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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 181 records · Page 10
All sourcesNASA NTRSDOE OSTI
DOE OSTI2021

Orienting an Organic Semiconductor into DNA 3D Arrays by Covalent Bonds

We report a quasi-one-dimensional organic semiconductor, hepta(p-phenylene vinylene) (HPV), was incorporated into a DNA tensegrity triangle motif using a covalent strategy. 3D arrays were self-assembled from an HPV-DNA pseudo-rhombohedron edge by rational design and characterized by X-ray diffraction. Templated by the DNA motif, HPV molecules exist as single-molecule fluorescence emitters at the concentration of 8 mM within the crystal lattice. The anisotropic fluorescence emission from HPV-DNA crystals indicates HPV molecules are well aligned in the macroscopic 3D DNA lattices. Sophisticated nanodevices and functional materials constructed from DNA can be developed from this strategy by addressing functional components with molecular accuracy.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2022

Planar 2D wireframe DNA origami

Two-dimensional (2D) DNA origami is widely used for applications ranging from excitonics to single-molecule biophysics. Conventional, single-layer 2D DNA origami exhibits flexibility and curvature in solution; however, that may limit its suitability as a 2D structural template. In contrast, 2D wireframe DNA origami rendered with six-helix bundle edges offers local control over duplex orientations with enhanced in-plane rigidity. Here, we investigate the 3D structure of these assemblies using cryo–electron microscopy (cryo-EM). 3D reconstructions reveal a high degree of planarity and homogeneity in solution for polygonal objects with and without internal mesh, enabling 10-Å resolution for a triangle. Coarse-grained simulations were in agreement with cryo-EM data, offering molecular structural insight into this class of 2D DNA origami. Our results suggest that these assemblies may be valuable for 2D material applications and geometries that require high structural fidelity together with local control over duplex orientations, rather than parallel duplex assembly.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2025

Phycobilisome core architecture influences photoprotective quenching by the Orange Carotenoid Protein

Photosynthetic organisms rely on sophisticated photoprotective mechanisms to prevent oxidative damage under high or fluctuating solar illumination. Cyanobacteria, which have evolved a unique, water-soluble light-harvesting complex—the phycobilisome—achieve photoprotection through a photoactivatable quencher called the Orange Carotenoid Protein (OCP). Phycobilisomes are highly symmetric and modular, formed by hierarchical assembly of conserved subunits into diverse geometries ranging from simple bundles to elaborate fan- or bouquet-like macromolecular architectures. Although OCP is known to provide photoprotection across species of cyanobacteria with different phycobilisome structures, it is not known whether or how these structural variations relate to changes in the photoprotective function of OCP. For example, OCP was recently discovered to bind as a dimer at two specific instances of an abundant structural motif on the tricylindrical phycobilisome of Synechocystis sp. PCC 6803, yet these sites are sterically inaccessible on a more common pentacylindrical phycobilisome ( Anabaena sp. PCC 7120). To understand how structural modularity and binding specificity contribute to conservation of OCP binding sites and function across different phycobilisome architectures, here we compare experimentally measured photophysical states accessible to these prototypical tricylindrical and pentacylindrical phycobilisomes, with and without OCP, at the single-molecule level. Together with Monte Carlo simulations of exciton transfer in OCP-quenched phycobilisomes, our results suggest that OCP binds at distinct and specific sites in each type of phycobilisome, yet provides nearly identical quenching strength to both phycobilisomes. Our findings highlight the utility of modular phycobilisome structures in balancing robust conservation of photoprotective function with adaptability of site-specific binding across species.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2022

Ligand-induced transmembrane conformational coupling in monomeric $\mathrm{EGFR}$

Single pass cell surface receptors regulate cellular processes by transmitting ligand-encoded signals across the plasma membrane via changes to their extracellular and intracellular conformations. This transmembrane signaling is generally initiated by ligand binding to the receptors in their monomeric form. While subsequent receptor-receptor interactions are established as key aspects of transmembrane signaling, the contribution of monomeric receptors has been challenging to isolate due to the complexity and ligand-dependence of these interactions. By combining membrane nanodiscs produced with cell-free expression, single-molecule Förster Resonance Energy Transfer measurements, and molecular dynamics simulations, we report that ligand binding induces intracellular conformational changes within monomeric, full-length epidermal growth factor receptor (EGFR). Our observations establish the existence of extracellular/intracellular conformational coupling within a single receptor molecule. We implicate a series of electrostatic interactions in the conformational coupling and find the coupling is inhibited by targeted therapeutics and mutations that also inhibit phosphorylation in cells. Collectively, these results introduce a facile mechanism to link the extracellular and intracellular regions through the single transmembrane helix of monomeric EGFR, and raise the possibility that intramolecular transmembrane conformational changes upon ligand binding are common to single-pass membrane proteins.

