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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 OSTI2025

LDRD 2024 Annual Report: Laboratory Directed Research and Development Program Activities

One fundamental question underlying all living organisms is the need to understand their hierarchical organizations and physical changes with the necessary spatial and temporal resolutions under physiological or pathological conditions. This is a multi-scale challenge requiring imaging from sub-nanometers to micrometers in a cellular context. While individual imaging techniques are available, there is a critical need to integrate them into a workflow capability. Our objective is to develop an integrated multi-disciplinary and multi-scale bioimaging capability at Brookhaven National Laboratory (BNL). The capability expands BNL’s existing facility operation program in bioimaging and positions BNL in a leadership position in bioimaging research. The capability also addresses the grand challenges of the Department of Energy (DOE) science programs for national bioenergy sustainability and security.

99 GENERAL AND MISCELLANEOUS↗
DOE OSTI2022

Hierarchical deep reinforcement learning reveals a modular mechanism of cell movement

Time-lapse images of cells and tissues contain rich information about dynamic cell behaviours, which reflect the underlying processes of proliferation, differentiation and morphogenesis. However, we lack computational tools for effective inference. Here we exploit deep reinforcement learning (DRL) to infer cell–cell interactions and collective cell behaviours in tissue morphogenesis from three-dimensional (3D) time-lapse images. We use hierarchical DRL (HDRL), known for multiscale learning and data efficiency, to examine cell migrations based on images with a ubiquitous nuclear label and simple rules formulated from empirical statistics of the images. When applied to Caenorhabditis elegans embryogenesis, HDRL reveals a multiphase, modular organization of cell movement. Imaging with additional cellular markers confirms the modular organization as a novel migration mechanism, which we term sequential rosettes. Furthermore, HDRL forms a transferable model that successfully differentiates sequential rosettes-based migration from others. Our study demonstrates a powerful approach to infer the underlying biology from time-lapse imaging without prior knowledge.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2025

Multiscale Mechanical Characterization of Mineral-Reinforced Wood Cell Walls

Studying the multiscale mechanics of bio-based composites offers unique perspectives on underlying structure–property relations. Cellular materials, such as wood, are highly organized, hierarchical assemblies of load-bearing structural elements that respond to mechanical stimuli at the microscopic, mesoscopic and macroscopic scale. In this study, we modified oak wood with nanocrystalline ferrihydrite, a widespread ferric oxyhydroxide mineral, and characterized the resulting mechanical properties of the composite at various levels of organization. Ferrihydrite nanoparticles were deposited inside the wood cell wall by an in situ chemical reaction, resulting in increased stiffness and hardness of the functionalized secondary cell wall, as evidenced by region-specific nanoindentation tests under an electron microscope. Chemically modified and pristine wood samples were characterized by using atomic force microscopy in the bimodal frequency modulation mode, which produced topographical images from the cellular ultrastructure with high lateral resolution and localized nanomechanical information across distinct cell wall layers. In conclusion, despite mineral reinforcement at the cell wall level, the macroscopic fracture behavior examined through three-point flexural testing remained unchanged upon modification, as cell–cell adhesion could be impaired by harsh chemical conditions.

Cells↗
DOE OSTI2024

Structure and identification of the native PLP synthase complex from Methanosarcina acetivorans lysate

Many protein-protein interactions behave differently in biochemically purified forms as compared to their in vivo states. As such, determining native protein structures may elucidate structural states previously unknown for even well-characterized proteins. Here, we apply the bottom-up structural proteomics method, cryoID , toward a model methanogenic archaeon. While they are keystone organisms in the global carbon cycle and active members of the human microbiome, there is a general lack of characterization of methanogen enzyme structure and function. Through the cryoID approach, we successfully reconstructed and identified the native Methanosarcina acetivorans pyridoxal 5′-phosphate (PLP) synthase (PdxS) complex directly from cryogenic electron microscopy (cryo-EM) images of fractionated cellular lysate. We found that the native PdxS complex exists as a homo-dodecamer of PdxS subunits, and the previously proposed supracomplex containing both the synthase (PdxS) and glutaminase (PdxT) was not observed in cellular lysate. Our structure shows that the native PdxS monomer fashions a single 8α/8β TIM-barrel domain, surrounded by seven additional helices to mediate solvent and interface contacts. A density is present at the active site in the cryo-EM map and is interpreted as ribose 5-phosphate. In addition to being the first reconstruction of the PdxS enzyme from a heterogeneous cellular sample, our results reveal a departure from previously published archaeal PdxS crystal structures, lacking the 37-amino-acid insertion present in these prior cases. This study demonstrates the potential of applying the cryoID workflow to capture native structural states at atomic resolution for archaeal systems, for which traditional biochemical sample preparation is nontrivial.

