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Results for “single molecule spectroscopy”

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 OSTI2023

Multi-level Force-dependent Allosteric Enhancement of αE-catenin Binding to F-actin by Vinculin

Classical cadherins are transmembrane proteins whose extracellular domains link neighboring cells, and whose intracellular domains connect to the actin cytoskeleton via β-catenin and α-catenin. The cadherin-catenin complex transmits forces that drive tissue morphogenesis and wound healing. In addition, tension-dependent changes in αE-catenin conformation enables it to recruit the actin-binding protein vinculin to cell-cell junctions, which contributes to junctional strengthening. How and whether multiple cadherin-complexes cooperate to reinforce cell-cell junctions in response to load remains poorly understood. Here, we used single-molecule optical trap measurements to examine how multiple cadherin-catenin complexes interact with F-actin under load, and how this interaction is influenced by the presence of vinculin. We show that force oriented toward the (-) end of the actin filament results in mean lifetimes 3-fold longer than when force was applied towards the barbed (+) end. We also measured force-dependent actin binding by a quaternary complex comprising the cadherin-catenin complex and the vinculin head region, which cannot itself bind actin. Binding lifetimes of this quaternary complex increased as additional complexes bound F-actin, but only when load was oriented toward the (-) end. In contrast, the cadherin-catenin complex alone did not show this form of cooperativity. Furthermore, these findings reveal multi-level, force-dependent regulation that enhances the strength of the association of multiple cadherin/catenin complexes with F-actin, conferring positive feedback that may strengthen the junction and polarize F-actin to facilitate the emergence of higher-order cytoskeletal organization.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2021

Fluorescence Microscopic Investigations of Molecular Dynamics in Self–Assembled Nanostructures

Many analytical methods employ self-assembled nanostructured materials as chemical recognition media. Molecular permeation through these materials exhibits unique selectivity owing to nanoconfinement-induced enhancement of permeant–nanostructure interactions. This Personal Account introduces our efforts to investigate the detailed dynamics of single or a small number of molecules in nanostructured materials. Here, we developed new experimental and analysis approaches built upon laser-based fluorescence microscopy to measure the detailed translational and orientational dynamics of molecules diffusing in horizontally-oriented, cylindrical nanostructures, including surfactant micelles, silica mesopores, block copolymer microdomains, and bolaamphiphile-based organic nanotubes. Our studies clarified nanoscale details on the structural/chemical heterogeneity of the nanostructures, and their impacts on molecular mass transport dynamics.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2023

Single-photon detection using high-temperature cuprate superconductors

The detection of individual quanta of light is important for quantum computation, fluorescence lifetime imaging, single-molecule detection, remote sensing, correlation spectroscopy, and more. Thanks to their broadband operation, high detection efficiency, exceptional signal-to-noise ratio, and fast recovery times, superconducting nanowire single-photon detectors (SNSPDs) have become a critical component in these applications. The operation of SNSPDs based on conventional superconductors, which have a low critical temperature (T c ), requires costly and bulky cryocoolers. This motivated exploration of other superconducting materials with higher T c that would enable single-photon detection at elevated temperatures, yet this task has proven exceedingly difficult. Here we show that with proper processing, high-T c cuprate superconductors can meet this challenge. We fabricated superconducting nanowires (SNWs) out of thin flakes of Bi 2 Sr 2 CaCu2O 8+δ and La 1.55 Sr 0.45 CuO 4 /La 2 CuO 4 (LSCO-LCO) bilayer films and demonstrated their single-photon response up to 25 and 8 K, respectively. The single-photon operation is revealed through the linear scaling of the photon count rate (PCR) on the radiation power. Both of our cuprate-based SNSPDs exhibited single-photon sensitivity at the technologically-important 1.5 μm telecommunications wavelength. Our work expands the family of superconducting materials for SNSPD technology, opens the prospects of raising the temperature ceiling, and raises important questions about the underlying mechanisms of single-photon detection by unconventional superconductors.

75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗
DOE OSTI2024

Localized Plasmonic Heating for Single-Molecule DNA Rupture Measurements in Optical Tweezers

To date, studies on the thermodynamic and kinetic processes that underlie biological function and nanomachine actuation in biological- and biology-inspired molecular constructs have primarily focused on photothermal heating of ensemble systems, highlighting the need for probes that are localized within the molecular construct and capable of resolving single-molecule response. Here we present an experimental demonstration of wavelength-selective, localized heating at the single-molecule level using the surface plasmon resonance of a 15 nm gold nanoparticle (AuNP). Our approach is compatible with force-spectroscopy measurements and can be applied to studies of the single-molecule thermodynamic properties of DNA origami nanomachines as well as biomolecular complexes. We further demonstrate wavelength selectivity and establish the temperature dependence of the reaction coordinate for base-pair disruption in the shear-rupture geometry, demonstrating the utility and flexibility of this approach for both fundamental studies of local (nanometer-scale) temperature gradients and rapid and multiplexed nanomachine actuation.

