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Search indexed NASA NTRS and DOE OSTI research on propulsion, heat transfer, battery materials and energy systems. Follow report and document links to the original sources.

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At least 91 records · Page 5
All sourcesNASA NTRSDOE OSTI
DOE OSTI2022

A Brief Overview of Reactive Transport Codes Used in CO 2 Applications

Reactive transport modelling consists of computational and numerical models that describe the coupled physical, chemical, mechanical, and biological processes interacting with each other over a broad range of spatial and temporal scales. This report reviews some of the reactive transport codes available in the literature for carbon dioxide (CO 2 ) applications and can assist the scientific community with the applicability of each code to solve a specific problem. Approaches implemented in these codes can be categorized in three groups: (i) continuum-scale, (ii) pore-scale, and (iii) hybrid-scale approaches. Theoretical foundations, numerical implementations, and application examples using the models are described. In the continuum approach, flow and transport are formulated in terms of a representative control volume of the medium and coupled with geochemical reactions. The medium is characterized by bulk parameters such as porosity, permeability, or reactive surface area. In the pore-scale approach, each point of space in the pore network is occupied by either a fluid or solid phase. The pore-scale approach requires an exact knowledge of the spatial and temporal phase distribution. In the hybrid-scale approach, media are described by multiple characteristic length-scales, with some regions using a pore-scale approach while others used a continuum approach.

01 COAL, LIGNITE, AND PEAT↗
DOE OSTI2023

Methods and systems of proteome analysis and imaging

Provided herein are methods and systems for proteome analysis that are at least partially automated and/or performed robotically. In some aspects, the methods and systems described herein can rapidly and efficiently provide protein identification of each of the proteins from a proteome, or a complement of proteins, obtained from extremely small amounts of biological samples. The identified proteins can be imaged quantitatively over a spatial region. Automation and robotics facilitates the throughput of the methods and systems, which enables protein imaging and/or rapid proteome analysis.

Piehowski, Paul D.↗
DOE OSTI2026

Spatial analysis of cell patterning to aid genetic and phenotypic understanding of grass stomatal density: A case study in maize

Biological processes involve complex hierarchies where composite traits result from multiple component traits. However, holistically understanding of how sets of component traits interact to underpin genotype-to-phenotype relationships is generally lacking. Stomatal density (SD) is a tractable model system for exploring how high-throughput phenotyping (HTP) data could be exploited by a new spatial analysis approach to better understand a developmentally and functionally important trait. SD is a composite trait, resulting from various components related to cell identity and size, which are themselves governed by a series of spatio-developmental processes. Data from 192 recombinant inbred lines of maize [Zea mays (L.)] were analyzed by a new stomatal patterning phenotype (SPP) to (1) describe the average spatial probability distribution of the nearest neighboring stomata; (2) derive a core set of component traits related to cell size, cell packing, and positional probabilities; (3) build a structural equation model of component traits underlying SD; and (4) identify stomatal patterning quantitative trait loci (QTL). The core set of SPP-derived traits explained 74% of the variation in SD. Analyzing SPP component traits allowed some loci previously identified as generic SD QTL to be recognized as specific to lateral versus longitudinal elements of stomatal patterning. Therefore, this study highlights how novel insights can be gained by decomposing a composite trait (e.g., SD) into a set of component traits that were present in HTP data but not previously exploited.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2020

Nanomechanical sampling of material for nanoscale mass spectrometry chemical analysis

The ability to spatially resolve the chemical distribution of compounds on a surface is important in many applications ranging from biological to material science. To this extent, we have recently introduced a hybrid atomic force microscopy (AFM)-mass spectrometry (MS) system for direct thermal desorption and pyrolysis of material with nanoscale chemical resolution. However, spatially resolved direct surface heating using local thermal desorption becomes challenging on material surfaces with low melting points, because the material will undergo a melting phase transition due to heat dissipation prior to onset of thermal desorption. Therefore, here we developed an approach using mechanical sampling and collection of surface materials on an AFM cantilever probe tip for real-time analysis directly from the AFM tip. This approach allows for material to be concentrated directly onto the probe for subsequent MS analysis. We evaluate the performance metrics of the technique and demonstrate localized MS sampling from a candelilla wax matrix containing UV stabilizers avobenzone and oxinoxate from areas down to 250 nm × 250 nm. Overall, this approach removes heat dissipation into the bulk material allowing for a faster desorption and concentration of the gas phase analyte from a single heating pulse enabling higher signal levels from a given amount of material in a single sampling spot.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2023

Enzymatically hydrolyzed fluorescence-based chemical probe enables in situ mapping of chitinase activity in the rhizosphere