Methanosarcina acetivorans↗
DOE OSTI2020

Efficacy and Delivery of Novel FAST Agents for Coronaviruses

We proposed to test and develop advanced delivery for novel agents from our collaborators Facile Accelerated Specific Therapeutics (FAST) platform to reduce coronavirus replication. Sachi Bioworks Inc., Prof. Anushree Chatterjee, and Prof. Prashant Nagpal at the University of Colorado Boulder have developed a bioinformatics and synthesis pipeline to produce sequence specific theranostic agents (agents that can be therapies and/or diagnostics) that are inherently transported into the cytoplasm of mammalian host cells and sequence-specifically interfere in nucleic acid replication. The agent comprises a small nanoparticle (2-5 nm) chosen for ideal cellular transport and/or imaging conjugated to a short, synthetic DNA analog oligomer designed for binding to one or more target viral sequences. The sequence specific binding of the FAST agent to its target prevents nucleic acid replication due to its high affinity binding. While the small nanoparticle facilitates delivery in vitro, we plan to package the FAST agents into a larger nanoparticle (80-300 nm) for future in vivo delivery applications. Our team at Sandia has expertise encapsulating biomolecules including protein, DNA, and RNA into solid lipid nanoparticles (LNP) and lipid coated mesoporous silica nanoparticles (LC-MSN) and shown successful delivery in mouse models to multiple tissues. Our team focused on formulation parameters for FAST agents into lipid nanoparticles (LNP) and lipid coated mesoporous silica nanoparticles (LC-MSN) for enhanced delivery and/or efficacy and in vivo translation. We used lipid formulas that have been shown in literature to facility in vitro and more importantly, in vivo delivery. In our work discussed below, we successfully demonstrate loading and release of FAST agents on silica core and stable LC-MSN in a reasonable size range for in vivo testing.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2023

Genomes to Structure and Function Workshop Report 2022

The goal of the U.S. Department of Energy (DOE) Biological and Environmental Research (BER) Program is to achieve a predictive understanding of complex biological, earth, and environmental systems with the aim of advancing the nation’s energy and infrastructure security. (https://www.energy.gov/science/ ber/biological-and-environmental-research). To pursue this goal, collaborations among experts in diverse research areas that lead to multidisciplinary projects are indispensable. The roles of DOE’s User Facilities, which offer unique and powerful resources for such research projects, are evolving, and expectations for the facilities are increasing. To respond to Users’ needs, the Joint Genome Institute (JGI) and Environmental Molecular Sciences Laboratory (EMSL) initiated the Facilities Integrating Collaborations for User Science (FICUS) program in 2014. This collaboration has grown into a popular and successful program, advancing more than 100 multidisciplinary projects to date. Similarly, the new interFacility collaborations among the JGI, EMSL, and User resources for BER structural biology and imaging at the Basic Energy Science (BES) Program’s synchrotron and neutron facilities are becoming essential for cutting-edge transdisciplinary science. To further explore the need for the BER research community to combine genomic, functional, and structural approaches to advance their research, an organizing committee was formed to develop and jointly host a 3-part workshop. The committee’s members represented seven DOE National Laboratory User Facilities (Appendix 1 lists the members). The “Genomes to Structure and Function” virtual workshop (see Appendices 2–5) was composed of three sessions. The first session, titled “Molecular Structures” (October 27– 28, 2021), highlighted diverse integrative experimental and computational approaches correlating structural data with sequencing and functional information, as well as predicting protein structures to model complex biological systems. The second session, “Intracellular Organization, and Material Synthesis and Decomposition” (December 15–16, 2021), covered imaging methods for observing, quantifying, and manipulating biosystems. The third session, “Imaging the Rhizosphere and Cellular Organization” (January 26–27, 2022) emphasized advanced and non-invasive imaging techniques applied to plant root-microbe-soil interactions.