59 BASIC BIOLOGICAL SCIENCES↗
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

Solution-phase sample-averaged single-particle spectroscopy of quantum emitters with femtosecond resolution

Here, the development of many optical quantum technologies depends on the availability of solid-state single quantum emitters with near-perfect optical coherence. However, a standing issue that limits systematic improvement is the significant sample heterogeneity and lack of mechanistic understanding of microscopic energy flow at the single emitter level and ultrafast timescales. Here we develop solution-phase single-particle pump-probe spectroscopy with photon correlation detection that captures sample-averaged dynamics in single molecules and/or defect states with unprecedented clarity at femtosecond resolution. We apply this technique to single quantum emitters in two-dimensional hexagonal boron nitride, which suffers from significant heterogeneity and low quantum efficiency. From millisecond to nanosecond timescales, the translation diffusion, metastable-state-related bunching shoulders, rotational dynamics, and antibunching features are disentangled by their distinct photon-correlation timescales, which collectively quantify the normalized two-photon emission quantum yield. Leveraging its femtosecond resolution, spectral selectivity and ultralow noise (two orders of magnitude improvement over solid-state methods), we visualize electron-phonon coupling in the time domain at the single defect level, and discover the acceleration of polaronic formation driven by multi-electron excitation. Corroborated with results from a theoretical polaron model, we show how this translates to sample-averaged photon fidelity characterization of cascaded emission efficiency and optical decoherence time. Our work provides a framework for ultrafast spectroscopy in single emitters, molecules, or defects prone to photoluminescence intermittency and heterogeneity, opening new avenues of extreme-scale characterization and synthetic improvements for quantum information applications.

36 MATERIALS SCIENCE↗
DOE OSTI2021

Spatially resolved photoluminescence brightening in individual single-walled carbon nanotubes

Single-molecule microscopy was used to image photoluminescence (PL) brightening of individual sodium-dodecyl-sulfate (SDS)-wrapped single-walled carbon nanotubes (SWCNTs) upon the addition of dithiothreitol (DTT). PL enhancement varied for each nanotube (NT), with some brightening by 16% and others by a factor of about 7. Interestingly, NTs that displayed lower initial QY values showed the largest increases in PL enhancement. SDS-SWCNTs longer than the diffraction limit were studied in order to spatially resolve the brightening phenomenon. Quite unexpectedly, a uniform, single-step PL brightening along the NT was consistently observed, suggesting that the PL enhancement is the result of a non-localized process. Furthermore, the even PL brightening seen over SWCNTs that are micrometers long implies that single point defect sites, which are known to be largely responsible for exciton nonradiative decay, play no significant role in the brightening process. Interestingly, affixing the SWCNT strongly to the substrate surface mitigated the PL brightening response, consistent with a hypothesis that surfactant reorganization upon the addition of DTT is responsible for exciton PL brightening.

71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗
DOE OSTI2023

Attosecond probing and control of charge migration in carbon-chain molecule

In quantum mechanics, when an electron is quickly ripped off from a molecule, a superposition of new eigenstates of the cation creates an electron wave packet that governs the charge flow inside, which has been called charge migration (CM). Experimentally, extracting such dynamics at its natural (attosecond) timescale is quite difficult. We report the first such experiment in a linear carbon-chain molecule, butadiyne (C 4 H 2 ), via high-harmonic spectroscopy (HHS). By employing advanced theoretical and computational tools, we showed that the wave packet and the CM of a single molecule are reconstructed from the harmonic spectra for each fixed-in-space angle of the molecule. For this one-dimensional molecule, we calculate the center of charge $\langle$ x $\rangle$ ( t ) to obtain v cm , to quantify the migration speed and how it depends on the orientation angle. The findings also uncover how the electron dynamics at the first few tens to hundreds of attoseconds depends on molecular structure. The method can be extended to other molecules where the HHS technique can be employed.

