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At least 559 records · Page 31

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DOE OSTI2022

Fungi-on-a-Chip: microfluidic platforms for single-cell studies on fungi

Abstract This review highlights new advances in the emerging field of ‘Fungi-on-a-Chip’ microfluidics for single-cell studies on fungi and discusses several future frontiers, where we envisage microfluidic technology development to be instrumental in aiding our understanding of fungal biology. Fungi, with their enormous diversity, bear essential roles both in nature and our everyday lives. They inhabit a range of ecosystems, such as soil, where they are involved in organic matter degradation and bioremediation processes. More recently, fungi have been recognized as key components of the microbiome in other eukaryotes, such as humans, where they play a fundamental role not only in human pathogenesis, but also likely as commensals. In the food sector, fungi are used either directly or as fermenting agents and are often key players in the biotechnological industry, where they are responsible for the production of both bulk chemicals and antibiotics. Although the macroscopic fruiting bodies are immediately recognizable by most observers, the structure, function, and interactions of fungi with other microbes at the microscopic scale still remain largely hidden. Herein, we shed light on new advances in the emerging field of Fungi-on-a-Chip microfluidic technologies for single-cell studies on fungi. We discuss the development and application of microfluidic tools in the fields of medicine and biotechnology, as well as in-depth biological studies having significance for ecology and general natural processes. Finally, a future perspective is provided, highlighting new frontiers in which microfluidic technology can benefit this field.

59 BASIC BIOLOGICAL SCIENCES↗

DOE OSTI2022

Cropbox: a declarative crop modelling framework

Abstract We introduce Cropbox, a novel modelling framework that supports various aspects of crop modelling in a unique yet concise style. Building a crop model can be easily riddled with technical details looking trivial at first but later becoming major obstacles that hamper the whole development or application process. This is particularly the case when implementing models from scratch without relying on an established framework. Cropbox adopts a declarative approach providing a domain-specific language to reduce technical debt and assist modellers to focus on high-level abstraction formed by relations between variables and enclosing systems, rather than tinkering with low-level implementation details. The syntax of Cropbox framework is based on the Julia programming language and is deliberately constrained to avoid unintended side effects caused by common mistakes while its architecture remains open to extension. We highlight key capabilities of the framework through case studies featuring a leaf gas-exchange model and a whole-plant simulation model. We also illustrate potential extensions for supporting functional-structural plant modelling by demonstrating a 3D root architectural model as an example.

Yun, Kyungdahm (ORCID:0000000322894386)↗

DOE OSTI2023

Quantitative elemental imaging in eukaryotic algae

Abstract All organisms, fundamentally, are made from the same raw material, namely the elements of the periodic table. Biochemical diversity is achieved by how these elements are utilized, for what purpose, and in which physical location. Determining elemental distributions, especially those of trace elements that facilitate metabolism as cofactors in the active centers of essential enzymes, can determine the state of metabolism, the nutritional status, or the developmental stage of an organism. Photosynthetic eukaryotes, especially algae, are excellent subjects for quantitative analysis of elemental distribution. These microbes utilize unique metabolic pathways that require various trace nutrients at their core to enable their operation. Photosynthetic microbes also have important environmental roles as primary producers in habitats with limited nutrient supplies or toxin contaminations. Accordingly, photosynthetic eukaryotes are of great interest for biotechnological exploitation, carbon sequestration, and bioremediation, with many of the applications involving various trace elements and consequently affecting their quota and intracellular distribution. A number of diverse applications were developed for elemental imaging, allowing subcellular resolution, with X-ray fluorescence microscopy (XFM, XRF) being at the forefront, enabling quantitative descriptions of intact cells in a non-destructive method. This Tutorial Review summarizes the workflow of a quantitative, single-cell elemental distribution analysis of a eukaryotic alga using XFM.