59 BASIC BIOLOGICAL SCIENCES↗
NASA NTRS1993

Nature's crucible: Manufacturing optical nonlinearities for high resolution, high sensitivity encoding in the compound eye of the fly, Musca domestica

The number of pixels per unit area sampling an image determines Nyquist resolution. Therefore, the highest pixel density is the goal. Unfortunately, as reduction in pixel size approaches the wavelength of light, sensitivity is lost and noise increases. Animals face the same problems and have achieved novel solutions. Emulating these solutions offers potentially unlimited sensitivity with detector size approaching the diffraction limit. Once an image is 'captured', cellular preprocessing of information allows extraction of high resolution information from the scene. Computer simulation of this system promises hyperacuity for machine vision.

Wilcox, Mike↗
DOE OSTI2021

Integrated and dynamic multi-spectroscopic in situ imaging of plant metabolism at the level of subcellular compartments. Final Report

The goals of this project was to develop integrated multi-spectral molecular imaging technologies (Raman, fluorescence, and mass spectrometry), that can assess, and image metabolic processes at the cellular and subcellular levels of plant organs. These imaging technologies were developed in the context of computational capabilities that integrated multi-spectral images with genome scale models of metabolism. The integrated molecular imaging technologies were developed in the biological context of autophagy that remodels membrane lipid topologies, which control spatially defined subcellular regions within plant cells and optimizes plant biomass productivity during environmental stresses that can limit biomass productivity.

09 BIOMASS FUELS↗
DOE OSTI2025

Spatial top-down proteomics for the functional characterization of human kidney

Background: The Human Proteome Project has credibly detected nearly 93% of the roughly 20,000 proteins which are predicted by the human genome. However, the proteome is enigmatic, where alterations in amino acid sequences from polymorphisms and alternative splicing, errors in translation, and post-translational modifications result in a proteome depth estimated at several million unique proteoforms. Recently mass spectrometry has been demonstrated in several landmark efforts mapping the human proteoform landscape in bulk analyses. Herein, we developed an integrated workflow for characterizing proteoforms from human tissue in a spatially resolved manner by coupling laser capture microdissection, nanoliter-scale sample preparation, and mass spectrometry imaging. Results: Using healthy human kidney sections as the case study, we focused our analyses on the major functional tissue units including glomeruli, tubules, and medullary rays. After laser capture microdissection, these isolated functional tissue units were processed with microPOTS (microdroplet processing in one-pot for trace samples) for sensitive top-down proteomics measurement. This provided a quantitative database of 616 proteoforms that was further leveraged as a library for mass spectrometry imaging with near-cellular spatial resolution over the entire section. Notably, several mitochondrial proteoforms were found to be differentially abundant between glomeruli and convoluted tubules, and further spatial contextualization was provided by mass spectrometry imaging confirming unique differences identified by microPOTS, and further expanding the field-of-view for unique distributions such as enhanced abundance of a truncated form (1-74) of ubiquitin within cortical regions. Conclusions: We developed an integrated workflow to directly identify proteoforms and reveal their spatial distributions. Where of the 20 differentially abundant proteoforms identified as discriminate between tubules and glomeruli by microPOTS, the vast majority of tubular proteoforms were of mitochondrial origin (8 of 10) where discriminate proteoforms in glomeruli were primarily hemoglobin subunits (9 of 10). These trends were also identified within ion images demonstrating spatially resolved characterization of proteoforms that has the potential to reshape discovery-based proteomics because the proteoforms are the ultimate effector of cellular functions. Applications of this technology have the potential to unravel etiology and pathophysiology of disease states, informing on biologically active proteoforms, which remodel the proteomic landscape in chronic and acute disorders.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2023

A combination interferometric and morphological image processing approach to rapid quality assessment of additively manufactured cellular truss core components

Advanced manufacturing (AM) processes such as laser powder bed fusion (LPBF) are increasingly capable of fabricating components with useful and unprecedented mechanical properties by incorporating complex internal bracing structures. From the standpoint of quality control and assessment, however, internally complex assemblies present significant build-verification challenges. Here we propose a hybrid approach to the inspection involving the application of computer-aided speckle interferometry (CASI) and morphological image processing as a rapid, inexpensive, and facile method for AM quality control. The described methodology has low capital equipment costs, is full-field and non-contact, can be used in an industrial setting, and has very low requirements in terms of operator training and expertise. Consisting primarily of the combination of image processing software with a simple optical system of variable sensitivity, the method is shown to be effective for inspection of a titanium honeycomb component subjected to differential pressure. Results are compared to those achieved with computed tomography (CT), immersion ultrasound testing (UT), and optical holographic interferometry. Here we propose several possible processing strategies for automated quality assessment based on this powerful hybrid approach.

