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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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All sourcesNASA NTRSDOE OSTI
DOE OSTI2024

In-vivo Raman microspectroscopy reveals differential nitrate concentration in different developmental zones in Arabidopsis roots

Abstract Background Nitrate (NO 3 − ) is one of the two major forms of inorganic nitrogen absorbed by plant roots, and the tissue nitrate concentration in roots is considered important for optimizing developmental programs. Technologies to quantify the expression levels of nitrate transporters and assimilating enzymes at the cellular level have improved drastically in the past decade. However, a technological gap remains for detecting nitrate at a high spatial resolution. Using extraction-based methods, it is challenging to reliably estimate nitrate concentration from a small volume of cells (i.e., with high spatial resolution), since targeting a small or specific group of cells is physically difficult. Alternatively, nitrate detection with microelectrodes offers subcellular resolution with high cell specificity, but this method has some limitations on cell accessibility and detection speed. Finally, optical nitrate biosensors have very good ( in-vivo ) sensitivity (below 1 mM) and cellular-level spatial resolution, but require plant transformation, limiting their applicability. In this work, we apply Raman microspectroscopy for high-dynamic range in-vivo mapping of nitrate in different developmental zones of Arabidopsis thaliana roots in-situ . Results As a proof of concept, we have used Raman microspectroscopy for in-vivo mapping of nitrate content in roots of Arabidopsis seedlings grown on agar media with different nitrate concentrations. Our results revealed that the root nitrate concentration increases gradually from the meristematic zone (~ 250 µm from the root cap) to the maturation zone (~ 3 mm from the root cap) in roots grown under typical growth conditions used for Arabidopsis, a trend that has not been previously reported. This trend was observed for plants grown in agar media with different nitrate concentrations (0.5–10 mM). These results were validated through destructive measurement of nitrate concentration. Conclusions We present a methodology based on Raman microspectroscopy for in-vivo label-free mapping of nitrate within small root tissue volumes in Arabidopsis. Measurements are done in-situ without additional sample preparation. Our measurements revealed nitrate concentration changes from lower to higher concentration from tip to mature root tissue. Accumulation of nitrate in the maturation zone tissue shows a saturation behavior. The presented Raman-based approach allows for in-situ non-destructive measurements of Raman-active compounds.

Fernández González, Alma↗
DOE OSTI2014

β1 and β4 integrins: from breast development to clinical practice

Following a highly dynamic and complex dialogue between the epithelium and the surrounding microenvironment, the mammary gland develops into a branching structure during puberty, buds during pregnancy, forms intricate polar acini during lactation and, once the babies are weaned, remodels and involutes. At every stage of menstrual and pregnancy cycles, interactions between the cells and the extracellular matrix (ECM) and homotypic and heterotypic cell–cell interactions give rise to the architecture and function of the gland at that junction. These orchestrated programs would not be possible without the important role of the ECM receptors, integrins being the prime examples. The ECM–integrin axis regulates many crucial cellular functions including survival, migration and quiescence; the imbalance in any of these processes could contribute to oncogenesis. In this review we spotlight the involvement of two prominent integrin subunits, β1 and β4 integrins, in cross-talk with tyrosine kinase receptors, and we discuss the roles of these integrin subunits in the biology of normal breast differentiation and as potential prognostic and therapeutic targets in breast cancer.

60 APPLIED LIFE SCIENCES↗
DOE OSTI2015

Athletic equipment microbiota are shaped by interactions with human skin

Background: Americans spend the vast majority of their lives in built environments. Even traditionally outdoor pursuits, such as exercising, are often now performed indoors. Bacteria that colonize these indoor ecosystems are primarily derived from the human microbiome. The modes of human interaction with indoor surfaces and the physical conditions associated with each surface type determine the steady-state ecology of the microbial community. Results: Bacterial assemblages associated with different surfaces in three athletic facilities, including floors, mats, benches, free weights, and elliptical handles, were sampled every other hour (8 am to 6 pm) for 2 days. Surface and equipment type had a stronger influence on bacterial community composition than the facility in which they were housed. Surfaces that were primarily in contact with human skin exhibited highly dynamic bacterial community composition and non-random co-occurrence patterns, suggesting that different host microbiomes—shaped by selective forces—were being deposited on these surfaces through time. Bacterial assemblages found on the floors and mats changed less over time, and species co-occurrence patterns appeared random, suggesting more neutral community assembly. Conclusions: These longitudinal patterns highlight the dramatic turnover of microbial communities on surfaces in regular contact with human skin. By uncovering these longitudinal patterns, this study promotes a better understanding of microbe-human interactions within the built environment.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2023

