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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 91 records · Page 5
All sourcesNASA NTRSDOE OSTI
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 OSTI2023

Strongly coupled intermediate electronic states in one-color two-photon single valence ionization of O 2

Here, we present an experimental and theoretical energy- and angle-resolved investigation on the non-dissociative photoionization dynamics of near-resonant, one-color, two-photon, single valence ionization of neutral O 2 molecules. Using 9.3 eV femtosecond pulses produced via high harmonic generation and a 3-D momentum imaging spectrometer, we detect the photoelectrons and O$^{+}_{2}$ cations produced from one-color, two-photon ionization in coincidence. The measured and calculated photoelectron angular distributions show agreement, which indicates that a superposition of two intermediate electronic states is dominantly involved and that wavepacket motion on those near-resonantly populated intermediate states does not play a significant role in the measured two-photon ionization dynamics. Here, we find greater utility in the diabatic representation compared to the adiabatic representation, where invoking a single valence-character diabat is sufficient to describe the underlying two-photon ionization mechanism.

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

A multi-material platform for imaging of single cell-cell junctions under tensile load fabricated with two-photon polymerization

We previously reported a single-cell adhesion micro tensile tester (SCAμTT) fabricated from IP-S photoresin with two-photon polymerization (TPP) for investigating the mechanics of a single cell-cell junction under defined tensile loading. A major limitation of the platform is the autofluorescence of IP-S, the photoresin for TPP fabrication, which significantly increases background signal and makes fluorescent imaging of stretched cells difficult. In this study, we report the design and fabrication of a new SCAμTT platform that mitigates autofluorescence and demonstrate its capability in imaging a single cell pair as its mutual junction is stretched. By employing a two-material design using IP-S and IP-Visio, a photoresin with reduced autofluorescence, we show a significant reduction in autofluorescence of the platform. Further, by integrating apertures onto the substrate with a gold coating, the influence of autofluorescence on imaging is almost completely mitigated. With this new platform, we demonstrate the ability to image a pair of epithelial cells as they are stretched up to 250% strain, allowing us to observe junction rupture and F-actin retraction while simultaneously recording the accumulation of over 800 kPa of stress in the junction. In conclusion, the platform and methodology presented here can potentially enable detailed investigation of the mechanics of and mechanotransduction in cell-cell junctions and improve the design of other TPP platforms in mechanobiology applications.

Autofluorescence↗
DOE OSTI2024

In situ visualisation of zeolite anisotropic framework flexibility during catalysis

Zeolites exhibit framework flexibility driving their chemical and catalytic properties. Since the zeolitic pores are extremely small, a slight strain generated in the crystal induces compelling changes in shape, connectivity, accessibility, and the framework chemical properties. These modifications affected the adsorption and desorption of reactants/products and the diffusion within the channels during reaction. Using in situ 3D Bragg coherent X-ray diffraction imaging, we unveil the dynamics of the zeolite structure during catalysis, contraction and/or expansion of its framework also known as zeolite framework flexibility. Here, we imaged three-dimensionally a single faujasite zeolite crystal during the ethanol dehydration reaction revealing anisotropic lattice dynamics simultaneously to guest molecules formation. Understanding zeolite flexibility could permit to tune zeolites properties towards potentially higher adsorption and selectivity.

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

Cooperative actin filament nucleation by the Arp2/3 complex and formins maintains the homeostatic cortical array in Arabidopsis epidermal cells