36 MATERIALS SCIENCE↗
DOE OSTI2025

Automated segmentation of soft X-ray tomography: Native cellular structure with submicron resolution at high-throughput for whole-cell quantitative imaging in yeast

Soft X-ray tomography (SXT) is an invaluable tool for quantitatively analyzing cellular structures at suboptical isotropic resolution. However, it has traditionally depended on manual segmentation, limiting its scalability for large datasets. Here, we leverage a deep learning-based autosegmentation pipeline to segment and label cellular structures in hundreds of cells across three Saccharomyces cerevisiae strains. This task-based pipeline uses manual iterative refinement to improve segmentation accuracy for key structures, including the cell body, nucleus, vacuole, and lipid droplets, enabling high-throughput and precise phenotypic analysis. Using this approach, we quantitatively compared the three-dimensional (3D) whole-cell morphometric characteristics of wild-type, VPH1-GFP, and vac14 strains, uncovering detailed strain-specific cell and organelle size and shape variations. We show the utility of SXT data for precise 3D curvature analysis of entire organelles and cells and detection of fine morphological features using surface meshes. Our approach facilitates comparative analyses with high spatial precision and statistical throughput, uncovering subtle morphological features at the single-cell and population level. This workflow significantly enhances our ability to characterize cell anatomy and supports scalable studies on the mesoscale, with applications in investigating cellular architecture, organelle biology, and genetic research across diverse biological contexts.

Chen, Jianhua [Lawrence Berkeley National Laborato↗
DOE OSTI2021

Quantitative phase microscopy monitors subcellular dynamics in single cells exposed to nanosecond pulsed electric fields

A substantial body of literature exists to study the dynamics of single cells exposed to short duration (<1 μs), high peak power (~1 MV/m) transient electric fields. Much of this research is limited to traditional fluorescence-based microscopy techniques, which introduce exogenous agents to the culture and are only sensitive to a single molecular target. Quantitative phase imaging (QPI) is a coherent imaging modality which uses optical path length as a label-free contrast mechanism, and has proven highly effective for the study of single-cell dynamics. In this work, we introduce QPI as a useful imaging tool for the study of cells undergoing cytoskeletal remodeling after nanosecond pulsed electric field (nsPEF) exposure. In particular, we use cell swelling, dry mass and disorder strength measurements derived from QPI phase images to monitor the cellular response to nsPEFs. We hope this demonstration of QPI's utility will lead to a further adoption of the technique for the study

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2025

Cryosectioning-enhanced super-resolution microscopy for single-protein imaging across cells and tissues

DNA-points accumulation for imaging in nanoscale topography (DNA-PAINT) enables nanoscale imaging with virtually unlimited multiplexing and molecular counting. Here, we address challenges, such as variable imaging performance and target accessibility, that can limit its broader applicability. Specifically, we enhance its capacity for robust single-protein imaging and molecular counting by optimizing the integration of total internal reflection fluorescence microscopy with physical sectioning, in particular, Tokuyasu cryosectioning. Our method, tomographic and kinetically enhanced DNA-PAINT (tkPAINT), achieves 3 nm localization precision across diverse samples, enhanced imager binding, and improved cellular integrity. tkPAINT can facilitate molecular counting with DNA-PAINT inside the nucleus, as demonstrated through its quantification of the in situ abundance of RNA Polymerase II in both HeLa cells as well as mouse tissues. Anticipating that tkPAINT could become a versatile tool for the exploration of biomolecular organization and interactions across cells and tissues, we also demonstrate its capacity to support multiplexing, multimodal targeting of proteins and nucleic acids, and three-dimensional (3D) imaging.