Methods for Continuously Resolving Spectral Shifts in Distributed Optical Fiber Sensors Irradiated to Extreme Neutron Fluence

Optical frequency domain reflectometry (OFDR) is a technique for interrogating distributed optical fiber sensors (DOFS) and involves correlating changes in the Rayleigh backscatter fingerprint for a fiber under test (FUT) with a reference measurement. Recently, under the WIRE-21 experiment sponsored by Nuclear Science User Facilities (NSUF) and performed at the High-Flux Isotope Reactor (HFIR) at Oak Ridge National Laboratory (ORNL), silica optical fibers were irradiated to a fast neutron fluence of 1x10^21 n/cm^2/s at temperatures from 200--400 C. As in the cases of high-temperature and high-strain conditions, such high levels of neutron bombardment result in a highly dynamic RBS that evades analysis with conventional methods. This work describes the further development and application of graphical signal processing techniques applied to OFDR-based distributed optical fiber sensors specifically deployed in in-pile applications. While the signal processing techniques developed in this work are applied to DOFS in nuclear environments, they provide a general framework for the analysis of OFDR measurements and a tangible method to yield higher quality data, without imposing additional hardware requirements.

Sweeney, Dan↗
DOE OSTI2020

High-speed fiber-based spectrometer for plasma Thomson scattering

Here we present a novel concept for a Thomson scattering diagnostic, based on a high-speed fiber optic spectrometer. The high-speed fiber optic spectrometer presented here translates a spectral measurement from the frequency domain into the time domain, thus requiring the use of only a single photodetector for spectral acquisition. The high temporal precision offered by the instrument gives rise to a number of advantages over traditional spectrometers, such as nearly background-free measurements and multiple uses of the same injected beam. Multiple uses of the same beam would enable greatly increased measurement rates, in the range of 10–100 MHz. The spectral range and resolution of the fiber spectrometer can be easily tailored to be optimized for the light source and experimental conditions by selecting different lengths of fiber, thus allowing for the proposed technique to exhibit high dynamic range when measuring many points simultaneously. Finally, due to the temporal separation of the background from the signal, these improvements are possible without the need for increased average input laser power.

47 OTHER INSTRUMENTATION↗
DOE OSTI2021

Evaluation of liquid-phase thermometry in impinging jet sprays using synchrotron x-ray scattering

Liquid thermometry during primary and secondary breakup of liquid sprays is challenging due to the presence of highly dynamic, optically complex flow features. This work evaluates the use of x-ray scattering from a focused, monochromatic beam of the Advanced Photon Source at Argonne National Laboratory for the measurement of liquid temperatures within the mixing zone of an impinging jet spray. The measured scattering profiles are converted to temperature through a previously developed two-component partial least squares (PLS) regression model. Transmitive mixing during jet merging is inferred through spatial mapping of temperatures within the impingement region. In this work, the technique exhibits uncertainties of ±2K in temperature and 2% in capturing the correct scattering profile, showing its potential utility for probing liquid temperature distributions in multiphase flows.