Rhizosphere microbiomes and root exudates play a pivotal biochemical role in helping to catalyze chitin catabolism. Chitin is a recalcitrant and ubiquitous soil biopolymer, estimated to be the second most abundant organic soil biopolymer on Earth. Despite its abundance, role as a source of C and N in soil, and importance to ecosystem function, the biochemical mechanisms controlling chitin fate in the rhizosphere are elusive and poorly understood. To enable spatial mapping of chitinase activity in the rhizosphere, we designed and synthesized an enzymatically activated fluorogenic substrate, chitotriose-TokyoGreen (chitotriose-TG), by incorporating a fluorescein derivative (TG) onto the trimeric unit of chitin. This non-fluorescent substrate is selectively hydrolyzed by chitinase to release TG and yield a high fluorescence signal, which can be used to spatially image and measure chitinase activity in the rhizosphere. To demonstrate the application of this technique, we grew switchgrass (Panicum virgatum) in rhizoboxes amended with a horizontal layer of chitin. We extracted mobile proteins from the rhizobox using a nitrocellulose membrane blotting technique which offer non-destructive enzyme extraction while preserving the 2D spatial position of the enzymes. We then subjected these membranes to the synthesized chitotriose-TG stain to spatially visualize the distribution of chitinase activity within the rhizosphere. Furthermore, we observed increased chitinase activity near plant roots and higher activity within the soil zone enriched in chitin, showing an adaptive response of chitinase activity with spatial focusing in areas of higher chitin abundance. Thus, the enzyme extraction and visualization strategy we describe here can help enlighten efforts to better understand spatial controls on chitin breakdown in rhizosphere, further elucidating the role of chitin as a C and N source in these systems.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2025

Confinement-induced chirality in phase-separated achiral polymer solutions

Self-organization of polymers in constrained geometries largely determines their applications in high-strength materials, photonics, and electronics. Chiral organization under confinement is well established for polymers with intrinsic molecular chirality; however, it has not been observed for achiral polymers. Here, we report the emergence of chirality in spatially confined solutions of achiral rigid-rod polymers. We show that kinetically arrested phase separation of polymer solutions confined to narrow capillaries resulted in alternating segments of isotropic and chiral nematic phases. The chiral structure of the nematic segments originated from the interplay between the constrained geometry, surface anchoring, orientational wetting, and elastic anisotropy of rigid-rod polymers. The catenoidal shape of the chiral structure recapitulated the morphology of biological chiral structures. These findings provide insight into the organization of soft matter under spatial confinement and offer a straightforward way to form chiral structures from achiral synthetic polymers.

Science & Technology - Other Topics↗
DOE OSTI2025

Challenges in spatial metabolomics and proteomics for functional tissue unit and single-cell resolution

While transcriptomics is the most broadly applied technology for global spatial and single cell measurements in healthy and diseased tissues. Transcripts are often used as a proxy for protein and even metabolite measurements, but it has become commonly accepted that extrapolating this kind of information is a poor proxy and not a substitute for direct measurement. Within the last decade advanced developments of mass spectrometry-based assays have made these direct measurements not only possible, but routine. Where mass spectrometry has become an enabling technology, and various methods can now detect hundreds of metabolites and thousands of proteins from samples. Not only can this be performed within bulk measurements, but much effort has been directed into translating these measurements to single cells and tissues at cellular resolution. The information obtained from mass spectrometry is now able to trace metabolic events and decipher feedback loops across anatomical regions, connecting genetic and metabolic networks that define phenotypes. Herein, we will broadly overview developments in the field over the past decade, leading into several case studies which highlight the direct measurement of metabolites, proteins, and proteoforms from thinly sliced tissues. Much of this work is feasible due to multidisciplinary team science, and we offer brief perspective on paths forward and the challenges that persist with adoption and application of spatial omics.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2020

Damage-free Analysis of Biological Materials by Vibrational Spectroscopy in the EM

In summary, vibrational spectroscopy in the electron microscope promises to probe biological materials in a way that is similar to infrared spectroscopy, at a spatial resolution of about 30-50 nm, while circumventing radiation damage. Herein we are now focused on developing this technique fully, using a side-entry cryotransfer holder in a Nion HERMES electron microscope equipped with a fast and efficient EELS direct detector [10], and capable of 5 meV (and better) energy resolution. The results of these investigations will be reported at the meeting.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2021

