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At least 955 records · Page 53
All sourcesNASA NTRSDOE OSTI
DOE OSTI2024

Combining compositional data sets introduces error in covariance network reconstruction

Microbial communities are diverse biological systems that include taxa from across multiple kingdoms of life. Notably, interactions between bacteria and fungi play a significant role in determining community structure. However, these statistical associations across kingdoms are more difficult to infer than intra-kingdom associations due to the nature of the data involved using standard network inference techniques. We quantify the challenges of cross-kingdom network inference from both theoretical and practical points of view using synthetic and real-world microbiome data. We detail the theoretical issue presented by combining compositional data sets drawn from the same environment, e.g. 16S and ITS sequencing of a single set of samples, and we survey common network inference techniques for their ability to handle this error. We then test these techniques for the accuracy and usefulness of their intra- and inter-kingdom associations by inferring networks from a set of simulated samples for which a ground-truth set of associations is known. We show that while the two methods mitigate the error of cross-kingdom inference, there is little difference between techniques for key practical applications including identification of strong correlations and identification of possible keystone taxa (i.e. hub nodes in the network). Furthermore, we identify a signature of the error caused by transkingdom network inference and demonstrate that it appears in networks constructed using real-world environmental microbiome data.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2024

Combining compositional data sets introduces error in covariance network reconstruction

Microbial communities are diverse biological systems that include taxa from across multiple kingdoms of life. Notably, interactions between bacteria and fungi play a significant role in determining community structure. However, these statistical associations across kingdoms are more difficult to infer than intra-kingdom associations due to the nature of the data involved using standard network inference techniques. We quantify the challenges of cross-kingdom network inference from both theoretical and practical points of view using synthetic and real-world microbiome data. We detail the theoretical issue presented by combining compositional data sets drawn from the same environment, e.g. 16S and ITS sequencing of a single set of samples, and we survey common network inference techniques for their ability to handle this error. We then test these techniques for the accuracy and usefulness of their intra- and interkingdom associations by inferring networks from a set of simulated samples for which a ground-truth set of associations is known. We show that while the two methods mitigate the error of cross-kingdom inference, there is little difference between techniques for key practical applications including identification of strong correlations and identification of possible keystone taxa (i.e. hub nodes in the network). Furthermore, we identify a signature of the error caused by transkingdom network inference and demonstrate that it appears in networks constructed using real-world environmental microbiome data.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2024

Haar-Like Wavelets on Hierarchical Trees

Here, discrete wavelet methods, originally formulated in the setting of regularly sampled signals, can be adapted to data defined on a point cloud if some multiresolution structure is imposed on the cloud. A wide variety of hierarchical clustering algorithms can be used for this purpose, and the multiresolution structure obtained can be encoded by a hierarchical tree of subsets of the cloud. Prior work introduced the use of Haar-like bases defined with respect to such trees for approximation and learning tasks on unstructured data. This paper builds on that work in two directions. First, we present an algorithm for constructing Haar-like bases on general discrete hierarchical trees. Second, with an eye towards data compression, we present thresholding techniques for data defined on a point cloud with error controlled in the $L$ $\infty$ norm and in a Hölder-type norm. In a concluding trio of numerical examples, we apply our methods to compress a point cloud dataset, study the tightness of the $L$ $\infty$ error bound, and use thresholding to identify MNIST classifiers with good generalizability.

97 MATHEMATICS AND COMPUTING↗
DOE OSTI2024

Anion-derived contact ion pairing as a unifying principle for electrolyte design

Enabling new electrochemical technologies requires systems that can operate under ever-more demanding conditions, and progress in energy storage applications reveals tantalizing opportunities to reimagine electrolyte design for performance at extreme potentials. Here, a common thread among these innovations is the formation of significant populations of contact ion pairs (CIPs) in the electrolyte, regardless of the specific cation chemistry or solvent system. The examples summarized in this review suggest that a set of general electrolyte design rules likely exists, where the purposeful selection of anion chemistry can yield CIP structures with tunable control over reaction thermodynamics, kinetics, and interphase chemistry. Identifying the relevant descriptors for high-performance, anion-derived CIP structures can be achieved utilizing a combined experimental and computational approach, aided by machine learning and artificial intelligence, to more rapidly survey the vast combinatorial space available and to enable a new generation of electrolytes for decarbonized electrochemical processes at scale.

