO and CO 2 into ethylene. To enhance both the activity and selectivity of ethylene production, we perform machine-learning-accelerated, first-principles molecular dynamics simulations at 298 K in an explicit solvent at pH 7 to elucidate the C–C coupling mechanism─the critical reaction step in forming C 2+ products. Among the six potential C–C coupling pathways, the most feasible are CO* dimerization and CO – CHO* and CHO* – CHO* couplings. Using the computational hydrogen electrode method, we demonstrate that all three pathways are equally accessible at −0.6 V vs RHE. At a potential below −1.0 V vs RHE, the thermodynamic barriers for the CO – CHO* and CHO* – CHO* pathways become negligible. Our computational findings explain the experimental observations, particularly the absence of C 2+ products above −0.4 V vs RHE and the peaks in ethylene production near −0.6 and −1.0 V vs RHE. Since CHO* acts as a key intermediate common to both C–C coupling and CH 4 formation, we propose that suppressing CHO* hydrogenation would inhibit CH 4 pathways, thereby maximizing ethylene selectivity.

CO2 reduction↗

DOE OSTI2020

Probing light-driven quantum materials with ultrafast resonant inelastic X-ray scattering

Abstract Ultrafast optical pulses are an increasingly important tool for controlling quantum materials and triggering novel photo-induced phase transitions. Understanding these dynamic phenomena requires a probe sensitive to spin, charge, and orbital degrees of freedom. Time-resolved resonant inelastic X-ray scattering (trRIXS) is an emerging spectroscopic method, which responds to this need by providing unprecedented access to the finite-momentum fluctuation spectrum of photoexcited solids. In this Perspective, we briefly review state-of-the-art trRIXS experiments on condensed matter systems, as well as recent theoretical advances. We then describe future research opportunities in the context of light control of quantum matter.

71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗

DOE OSTI2024

Neural simulation-based inference of the neutron star equation of state directly from telescope spectra

Neutron stars provide a unique opportunity to study strongly interacting matter under extreme density conditions. The intricacies of matter inside neutron stars and their equation of state are not directly visible, but determine bulk properties, such as mass and radius, which affect the star's thermal X-ray emissions. However, the telescope spectra of these emissions are also affected by the stellar distance, hydrogen column, and effective surface temperature, which are not always well-constrained. Uncertainties on these nuisance parameters must be accounted for when making a robust estimation of the equation of state. In this study, we develop a novel methodology that, for the first time, can infer the full posterior distribution of both the equation of state and nuisance parameters directly from telescope observations. This method relies on the use of neural likelihood estimation, in which normalizing flows use samples of simulated telescope data to learn the likelihood of the neutron star spectra as a function of these parameters, coupled with Hamiltonian Monte Carlo methods to efficiently sample from the corresponding posterior distribution. Our approach surpasses the accuracy of previous methods, improves the interpretability of the results by providing access to the full posterior distribution, and naturally scales to a growing number of neutron star observations expected in the coming years.

79 ASTRONOMY AND ASTROPHYSICS↗

DOE OSTI2021

Increased seminal root number associated with domestication improves nitrogen and phosphorus acquisition in maize seedlings

