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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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70 records · Page 4
All sourcesNASA NTRSDOE OSTI
DOE OSTI2024

Differential roles of kinetic on- and off-rates in T-cell receptor signal integration revealed with a modified Fab’-DNA ligand

Antibody-derived T-cell receptor (TCR) agonists are commonly used to activate T cells. While antibodies can trigger TCRs regardless of clonotype, they bypass native T cell signal integration mechanisms that rely on monovalent, membrane-associated, and relatively weakly binding ligand in the context of cellular adhesion. Commonly used antibodies and their derivatives bind much more strongly than native peptide major histocompatibility complex (pMHC) ligands bind their cognate TCRs. Because ligand dwell time is a critical parameter that tightly correlates with physiological function of the TCR signaling system, there is a general need, both in research and therapeutics, for universal TCR ligands with controlled kinetic binding parameters. To this end, we have introduced point mutations into recombinantly expressed α-TCRβ H57 Fab to modulate the dwell time of monovalent Fab binding to TCR. When tethered to a supported lipid bilayer via DNA complementation, these monovalent Fab’-DNA ligands activate T cells with potencies well-correlated with their TCR binding dwell time. Single-molecule tracking studies in live T cells reveal that individual binding events between Fab'-DNA ligands and TCRs elicit local signaling responses closely resembling native pMHC. The unique combination of high on- and off-rates of the H57 R97L mutant enables direct observations of cooperative interplay between ligand binding and TCR-proximal condensation of the linker for activation of T cells, which is not readily visualized with pMHC. This work provides insights into how T cells integrate kinetic information from TCR ligands and introduces a method to develop affinity panels for polyclonal T cells, such as cells from a human patient.

Science & Technology - Other Topics↗
DOE OSTI2025

Emerging protein sequencing technologies: proteomics without mass spectrometry?

Liquid chromatography-tandem mass spectrometry (LC-MS/MS) has been a leading method for proteomics for 30 years. Advantages provided by LC-MS/MS are offset by significant disadvantages, including cost. Recently, several non-mass spectrometric methods have emerged, but little information is available about their capacity to analyze the complex mixtures routine for mass spectrometry. Areas Covered: We review recent non-mass-spectrometric methods for sequencing proteins and peptides, including those using nanopores, sequencing by degradation, reverse translation, and short-epitope mapping, with comments on bioinformatics challenges, fundamental limitations, and areas where new technologies will be more or less competitive with LC-MS/MS. In addition to conventional literature searches, instrument vendor websites, patents, webinars, and preprints were also consulted to give a more up-to-date picture. Expert Opinion: Many new technologies are promising. However, demonstrations that they outperform mass spectrometry in terms of peptides and proteins identified have not yet been published, and astute observers note important disadvantages, especially relating to the dynamic range of single-molecule measurements of complex mixtures. Still, even if the performance of emerging methods proves inferior to LC-MS/MS, their low cost could create a different kind of revolution: a dramatic increase in the number of biology laboratories engaging in new forms of proteomics research.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2024

Partial wrapping of single-stranded DNA by replication protein A and modulation through phosphorylation

Abstract Single-stranded DNA (ssDNA) intermediates which emerge during DNA metabolic processes are shielded by replication protein A (RPA). RPA binds to ssDNA and acts as a gatekeeper to direct the ssDNA towards downstream DNA metabolic pathways with exceptional specificity. Understanding the mechanistic basis for such RPA-dependent functional specificity requires knowledge of the structural conformation of ssDNA when RPA-bound. Previous studies suggested a stretching of ssDNA by RPA. However, structural investigations uncovered a partial wrapping of ssDNA around RPA. Therefore, to reconcile the models, in this study, we measured the end-to-end distances of free ssDNA and RPA–ssDNA complexes using single-molecule FRET and double electron–electron resonance (DEER) spectroscopy and found only a small systematic increase in the end-to-end distance of ssDNA upon RPA binding. This change does not align with a linear stretching model but rather supports partial wrapping of ssDNA around the contour of DNA binding domains of RPA. Furthermore, we reveal how phosphorylation at the key Ser-384 site in the RPA70 subunit provides access to the wrapped ssDNA by remodeling the DNA-binding domains. These findings establish a precise structural model for RPA-bound ssDNA, providing valuable insights into how RPA facilitates the remodeling of ssDNA for subsequent downstream processes.