59 BASIC BIOLOGICAL SCIENCES↗

DOE OSTI2025

Superconducting coherence peak in near-field radiative heat transfer

Enhancement and peaks in near-field radiative heat transfer (NFRHT) typically arise due to surface phonon-polaritons, plasmon-polaritons, and electromagnetic (EM) modes in structured materials. However, the role of material quantum coherence in enhancing near-field radiative heat transfer remains unexplored. Here, we unravel that NFRHT in superconductor-ferromagnetic systems displays a unique peak at the superconducting phase transition that originates from the quantum coherence of Bogoliubov quasiparticles in superconductors. Our theory takes into account evanescent EM radiation emanating from fluctuating currents related to Cooper pairs and Bogoliubov quasiparticles in stark contrast to the current-current correlations induced by free electrons in conventional materials. Our proposed NFRHT configuration exploits ferromagnetic resonance at frequencies deep inside the superconducting band gap to isolate this superconducting coherence peak. Furthermore, we reveal that Cooper pairs and Bogoliubov quasiparticles have opposite effects on near-field thermal radiation and isolate their effects on many-body radiative heat transfer near superconductors. As a result, our proposed phenomenon can have applications for developing thermal isolators and heat sinks in superconducting circuits.

Dipole approximation↗

DOE OSTI2021

Simulations of multicomponent relativistic thermalization

Multicomponent relativistic fluids have been studied for decades. However, simulating the dynamics of the particles and fluids in such a mixture has been a challenge due to the fact that such simulations are computationally expensive in three spatial dimensions. Here, we report on the development and application of a multidimensional relativistic Monte Carlo code to explore the thermalization process in a relativistic multicomponent environment in a computationally inexpensive way. As an illustration we simulate the fully relativistic three-dimensional Brownian-motion-like solution to the thermalization of a high-mass particle (proton) in a bath of relativistic low-mass particles (electrons). Here, we follow the thermalization and ultimate equilibrium distribution of the Brownian-like particle as can happen in the cosmic plasma during big-bang nucleosynthesis. We also simulate the thermalization of energetic particles injected into the plasma as can occur, for example, by the decay of massive unstable particles during the big bang.

79 ASTRONOMY AND ASTROPHYSICS↗

DOE OSTI2021

Reduction of bright exciton lifetimes by radiation-induced disorder

Quantum-radiative decay is a fundamental process in many optoelectronic systems such as laser diodes and solar cells. The bright exciton lifetime is a critical factor in determining the performance of these systems. Motivated by the ever-increasing need for laser systems in space and nuclear applications, we develop a many-particle approach to predict the radiative lifetime under harsh radiation environments. Here, using GaAs as a model system, we find that radiation-induced band tailing reduces the bright exciton lifetime. This result shows that the efficiency of radiative recombination, in addition to nonradiative recombination, can be affected by ionization radiation. Our approach enables a detailed understanding of the interplay between correlation, localization, and radiation that affect the performance of gain media.

36 MATERIALS SCIENCE↗

DOE OSTI2025

Relativistic approach to manipulating angular distribution of charged particles via kinetic equations

Deflection angles of charged particles interacting with materials play a critical role in various plasma applications. The development of a mathematically well-posed kinetic collision operator that accounts for deflection angles of strong Coulomb interactions remains a fundamental open problem. This paper presents a relativistic method for modifying the electromagnetic field in an anisotropic and adjustable manner to manipulate a system of charged particles, specifically by the transfer of angular momentum from a superluminal wave source to particles at specific times and locations. The method provides a mechanism to influence the scattering outcomes of strong interactions by manipulating the angular distribution of particles, and thus the deflection angles of their interactions with a solid surface, without requiring detailed knowledge of the kinetic collision operator. To this end, we demonstrate how a specific type of singularity, generated by Maxwell's equations for a superluminal wave source at the boundary of the plasma, can modify the electromagnetic field in a highly directional manner. The proposed method can lead to the development of novel approaches for controlling interactions of charged particles with a material in plasma systems. Published by the American Physical Society 2025

Moini, Nima (ORCID:0009000929568824)↗

DOE OSTI2022

Transactional Knowledge Graph Generation To Model Adversarial Activities

A Knowledge Graph (KG) is a formal and structured representation of facts, relationships, and semantic descriptions of a set of entities. Traditionally, KGs are used to describe metadata about entities and to provide additional context to target application results. Many real-world domains also involve temporal interactions between entities in addition to the metadata data. Modeling these attributed transactions is a critical requirement when using KGs in complex real-world applications. Modeling adversarial activities is one such application that develops methodology and tools to produce realistic large-scale background activity graphs that include embedded Weapons of Mass Destruction (WMD) activity patterns. We present a novel platform for constructing a transactional knowledge graph from a diverse set of sources. We present the core components and architecture of the framework, and a use case for generating a background knowledge graph and WMD activity template to evaluate network alignment and subgraph matching algorithms.