42 ENGINEERING↗
DOE OSTI2023

Modeling suggests that virion production cycles within individual cells is key to understanding acute hepatitis B virus infection kinetics

Hepatitis B virus (HBV) infection kinetics in immunodeficient mice reconstituted with humanized livers from inoculation to steady state is highly dynamic despite the absence of an adaptive immune response. To recapitulate the multiphasic viral kinetic patterns, we developed an agent-based model that includes intracellular virion production cycles reflecting the cyclic nature of each individual virus lifecycle. The model fits the data well predicting an increase in production cycles initially starting with a long production cycle of 1 virion per 20 hours that gradually reaches 1 virion per hour after approximately 3–4 days before virion production increases dramatically to reach to a steady state rate of 4 virions per hour per cell. Together, modeling suggests that it is the cyclic nature of the virus lifecycle combined with an initial slow but increasing rate of HBV production from each cell that plays a role in generating the observed multiphasic HBV kinetic patterns in humanized mice.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2015

A Geographic Mosaic of Climate Change Impacts on Terrestrial Vegetation: Which Areas Are Most at Risk?

Changes in climate projected for the 21st century are expected to trigger widespread and pervasive biotic impacts. Forecasting these changes and their implications for ecosystem services is a major research goal. Much of the research on biotic responses to climate change has focused on either projected shifts in individual species distributions or broad-scale changes in biome distributions. Here, we introduce a novel application of multinomial logistic regression as a powerful approach to model vegetation distributions and potential responses to 21st century climate change. We modeled the distribution of 22 major vegetation types, most defined by a single dominant woody species, across the San Francisco Bay Area. Predictor variables included climate and topographic variables. The novel aspect of our model is the output: a vector of relative probabilities for each vegetation type in each location within the study domain. The model was then projected for 54 future climate scenarios, spanning a representative range of temperature and precipitation projections from the CMIP3 and CMIP5 ensembles. We found that sensitivity of vegetation to climate change is highly heterogeneous across the region. Surprisingly, sensitivity to climate change is higher closer to the coast, on lower insolation, north-facing slopes and in areas of higher precipitation. While such sites may provide refugia for mesic and cool-adapted vegetation in the face of a warming climate, the model suggests they will still be highly dynamic and relatively sensitive to climate-driven vegetation transitions. The greater sensitivity of moist and low insolation sites is an unexpected outcome that challenges views on the location and stability of climate refugia. Projections provide a foundation for conservation planning and land management, and highlight the need for a greater understanding of the mechanisms and time scales of potential climate-driven vegetation transitions.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2019

Single-cell correlations of mRNA and protein content in a human monocytic cell line after LPS stimulation

The heterogeneity of mRNA and protein expression at the single-cell level can reveal fundamental information about cellular response to external stimuli, including the sensitivity, timing, and regulatory interactions of genes. Here we describe a fully automated system to digitally count the intron, mRNA, and protein content of up to five genes of interest simultaneously in single-cells. Full system automation of 3D microscope scans and custom image analysis routines allows hundreds of individual cells to be automatically segmented and the mRNA-protein content to be digitally counted. Single-molecule intron and mRNA content is measured by single-molecule fluorescence in-situ hybridization (smFISH), while protein content is quantified though the use of antibody probes. To mimic immune response to bacterial infection, human monocytic leukemia cells (THP-1) were stimulated with lipopolysaccharide (LPS), and the expression of two inflammatory genes, IL1β (interleukin 1β) and TNF-α (tumor necrosis factor α), were simultaneously quantified by monitoring the intron, mRNA, and protein levels over time. The simultaneous labeling of cellular content allowed for a series of correlations at the single-cell level to be explored, both in the progressive maturation of a single gene (intron-mRNA-protein) and comparative analysis between the two immune response genes. In the absence of LPS stimulation, mRNA expression of IL1β and TNF-α were uncorrelated. Following LPS stimulation, mRNA expression of the two genes became more correlated, consistent with a model in which IL1β and TNF-α upregulation occurs in parallel through independent mechanistic pathways. This smFISH methodology can be applied to different complex biological systems to provide valuable insight into highly dynamic gene mechanisms that determine cell plasticity and heterogeneity of cellular response.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2024

Data for: Time to anoxia: Observations and predictions of oxygen drawdown following coastal flood events