Abstract Background and Aims Domesticated maize (Zea mays ssp. mays) generally forms between two and six seminal roots, while its wild ancestor, Mexican annual teosinte (Zea mays ssp. parviglumis), typically lacks seminal roots. Maize also produces larger seeds than teosinte, and it generally has higher growth rates as a seedling. Maize was originally domesticated in the tropical soils of southern Mexico, but it was later brought to the Mexican highlands before spreading to other parts of the continent, where it experienced different soil resource constraints. The aims of this study were to understand the impacts of increased seminal root number on seedling nitrogen and phosphorus acquisition and to model how differences in maize and teosinte phenotypes might have contributed to increased seminal root number in domesticated maize. Methods Seedling root system architectural models of a teosinte accession and a maize landrace were constructed by parameterizing the functional–structural plant model OpenSimRoot using plants grown in mesocosms. Seedling growth was simulated in a low-phosphorus environment, multiple low-nitrogen environments, and at variable planting densities. Models were also constructed to combine individual components of the maize and teosinte phenotypes. Key Results Seminal roots contributed ~35 % of the nitrogen and phosphorus acquired by maize landrace seedlings in the first 25 d after planting. Increased seminal root number improved plant nitrogen acquisition under low-nitrogen environments with varying precipitation patterns, fertilization rates, soil textures and planting densities. Models suggested that the optimal number of seminal roots for nutrient acquisition in teosinte is constrained by its limited seed carbohydrate reserves. Conclusions Seminal roots can improve the acquisition of both nitrogen and phosphorus in maize seedlings, and the increase in seed size associated with maize domestication may have facilitated increased seminal root number.

59 BASIC BIOLOGICAL SCIENCES↗

DOE OSTI2021

New high-throughput endstation to accelerate the experimental optimization pipeline for synchrotron X-ray footprinting

Synchrotron X-ray footprinting (XF) is a growing structural biology technique that leverages radiation-induced chemical modifications via X-ray radiolysis of water to produce hydroxyl radicals that probe changes in macromolecular structure and dynamics in solution states of interest. The X-ray Footprinting of Biological Materials (XFP) beamline at the National Synchrotron Light Source II provides the structural biology community with access to instrumentation and expert support in the XF method, and is also a platform for development of new technological capabilities in this field. Hee, the design and implementation of a new high-throughput endstation device based around use of a 96-well PCR plate form factor and supporting diagnostic instrumentation for synchrotron XF is described. This development enables a pipeline for rapid comprehensive screening of the influence of sample chemistry on hydroxyl radical dose using a convenient fluorescent assay, illustrated here with a study of 26 organic compounds. The new high-throughput endstation device and sample evaluation pipeline now available at the XFP beamline provide the worldwide structural biology community with a robust resource for carrying out well optimized synchrotron XF studies of challenging biological systems with complex sample compositions.

38 RADIATION CHEMISTRY, RADIOCHEMISTRY, AND NUCLEA↗

DOE OSTI2024

MemFriend: Understanding Memory Performance with Spatial-Temporal Affinity

In HPC applications, memory access behavior is one of the main factors affecting performance. Improving an application’s memory access behavior involves optimizing data layout and/or restructuring code, and requires studying spatial-temporal data locality. Existing data locality analyses focus on single-location metrics and are restricted to evaluating temporal locality. We introduce spatial-temporal affinity metrics that quantify temporal access proximity, forward access correlation, and nearby access correlation between pairs of memory locations. We describe methods for distinguishing between potential vs. realized affinity and for reasoning about affinity at multiple resolutions (3D, 2D, 1D). Finally, we construct spatial-temporal affinity signatures that classify memory behavior and that be used to reason about changes in software (data relayout, code refactoring) or hardware (caching, prefetching). We describe methods for signature visualization, interpretation, and quantitative comparison of signatures. We evaluate our methodology using applications with variants that contrast data structures, data layouts and algorithms. We show that spatial-temporal affinity analysis provides novel insights and enables predictive reasoning about application performance when contrasted with reuse distance analysis.

Suriyakumar, Yasodhadevi↗

DOE OSTI2023

Missing data in multi-omics integration: Recent advances through artificial intelligence

Biological systems function through complex interactions between various ‘omics (biomolecules), and a more complete understanding of these systems is only possible through an integrated, multi-omic perspective. This has presented the need for the development of integration approaches that are able to capture the complex, often non-linear, interactions that define these biological systems and are adapted to the challenges of combining the heterogenous data across ‘omic views. A principal challenge to multi-omic integration is missing data because all biomolecules are not measured in all samples. Due to either cost, instrument sensitivity, or other experimental factors, data for a biological sample may be missing for one or more ‘omic techologies. Recent methodological developments in artificial intelligence and statistical learning have greatly facilitated the analyses of multi-omics data, however many of these techniques assume access to completely observed data. A subset of these methods incorporate mechanisms for handling partially observed samples, and these methods are the focus of this review. We describe recently developed approaches, noting their primary use cases and highlighting each method's approach to handling missing data. We additionally provide an overview of the more traditional missing data workflows and their limitations; and we discuss potential avenues for further developments as well as how the missing data issue and its current solutions may generalize beyond the multi-omics context.