WORKSHOP ON URBAN SCALE PROCESSES AND THEIR REPRESENTATION IN HIGH SPATIAL RESOLUTION EARTH SYSTEM MODELS

It is essential that numerical models used to study physics, chemistry, and biology affecting the Earth system at regional and global scales represent the effects of urban areas on climate and the effects of changing the climate on urban areas. At the same time, it is essential to develop state of the art, simple and accurate urban models to better understand the relevant processes and also toaddress issues related to urban security against the spectra of chemical, biological and radiological (CBR) hazards. Towards bringing these communities together, a 2.5-day international workshop was held at Argonne National Laboratory (ANL) in the Chicago area on May 22-24, 2019. This workshop brought together national and international experts to develop a roadmap for a better understanding of the issues associated with urban areas and at enhancing the capabilities of regional and global Earth System models (ESMs) in representing the atmospheric dynamics and chemistry, unique aspects of the biosphere and land use, and human dimensions of the urban environment. This workshop was especially important to those developing very high-resolution versions of regional and global models. The workshop also discussed existing datasets, including in situ and satellite observations, and the emerging smart city sensing technologies and their possible use in model development (e.g., the NSF-funded Array of Things network currently operating in Chicago and expanding to other cities).

54 ENVIRONMENTAL SCIENCES↗
DOE OSTI2026

Desorption Electrospray Ionization–Mass Spectrometry Imaging Provides Spatiochemical Information on Potential Biocontrol Agents against Phytophthora capsici Infection in Tomato Plants

Biological control agents can offer an eco-friendly and more sustainable alternative to conventional chemical pesticides, providing protection against destructive pathogens, such as Phytophthora capsici, while reducing potential environmental harm associated with synthetic pesticide use in agricultural systems. This work evaluates the biocontrol effectiveness of Bacillus vallismortis, Bacillus amyloliquefaciens, Bacillus thuringiensis, and Bacillus subtilis, against the widespread plant pathogen Phytophthora capsici. Our studies showed that Bacillus thuringiensis and Bacillus subtilis promote plant growth and provide protection against Phytophthora capsici in both in vitro and in vivo greenhouse studies, while Bacillus vallismortis and Bacillus amyloliquefaciens were effective in vitro but not in vivo. Specifically, Bacillus thuringiensis was observed to both hinder the growth of Phytophthora capsici and enhance plant resilience to this pathogen, with B. thuringiensis-treated, pathogen-exposed plants displaying a 94.4% increase in root length and a 74.0% increase in shoot height compared to plants with only oomycete exposure. To probe the molecular interactions between the biocontrol agent and pathogen, a dual culture of Bacillus thuringiensis and Phytophthora capsici was analyzed in situ using a desorption electrospray ionization–mass spectrometry imaging (DESI-MSI) workflow. This approach interrogated the spatially oriented biochemical interactions that may serve as the molecular foundation for the effectiveness of these biological control agents in crop protection, identifying seven unique phenotypic regions within the dual culture. Herein, we demonstrate the benefits of biological control agent application in tomato cultivation and showcase the strengths of desorption electrospray ionization–mass spectrometry imaging when applied to the spatially resolved molecular characterization of agriculturally relevant microorganisms.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2023

Home range and resource selection of Virginia opossums in the rural southeastern United States

The Virginia opossum (Didelphis virginiana) has a rapidly expanding distribution in North America, but many aspects of its ecology remain relatively understudied, particularly in rural areas of its core range. We collected GPS telemetry data from 93 opossums in a rural, non-agricultural landscape in South Carolina, USA (2018–2019) to examine factors influencing space use and resource selection. Estimated male home ranges (99% utilization distributions) were on average 50% larger than those of females (mean home range 115.9 ± 103.7 ha vs 76.7 ± 75.0 ha). The home range size decreased on average by 20% with each 20% increase in deciduous land cover but was not affected by season or other landscape factors. Core area sizes (65% utilization distributions) were not influenced by sex (mean core area size 29.1 ± 23.7 ha and 22.4 ha ± 13.8 for males and females, respectively) or season, but the core area size decreased by 14% with each 400 m increase in distance from a permanent water source. Resource selection by opossums primarily occurred at the landscape level. Both males and females generally selected for wetlands while avoiding pine forests and developed/open areas, likely the result of differences in resource availability and predation risk between habitats. Opossums also tended to select for linear features such as unpaved roads and edge habitat, which may facilitate movement across the landscape. Finally, the home ranges we documented are among the largest recorded for opossums in the USA, likely the result of the relatively low resource abundance throughout our study area due to comparatively minimal anthropogenic influence.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2024

Integrating in situ environmental covariates in an American lobster catch model to improve impact assessment