Abstract Precise control over how and where actin filaments are created leads to the construction of unique cytoskeletal arrays within a common cytoplasm. Actin filament nucleators are key players in this activity and include the conserved actin-related protein 2/3 (Arp2/3) complex as well as a large family of formins. In some eukaryotic cells, these nucleators compete for a common pool of actin monomers and loss of one favors the activity of the other. To test whether this mechanism is conserved, we combined the ability to image single filament dynamics in the homeostatic cortical actin array of living Arabidopsis (Arabidopsis thaliana) epidermal cells with genetic and/or small molecule inhibitor approaches to stably or acutely disrupt nucleator activity. We found that Arp2/3 mutants or acute CK-666 treatment markedly reduced the frequency of side-branched nucleation events as well as overall actin filament abundance. We also confirmed that plant formins contribute to side-branched filament nucleation in vivo. Surprisingly, simultaneous inhibition of both classes of nucleator increased overall actin filament abundance and enhanced the frequency of de novo nucleation events by an unknown mechanism. Collectively, our findings suggest that multiple actin nucleation mechanisms cooperate to generate and maintain the homeostatic cortical array of plant epidermal cells.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2021

Application of transport-based metric for continuous interpolation between cryo-EM density maps

Cryogenic electron microscopy (cryo-EM) has become widely used for the past few years in structural biology, to collect single images of macromolecules "frozen in time". As this technique facilitates the identification of multiple conformational states adopted by the same molecule, a direct product of it is a set of 3D volumes, also called EM maps. To gain more insights on the possible mechanisms that govern transitions between different states, and hence the mode of action of a molecule, we recently introduced a bioinformatic tool that interpolates and generates morphing trajectories joining two given EM maps. This tool is based on recent advances made in optimal transport, that allow efficient evaluation of Wasserstein barycenters of 3D shapes. As the overall performance of the method depends on various key parameters, including the sensitivity of the regularization parameter, we performed various numerical experiments to demonstrate how MorphOT can be applied in different contexts and settings. Finally, we discuss current limitations and further potential connections between other optimal transport theories and the conformational heterogeneity problem inherent with cryo-EM data.

3D shapes↗
DOE OSTI2020

LoTToR: An Algorithm for Missing-Wedge Correction of the Low-Tilt Tomographic 3D Reconstruction of a Single-Molecule Structure

A single-molecule three-dimensional (3D) structure is essential for understanding the thermal vibrations and dynamics as well as the conformational changes during the chemical reaction of macromolecules. Individual-particle electron tomography (IPET) is an approach for obtaining a snap-shot 3D structure of an individual macromolecule particle by aligning the tilt series of electron tomographic (ET) images of a targeted particle through a focused iterative 3D reconstruction method. The method can reduce the influence on the 3D reconstruction from large-scale image distortion and deformation. Due to the mechanical tilt limitation, 3D reconstruction often contains missing-wedge artifacts, presented as elongation and an anisotropic resolution. Here, we report a post-processing method to correct the missing-wedge artifact. This low-tilt tomographic reconstruction (LoTToR) method contains a model-free iteration process under a set of constraints in real and reciprocal spaces. A proof of concept is conducted by using the LoTToR on a phantom, i.e., a simulated 3D reconstruction from a low-tilt series of images, including that within a tilt range of ±15°. The method is validated by using both negative-staining (NS) and cryo-electron tomography (cryo-ET) experimental data. A significantly reduced missing-wedge artifact verifies the capability of LoTToR, suggesting a new tool to support the future study of macromolecular dynamics, fluctuation and chemical activity from the viewpoint of single-molecule 3D structure determination.

97 MATHEMATICS AND COMPUTING↗
DOE OSTI2020

Toward nanoscale molecular mass spectrometry imaging via physically constrained machine learning on co-registered multimodal data

Mass spectrometry imaging (MSI) plays a pivotal role in investigating the chemical nature of complex systems that underly our understanding in biology and medicine. Multiple fields of life science such as proteomics, lipidomics and metabolomics benefit from the ability to simultaneously identify molecules and pinpoint their distribution across a sample. However, achieving the necessary submicron spatial resolution to distinguish chemical differences between individual cells and generating intact molecular spectra is still a challenge with any single imaging approach. Here, we developed an approach that combines two MSI techniques, matrix-assisted laser desorption/ionization (MALDI) and time-of-flight secondary ion mass spectrometry (ToF-SIMS), one with low spatial resolution but intact molecular spectra and the other with nanometer spatial resolution but fragmented molecular signatures, to predict molecular MSI spectra with submicron spatial resolution. The known relationships between the two MSI channels of information are enforced via a physically constrained machine-learning approach and directly incorporated in the data processing. We demonstrate the robustness of this method by generating intact molecular MALDI-type spectra and chemical maps at ToF-SIMS resolution when imaging mouse brain thin tissue sections. This approach can be readily adopted for other types of bioimaging where physical relationships between methods have to be considered to boost the confidence in the reconstruction product.