77 NANOSCIENCE AND NANOTECHNOLOGY↗
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 OSTI2020

Cryogenic Correlative Single-Particle Photoluminescence Spectroscopy and Electron Tomography for Investigation of Nanomaterials

Cryogenic single-particle photoluminescence (PL) spectroscopy has been used with great success to directly observe the heterogeneous photophysical states present in a population of luminescent particles. Cryogenic electron tomography provides complementary nanometer scale structural information to PL spectroscopy, but the two techniques have not been correlated due to technical challenges. Here, we present a method for correlating single-particle information from these two powerful microscopy modalities. We simultaneously observe PL brightness, emission spectrum, and in-plane excitation dipole orientation of CdSSe/ZnS quantum dots suspended in vitreous ice. Stable and fluctuating emitters were observed, as well as a surprising splitting of the PL spectrum into two bands with an average energy separation of 80 meV. In some cases, the onset of the splitting corresponded to changes in the in-plane excitation dipole orientation. These dynamics were assigned to structures of individual quantum dots and the excitation dipoles were visualized in the context of structural features.

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

Imaging from Macro to Nanoscale: Multimodal Advances in Chemical and Biomedical Imaging

Imaging increasingly serves as a multiscale framework for linking molecular mechanisms to cellular behavior, tissue architecture, and organ phenotypes in biology and unraveling fundamental processes in chemistry, physics and materials science. This Perspective highlights recent advances in chemical and biomedical imaging across macro-, micro-, and nanoscales, using representative examples published in Chemical and Biomedical Imaging (CBMI). At the macroscale, we discuss chemically selective MRI, including endogenous and exogenous CEST strategies, together with photoacoustic imaging as a hybrid modality with functional and chemical contrast. At the microscale, we consider fluorescence, label-free optical and vibrational imaging, and selected X-ray approaches that expand sensitivity, specificity, and temporal resolution in biological and materials systems. At the nanoscale, we highlight super-resolution fluorescence microscopy, single-molecule methods, tip-enhanced Raman spectroscopy, and correlative imaging strategies that resolve local heterogeneity and molecular organization. Across scales, a common theme emerges that advances in probes, contrast mechanisms, instrumentation, and sample handling are enabling chemically informed imaging that connects molecular specificity with biological context.

multiscale imaging↗
DOE OSTI2024

Membrane lipids drive formation of KRAS4b-RAF1 RBDCRD nanoclusters on the membrane

The oncogene RAS, extensively studied for decades, presents persistent gaps in understanding, hindering the development of effective therapeutic strategies due to a lack of precise details on how RAS initiates MAPK signaling with RAF effector proteins at the plasma membrane. Recent advances in X-ray crystallography, cryo-EM, and super-resolution fluorescence microscopy offer structural and spatial insights, yet the molecular mechanisms involving protein-protein and protein-lipid interactions in RAS-mediated signaling require further characterization. This study utilizes single-molecule experimental techniques, nuclear magnetic resonance spectroscopy, and the computational Machine-Learned Modeling Infrastructure (MuMMI) to examine KRAS4b and RAF1 on a biologically relevant lipid bilayer. MuMMI captures long-timescale events while preserving detailed atomic descriptions, providing testable models for experimental validation. Both in vitro and computational studies reveal that RBDCRD binding alters KRAS lateral diffusion on the lipid bilayer, increasing cluster size and decreasing diffusion. RAS and membrane binding cause hydrophobic residues in the CRD region to penetrate the bilayer, stabilizing complexes through β-strand elongation. These cooperative interactions among lipids, KRAS4b, and RAF1 are proposed as essential for forming nanoclusters, potentially a critical step in MAP kinase signal activation.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2022

All-Inorganic Open-Framework Chalcogenides, A 3 Ga 5 S 9 · x H 2 O ( A = Rb and Cs), Exhibiting Ultrafast Uranyl Remediation and Illustrating a Novel Post-Synthetic Preparation of Open-Framework Oxychalcogenides