The installation and operation of floating offshore wind power is an integral component of societal transition to renewable energy generation where fixed bottom offshore wind is not possible. However, it will cause unique ecosystem changes. To disentangle the effects of offshore wind installations from the concurrent effects of climate change and the fishing practices on commercially significant resources, we must develop detailed characterizations of the resources before development occurs. In the Gulf of Maine, American lobster is the most commercially and culturally important fishery. At the time of writing, this is the largest fishery by value in North America. Our understanding of baseline localized parameters (such as catch per trap at the spatial scale of individual turbines) should be informed by relationships to environmental, biological, and survey-specific functional drivers of catch. A more mechanistic understanding of catch will allow for strategic adjustments to Post- Deployment fishery responses and ultimately, the development of research- and commercial-scale floating offshore wind development. Here, we used survey data from the New England Aqua Ventus Pre-Construction Commercial Trapping Survey to develop Generalized Additive Models describing seasonal catch per trap for legal and sublegal lobsters. We found fall catch to be nearly twice that of spring. Bottom temperature dynamics could be used to predict catch, and the Fall survey was associated with a warmer temperature regime. By using analytical tools that incorporate environmental heterogeneity, we developed monitoring methods from preconstruction baseline data that will be applicable over the post-construction operating period of an offshore wind farm.

BACI↗
DOE OSTI2026

Protonic nickelate device networks for spatiotemporal neuromorphic computing

Computation in biological neural circuits arises from the interplay of nonlinear temporal responses and spatially distributed dynamic network interactions. Replicating this richness in hardware has remained challenging, as most neuromorphic devices emulate only isolated neuron- or synapse-like functions. Here we introduce an integrated neuromorphic computing platform in which both nonlinear spatiotemporal processing and programmable memory are realized within a single perovskite nickelate material system. By engineering symmetric and asymmetric hydrogenated NdNiO 3 junction devices on the same wafer, we combine ultrafast, proton-mediated transient dynamics with stable multilevel resistance states. Networks of symmetric NdNiO 3 junctions exhibit emergent spatial interactions mediated by proton redistribution, while each node simultaneously provides short-term temporal memory, enabling nanosecond-scale operation with an energy cost of ~0.2 nJ per input. When interfaced with asymmetric output units serving as reconfigurable long-term weights, these networks allow both feature transformation and linear classification in the same material system. Leveraging these emergent interactions, the platform enables real-time pattern recognition and achieves high accuracy in spoken digit classification and early seizure detection, outperforming temporal-only or uncoupled architectures. These results position protonic nickelates as a compact, energy-efficient, CMOS-compatible platform that integrates processing and memory for scalable intelligent hardware.

Electrical and electronic engineering↗
DOE OSTI2021

Prospects for sub-nanometer scale imaging of optical phenomena using electron microscopy

Imaging of optical phenomena at the sub-nanometer scale can offer fundamental insights into the electronic or vibrational states in atomic-scale defects, molecules, and nanoparticles, which are important in quantum information, heterogeneous catalysis, optoelectronics, and structural biology. Several techniques have surpassed the traditional Abbe diffraction limit and attained spatial resolutions down to a few nanometers, but sub-nanometer scale optics has remained elusive. Here, we propose an approach that combines spectrally specific photoabsorption with sub-nanometer scale resolution transmission electron microscopy (TEM) of photoexcited electrons. We first estimate the signal level and conditions required for imaging nanoscale optical phenomena in core-shell quantum dots (QDs) like CdS/CdTe. Furthermore, we show the possibility of imaging photoexcited states of atomic-scale defects in a monolayer hexagonal boron nitride (h-BN) using ab initio and high resolution (HR)TEM simulations. The ability to directly visualize photoexcited states at the sub-nanometer scale opens opportunities to study properties of individual quantum dots and atomic defects.