electrochemistry↗
DOE OSTI2023

Nanomaterials and Sustainability

Nanostructuring adds a tremendous degree of tunability to the optical, electronic, magnetic, tribological, and chemical properties of matter. As a result, nanostructured materials already play major roles in the many technologies and industries that provide the comfort and convenience of our everyday lives. Although there are examples of nanostructured materials that currently enhance sustainable technologies, such as for batteries and electrolyzers, the potential impact of nanoscale materials on sustainability has likely not nearly been realized when one considers that the nanostructure–property–composition exploration phase space is almost infinite. We can find inspiration from nature, which builds and assembles nanostructured materials into hierarchical biological structures to perform the enormously complex functions of life, all the while doing so with a relatively small set of elements that are sustainably sourced. This contrasts with current technology, where performance demands often require a greater and greater diversity of elements from the periodic table, some of which are very challenging to be sustainably sourced or recycled.

77 NANOSCIENCE AND NANOTECHNOLOGY↗
DOE OSTI2021

Turning Rubber into a Glass: Mechanical Reinforcement by Microphase Separation

Supramolecular associations provide a promising route to functional materials with properties such as self-healing, easy recyclability or extraordinary mechanical strength and toughness. The latter benefit especially from the transient character of the formed network, which enables dissipation of energy as well as regeneration of the internal structures. However, recent investigations revealed intrinsic limitations in the achievable mechanical enhancement. Here we present studies of a set of telechelic polymers with hydrogen-bonding chain ends exhibiting an extraordinarily high, almost glass-like, rubbery plateau. This is ascribed to the segregation of the associative ends into clusters and formation of an interfacial layer surrounding these clusters. An approach adopted from the field of polymer nanocomposites provides a quantitative description of the data and reveals the strongly altered mechanical properties of the polymer in the interfacial layer. These results demonstrate how employing phase separating dynamic bonds can lead to the creation of high-performance materials.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2026

High-throughput computation of electric polarization in solids via Berry flux diagonalization

Electric polarization in the absence of an externally applied electric field is a key property of polar materials, but the standard interpolation-based ab initio approach to compute polarization differences within the modern theory of polarization presents challenges for automated high-throughput calculations. Berry flux diagonalization [J. Bonini et al., Phys. Rev. B 102, 045141 (2020)] has been proposed as an efficient and reliable alternative, though it has yet to be widely deployed. Here, we assess Berry flux diagonalization using ab initio calculations of a large set of materials, introducing and validating heuristics that ensure branch alignment with a minimal number of intermediate interpolated structures. Our automated implementation of Berry flux diagonalization succeeds in cases where prior interpolation-based workflows fail due to band-gap closures or branch ambiguities. Benchmarking with ab initio calculations of 176 candidate ferroelectrics, we demonstrate the efficacy of the approach on a broad range of insulating materials and obtain accurate effective polarization values with fewer interpolated structures than prior automated interpolation-based workflows. Our real-space heuristics that can predict gauge stability a priori from ionic displacements enable a general automated framework for reliable polarization calculations and efficient high-throughput screening of chemically and structurally diverse polar insulators. These results establish Berry flux diagonalization as a robust and efficient method to compute the effective polarization of solids and to accelerate the data-driven discovery of functional polar materials.

Poteshman, Abigail N. [University of Chicago, IL (↗
DOE OSTI2024

Quantifying motion blur by imaging shock front propagation with broadband and narrowband X-ray sources

Time-integrated radiography using MeV Bremsstrahlung X-ray sources is the norm for imaging during system-level testing of components and structures under dynamic condition. One source of error in the analysis of the time-integrated radiography data sets stems from motion blur which smears out sharp interfaces to a greater degree with longer exposure times, which become necessary to provide sufficient signal-to-noise with low X-ray penetration of objects of interest. To quantify motion blur, a 1D shock wave through PMMA was investigated experimentally at The Dynamic Compression Sector at The Advanced Photon Source (DCS@APS) with tapered broadband and 25.46 ± 1.06 keV narrowband X-rays. Four cameras with different exposure times were used for each experiment to compare the effect that exposure time has on motion blur. In addition, our methodology to accurately simulate motion blur in terms of transmission and shape is presented and compared to our experimental results and quantified. There is a high level of agreement between the experimental and simulation results across the range of data sets investigated in this study with a percent difference range of 0.29–1.31% for the four shots. The methodology of this work serves as a steppingstone towards a physically validated model that could be used in conjunction with experimental results to deconvolve physical parameters, densities, and interfaces of interest in a way that would not be possible with experimental results alone.