Science & Technology - Other Topics↗
NASA NTRS2001

Latitudinal Transport of Angular Momentum by Cellular Flows Observed with MDI

We have analyzed Doppler velocity images from the MDI instrument on SOHO to determine the latitudinal transport of angular momentum by the cellular photospheric flows. Doppler velocity images from 60-days in May to July of 1996 were processed to remove the p-mode oscillations, the convective blue shift, the axisymmetric flows, and any instrumental artifacts. The remaining cellular flows were examined for evidence of latitudinal angular momentum transport. Small cells show no evidence of any such transport. Cells the size of supergranules (30,000 km in diameter) show strong evidence for a poleward transport of angular momentum. This would be expected if supergranules are influenced by the Coriolis force, and if the cells are elongated in an east-west direction. We find good evidence for just such an east-west elongation of the supergranules. This elongation may be the result of differential rotation shearing the cellular structures. Data simulations of this effect support the conclusion that elongated supergranules transport angular momentum from the equator toward the poles, Cells somewhat larger than supergranules do not show evidence for this poleward transport. Further analysis of the data is planned to determine if the direction of angular momentum transport reverses for even larger cellular structures. The Sun's rapidly rotating equator must be maintained by such transport somewhere within the convection zone.

Hathaway, David H.↗
DOE OSTI2023

Controlling solute channel formation using magnetic fields

Solute channel formation introduces compositional and microstructural variations in a range of processes, from metallic alloy solidification, to salt fingers in ocean and water reservoir flows. Applying an external magnetic field interacts with thermoelectric currents at solid/liquid interfaces generating additional flow fields. This thermoelectric (TE) magnetohydrodynamic (TEMHD) effect can impact on solute channel formation, via a mechanism recently drawing increasing attention. To investigate this phenomenon, we combined in situ synchrotron X-ray imaging and Parallel-Cellular-Automata-Lattice-Boltzmann based numerical simulations to study the characteristics of flow and solute transport under TEMHD. Observations suggest the macroscopic TEMHD flow appearing ahead of the solidification front, coupled with the microscopic TEMHD flow arising within the mushy zone are the primary mechanisms controlling plume migration and channel bias. Two TE regimes were revealed, each with distinctive mechanisms that dominate the flow. Further, we show that grain orientation modifies solute flow through anisotropic permeability. These insights led to a proposed strategy for producing solute channel-free solidification using a time-modulated magnetic field.

36 MATERIALS SCIENCE↗
NASA NTRS1999

Avian Blood-Vessel Formation in Space

Based on previous studies, we hypothesized that the developmental anomalies observed in the past might be related to or caused by delayed or improper vascular development. The objective of our research is to test the hypothesis that exposure to microgravity during space flight cause delayed or improper vascular development during embryogenesis. The effects of microgravity on the time course and extent of avian blood-vessel formation are assessed using two models, one for angiogenesis and one for vasculogenesis. The methodological approach is dictated by the constraints of the tissue preservation method used in space. Thus, both in the chorioallantoic membrane (CAM) and in the adrenal, we will evaluate microscopically the vascular architecture and immunostain endothelial cells with specific antibodies (anti- vWF and QH1). The extent of ECM protein deposition will be assessed by immunohistochemistry and correlated with the degree of vascularization, using computer-based image analysis. Also, the cellular source for ECM proteins will be assessed by in situ hybridization.

Lelkes, Peter I.↗
NASA NTRS1995

Comparison of DNA fragmentation and color thresholding for objective quantitation of apoptotic cells

Apoptosis is a process of cell death characterized by distinctive morphological changes and fragmentation of cellular DNA. Using video imaging and color thresholding techniques, we objectively quantitated the number of cultured CD4+ T-lymphoblastoid cells (HUT78 cells, RH9 subclone) displaying morphological signs of apoptosis before and after exposure to gamma-irradiation. The numbers of apoptotic cells measured by objective video imaging techniques were compared to numbers of apoptotic cells measured in the same samples by sensitive apoptotic assays that quantitate DNA fragmentation. DNA fragmentation assays gave consistently higher values compared with the video imaging assays that measured morphological changes associated with apoptosis. These results suggest that substantial DNA fragmentation can precede or occur in the absence of the morphological changes which are associated with apoptosis in gamma-irradiated RH9 cells.

Non-NASA Center↗