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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 55 records · Page 3
All sourcesNASA NTRSDOE OSTI
DOE OSTI2025

Dynamic basis of supercoiling-dependent DNA interrogation by Cas12a via R-loop intermediates

The sequence specificity and programmability of DNA binding and cleavage have enabled widespread applications of CRISPR-Cas12a in genetic engineering. As an RNA-guided CRISPR endonuclease, Cas12a engages a 20-base pair (bp) DNA segment by forming a three-stranded R-loop structure in which the guide RNA hybridizes to the DNA target. Here we use single-molecule torque spectroscopy to investigate the dynamics and mechanics of R-loop formation of two widely used Cas12a orthologs at base-pair resolution. We directly observe kinetic intermediates corresponding to a ~5 bp initial RNA-DNA hybridization and a ~17 bp intermediate preceding R-loop completion, followed by transient DNA unwinding that extends beyond the 20 bp R-loop. The complex multistate landscape of R-loop formation is ortholog-dependent and shaped by target sequence, mismatches, and DNA supercoiling. A four-state kinetic model captures essential features of Cas12a R-loop dynamics and provides a biophysical framework for understanding Cas12a activity and specificity.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2025

Sub-10 nm upconversion nanocrystals for long-term single-particle tracking

Lanthanide-doped upconversion nanoparticles are attractive single-molecule imaging probes due to their high photostability and anti-Stokes luminescence. However, achieving both small particle size and strong brightness has remained a major challenge, as reducing size often leads to dimmer emission. Herein, we fabricate a sub-10 nm cascade actively protected upconversion nanoparticles, which shows a 33-fold enhanced upconversion efficiency at the single-particle level compared to larger ~19 nm conventional nanoparticles. Theoretical modeling and time-resolved measurements show that emission loss mainly comes from energy leakage of Er 3+ ions to surface defects. By introducing a NaYbF 4 layer as photon-harvesting and protective intermediate layer, we minimize this energy loss and significantly boost brightness. A monolayer of inert NaLuF 4 can effectively suppress the surface quenching to Yb 3+ . Using these ultra-small bright probes, we successfully tracked single epidermal growth factor receptor molecules on live cells for up to one hour, revealing dynamic switching between different diffusion modes.

Qiu, Xiaochen [Fudan Univ., Shanghai (China); Shen↗
DOE OSTI2026

PARP1-HPF1 structure and dynamics on nicked DNA suggest a mechanism for acute and localized ADP-ribosylation

PARP1 detection of DNA strand breaks allosterically leads to PARP1 synthesis of poly(ADP-ribose) modifications that signal DNA damage. HPF1 engages activated PARP1 to control modification site selection. Understanding of the mechanism of DNA break detection and catalytic activation is incomplete, due largely to limited structural information for full-length PARP1. Here, single-particle cryo-EM provides views of the full complement of PARP1 domains engaging a DNA single-strand break in the presence of HPF1 and a fragment of binding partner Timeless. Cryo-EM, single-molecule DNA dynamics, and small-angle X-ray scattering analysis indicate that PARP1 remains dynamic even when the multi-domain structure is organized on a DNA break, with the minimal catalytic region displaying high mobility relative to domains engaging damage. We propose that the organization of PARP1 domains on a DNA break releases a tethered, constitutively active catalytic region to modify molecules in a radius surrounding the DNA break site.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2025

Domain coupling in activation of a family C GPCR

Abstract The G protein-coupled metabotropic glutamate receptors form homodimers and heterodimers with highly diverse responses to glutamate and varying physiological functions. We employ molecular dynamics, single-molecule spectroscopy and hydrogen–deuterium exchange to dissect the activation pathway triggered by glutamate. We find that activation entails multiple loosely coupled steps, including formation of an agonist-bound, pre-active intermediate whose transition to active conformations forms dimerization interface contacts that set efficacy. The agonist-bound receptor populates at least two additional intermediates en route to G protein-coupling conformations. Sequential transitions into these states act as ‘gates’, which attenuate the effects of glutamate. Thus, the agonist-bound receptor is remarkably dynamic, with low occupancy of G protein-coupling conformations, providing considerable headroom for modulation by allosteric ligands. Sequence variation within the dimerization interface, as well as altered conformational coupling in receptor heterodimers, may contribute to precise decoding of glutamate signals over broad spatial and temporal scales.

Biochemistry & Molecular Biology↗
DOE OSTI2025

When do molecular polaritons behave like optical filters?

This review outlines several linear optical effects featured by molecular polaritons arising in the collective strong light–matter coupling regime. Under weak laser irradiation and when the single-molecule light–matter coupling can be neglected (often in the limit when the number of molecules per photon mode is large), we show that the excited-state molecular dynamics under collective strong coupling can be exactly replicated without the cavity using a shaped (or “filtered”) laser, whose field amplitude is enhanced by the cavity quality factor, shining on the bare molecules. As a consequence, the absorption within a cavity can be understood as the overlap between the polariton transmission and the bare molecular absorption, suggesting that polaritons act in part as optical filters. This framework demystifies and provides a straightforward explanation for a large class of experiments and theoretical models in molecular polaritonics, highlighting that the same effects can be achieved without the cavity with shaped laser pulses. With a few modifications, this simple conceptual picture can also be adapted to understand the incoherent nonlinear response of polaritonic systems. This review establishes a clear distinction between polaritonic phenomena that can be fully explained through classical linear optics and those that require a quantum electrodynamics approach. It also highlights the need to differentiate between effects that necessitate polaritons (i.e., hybrid light–matter states) and those that can occur in the weak coupling regime. Here, we further discuss that certain quantum optical effects like fluorescence can be partially described as optical filtering, whereas some others like cavity-induced Raman scattering go beyond this. Further exploration in these areas is needed to uncover novel polaritonic phenomena beyond optical filtering.

Schwennicke, Kai [University of California, San Di↗
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 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↗
NASA NTRS2002

Biosensors for DNA sequence detection

DNA biosensors are being developed as alternatives to conventional DNA microarrays. These devices couple signal transduction directly to sequence recognition. Some of the most sensitive and functional technologies use fibre optics or electrochemical sensors in combination with DNA hybridization. In a shift from sequence recognition by hybridization, two emerging single-molecule techniques read sequence composition using zero-mode waveguides or electrical impedance in nanoscale pores.

Review↗
NASA NTRS2005

Three-dimensional characterization of tethered microspheres by total internal reflection fluorescence microscopy

Tethered particle microscopy is a powerful tool to study the dynamics of DNA molecules and DNA-protein complexes in single-molecule experiments. We demonstrate that stroboscopic total internal reflection microscopy can be used to characterize the three-dimensional spatiotemporal motion of DNA-tethered particles. By calculating characteristic measures such as symmetry and time constants of the motion, well-formed tethers can be distinguished from defective ones for which the motion is dominated by aberrant surface effects. This improves the reliability of measurements on tether dynamics. For instance, in observations of protein-mediated DNA looping, loop formation is distinguished from adsorption and other nonspecific events.

Non-NASA Center↗