This dataset contains data and code associated with the paper Patel et al. "Time to anoxia: Observations and predictions of oxygen drawdown following coastal flood events".The coastal terrestrial-aquatic interface (TAI) is a highly dynamic system characterized by strong physical, chemical, and biological gradients. In particular, shifting soil redox conditions and consumption of terminal electron acceptors, due in part to dynamic hydrologic conditions, is a strong driver of carbon availability and transformations across TAIs. However, while redox dynamics are well described, our ability to quantitatively forecast rates of oxic to anoxic shifts in soils with different characteristics and inundation regimes is limited. We integrated field measurements, laboratory incubations, and model simulations to improve mechanistic understanding of oxygen consumption dynamics in coastal soils. Continuous in situ monitoring unexpectedly revealed that flooding caused temporary spikes in subsurface dissolved oxygen followed by rapid consumption in the wetlands. To further investigate these mechanisms in a controlled setting, we performed laboratory incubations using surface and subsurface soils from a TAI gradient (defined here as upland forest to transitional forest to wetland) in Western Lake Erie to measure oxygen consumption rates in TAI soils during flood events. In our experiments, wetland soils reached anoxia the fastest, in ∼ 9 h on average, whereas upland soils turned anoxic in ∼ 18 h. Subsurface upland soils did not turn anoxic even after two weeks of saturation in the lab, and their oxygen consumption patterns suggested carbon and/or nutrient limitation. These results are consistent with in-situ groundwater redox and oxygen measurements in the field, where wetland soils exhibited the highest rates of oxygen consumption along the TAI. Model simulations of oxygen consumption suggested that oxygen consumption had stronger abiotic controls in wetland soils but stronger biotic controls in upland soils, providing a useful framework for future incubation experiments. Microbial activity is a strong driver of oxygen consumption in TAI soils, although it is constrained by the availability of dissolved carbon in subsurface soils.This dataset contains a compressed (.zip) archive of the data and R scripts used for this manuscript. The dataset includes files in .csv format, which can be accessed and processed using MS Excel or R. This archive can also be accessed on GitHub at https://github.com/COMPASS-DOE/cmps-time_to_anoxia (DOI: 10.5281/zenodo.10815374).

54 ENVIRONMENTAL SCIENCES↗
DOE OSTI2025

Catalyst Deactivation Modes of PdO/γ-Al 2 O 3 Catalysts for Lean Methane Oxidation

PdO/γ-Al 2 O 3 catalysts are one of the most active catalytic components for the complete oxidation of methane. Under reaction conditions, especially in a wet feed, the catalysts suffer severe performance degradation. This study establishes a series of testing protocols to systematically investigate the causes of catalyst deactivation under methane oxidation reaction conditions. Four distinct catalyst deactivation modes are identified. Two of the deactivation modes are directly related to H 2 O, either from the feed gas or as a part of the reaction products, with one (Mode 2) being attributed to the formation of surface hydroxyl groups and the other (Mode 3) to the competitive adsorption of H 2 O on the catalysts. The impact of the two deactivation modes is acute and severe but reversible. In contrast, the other two deactivation modes are gradual and persistent but irreversible. Both modes are induced by CH 4 oxidation reaction, with the impact of a wet feed (Mode 4) being substantially more severe than that of a dry feed (Mode 1). The major cause of the irreversible catalyst deactivation is attributed to surface reconstruction of PdO nanoparticles, which behaves as a passivation layer lowering the number of coordinately unsaturated Pd sites for CH 4 activation. Although the passivation layer is relatively stable against thermal or hydrothermal treatment, it is not completely inert. Formation and partial regeneration of the passivation layer is a highly dynamic process and heavily depends on the reaction temperature: a lower reaction temperature (≤ 450 ℃) can lead to quicker catalyst deactivation; but a higher reaction temperature (between 500 – 550 ℃) can result in a greater extent of catalyst deactivation.

PdO/γ-Al2O3↗
DOE OSTI2019

Synchrotron Radiation Beam Diagnostics at IOTA - Commissioning Performance and Upgrade Efforts

The Integrable Optics Test Accelerator is a research electron and proton storage ring recently commissioned at the Fermilab Accelerator Science and Technology facility. A key part of its beam diagnostics suite are synchrotron radiation monitors, used for measuring transverse beam profile, position, and intensity. In this paper, we report on the performance and uses of this system during the year 1 run. We demonstrate sub-100nm statistical beam position uncertainty and high dynamic range from 10⁹ electrons down to a single electron. Commissioning challenges and operational issues are discussed. We conclude by outlining current upgrade efforts, including improved modularity, small emittance measurements, and a multi-anode photomultiplier system for turn-by-turn acquisition.