72 PHYSICS OF ELEMENTARY PARTICLES AND FIELDS↗
DOE OSTI2023

Simulating the Excited-State Dynamics of Polaritons with Ab Initio Multiple Spawning

Over the past decade, there has been a growth of interest in polaritonic chemistry, where the formation of hybrid light–matter states (polaritons) can alter the course of photochemical reactions. These hybrid states are created by strong coupling between molecules and photons in resonant optical cavities and can even occur in the absence of light when the molecule is strongly coupled with the electromagnetic fluctuations of the vacuum field. Here, we present a first-principles model to simulate nonadiabatic dynamics of such polaritonic states inside optical cavities by leveraging graphical processing units (GPUs). Our first implementation of this model is specialized for a single molecule coupled to a single-photon mode confined inside the optical cavity but with any number of excited states computed using complete active space configuration interaction (CASCI) and a Jaynes–Cummings-type Hamiltonian. Using this model, we have simulated the excited-state dynamics of a single salicylideneaniline (SA) molecule strongly coupled to a cavity photon with the ab initio multiple spawning (AIMS) method. We demonstrate how the branching ratios of the photodeactivation pathways for this molecule can be manipulated by coupling to the cavity. We also show how one can stop the photoreaction from happening inside of an optical cavity. Finally, we also investigate cavity-based control of the ordering of two excited states (one optically bright and the other optically dark) inside a cavity for a set of molecules, where the dark and bright states are close in energy.

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

Quantitative multiplexed analysis of gene and protein expression patterns in Yarrowia lipolytica

In this report, we present coordinated observations of protein and mRNA transcript counts at the single-cell level in the oleaginous yeast model Yarrowia lipolytica. The transcription factor Xbp1p regulates entry into a quiescent state, representing a shift of resources to sequestration of nutrients rather than cell division. We observed the responses of wild-type and Δxbp1 cells to protein (by fluorescence) and transcript quantification and localization at both single-cell and population-averaged levels. Data were collected via single-molecule fluorescence in situ hybridization (smFISH) and qPCR under nitrogen depletion, a condition that drives lipid accumulation. These techniques reveal a complex and heterogeneous population of Xbp1p dynamics and downstream regulation. Our findings highlight the need for single-cell resolution analyses to describe cellular dynamics and regulatory processes.

Yarrowia lipolytica↗
DOE OSTI2024

A Nanosized {Ni II 18 } Cluster with a ‘Flying Saucer’ Topology Exhibiting Slow Relaxation of Magnetisation Phenomena at Both 15 K and 1.3 K

A high-nuclearity {Ni 18 } complex (1) with a unique ‘flying saucer’ motif has been prepared from the organic chelate, α-methyl-2-pyridine-methanol (mpmH), in conjunction with bridging azido (N 3 - ) and peroxido (O 2 2- ) ligands. Magnetic susceptibility measurements revealed the presence of both ferro- and antiferromagnetic exchange interactions between the metal centres in 1, and the stabilization of spin states with appreciable S values at two different temperature regimes. The end-on bridging azido and alkoxido groups are in all likelihood the ferromagnetic mediators, while the η 3 :η 3 :μ 6 -bridging peroxides most likely promote the antiparallel alignment of the metals’ spin vectors, yielding an overall non-zero spin ground state for the centrosymmetric compound 1. Furthermore, the {Ni 18 } nanosized cluster behaves as a single-molecule magnet, exhibiting magnetic hysteresis at low temperatures and two relaxation processes at 15 K and 1.3 K, a very rare phenomenon in polynuclear magnetic 3d-metal clusters.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2026

A Unified Analytical Method Greenness Score ( uAMGS ) Quantifies How Microscopic Imaging Is Greener Than Conventional Liquid Chromatography