46 INSTRUMENTATION RELATED TO NUCLEAR SCIENCE AND ↗
DOE OSTI2025

Invariant discovery of features across multiple length scales: Applications in microscopy and autonomous materials characterization

Physical imaging is a foundational characterization method in areas from condensed matter physics and chemistry to astronomy and spans length scales from atomic to universe. Images encapsulate crucial data regarding atomic bonding, materials microstructures, and dynamic phenomena such as microstructural evolution and turbulence, among other phenomena. The challenge lies in effectively extracting and interpreting this information. Variational Autoencoders (VAEs) have emerged as powerful tools for identifying the underlying factors of variation in image data, providing a systematic approach to distilling meaningful patterns from complex data sets. However, a significant hurdle in their application is the definition and selection of appropriate descriptors reflecting local structures. Here, we introduce the scale-invariant VAE approach (SI-VAE) based on the progressive training of the VAE with the descriptors sampled at different length scales. The SI-VAE allows the discovery of the length scale-dependent factors of variation in the system. Here, we illustrate this approach using the ferroelectric domain images and generalize it to the movies of the electron-beam induced phenomena in graphene and topography evolution across combinatorial libraries. This approach can further be used to initialize the decision making in automated experiments including structure–property discovery and can be applied across a broad range of imaging methods. This approach is universal and can be applied to any spatially resolved data including both experimental imaging studies and simulations, and can be particularly useful for exploration of phenomena such as turbulence and scale-invariant transformation fronts.

36 MATERIALS SCIENCE↗
DOE OSTI2026

Knowledge-guided learning with curated prior genetic biomarkers for robust model interpretation

Abstract Motivation Knowledge-guided learning offers effective and robust model training strategies in data-scarce settings by incorporating established domain knowledge, thereby enhancing generalization, robustness, and interpretability. By contrast, conventional deep learning approaches rely purely on data-driven learning, which can limit robust model interpretability, particularly in high-dimensional settings with limited size samples. In computational biology, knowledge-guided learning has primarily leveraged network- and structural-based knowledge, leading to biologically interpretable representations and enhanced predictive performance compared to conventional approaches. However, curated biomarkers, one of the most accessible forms of biological knowledge, remain largely unexplored within knowledge-guided paradigms. Results In this study, we propose a model-agnostic training paradigm, Biomarker-driven Explainable Prior-guided Learning (BioExPL), that can be applied to any neural networks that incorporates curated prior knowledge. BioExPL enforces neural networks to reflect curated biomarker priors in their latent representations through a novel knowledge-alignment loss. BioExPL consistently demonstrated significantly improved predictive performance and enhanced model interpretability with minimized computational overhead in simulation studies and intensive experiments on multiple cancer datasets. BioExPL not only integrates prior curated knowledge into the model but also accurately identifies unknown associated signals additionally. BioExPL is model-agnostic and domain-independent, enabling its integration into diverse neural network architectures. Availability and implementation The open-source is publicly available at: https://github.com/datax-lab/BioExPL.

Baek, Beomsu [Department of Computer Science, Univ↗
DOE OSTI2023

Dynamics of a relativistic jet through magnetized media

The merger of two neutron stars (NSs) produces the emission of gravitational waves, the formation of a compact object surrounded by a dense and magnetized environment. If the binary undergoes delayed collapse a collimated and relativistic jet, which will eventually produce a short gamma-ray burst (SGRB), may be launched. The interaction of the jet with the environment has been shown to play a major role in shaping the structure of the outflow that eventually powers the gamma-ray emission. In this paper, we present a set of 2.5D RMHD simulations that follow the evolution of a relativistic non-magnetized jet through a medium with different magnetization levels, as produced after the merger of two NSs. We find that the predominant consequence of a magnetized ambient medium is that of suppressing instabilities within the jet and preventing the formation of a series of collimation shocks. One implication of this is that internal shocks lose efficiency, causing bursts with low-luminosity prompt emission. On the other hand, the jet-head velocity and the induced magnetization within the jet are fairly independent of the magnetization of the ambient medium. Future numerical studies with a larger domain are necessary to obtain light curves and spectra in order to better understand the role of magnetized media.