97 MATHEMATICS AND COMPUTING↗

DOE OSTI2024

Model and remote-sensing-guided experimental design and hypothesis generation for monitoring snow-soil–plant interactions

In this study, we develop a machine-learning (ML)-enabled strategy for selecting hillslope-scale ecohydrological monitoring sites within snow-dominated mountainous watersheds, with a particular focus on snow-soil–plant interactions. Data layers rely on spatial data layers from both remote sensing and hydrological model simulations. Specifically, a Landsat-based foresummer drought sensitivity index is used to define the dependency of the annual peak plant productivity on the Palmer drought severity index in the early growing season. Hydrological simulations provide the spatiotemporal dynamics of near-surface soil moisture and snow depth. In this framework, a regression analysis identifies the key hydrological variables relevant to the spatial heterogeneity of drought sensitivity. We then apply unsupervised clustering to these key variables, using the Gaussian mixture model, to group hillslopes into several zones that have divergent relationships regarding soil moisture, snow dynamics, and drought sensitivity. Using the datasets collected in the East River Watershed (Crested Butte, Colorado, United States), results show that drought sensitivity is significantly correlated with model-derived soil moisture and snow-free timing over space and time. The relationship is, however, non-linear, such that the correlation decreases above a threshold elevation and in a heavy snow year due to large snowpacks, lateral flow, and soil storage limitations. Clustering is then able to define the zones that have high or low sensitivity to drought, as well as the mid-elevation regions where sensitivity is associated with the topographic aspect and net potential radiation. In addition, the algorithm identifies the most representative hillslopes with road/trail access within each zone for installing monitoring sites. Our method also aims to significantly increase the use of ML and model-simulation results to guide critical zone and watershed monitoring activities.

54 ENVIRONMENTAL SCIENCES↗

DOE OSTI2021

Multi-device Studies of Pedestal Physics and Confinement in the I-mode Regime

This paper describes joint ITPA studies of the I-mode regime, which features an edge thermal barrier but with L-mode-like particle and impurity transport, and without ELMs. The regime has been demonstrated on Alcator C-Mod, ASDEX Upgrade and DIII-D tokamaks, over a wide range of device parameters and pedestal conditions, including low collisionality. Access to I-mode is independent of heating method (neutral beam injection, ICRH and/or ECRH). Normalized energy confinement H98y,2 ≥ 1 has been achieved for a range of 3≤q95≤4.9 and scales favourably with power. Changes in turbulence in the pedestal region accompany the transition from L-mode to I-mode. The L-I threshold increases with plasma density and current, and with device size, but weakly with BT. The upper limit of power for I-modes increases with toroidal field, and is largest on Alcator C-Mod at B > 5 T. Issues for extrapolation to ITER and other future fusion devices are discussed.

70 PLASMA PHYSICS AND FUSION TECHNOLOGY↗

DOE OSTI2023

Method and apparatus for a page-local delta-based prefetcher

A method includes recording a first set of consecutive memory access deltas, where each of the consecutive memory access deltas represents a difference between two memory addresses accessed by an application, updating values in a prefetch training table based on the first set of memory access deltas, and predicting one or more memory addresses for prefetching responsive to a second set of consecutive memory access deltas and based on values in the prefetch training table.