Biochemistry & Molecular Biology↗
DOE OSTI2025

Scalable Parallel Measurement of Individual Nitrogen-Vacancy Centers

The nitrogen-vacancy (NV) center in diamond is a solid-state spin defect that has been widely adopted for quantum sensing and quantum information processing applications. Typically, experiments are performed either with a single isolated NV center or with an unresolved ensemble of many NV centers, resulting in a trade-off between measurement speed and spatial resolution or control over individual defects. In this work, we introduce an experimental platform that bypasses this trade-off by addressing multiple optically resolved NV centers in parallel. We perform charge- and spin-state manipulations selectively on multiple NV centers from within a larger set, and we manipulate and measure the electronic spin states of over 100 NV centers in parallel. We show that the high signal-to-noise ratio of the measurements enables the detection of shot-to-shot pairwise correlations between the spin states of 108 NV centers, corresponding to the simultaneous measurement of 5778 unique correlation coefficients. We discuss how our platform can be scaled to parallel experiments with thousands of individually resolved NV centers. These results enable parallelized high-throughput sensing experiments that retain the spatial resolution of single defects and will, thereby, help to unlock advances in applications such as single-molecule NMR and characterization of integrated circuits. In addition, our approach to multiplexing provides a natural platform for the application of recently developed correlated sensing techniques.

NV centers↗
DOE OSTI2025

Super-resolution imaging reveals resistance to mass transfer in functionalized stationary phases

Chemical separations are costly in terms of energy, time, and money. Separation methods are optimized with inefficient trial-and-error approaches that lack insight into the molecular dynamics that lead to the success or failure of a separation and, hence, ways to improve the process. We perform super-resolution imaging of fluorescent analytes in five different commercial liquid chromatography materials. Unexpectedly, we observe that chemical functionalization can block more than 50% of the material’s porous interior, rendering it inaccessible to small-molecule analytes. Only in situ imaging unveils the inaccessibility when compared to the industry-accepted ex situ characterization methods. Selectively removing some of the functionalization with solvent restores pore access without substantially altering the single-molecule kinetics that underlie the separation and agree with bulk chromatography measurements. Our molecular results determine that commercial “fully porous” stationary phases are over-functionalized and provide an alternative avenue to characterize and direct separation material design from the bottom-up.

Science & Technology - Other Topics↗
DOE OSTI2025

Tunable phononic quantum interference induced by two-dimensional metals

Harnessing quantum interference among bosons provides opportunities due to their longer coherence time than fermions. Fano resonance, an example of quantum interference between discrete and continuous states, is marked by an asymmetric lineshape. While photon-based Fano resonance has enabled high-sensitivity molecule sensing, phonon-based Fano resonance remains underexplored because of ineffective interference between discrete phonons and electronic continuum. In this work, we report phonon-based Fano resonance in a graphene/2D Ag/SiC heterostructure, arising from frequency and lifetime matching between discrete and continuous phonons of SiC. The observed Fano asymmetry is tunable over two orders of magnitude, surpassing previously reported phonon-based systems. The 2D Ag layer restructures the interfacial SiC and facilitates resonant scattering to enhance Fano asymmetry, which is unattainable in conventional Ag. We further demonstrated that this Fano resonance allows ultrasensitive molecule detection at the single-molecule level. Our work highlights phonon-based Fano resonance, opening avenues for engineering quantum interference with phonons.