97 MATHEMATICS AND COMPUTING↗
DOE OSTI2023

Single- and multi-photon-induced ultraviolet excitation and photodissociation of CH 3 I probed by coincident ion momentum imaging

The UV-induced photodissociation dynamics of iodomethane (CH 3 I) in its A-band are investigated by time-resolved coincident ion momentum imaging using strong-field ionization as a probe. The delay-dependent kinetic energy distribution of the photofragments resulting from double ionization of the molecule maps the cleavage of the carbon–iodine bond and shows how the existence of a potential well in the di-cationic potential energy surfaces shapes the observed distribution at small pump–probe delays. Furthermore, the competition between single- and multi-photon excitation and ionization of the molecule is studied as a function of the intensity of the UV-pump laser pulse. Two-photon excitation to Rydberg states is identified by tracking the transformation of the delay-dependent singly-charged iodomethane yield from a pure Gaussian distribution at low intensity to a Gaussian with an exponentially decaying tail at higher intensities. In conclusion, dissociative ionization induced by absorption of three UV photons is resolved as an additional delay-dependent feature in the kinetic energy of the fragment ions detected in coincidence.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2021

Low-dose high-resolution $\mathrm{TOF}$-$\mathrm{PET}$ using ionization-activated multi-state low-$\mathrm{Z}$ detector media

We propose PET scanners using low atomic number media that undergo a persistent local change of state along the paths of the Compton recoil electrons. Measurement of the individual scattering locations and angles, deposited energies, and recoil electron directions allows using the kinematical constraints of the 2-body Compton scattering process to perform a statistical time-ordering of the scatterings, with a high probability of precisely identifying where the gamma first interacted in the detector. In these cases the Line-of-Response is measured with high resolution, determined by the underlying physics processes and not the detector segmentation. There are multiple such media that act through different mechanisms. As an example in which the change of state is quantum-mechanical through a change in molecular configuration, rather than thermodynamic, as in a bubble chamber, we present simulations of a two-state photoswitchable organic dye, a ‘Switchillator’, that is activated to a fluorescent-capable state by the ionization of the recoil electrons. The activated state is persistent, and can be optically excited multiple times to image individual activated molecules. Energy resolution is provided by counting the activated molecules. Location along the LOR is implemented by large-area time-of-flight MCP-PMT photodetectors with single photon time resolution in the tens of ps and sub-mm spatial resolution. Simulations indicate a large reduction of dose.

46 INSTRUMENTATION RELATED TO NUCLEAR SCIENCE AND ↗
DOE OSTI2025

Spectroscopic and Computational Studies of Spin-Orbit Coupling of Lanthanide Oxides

Spin-orbit (SO) coupling makes it possible for spin forbidden transitions or reactions within non-relativistic quantum theory feasible. Thus, quantification of such interactions has important implications in photophysics and chemical catalysis. This work aims to quantify SO interactions using lanthanide (Ln) oxides as target molecular systems. Through these systems, we examine the impact on the SO coupling by electron configurations and 4f orbital occupancies of Ln elements and sizes of the metal oxides. By examining these factors, we explore how SO coupling is affected by the number of Ln 4f electrons for a given size of molecules and if the Ln 4f orbitals remain atomic in nature in these small clusters. Ln oxides are produced in laser ablation molecular beams, identified with time-of-fight mass spectrometry, and characterized with laser spectroscopy and relativistic quantum chemical computations. Spectroscopic measurements include mass-analyzed threshold ionization (MATI), zero electron kinetic energy, and slow electron velocity-map imaging spectroscopies. Relativistic computations treat scalar relativistic corrections, electron correlations, and SO interactions. The main results are SO terms and energies of the neutral molecules and singly charged cations, ionization energies of the neutral species, metal-metal and metal-oxygen vibrational frequencies of the ions and, in some cases, neutrals as well, and charge effects on the bonding and structures.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2021