(magnetohydrodynamics) MHD↗
DOE OSTI2025

Forecasting constraints on the high-z IGM thermal state from the Lyman-α forest flux autocorrelation function

ABSTRACT The autocorrelation function of the Lyman-$\alpha$ (Ly $\alpha$) forest flux from high-z quasars probes the small-scale structure of the intergalactic medium (IGM). The thermal state of the IGM, determined by the physics of reionization, sets the small-scale power observed in the Ly $\alpha$ forest. To explore the sensitivity of the autocorrelation function to the IGM’s thermal state, we compute the autocorrelation function from a cosmological hydrodynamical simulation with an instantaneous reionization model and 135 post-processed thermal states. Using mock data sets of 20 quasars, we forecast constraints on $T_0$ and $\gamma$, which characterize the post-processed IGM thermal state, at $5.4 \le z \le 6$. While this model simplifies the IGM’s thermal state, it serves as a key first step in assessing future observational prospects. We also perform an inference test on mocks and re-weight out posterior distributions to guarantee that they exhibit statistically correct behaviour. At $z = 5.4$, we find that an idealized data set constrains $T_0$ to 59 per cent and $\gamma$ to 16 per cent at the 1$\sigma$ equivalent confidence level. To explore more realistic, non-instantaneous reionization scenarios, we analyse four models combining temperature and ultraviolet background (UVB) fluctuations at $z = 5.8$. We find that mock data generated from a model with both temperature and UVB fluctuations can rule out a model with only temperature fluctuations at the $> 1\sigma$ level 73.9 per cent of the time.

Wolfson, Molly↗
DOE OSTI2025

Clear as mud redefined: Tunable transparent mineral scaffolds for visualizing microbial processes below ground

Microbes inhabiting complex porous microenvironments in sediments and aquifers catalyze reactions that are critical to global biogeochemical cycles and ecosystem health. However, the opacity and complexity of porous sediment and rock matrices have considerably hindered the study of microbial processes occurring within these habitats. Here, we generated microbially compatible, optically transparent mineral scaffolds to visualize and investigate microbial colonization and activities occurring in these environments, in laboratory settings and in situ. Using inexpensive synthetic cryolite mineral, we produced optically transparent scaffolds mimicking the complex 3D structure of sediments and rocks by adapting a suspension-based, freeze-casting technique commonly used in materials science. Fine-tuning of parameters, such as freezing rate and choice of solvent, provided full control of pore size and architecture. The combined effects of scaffold porosity and structure on the movement of microbe-sized particles, tested using velocity tracking of fluorescent beads, showed diverse yet reproducible behaviors. The scaffolds we produced are compatible with epifluorescence microscopy, allowing the fluorescence-based identification of colonizing microbes by DNA-based staining and fluorescence in situ hybridization (FISH) to depths of 100 µm. Additionally, Raman spectroscopy analysis indicates minimal background signal in regions used for measuring deuterium and 13 C enrichment in microorganisms, highlighting the potential to directly couple D 2 O or 13 C stable isotope probing and Raman-FISH for quantifying microbial activity at the single-cell level. To demonstrate the relevance of cryolite scaffolds for environmental field studies, we visualized their colonization by diverse microorganisms within rhizosphere sediments of a coastal seagrass plant using epifluorescence microscopy. The tool presented here enables highly resolved, spatially explicit, and multimodal investigations into the distribution, activities, and interactions of underground microbes typically obscured within opaque geological materials until now.