Science & Technology - Other Topics↗
DOE OSTI2024

SISGR: The regulation of carbon fixation in plant and green algae: Rubisco activase and the origin of heat inactivation of CO 2 assimilation

Rubisco activase (Rca) is a critical AAA+ ATPase protein complex that remodels and promotes the Rubisco enzyme, a key player in photosynthetic performance and carbon fixation. The assembly and function of the Rca protein complex are regulated by a range of factors, including subunit concentration, nucleotide-binding states, thermal conditions, metal-ion coordination, and post-translational modifications, such as phosphorylation. Despite its importance in photosynthesis, the detailed molecular mechanisms underlying the regulation of plant Rca and how it activates Rubisco remain elusive. This project aims to bridge this knowledge gap by integrating sophisticated enzymology tools with single-molecule methods and high-resolution electron microscopy to elucidate the structure and function of plant Rca. Through these multiple approaches, we have systematically investigated how the activity of plant Rca is impacted by various factors, such as phosphorylation and metal-ion coordination. The Rca complex assembly/disassembly dynamics were captured using anti-Brownian electrokinetic (ABEL) trap-based measurements, providing unprecedented insight into its structural flexibility and diverse assembly states. Furthermore, the structural analysis of Rca through electron crystallography and single-particle cryogenic electron microscopy (cryo-EM) reveals novel assembly states of the spinach Rca, providing insight into the mechanistic action for Rubisco remodeling. By combining cutting-edge tools and approaches, this work uncovers critical aspects of Rca’s regulation and assembly, paving the way for a deeper understanding of its role in photosynthetic efficiency and the potential for enhancing carbon fixation in crops.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2024

Toward a better understanding of Ni coarsening in solid oxide cells: NiH on Ni (111) examined at the level of density-functional theory (and KMC)

Ni coarsening in the fuel electrode of solid oxide cells (SOCs) is known to be significantly faster under a humid atmosphere. In this talk, density-functional theory and kinetic Monte Carlo methods are used to explore the hypothesis that the surface diffusion of NiH on Ni may promote Ni coarsening in the SOC operated in electrolysis cell mode. Defining the surface diffusivity as the product of the fractional surface coverage and single-molecule surface diffusivity, the surface diffusivity of NiH on Ni (111) is found to be large enough under a significant overpotential to support the above hypothesis. However, as NiH could dissociate on Ni (111), more work is needed to show that NiH may promote Ni coarsening.

Mantz, Yves↗
DOE OSTI2025

Examining Ni Coarsening in Solid Oxide Electrolysis Cells by Characterizing NiH on Ni (111) Using a Combined Theoretical Approach

Ni coarsening in the fuel electrode of solid oxide cells (SOCs) is an important degradation mechanism. In this talk, density-functional theory and kinetic Monte Carlo methods are used to explore the hypothesis that the surface diffusion of NiH on Ni may promote Ni coarsening in the SOC operated in electrolysis cell mode. Using both methods and defining the diffusivity as the product of the surface coverage and single-molecule diffusivity, the diffusivity of NiH on Ni (111) is found to be sufficiently large under a significant overpotential to support the above hypothesis. Also, the time between the formation and dissociation of NiH on Ni (111) is predicted to be short at low coverages of H on Ni (111). Thus, significant progress is made toward developing a model of Ni coarsening considering both molecular and dissociated forms of NiH on Ni (111).

density functional theory (DFT)↗
DOE OSTI2026

Unraveling the Dynamics of Nucleosome Arrays

The organization of genomic DNA into chromatin is a fundamental determinant of genome stability, regulation, and cellular function. Nucleosomes, the basic repeating units of chromatin, assemble into higher-order structures whose organization and heterogeneity remain difficult to characterize using conventional ensemble-averaged techniques. A key need in the field is the development of experimental approaches capable of directly visualizing nucleosome assemblies and their structural variability at the single-molecule level. This LDRD Lab-Wide project focused on establishing and evaluating atomic force microscopy (AFM)–based approaches for the characterization of nucleosome assemblies. The work emphasized experimental workflows for preparing, imaging, and assessing multi-nucleosome systems, rather than isolated single nucleosomes. Through method development and exploratory measurements, the project demonstrated the feasibility of applying scanning probe microscopy to investigate chromatin-relevant assemblies and provided preliminary insight into the strengths and limitations of this approach for future quantitative studies. Results and lessons learned from this effort were disseminated to the broader scientific community through multiple national conference presentations, helping to position LLNL for continued work in chromatin and genome organization research.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2026