Fast and effective uranyl sequestration is of interest to the nuclear industry. Recently layered chalcogenide materials have demonstrated fast, selective, and efficient sorption properties towards uranyl cations and the development and investigation of new types of chalcogenide materials continues to be of interest and represents an intriguing option for uranyl remediation. Three new all-inorganic A 3 Ga 5 S 9 ·xH 2 O (A = Rb, Rb/Cs, and Cs) open-framework chalcogenides were obtained via an in-situ alkali carbonate to alkali sulfide conversion process achieved under mild hydrothermal conditions. The structures of the all-inorganic open framework chalcogenides consist of a 2-fold interpenetrated diamond-like 3D framework containing pseudo-T 3 [Ga 10 S 20 ] 10– supertetrahedra. 48% of the structural volume is occupied by A + cations and water species, as established by single-crystal X-ray diffraction (SCXRD), infrared (IR) and energy-dispersive (EDS) spectroscopies. The dynamic nature of the A + cations and water molecules within the pores was investigated via single crystal X-ray diffraction as well as by IR spectroscopy monitored H 2 O to D 2 O exchange experiments. Framework stability was probed with post-synthetic treatment of A 3 Ga 5 S 9 ·xH 2 O (A = Rb and Cs) samples in acidic solutions that resulted in the formation of the oxysulfide (A/H) 3 Ga 5 S 9–y O y ·xH 2 O (A = Rb and Cs; y = 0–1), as shown by SCXRD and IR. Ion-exchange studies on A 3 Ga 5 S 9 ·xH 2 O (A = Rb and Cs) samples were carried out utilizing a uranyl acetate solution. The presence of the UO 2 2+ species in the ion-exchanged product was supported by IR and EDS spectroscopies. Batch method ion-exchange experiments on Cs 3 Ga 5 S 9 ·xH 2 O powder demonstrated fast kinetics with 95% uranyl removal from the uranyl acetate solution during the first minute, a maximum uranyl uptake capacity of 15mg/g, and the subsequent elution of uranyl species with KCl solution. Furthermore, the porous and dynamic nature of the A 3 Ga 5 S 9 ·xH 2 O framework coupled with effective UO 2 2+ ···S 2– bonding interactions makes it a good potential sorbent for uranyl remediation from aqueous media.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2020

Single-molecule diffusometry reveals no catalysis-induced diffusion enhancement of alkaline phosphatase as proposed by FCS experiments

Significance Recent experiments have suggested that the energy released by a chemical reaction can propel its enzyme catalyst (for example, alkaline phosphatase). However, this topic remains controversial, partially due to the indirect and ensemble nature of existing measurements. Here, we used recently developed single-molecule approaches to monitor directly the motions of individual proteins in aqueous solution and find that single alkaline phosphatase enzymes do not diffuse faster under catalysis. Instead, we demonstrate that interactions between the fluorescent dye and the enzyme’s substrate can produce the signature of apparent diffusion enhancement in fluorescence correlation spectroscopy, the standard ensemble assay currently used to study enzyme diffusion and indicate that single-molecule approaches provide a more robust means to investigate diffusion at the nanoscale.

36 MATERIALS SCIENCE↗
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 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 OSTI2020

Role of dipole-forbidden autoionizing resonances in nonresonant one-color two-photon single ionization of N 2

We present an experimental and theoretical energy- and angle-resolved study on the photoionization dynamics of non-resonant one-color two-photon single valence ionization of neutral N$_2$ molecules. Using 9.3 eV photons produced via high harmonic generation and a 3-D momentum imaging spectrometer, we detect the photoelectrons and ions produced from one-color two-photon ionization in coincidence. Photoionization of N$_2$ populates the X $^2\Sigma^+_g$, A $^2\Pi_u$, and B $^2\Sigma^+_u$ ionic states of N$_2^+$, where the photoelectron angular distributions associated with the X $^2\Sigma^+_g$ and A $^2\Pi_u$ states both vary with changes in photoelectron kinetic energy of only a few hundred meV. We attribute the rapid evolution in the photoelectron angular distributions to the excitation and decay of dipole-forbidden autoionizing resonances that belong to series of different symmetries, all of which are members of the Hopfield series, and compete with the direct two-photon single ionization.

74 ATOMIC AND MOLECULAR PHYSICS↗
DOE OSTI2022

Random Walks and Sticky Surfaces: Single-Molecule Measurements of Solute Diffusion in Ethanol/Water-Filled Anodic Alumina Nanopores

Nanoporous anodic aluminum oxide (AAO) membranes are now being explored for use in advanced chemical separations, including in the dehydration of biofuels such as ethanol. Optimization of membrane performance requires an in-depth understanding of how solvent mixtures and solutes behave under nanoconfinement. In this work, the diffusion of rhodamine B (RhB) dye through 10 nm and 20 nm AAO nanopores filled with a series of ethanol/water mixtures (0 - 33% water) is explored by fluorescence correlation spectroscopy (FCS). RhB was found to diffuse through the pores by two distinct mechanisms with mean diffusion coefficients, $D_f$ and $D_s$, reflecting fast and slow diffusive motions, respectively, with values that differ by nearly two orders of magnitude. Further, both $D_f$ and $D_s$ increased with pore size and were significantly smaller than $D_b$, the RhB diffusion coefficient in bulk liquid. Mean $D_f$ values follow a composition-dependent trend that closely mimics the viscosity dependence of $D_b$. Additional slowing of fast RhB diffusion is attributed to both hydrodynamic drag and electrostatic interactions with the nanopore surface. The mean $D_s$ values exhibit a different trend with increasing water content, revealing an increase in $D_s$ and a decrease in the contributions of slow diffusion to the observed dynamics. The fluorescence time transient data used in the analysis show that the slow diffusion process is strongly hindered and likely involves frequent adsorption of RhB to the pore surfaces. These results provide new insights into the detailed molecular-level mechanisms of mass transport in nanoporous AAO membranes.