43 PARTICLE ACCELERATORS↗
DOE OSTI2023

Measurements at peak operational beam current in the SNS beam test facility

Work at the SNS beam test facility has focused on high dimensional and high dynamic range measurements of the medium energy (2.5 Mev) beam distribution. This is motivated by the need to understand and predict beam losses down to one-part-per-million. The initial demonstration of full-and-direct 6D phase space measurement was done at a current of 40 mA transported through the RFQ. Since that demonstration, more detailed studies have been performed at lower transported currents (in the range 30 mA and below). This is due to a hardware change - recent runs utilize the original SNS RFQ, which after a decade of service in the SNS achieves transmission significantly below design (50-60%, vs >80%). A short run in 2023 with a newly-commissioned RFQ enables maximum transmission. Preliminary results from beam distribution measurements during this run are discussed.

Ruisard, Kiersten↗
DOE OSTI2012

The Arabidopsis Wave Complex: Mechanisms of Localized Actin Polymerization and Growth

Plant cells are complex energy storage systems that convert solar radiation to reduced carbon. The chemical form of the storage molecule varies depending on the species and cell type, but sucrose, fructans, starch, or lipids are common examples. The compartmentation of metabolic activities within specific organelles and the intracellular transport and fusion of specialized compartments are key components to energy storage. In the context of cellular engineering, is critical to gain a deep understanding of how metabolic activities are integrated with the organelles and inter-organelle transport. In plant cells, actin filaments are highly dynamic structural elements that define the overall architecture of the cytoplasm and organelle transport activities in the cell. Stable actin bundles are critical architectural elements that position organelles and serves as tracks for motor-dependent organelle trafficking. Subsets of dynamic actin do work by generating membrane tension or by driving organelle fusion, and organelle motility. However, in plants we know very little about when and how particular actin filament arrays are generated and their cellular function. The lack of knowledge impedes efforts to use protein assemblies to dictate the trafficking and growth behaviors of cells. The objective of this project was to discover the protein complexes and control mechanisms that determine the location of actin filament roadways in plant cells. Our work provided the first molecular description of protein complexes that are converted from inactive complexes to active actin filament nucleators in the cell. These discoveries provided a conceptual framework to control to roadways in plant cells that determine the location and delivery of plant metabolites and storage molecules that are relevant to the bioenergy economy.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2013

Distributed Sensor Coordination for Advanced Energy Systems

The ability to collect key system level information is critical to the safe, efficient and reliable operation of advanced energy systems. With recent advances in sensor development, it is now possible to push some level of decision making directly to computationally sophisticated sensors, rather than wait for data to arrive to a massive centralized location before a decision is made. This type of approach relies on networked sensors (called “agents” from here on) to actively collect and process data, and provide key control decisions to significantly improve both the quality/relevance of the collected data and the associating decision making. The technological bottlenecks for such sensor networks stem from a lack of mathematics and algorithms to manage the systems, rather than difficulties associated with building and deploying them. Indeed, traditional sensor coordination strategies do not provide adequate solutions for this problem. Passive data collection methods (e.g., large sensor webs) can scale to large systems, but are generally not suited to highly dynamic environments, such as advanced energy systems, where crucial decisions may need to be reached quickly and locally. Approaches based on local decisions on the other hand cannot guarantee that each agent performing its task (maximize an agent objective) will lead to good network wide solution (maximize a network objective) without invoking cumbersome coordination routines. There is currently a lack of algorithms that will enable self-organization and blend the efficiency of local decision making with the system level guarantees of global decision making, particularly when the systems operate in dynamic and stochastic environments. In this work we addressed this critical gap and provided a comprehensive solution to the problem of sensor coordination to ensure the safe, reliable, and robust operation of advanced energy systems. The differentiating aspect of the proposed work is in shifting the focus towards “what to observe” rather than “how to observe” in large sensor networks, allowing the agents to actively determine both the structure of the network and the relevance of the information they are seeking to collect. In addition to providing an implicit coordination mechanism, this approach allows the system to be reconfigured in response to changing needs (e.g., sudden external events requiring new responses) or changing sensor network characteristics (e.g., sudden changes to plant condition). Outcome Summary: All milestones associated with this project have been completed. In particular, private sensor objective functions were developed which are aligned with the global objective function, sensor effectiveness has been improved by using “sensor teams,” system efficiency has been improved by 30% using difference evaluation functions, we have demonstrated system reconfigurability for 20% changes in system conditions, we have demonstrated extreme scalability of our proposed algorithm, we have demonstrated that sensor networks can overcome disruptions of up to 20% in network conditions, and have demonstrated system reconfigurability to 20% changes in system conditions in hardware-based simulations. This final report summarizes how each of these milestones was achieved, and gives insight into future research possibilities past the work which has been completed. The following publications support these milestones [6, 8, 9, 10, 16, 18, 19].