36 MATERIALS SCIENCE↗
DOE OSTI2025

Spin-lattice entanglement in CoPS 3

Complex chalcogenides in the 𝑀⁢PS 3 family of materials (𝑀 =Mn, Fe, Co, and Ni) display remarkably different phase progressions depending upon the metal center orbital filling, character of the P–P linkage, and size of the van der Waals gap. There is also a stacking pattern and spin-state difference between the “lighter” and “heavier” transition-metal-containing systems that places CoPS 3 at the nexus of these activities. Despite these unique properties, this compound is underexplored. Here, we bring together Raman scattering spectroscopy and infrared absorption spectroscopy with x-ray techniques to identify a structural component to the 119 K magnetic ordering transition. With temperature-dependent Raman scattering, we discover a set of magnon-phonon pairs that engages in avoided crossings below 𝑇 Néel . Lastly, these findings point to strong spin-phonon entanglement as well as opportunities to control these effects under external stimuli.

Magnetism↗
DOE OSTI2020

Confinement Controls the Bend Instability of Three-Dimensional Active Liquid Crystals

Spontaneous growth of long-wavelength deformations is a defining feature of active liquid crystals. We investigate the effect of confinement on the instability of 3D active liquid crystals in the isotropic phase composed of extensile microtubule bundles and kinesin molecular motors. When shear aligned, such fluids exhibit finite-wavelength self-amplifying bend deformations. By systematically changing the channel size we elucidate how the instability wavelength and its growth rate depend on the channel dimensions. Experimental findings are qualitatively consistent with a minimal hydrodynamic model, where the fastest growing deformation is set by a balance of active driving and elastic relaxation. Furthermore, our results demonstrate that confinement determines the structure and dynamics of active fluids on all experimentally accessible length scales.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2026

Magnetoelectric properties at the Co/AlN(0001) interface

AlN nitride is a large-band-gap polar material that has gained interest due to its ability to become ferroelectric and its compatibility with Si- and GaN-based technologies. This compound could, therefore, be a good candidate to design new artificial multiferroics if combined with a ferromagnetic electrode. For this work, we performed first-principles calculations to investigate the set up of the magnetoelectric coupling at the Co/AlN(0001) interface. Our results describe a complex interfacial atomic structure with variable local magnetic properties as a function of the atom alignment. We predict an average variation of interface spin magnetization, when the polarization is reversed, of 3.83 𝜇B nm −2 , close to the values already reported in the literature at metal/oxide interfaces. This confirms the potential of this AlN-based ferroelectric compound to be used in future voltage-controlled spintronic devices.

36 MATERIALS SCIENCE↗
DOE OSTI2025

Impulse Response Functions for Characterizing Pulse-to-Pulse Junction Temperature Behavior in Laser Diode Pulse Trains

A method is proposed for determination of the pulse-to-pulse variation in junction temperature and emission wavelength of a semiconductor laser diode during a train of pulses. Here, this approach, based on impulse response functions, enables predictions for pulse trains with arbitrary pulse-to-pulse variations in output power, pulse width, and pulse delay using a limited set of experimental characterization data. The use of this approach is illustrated by application to a particular device structure.

Deri, Robert J. [Lawrence Livermore National Labor↗
DOE OSTI2021

A Novel Framework for Optimizing Ramping Capability of Hybrid Energy Storage Systems

Hybrid Energy Storage System has been widely applied in aerospace, electric vehicle, and microgrid applications. The advantages are that they include complimentary technologies with both high power and energy capabilities. HESS have the potential to be useful to the bulk power systems, for example to increase the value of energy produced by variable generation resource through enabling participation in ancillary service markets. Actualizing the benefits of HESSs requires optimizing the combined ramping capability of aggregated HESS resources. To provide quality ancillary service, source of HESSs locating at multiple sites of variable generation resource must be optimally sized and cohesively controlled. Optimizing aggregated resources can be formulated as an optimization problem. Successfully solving this problem not only requires using effective solution methods but also depends on accurately and rapidly setting the necessary parameters in the problem formula. This article proposes a novel framework with double-layer structure to solve the optimization problem of aggregating ramping capability. Program developed on the upper layer focuses on solving the optimization of aggregating ramping capability among multiple HESSs and is compatible with most existing optimization algorithms. Program on lower layer of the framework targets at optimizing the local control of a single HESS based on a thorough analytics of HESS operation strategy presented in this article. Result of local optimization is also provided to upper layer program for updating the parameters in formula of optimization problem. Real time hardware-in-the-loop test is conducted to verify the performance of the optimization framework developed. The work presented is expected to provide guidance for implementing this framework in practical operation.

Luo, Yushen↗