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

Charge Transport Characteristics of Molecular Electronic Junctions Studied by Transition Voltage Spectroscopy

The field of molecular electronics is prompted by tremendous opportunities for using a single-molecule and molecular monolayers as active components in integrated circuits. Until now, a wide range of molecular devices exhibiting characteristic functions, such as diodes, transistors, switches, and memory, have been demonstrated. However, a full understanding of the crucial factors that affect charge transport through molecular electronic junctions should yet be accomplished. Remarkably, recent advances in transition voltage spectroscopy (TVS) elucidate that it can provide key quantities for probing the transport characteristics of the junctions, including, for example, the position of the frontier molecular orbital energy relative to the electrode Fermi level and the strength of the molecule–electrode interactions. These parameters are known to be highly associated with charge transport behaviors in molecular systems and can then be used in the design of molecule-based devices with rationally tuned electronic properties. This article highlights the fundamental principle of TVS and then demonstrates its major applications to study the charge transport properties of molecular electronic junctions.

36 MATERIALS SCIENCE↗
DOE OSTI2025

Electrochemically Mediated Au–C(sp 2 ) Anchors for Molecular Electronics

Terminal anchor groups play a key role in the stability and electronic properties of molecular junctions. Single molecule junctions typically consist of two preinstalled terminal anchors linking organic molecules to metal electrodes. Here, in this work, we show that p -terphenyl derivatives containing only a single terminal anchor show conductance features similar to junctions with two preinstalled terminal anchors. A set of p -terphenyl derivatives with one terminal anchor was prepared using automated chemical synthesis and characterized using single molecule electronics experiments, molecular dynamics (MD) simulations, bulk electrochemistry and spectroscopy, and nonequilibrium Green’s function-density functional theory (NEGF-DFT) calculations. Our results show that 4-amino- p -terphenyl (PPP) and related analogs exhibit a well-defined high conductance state that is diminished or absent in other p-terphenyl derivatives lacking a preinstalled amine terminal anchor or fluorine or methyl substitutions at the terminal para position. However, a low conductance state is observed in all amino- p -terphenyl derivatives with one preinstalled anchor due to molecular junctions formed by noncovalent dimeric π–π stacking interactions. The observed high conductance state diminishes upon the addition of reducing agents and is restored upon the addition of an oxidizing agent. Our results suggest that the high conductance state arises due to Au–C(sp 2 ) bond formation facilitated by a single electron oxidation event at the electrode surface. A series of control experiments with different anchor groups shows that primary amines play a key role in forming Au–C bonds for molecular junctions. Overall, these results suggest that Au–C bond formation gives rise to high conductance pathways in organic molecules containing only one preinstalled terminal anchor. Insights from this work can be leveraged in the design of molecular electronic devices, particularly in understanding the mechanisms of molecular binding and junction formation.

charge transport↗
DOE OSTI2022

Phosphorothioate-Based Site-Specific Labeling of Large RNAs for Structural and Dynamic Studies

Pulsed electron-electron double resonance (PELDOR) spectroscopy, X-ray scattering interferometry (XSI), and single-molecule Forster resonance energy transfer (smFRET) are molecular rulers that provide inter- or intramolecular pair-wise distance distributions in the nanometer range, thus being ideally suitable for structural and dynamic studies of biomolecules including RNAs. The prerequisite for such applications requires site-specific labeling of biomolecules with spin labels, gold nanoparticles, and fluorescent tags, respectively. Recently, site-specific labeling of large RNAs has been achieved by a combination of transcription of an expanded genetic alphabet containing A-T/G-C base pairs and NaM-TPT3 unnatural base pair (UBP) with posttranscriptional modifications at UBP bases by click chemistry or amine-NHS ester reactions. However, due to the bulky sizes of functional groups or labeling probes used, such strategies might cause structural perturbation and decrease the accuracy of distance measurements. Here, we synthesize an a-thiophosphorylated variant of rTPT3TP (rTPT3aS), which allows for post-transcriptional site-specific labeling of large RNAs at the internal a-phosphate backbone via maleimide-modified probes. Subsequent PELDOR, XSI, and smFRET measurements result in narrower distance distributions than labeling at the TPT3 base. The presented strategy provides a new route to empower the molecular rulers for structural and dynamic studies of large RNA and its complex.

59 BASIC BIOLOGICAL SCIENCES↗