Purohit, Sumit↗

DOE OSTI2022

SparseLU, A Novel Algorithm and Math Library for Sparse LU Factorization

Decomposing sparse matrices into lower and upper triangular matrices (sparse LU factorization) is a key operation in many computational scientific applications. We developed SparseLU, a sparse linear algebra library that implements a new algorithm for LU factorization on general sparse matrices. The new algorithm divides the input matrix into tiles to which OpenMP tasks are created for factorization computation, where only tiles that contain nonzero elements are computed. For comparative performance analysis, we used the reference library SuperLU. Testing was performed on synthetically generated matrices which replicate the conditions of the real-world matrices. SparseLU is able to reach a mean speedup of ~29× compared to SuperLU.

Valero Lara, Pedro↗

DOE OSTI2021

Metamorphic Tunnel Junctions Grown Via MOCVD Designed for GaAs 0.75 P 0.25 /Si Tandem Solar Cells

A high-performance metamorphic Al 0.2 Ga 0.8 As 0.75 P 0.25 /GaAs 0.75 P 0.25 heterojunction tunnel junction structure was developed for application to monolithic epitaxial GaAs 0.75 P 0.25 /Si 1.7 eV/1.1 eV bandgap tandem solar cells produced via metal-organic chemical vapor deposition. Doping optimization focused on both bulk doping concentrations and mitigating the transient incorporation effects that otherwise causes non-abrupt doping profiles in the Te doped layer. Furthermore, these efforts resulted in a fully-relaxed metamorphic tunnel diode at the target lattice constant having a peak tunneling current density (JP) of 279.1 A·cm –2 and a zero-bias resistance area product (RA) of 3.0×10 –4 Ω·cm 2 . After post-growth annealing to emulate the thermal load of the GaAs 0.75 P 0.25 top cell growth and elimination of the performance enhancing carbon activation anneal, the device achieved JP = 13.1 A·cm –2 and RA = 1.5×10 –3 Ω·cm 2 . These worst-case values are very promising as they enable the operation of GaAs 0.75 P 0.25 /Si tandems under one-sun AM1.5G illumination with negligible series resistance and at AM1.5D concentrations up to 240 suns with only 0.1% absolute efficiency loss.

14 SOLAR ENERGY↗

DOE OSTI2025

A Perspective on Data and Privacy for AI in Healthcare [Industrial and Governmental Activities]

As large language models continue to push the bounds of AI model size, they are also being trained on unprecedented volumes of data. While individual hospitals are estimated to produce petabytes of data per year, only a small fraction is currently being used for developing AI models. Additionally, with such data resources available, healthcare is well-positioned to benefit from the current trends in AI. Moreover, the inherently multi-modal and longitudinal nature of clinical data – from omics to imaging to unstructured notes – provides a fertile ground for the development and application of cutting-edge architectures like foundation models.

Gounley, John [Oak Ridge National Laboratory (ORNL↗

DOE OSTI2025

Vision Foundation Models in Remote Sensing: A survey

Artificial intelligence (AI) technologies have profoundly transformed the field of remote sensing (RS), revolutionizing data collection, processing, and analysis. Traditionally reliant on manual interpretation and task-specific models, RS research has been significantly enhanced by the advent of foundation models (FMs)—large-scale pretrained AI models capable of performing a wide array of tasks with unprecedented accuracy and efficiency. This article provides a comprehensive survey of FMs in the RS domain. We categorize these models based on their architectures, pretraining datasets, and methodologies. Through detailed performance comparisons, we highlight emerging trends and the significant advancements achieved by those FMs. Additionally, we discuss technical challenges, practical implications, and future research directions, addressing the need for high-quality data, computational resources, and improved model generalization. Our research also finds that pretraining methods, particularly self-supervised learning (SSL) techniques like contrastive learning (CL) and masked autoencoders (MAEs), remarkably enhance the performance and robustness of FMs. This survey aims to serve as a resource for researchers and practitioners by providing a panorama of advances and promising pathways for the continued development and application of FMs in RS.

data models↗

DOE OSTI2021

In Situ Transmission Electron Microscopy: Signal processing challenges and examples

Transmission electron microscopy (TEM) is a powerful tool for imaging material structure and characterizing material chemistry. Recent advances in data collection technology for TEM have enabled high-volume and high-resolution data collection at a microsecond frame rate. Here, taking advantage of these advances in data collection rates requires the development and application of data processing tools, including image analysis, feature extraction, and streaming data processing techniques. In this article, we highlight a few areas in materials science that have benefited from combining signal processing and statistical analysis with data collection capabilities in TEM and present a future outlook on opportunities of integrating signal processing with automated TEM data analysis.