Mashimo, Susumu↗

DOE OSTI2024

Internet of things and operational technology detection and visualization platform

A computer-implemented method of monitoring activity of devices in a network is provided. The method comprises passively collecting data regarding how the devices access the network, and for each device on the network, identifying all other devices on the network with which the device communicates. All communication traffic from the devices to outside the network is identified. A determination is made if there are any required updates and if patches for the devices execute in a fashion defined as safe. A number of risk indicators for privacy risks are determined according to device communication within the network, device communication to outside the network, and update and patch execution. A visualization of any identified risk factors is displayed to a user through a user interface.

Urias, Vincent↗

DOE OSTI2021

Characterization of Mammalian In Vivo Enhancers Using Mouse Transgenesis and CRISPR Genome Editing [Book Chapter]

Embryonic morphogenesis is strictly dependent on tight spatiotemporal control of developmental gene expression, which is typically achieved through the concerted activity of multiple enhancers driving cell type-specific expression of a target gene. Mammalian genomes are organized in topologically associated domains, providing a preferred environment and framework for interactions between transcriptional enhancers and gene promoters. While epigenomic profiling and three-dimensional chromatin conformation capture have significantly increased the accuracy of identifying enhancers, assessment of subregional enhancer activities via transgenic reporter assays in mice remains the gold standard for assigning enhancer activity in vivo. Once this activity is defined, the ideal method to explore the functional necessity of a transcriptional enhancer and its contribution to target gene dosage and morphological or physiological processes is deletion of the enhancer sequence from the mouse genome. Here we present detailed protocols for efficient introduction of enhancer-reporter transgenes and CRISPR-mediated genomic deletions into the mouse genome, including a step-by-step guide for pronuclear microinjection of fertilized mouse eggs. We provide instructions for the assembly and genomic integration of enhancer-reporter cassettes that have been used for validation of thousands of putative enhancer sequences accessible through the VISTA enhancer browser, including a recently published method for robust site-directed transgenesis at the H11 safe-harbor locus. Together, these methods enable rapid and large-scale assessment of enhancer activities and sequence variants in mice, which is essential to understand mammalian genome function and genetic diseases.

cis-regulatory elements↗

DOE OSTI2024

Heterogeneous Fe-N-C Catalyst for Aerobic Dehydrogenation of Hydrazones to Diazo Compounds Used for Carbene Transfer

Organic diazo compounds are versatile reagents in chemical synthesis and would benefit from improved synthetic accessibility, especially for larger scale applications. Here, we report a mild method for the synthesis of diazo compounds from hydrazones using a heterogeneous Fe-N-C catalyst, which has Fe ions dispersed within a graphitic nitrogen-doped carbon support. The reactions proceed readily at room temperature using O 2 (1 atm) as the oxidant. Aryl diazoesters, ketones, and amides are accessible, in addition to less stable diaryl diazo compounds. Initial-rate data show that the Fe-N-C catalyst achieves faster rates than a heterogeneous Pt/C catalyst. The oxidative dehydrogenation of hydrazones may be performed in tandem with Rh-catalyzed enantioselective C–H insertion and cyclopropanation of alkenes, without requiring isolation of the diazo intermediate. Furthermore, this sequence is showcased by using a flow reactor for continuous synthesis of diazo compounds.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

DOE OSTI2021

Filtering states with total spin on a quantum computer

Starting from a general wave-function described on a set of spins or qubits, we propose several quantum algorithms to extract the components of this state on eigenstates of total spin S 2 and its z component S z . The method plays the role of total spin projection and gives access to the amplitudes of the initial state on a total spin basis. Here, the different algorithms have various degrees of sophistication depending on the requested tasks. They can either solely project onto the subspace with good total spin or completely uplift the degeneracy in this subspace. In the former case, when the projection on the total spin j is made, we show that the number of operations for the projection can be reduced from a quadratic to a linear dependence in j. After each measurement, the state collapses to one of the spin eigenstates that could be used for postprocessing. For this reason, we call the method total quantum spin filtering.

72 PHYSICS OF ELEMENTARY PARTICLES AND FIELDS↗