Carbon-Based Quantum Information Science with Symmetry Protected Topological States (Final Report, DOE-BES award DE-SC0023105)

This research program established the scientific foundation for the rational, bottom-up design, synthesis, isolation, and investigation of symmetry-protected topological (SPT) electron spin qubits embedded in graphene nanoribbons (GNRs). The work focused on integrating atomically precise low-dimensional carbon nanostructures with emerging quantum logic architectures, providing a pathway toward scalable quantum materials for next-generation computing and sensing technologies. A central component of the program was the elucidation of fundamental relationships between real-space molecular architecture, local spin density distributions, electronic band dispersion, and energy level alignment in atomically precise GNR systems. These correlations define key operational parameters of SPT qubits and were systematically investigated to establish quantitative benchmarks against established molecular and solid-state spin qubit platforms. Attention was given to properties critical for quantum device performance, e.g. decoherence times, spectral sharpness of energy transitions, and tunable exchange interactions between spin states. The research demonstrated that these parameters can be engineered with atomic precision through scalable bottom-up synthetic strategies. Theory-guided design played a central role in identifying candidate structures hosting topologically protected spin states. Experimental validation was performed using both ensemble measurements and single-molecule characterization. In addition to advances in quantum materials synthesis, the program developed and applied spin-sensitive scanning probe microscopy techniques capable of directly probing quantum states and dynamic processes with atomic-scale spatial resolution. These capabilities enabled direct observation and characterization of quantum structures at the single-atom level. While the research activities were primarily hypothesis-driven fundamental investigations, the program adopted a comprehensive materials-by-design framework aimed at translating scientific discoveries into technological concepts compatible with scalable and intelligent manufacturing approaches.

36 MATERIALS SCIENCE↗
DOE OSTI2026

Development of high throughput light-sheet fluorescence lifetime imaging microscopy for 3D functional imaging of metabolic pathways in plant and microorganisms (Final Technical Report)

This research program will enable new biochemical contrast in the nanosecond lifetime domain through use of the recently demonstrated electro-optic fluorescence lifetime imaging technique (EO-FLIM) for wide-field lifetime imaging. The Stanford/Stanford Linear Accelerator Center multidisciplinary collaboration -- physics, applied physics, and structural biology -- will develop a light-sheet fluorescence lifetime imaging microscope for functional studies of microbial and plant metabolic pathways and dynamic interactions between plants and microorganisms in the rhizosphere. The proposed approach overcomes the imaging time bottleneck associated with existing fluorescence lifetime imaging methods. Initial demonstrations have shown a factor of 100,000 improvement in photon throughput compared to existing methods. High photon efficiency allowed the first wide-field fluorescence lifetime imaging of single molecules. Recent work has improved the technique’s repetition rate to enable compatibility with mode-locked lasers and demonstrated the combination of wide-field fluorescence lifetime imaging with super-resolution localization microscopy, observations of single molecule dynamics, and observation of donor lifetime quenching in single-molecule imaging. These results were achieved on standard camera sensors and would not have been possible with other wide-field approaches. The throughput and photon economy of the EO-FLIM method enables new BER-relevant imaging opportunities. In particular, scanned single- and two-photon light-sheet excitation will be used to achieve volumetric imaging with time-domain contrast.

47 OTHER INSTRUMENTATION↗
DOE OSTI2026

Edge‐Driven Fringe‐Field Effects, Reduced Screening, and Bandgap Widening in Graphene Nanoribbons Enable Single‑Molecule Sensitivity