74 ATOMIC AND MOLECULAR PHYSICS↗
DOE OSTI2024

Wildfire smoke impacts lake ecosystems

Abstract Wildfire activity is increasing globally. The resulting smoke plumes can travel hundreds to thousands of kilometers, reflecting or scattering sunlight and depositing particles within ecosystems. Several key physical, chemical, and biological processes in lakes are controlled by factors affected by smoke. The spatial and temporal scales of lake exposure to smoke are extensive and under‐recognized. We introduce the concept of the lake smoke‐day, or the number of days any given lake is exposed to smoke in any given fire season, and quantify the total lake smoke‐day exposure in North America from 2019 to 2021. Because smoke can be transported at continental to intercontinental scales, even regions that may not typically experience direct burning of landscapes by wildfire are at risk of smoke exposure. We found that 99.3% of North America was covered by smoke, affecting a total of 1,333,687 lakes ≥10 ha. An incredible 98.9% of lakes experienced at least 10 smoke‐days a year, with 89.6% of lakes receiving over 30 lake smoke‐days, and lakes in some regions experiencing up to 4 months of cumulative smoke‐days. Herein we review the mechanisms through which smoke and ash can affect lakes by altering the amount and spectral composition of incoming solar radiation and depositing carbon, nutrients, or toxic compounds that could alter chemical conditions and impact biota. We develop a conceptual framework that synthesizes known and theoretical impacts of smoke on lakes to guide future research. Finally, we identify emerging research priorities that can help us better understand how lakes will be affected by smoke as wildfire activity increases due to climate change and other anthropogenic activities.

54 ENVIRONMENTAL SCIENCES↗
DOE OSTI2024

From individual leaves to forest stands: importance of niche, distance decay, and stochasticity vary by ecosystem type and functional group for fungal community composition

Abstract Community assembly is influenced by environmental niche processes as well as stochastic processes that can be spatially dependent (e.g. dispersal limitation) or independent (e.g. priority effects). Here, we sampled senesced tree leaves as unit habitats to investigate fungal community assembly at two spatial scales: (i) small neighborhoods of overlapping leaves from differing tree species and (ii) forest stands of differing ecosystem types. Among forest stands, ecosystem type explained the most variation in community composition. Among adjacent leaves within stands, variability in fungal composition was surprisingly high. Leaf type was more important in stands with high soil fertility and dominated by differing tree mycorrhizal types (sugar maple vs. basswood or red oak), whereas distance decay was more important in oak-dominated forest stands with low soil fertility. Abundance of functional groups was explained by environmental factors, but predictors of taxonomic composition within differing functional groups were highly variable. These results suggest that fungal community assembly processes are clearest for functional group abundances and large spatial scales. Understanding fungal community assembly at smaller spatial scales will benefit from further study focusing on differences in drivers for different ecosystems and functional groups, as well as the importance of spatially independent factors such as priority effects.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2026

Single-cell and spatial omics in plants: from cellular atlases to regulatory mechanisms

Single-cell RNA sequencing (scRNA-seq) has transformed transcriptomic studies by enabling gene expression profiling at the resolution of individual cells within and across a broad range of tissue types, revealing cellular heterogeneity that is obscured in bulk tissue transcriptomes. Over the past decade, improvements in microfluidics and library preparation have drastically increased throughput, allowing tens of thousands of cells to be assayed in a single experiment. Although initially developed in animal systems, scRNA-seq has rapidly emerged as a powerful and widely adopted approach in plant biology. Beyond transcriptomics, the integration of single-cell data with chromatin accessibility, proteomics, metabolomics, and spatial omics is enabling a system-level understanding of plant gene regulation and cellular organization. Network-based analytical frameworks further support the reconstruction of gene regulatory networks and the interpretation of complex single-cell data. In this review, we summarize the current technological landscape of plant single-cell studies, discuss key experimental and analytical challenges, and review emerging strategies for validating single-cell discoveries. We also discuss future directions in applying single-cell technologies to woody perennials plants and bioenergy-relevant crops, emphasizing their potential to accelerate the discovery of cell type-specific regulatory mechanisms underlying growth, stress resilience, and biomass production.

Li, Miaomiao [ORNL] (ORCID:0000000321326168)↗
DOE OSTI2021

Rapid Automated Annotation and Analysis of N-Glycan Mass Spectrometry Imaging Data Sets Using NGlycDB in METASPACE

Imaging N-glycan spatial distribution in tissues using mass spectrometry imaging (MSI) is emerging as a promising tool in biological and clinical applications. However, there is currently no high throughput tool for visualization and molecular annotation of N-glycans in MSI data, which significantly slows down data processing and hampers the applicability of this approach. In this work, we present how METASPACE, an open-source cloud engine for molecular annotation of MSI data, can be used to automatically annotate, visualize, analyze, and interpret high-resolution mass spectrometry-based spatial N-glycomics data. METASPACE is an emerging tool in spatial metabolomics, but the lack of compatible glycan databases has limited its application for comprehensive N-glycan annotations from MSI datasets. We created NGlycDB, a public database of N-glycans, by adapting available glycan databases. We demonstrate the applicability of NGlycDB in METASPACE by analyzing MALDI-MSI data from formalin-fixed paraffin-embedded (FFPE) human kidney and mouse lung tissue sections. We added NGlycDB to METASPACE for public use, thus facilitating applications of MSI in glycobiology.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