97 MATHEMATICS AND COMPUTING↗
DOE OSTI2014

Advanced Kalman Filter for Real-Time Responsiveness in Complex Systems

Complex engineering systems pose fundamental challenges in real-time operations and control because they are highly dynamic systems consisting of a large number of elements with severe nonlinearities and discontinuities. Today’s tools for real-time complex system operations are mostly based on steady state models, unable to capture the dynamic nature and too slow to prevent system failures. We developed advanced Kalman filtering techniques and the formulation of dynamic state estimation using Kalman filtering techniques to capture complex system dynamics in aiding real-time operations and control. In this work, we looked at complex system issues including severe nonlinearity of system equations, discontinuities caused by system controls and network switches, sparse measurements in space and time, and real-time requirements of power grid operations. We sought to bridge the disciplinary boundaries between Computer Science and Power Systems Engineering, by introducing methods that leverage both existing and new techniques. While our methods were developed in the context of electrical power systems, they should generalize to other large-scale scientific and engineering applications.

97 MATHEMATICS AND COMPUTING↗
DOE OSTI2014

EMAPS: An Efficient Multiscale Approach to Plasma Systems with Non-MHD Scale Effects

Using Discrete-Event Simulation (DES) as a novel paradigm for time integration of large-scale physics-driven systems, we have achieved significant breakthroughs in simulations of multi-dimensional magnetized plasmas where ion kinetic and finite Larmor radius (FLR) and Hall effects play a crucial role. For these purposes we apply a unique asynchronous simulation tool: a parallel, electromagnetic Particle-in-Cell (PIC) code, HYPERS (Hybrid Particle Event-Resolved Simulator), which treats plasma electrons as a charge neutralizing fluid and solves a self-consistent set of non-radiative Maxwell, electron fluid equations and ion particle equations on a structured computational grid. HYPERS enables adaptive local time steps for particles, fluid elements and electromagnetic fields. This ensures robustness (stability) and efficiency (speed) of highly dynamic and nonlinear simulations of compact plasma systems such spheromaks, FRCs, ion beams and edge plasmas. HYPERS is a unique asynchronous code that has been designed to serve as a test bed for developing multi-physics applications not only for laboratory plasma devices but generally across a number of plasma physics fields, including astrophysics, space physics and electronic devices. We have made significant improvements to the HYPERS core: (1) implemented a new asynchronous magnetic field integration scheme that preserves local divB=0 to within round-off errors; (2) Improved staggered-grid discretizations of electric and magnetic fields. These modifications have significantly enhanced the accuracy and robustness of 3D simulations. We have conducted first-ever end-to-end 3D simulations of merging spheromak plasmas. The preliminary results show: (1) tilt-driven relaxation of a freely expanding spheromak to an m=1 Taylor helix configuration and (2) possibility of formation of a tilt-stable field-reversed configuration via merging and magnetic reconnection of two double-sided spheromaks with opposite helicities.

70 PLASMA PHYSICS AND FUSION TECHNOLOGY↗