Graphene nanoribbons (GNRs) offer promising platforms for single‐molecule sensing due to their quasi‐1D channels and discrete electronic states, providing superior sensitivity toward molecular perturbations. While prior studies emphasize smoother edges as essential for optimal performance, the potential benefits of controlled edge roughness remain largely unexplored. Additionally, most investigations focus on GNR arrays, leaving critical edge‐ and width‐dependent factors, including fringe fields, bandgap widening, interactions between adsorbing molecules and GNR atoms, density of states (DOS) suppression, and electrostatic screening lengths, and their collective impact on sensitivity, poorly understood. Here, in this work, we fabricated field‐effect transistors using individual GNRs (widths: 200–20 nm) and characterized their response to molecular adsorption with perfluorooctanoic acid as the model analyte. Narrower ribbons displayed significantly enhanced sensitivity, yielding a coverage‐normalized response of 116 ± 10 mV per molecule in 20 nm‐wide GNRs (from calibrated ensemble Dirac‐point shifts). Experimental and theoretical analyses reveal that this heightened sensitivity arises from stronger fringe fields, width‐dependent quantum confinement effects, reduced DOS, and increased edge roughness that facilitates molecular anchoring, enhanced orbital overlap, and improved charge transfer efficiency. Our findings challenge the conventional assumption that smoother edges inherently enhance sensor performance, demonstrating that controlled edge disorder substantially boosts molecular sensitivity in GNR sensors.

36 MATERIALS SCIENCE↗
DOE OSTI2024

Angle between DNA linker and nucleosome core particle regulates array compaction revealed by individual-particle cryo-electron tomography

Abstract The conformational dynamics of nucleosome arrays generate a diverse spectrum of microscopic states, posing challenges to their structural determination. Leveraging cryogenic electron tomography (cryo-ET), we determine the three-dimensional (3D) structures of individual mononucleosomes and arrays comprising di-, tri-, and tetranucleosomes. By slowing the rate of condensation through a reduction in ionic strength, we probe the intra-array structural transitions that precede inter-array interactions and liquid droplet formation. Under these conditions, the arrays exhibite irregular zig-zag conformations with loose packing. Increasing the ionic strength promoted intra-array compaction, yet we do not observe the previously reported regular 30-nanometer fibers. Interestingly, the presence of H1 do not induce array compaction; instead, one-third of the arrays display nucleosomes invaded by foreign DNA, suggesting an alternative role for H1 in chromatin network construction. We also find that the crucial parameter determining the structure adopted by chromatin arrays is the angle between the entry and exit of the DNA and the corresponding tangents to the nucleosomal disc. Our results provide insights into the initial stages of intra-array compaction, a critical precursor to condensation in the regulation of chromatin organization.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2025

Gating Single Molecules with Counterions

We report atomic-scale gating and visualization of local charge distribution within individual rare-earth-based molecular complexes on a metallic surface. The complexes are formed by a positively charged lanthanum ion coordinated to a (pcam)3 molecule and a negatively charged counterion trapped underneath via electrostatic interactions on a Au(111) surface. Local gating is performed by adding an additional negatively charged counterion to one side of the complex, which results in the redistribution of charges within the complex and a positive shift of the frontier orbitals. This is caused by the internal Stark effect induced by the added counterion. This effect is directly captured using tunneling spectroscopy and spectroscopic mapping at 5 K substrate temperature. The polarizability of the complex is corroborated by density functional theory and analytical calculations based on experimental findings. Furthermore, the influence of charge polarization on nearby complexes is investigated in a cluster purposely assembled using three complexes, which reveals maintaining the charge states as in single complexes. These findings will enable the design of robust charged rare-earth complexes to be tailored for potential solid-state applications.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2025

DNA-PAINT Imaging with Hydrogel Imprinting and Clearing

Hydrogel-embedding is a versatile technique in fluorescence microscopy, offering stabilization, optical clearing, and the physical expansion of biological specimens. DNA-PAINT is a super-resolution microscopy approach based on the diffusion and transient binding of fluorescently labeled oligos, but its feasibility in hydrogels has not yet been explored. In this study, we demonstrate that polyacrylamide hydrogels support sufficient diffusion for effective DNA-PAINT imaging. Using acrydite-anchored oligonucleotides imprinted from patterned DNA origami nanostructures and microtubule filaments in fixed cells, we find that hydrogel embedding preserves docking strand positioning at the nanoscale. Sample clearing via protease treatment had minor structural effects on the microtubule structure and enhanced diffusion and accessibility to hydrogel-imprinted docking strands. Our work demonstrates promising potential for diffusion and binding-based fluorescence imaging applications in hydrogel-embedded samples.

DNA origami↗