Green chemistry is a set of principles for assessing, developing, and implementing methods that are safer, more efficient, and less detrimental to the environment. The analytical method greenness score (AMGS) is one of many metrics that attempt to evaluate traditional liquid chromatography (LC) based on the energy consumption of the instrument and the safety, health risks, and environmental impact of the solvents employed. Unfortunately, in practice, the AMGS is primarily focused on traditional separation methods in the pharmaceutical industry and is not amenable to cutting-edge separation science, including miniaturization. To broaden this scope, the unified Analytical Method Greenness Score (uAMGS) is presented here, which clarifies and expands on the underlying mathematics and incorporates both dimensional and uncertainty analysis, enabling its application to a broader range of analytical techniques. The uAMGS is used to compare the greenness of two distinct methods: single-molecule microscopy (SMM) and high-performance liquid chromatography (HPLC), which were used to collect equivalent data. uAMGS determines that SMM is significantly greener than HPLC due primarily to decreased solvent consumption. Overall, the uAMGS should allow chemists ranging from undergraduates to industrial PhDs to assess the greenness of a wide range of separations.

chemical separations↗
DOE OSTI2020

Biased localization of actin binding proteins by actin filament conformation

The assembly of actin filaments into distinct cytoskeletal structures plays a critical role in cell physiology, but how proteins localize differentially to these structures within a shared cytoplasm remains unclear. Here, we show that the actin-binding domains of accessory proteins can be sensitive to filament conformational changes. Using a combination of live cell imaging and in vitro single molecule binding measurements, we show that tandem calponin homology domains (CH1–CH2) can be mutated to preferentially bind actin networks at the front or rear of motile cells. We demonstrate that the binding kinetics of CH1–CH2 domain mutants varies as actin filament conformation is altered by perturbations that include stabilizing drugs and other binding proteins. These findings suggest that conformational changes of actin filaments in cells could help to direct accessory binding proteins to different actin cytoskeletal structures through a biophysical feedback loop.

42 ENGINEERING↗
DOE OSTI2023

Structural and dynamic mechanisms for coupled folding and tRNA recognition of a translational T-box riboswitch

T-box riboswitches are unique riboregulators where gene regulation is mediated through interactions between two highly structured RNAs. Despite extensive structural insights, how RNA-RNA interactions drive the folding and structural transitions of T-box to achieve functional conformations remains unclear. Here, by combining SAXS, single-molecule FRET and computational modeling, we elaborate the folding energy landscape of a translational T-box aptamer consisting of stems I, II and IIA/B, which Mg 2+ -induced global folding and tRNA binding are cooperatively coupled. smFRET measurements reveal that high Mg 2+ stabilizes IIA/B and its stacking on II, which drives the pre-docking of I and II into a competent conformation, subsequent tRNA binding promotes docking of I and II to form a high-affinity tRNA binding groove, of which the essentiality of IIA/B and S-turn in II is substantiated with mutational analysis. We highlight a delicate balance among Mg 2+ , the intra- and intermolecular RNA-RNA interactions in modulating RNA folding and function.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2023

Direct observation of tRNA-chaperoned folding of a dynamic mRNA ensemble

T-box riboswitches are multi-domain noncoding RNAs that surveil individual amino acid availabilities in most Gram-positive bacteria. T-boxes directly bind specific tRNAs, query their aminoacylation status to detect starvation, and feedback control the transcription or translation of downstream amino-acid metabolic genes. Most T-boxes rapidly recruit their cognate tRNA ligands through an intricate three-way stem I-stem II-tRNA interaction, whose establishment is not understood. Using single-molecule FRET, SAXS, and time-resolved fluorescence, we find that the free T-box RNA assumes a broad distribution of open, semi-open, and closed conformations that only slowly interconvert. tRNA directly binds all three conformers with distinct kinetics, triggers nearly instantaneous collapses of the open conformations, and returns the T-box RNA to their pre-binding conformations upon dissociation. This scissors-like dynamic behavior is enabled by a hinge-like pseudoknot domain which poises the T-box for rapid tRNA-induced domain closure. This study reveals tRNA-chaperoned folding of flexible, multi-domain mRNAs through a Venus flytrap-like mechanism.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2024