36 MATERIALS SCIENCE↗

DOE OSTI2025

Linear Solver for Electromagnetic Simulation of General Distribution Feeders

High-fidelity electromagnetic transient (EMT) modeling is required for accurate simulation and analysis of power system dynamics in modern distribution feeders. However, the high-fidelity of EMT models often leads to significant computational challenges, particularly in terms of computational resources and simulation time. This paper investigates the development and application of a detailed EMT model for general distribution feeders, with a focus on improving computational efficiency. A direct linear solver is proposed for a bordered block diagonal (BBD) matrix structure commonly encountered in a EMT model of distribution feeders. The solver integrates the Schur complement method with the block tridiagonal matrix algorithm to enhance the computational performance. The proposed solver is validated using the primary feeder of the IEEE 342-node test system, demonstrating its accuracy and efficiency in EMT simulations. Furthermore, the solver’s performance is benchmarked against MATLAB’s built-in linear solvers, showing significant improvements in computation time while maintaining high fidelity and accuracy in simulation results.

Choi, Jongchan [ORNL] (ORCID:000000025952455X)↗

DOE OSTI2021

Soil enzymes as indicators of soil function: A step toward greater realism in microbial ecological modeling

Soil carbon (C) and nitrogen (N) cycles and their complex responses to environmental changes have received increasing attention. However, large uncertainties in model predictions remain, partially due to the lack of explicit representation and parameterization of microbial processes. One great challenge is to effectively integrate rich microbial functional traits into ecosystem modeling for better predictions. Here, using soil enzymes as indicators of soil function, we developed a competitive dynamic enzyme allocation scheme and detailed enzyme-mediated soil inorganic N processes in the Microbial-ENzyme Decomposition (MEND) model. We conducted a rigorous calibration and validation of MEND with diverse soil C-N fluxes, microbial C:N ratios, and functional gene abundances from a 12-year CO 2 × N grassland experiment (BioCON) in Minnesota, USA. In addition to accurately simulating soil CO 2 fluxes and multiple N variables, the model correctly predicted microbial C:N ratios and their negative response to enriched N supply. Model validation further showed that, compared to the changes in simulated enzyme concentrations and decomposition rates, the changes in simulated activities of eight C-N-associated enzymes were better explained by the measured gene abundances in responses to elevated atmospheric CO 2 concentration. In conclusion, our results demonstrated that using enzymes as indicators of soil function and validating model predictions with functional gene abundances in ecosystem modeling can provide a basis for testing hypotheses about microbially mediated biogeochemical processes in response to environmental changes. Further development and applications of the modeling framework presented here will enable microbial ecologists to address ecosystem-level questions beyond empirical observations, toward more predictive understanding, an ultimate goal of microbial ecology.

59 BASIC BIOLOGICAL SCIENCES↗

DOE OSTI2025

Combining Observations and Models: A Review of the CARDAMOM Framework for Data‐Constrained Terrestrial Ecosystem Modeling

The rapid increase in the volume and variety of terrestrial biosphere observations (i.e., remote sensing data and in situ measurements) offers a unique opportunity to derive ecological insights, refine process‐based models, and improve forecasting for decision support. However, despite their potential, ecological observations have primarily been used to benchmark process‐based models, as many past and current models lack the capability to directly integrate observations and their associated uncertainties for parameterization. In contrast, data assimilation frameworks such as the CARbon DAta MOdel fraMework (CARDAMOM) and its suite of process‐based models, known as the Data Assimilation Linked Ecosystem Carbon Model (DALEC), are specifically designed for model‐data fusion. This review, motivated by a recent CARDAMOM community workshop, examines the development and applications of CARDAMOM, with an emphasis on its role in advancing ecosystem process understanding. CARDAMOM employs a Bayesian approach, using a Markov Chain Monte Carlo algorithm to enable data‐driven calibration of DALEC parameters and initial states (i.e., carbon pool sizes) through observation operators. CARDAMOM's unique ability to retrieve localized model process parameters from diverse datasets—ranging from in situ measurements to global satellite observations—makes it a highly flexible tool for analyzing spatially variable ecosystem responses to environmental change. However, assimilating these data also presents challenges, including data quality issues that propagate into model skill, as well as trade‐offs between model complexity, parameter equifinality, and predictive performance. We discuss potential solutions to these challenges, such as reducing parameter equifinality by incorporating new observations. This review also offers community recommendations for incorporating emerging datasets, integrating machine learning techniques, strengthening collaboration with remote sensing, field, and modeling communities, and expanding CARDAMOM's relevance for localized ecosystem monitoring and decision‐making. CARDAMOM enables a deep, mechanistic understanding of terrestrial ecosystem dynamics that cannot be achieved through empirical analyses of observational datasets or weakly constrained models alone.