Hub stability in the calcium calmodulin-dependent protein kinase II

The calcium calmodulin protein kinase II (CaMKII) is a multi-subunit ring assembly with a central hub formed by the association domains. There is evidence for hub polymorphism between and within CaMKII isoforms, but the link between polymorphism and subunit exchange has not been resolved. Here, we present near-atomic resolution cryogenic electron microscopy (cryo-EM) structures revealing that hubs from the α and β isoforms, either standalone or within an β holoenzyme, coexist as 12 and 14 subunit assemblies. Single-molecule fluorescence microscopy of Venus-tagged holoenzymes detects intermediate assemblies and progressive dimer loss due to intrinsic holoenzyme lability, and holoenzyme disassembly into dimers upon mutagenesis of a conserved inter-domain contact. Molecular dynamics (MD) simulations show the flexibility of 4-subunit precursors, extracted in-silico from the β hub polymorphs, encompassing the curvature of both polymorphs. The MD explains how an open hub structure also obtained from the β holoenzyme sample could be created by dimer loss and analysis of its cryo-EM dataset reveals how the gap could open further. An assembly model, considering dimer concentration dependence and strain differences between polymorphs, proposes a mechanism for intrinsic hub lability to fine-tune the stoichiometry of αβ heterooligomers for their dynamic localization within synapses in neurons.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2023

Homo- and hetero-dimeric subunit interactions set affinity and efficacy in metabotropic glutamate receptors

Metabotropic glutamate receptors (mGluRs) are dimeric class C G-protein–coupled receptors that operate in glia and neurons. Glutamate affinity and efficacy vary greatly between the eight mGluRs. The molecular basis of this diversity is not understood. We used single-molecule fluorescence energy transfer to monitor the structural rearrangements of activation in the mGluR ligand binding domain (LBD). In saturating glutamate, group II homodimers fully occupy the activated LBD conformation (full efficacy) but homodimers of group III mGluRs do not. Strikingly, the reduced efficacy of Group III homodimers does not arise from differences in the glutamate binding pocket but, instead, from interactions within the extracellular dimerization interface that impede active state occupancy. By contrast, the functionally boosted mGluR II/III heterodimers lack these interface ‘brakes’ to activation and heterodimer asymmetry in the flexibility of a disulfide loop connecting LBDs greatly favors occupancy of the activated conformation. Our results suggest that dimerization interface interactions generate substantial functional diversity by differentially stabilizing the activated conformation. This diversity may optimize mGluR responsiveness for the distinct spatio-temporal profiles of synaptic versus extrasynaptic glutamate.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2024

Adsorption and Solvation Modulate Rhodamine B Diffusion in Ethanol/Water-Filled Anodic Alumina Nanopores

Confinement of solvents and solutes within nanoporous materials frequently leads to the emergence of unique mass transport behaviors that, once fully understood, may lead to improved chemical separations. Here, the diffusion of Rhodamine B (RhB) dye within 10 and 20 nm diameter anodic aluminum oxide (AAO) nanopores filled with binary ethanol/water mixtures is investigated. Mixture compositions spanning from pure ethanol to pure water are employed. The results of confocal fluorescence correlation spectroscopy studies reveal that RhB diffusion occurs by a two-component mechanism comprising composition-dependent fast and slow motions, characterized by diffusion coefficients D f and D s . The results are consistent with those of previous studies performed under more limited conditions [J. Phys. Chem. C, 2023, 127, 411-420]. The fast component scales with mixture viscosity and is assigned to hindered bulk-like diffusion in central pore regions. Slow diffusion likely involves adsorption of RhB to the pore surface and may be described by a desorption mediated mechanism. The occurrence of RhB adsorption to the AAO surface is verified at the single-molecule level by wide-field fluorescence imaging of membrane cross-sectional surfaces. Unique composition dependent trends in the autocorrelation amplitude and in D s that mimic bulk RhB solubility are revealed. D s is found to be smallest in pure ethanol and pure water and largest in intermediate mixtures. These results suggest that RhB surface adsorption is strongest in the pure liquids and weakest in mixtures of intermediate composition, where the dye is least soluble, and most soluble, respectively. As a result, molecular dynamics simulations reveal that a water layer appears on the pore surface under most conditions, while RhB is solvated primarily by ethanol. The composition dependence of RhB diffusion is concluded to reflect its solvation dependent interactions with the pore walls.

36 MATERIALS SCIENCE↗