Bayesian inference↗

DOE OSTI2020

First-principles study of magnetism and electric field effects in 2D systems

This review article provides a bird's-eye view of what first-principles based methods can contribute to next-generation device design and simulation. After a brief overview of methods and capabilities in the area, the authors focus on published work by their group since 2015 and current work on CrI3. The authors introduce both single- and dual-gate models in the framework of density functional theory and the constrained random phase approximation in estimating the Hubbard U for 2D systems vs their 3D counterparts. A wide range of systems, including graphene-based heterogeneous systems, transition metal dichalcogenides, and topological insulators, and a rich array of physical phenomena, including the macroscopic origin of polarization, field effects on magnetic order, interface state resonance induced peak in transmission coefficients, spin filtration, etc., are covered. For CrI3, the authors present their new results on bilayer systems such as the interplay between stacking and magnetic order, pressure dependence, and electric field induced magnetic phase transitions. The authors find that a bare bilayer CrI3, graphene|bilayer CrI3|graphene, hexagonal boron nitride (h-BN)|bilayer CrI3|h-BN, and h-BN|bilayer CrI3|graphene all have a different response at high field, while at small field, the difference is small except for graphene|bilayer CrI3|graphene. The authors conclude with discussion of some ongoing work and work planned in the near future, with the inclusion of further method development and applications.

Cheng, Hai-Ping (ORCID:0000000159901725)↗

DOE OSTI2021

X-ray spectroscopic identification of strain and structure-based resonances in a series of saturated carbon-cage molecules: Adamantane, twistane, octahedrane, and cubane

Novel nanocarbons such as fullerenes, nanotubes, graphene, and nanodiamond reside at the cutting edge of nanoscience and technology. Along with chemical functionalization, geometric constraints (such as extreme curvature in nanotubes or defects within or at the surfaces of diamond nanoparticles) significantly alter the electronic states of the nanocarbon material. Understanding the effects of steric strain on the electronic structure is critical to developing nanoelectronic applications based on these materials. This paper presents a fundamental study of how strain affects the electronic structure in a benchmark series of some fundamental saturated carbon cage compounds. Adamantane, C10H16, the smallest diamondoid and arguably the smallest nanodiamond crystallite, has carbon atoms essentially commensurate with diamond lattice positions and possesses by far the least molecular strain of this series. Twistane also is a C10H16 isomer but the fixed cyclohexane twist conformation of the central ring introduces additional strain into the cage. Octahedrane [(CH)12] and cubane [(CH)8] are considerably more strained, culminating in cubane where carbon–carbon bonds lie either parallel or orthogonal to one another. Using gas-phase near-edge x-ray absorption fine structure spectroscopy to probe the unoccupied electronic states, we observe two major progressions across this series. First, a broad C–C σ* resonance in the absorption splits into two more narrow and intense resonances with increasing strain. Second, the first manifold of states previously associated with tertiary C–H σ* in the diamondoid series appears to broaden and shift to lower energy. This feature is more than twice as intense in cubane than in octahedrane, even though these two molecules have only tertiary carbons, with the chemical formula (CH)x. The spectral differences are entirely due to the shape of the molecules; in particular, in cubane, the features arise from a high degree of p-p interaction between parallel C–C bonds. In contrast to the conventional wisdom that near-edge x-ray absorption is primarily an atomically localized spectroscopy, molecular shape and associated strain lead to the dominant features in spectra acquired from this fundamental series of carbon cage structures.

36 MATERIALS SCIENCE↗