Selecting XFEL single-particle snapshots by geometric machine learning

A promising new route for structural biology is single-particle imaging with an X-ray Free-Electron Laser (XFEL). This method has the advantage that the samples do not require crystallization and can be examined at room temperature. However, high-resolution structures can only be obtained from a sufficiently large number of diffraction patterns of individual molecules, so-called single particles. Here, we present a method that allows for efficient identification of single particles in very large XFEL datasets, operates at low signal levels, and is tolerant to background. This method uses supervised Geometric Machine Learning (GML) to extract low-dimensional feature vectors from a training dataset, fuse test datasets into the feature space of training datasets, and separate the data into binary distributions of “single particles” and “non-single particles.” As a proof of principle, we tested simulated and experimental datasets of the Coliphage PR772 virus. We created a training dataset and classified three types of test datasets: First, a noise-free simulated test dataset, which gave near perfect separation. Second, simulated test datasets that were modified to reflect different levels of photon counts and background noise. These modified datasets were used to quantify the predictive limits of our approach. Third, an experimental dataset collected at the Stanford Linear Accelerator Center. The single-particle identification for this experimental dataset was compared with previously published results and it was found that GML covers a wide photon-count range, outperforming other single-particle identification methods. Moreover, a major advantage of GML is its ability to retrieve single particles in the presence of structural variability.

71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗
DOE OSTI2024

Single-colony MALDI mass spectrometry imaging reveals spatial differences in metabolite abundance between natural and cultured Trichodesmium morphotypes

Trichodesmium, a globally significant N 2 -fixing marine cyanobacterium, forms extensive surface blooms in nutrient-poor ocean regions. These blooms consist of a dynamic assemblage of Trichodesmium species that form distinct colony morphotypes and are inhabited by diverse microorganisms. Trichodesmium colony morphotypes vary in ecological niche, nutrient uptake, and organic molecule release, differentially impacting ocean carbon and nitrogen biogeochemical cycles. Here, we assessed the poorly studied spatial abundance of metabolites within and between three morphologically distinct Trichodesmium colonies collected from the Red Sea. We also compared these results with two morphotypes of the cultivable Trichodesmium strain IMS101. Using matrix-assisted laser desorption/ionization (MALDI) mass spectrometry imaging (MSI) coupled with liquid extraction surface analysis (LESA) tandem mass spectrometry (MS2), we identified and localized a wide range of small metabolites associated with single-colony Trichodesmium morphotypes. Our untargeted MALDI-MSI approach revealed 80 unique features (metabolites) shared between Trichodesmium morphotypes. Discrimination analysis showed spatial variations in 57 shared metabolites, accounting for 62% of the observed variation between morphotypes. The greatest variations in metabolite abundance were observed between the cultured morphotypes compared to the natural colony morphotypes, suggesting substantial differences in metabolite production between the cultivable strain IMS101 and the naturally occurring colony morphotypes that the cultivable strain is meant to represent. This study highlights the variations in metabolite abundance between natural and cultured Trichodesmium morphotypes and provides valuable insights into metabolites common to morphologically distinct Trichodesmium colonies, offering a foundation for future targeted metabolomic investigations.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2024

Fluorescence imaging of individual ions and molecules in pressurized noble gases for barium tagging in 136Xe

Abstract The imaging of individual Ba 2+ ions in high pressure xenon gas is one possible way to attain background-free sensitivity to neutrinoless double beta decay and hence establish the Majorana nature of the neutrino. In this paper we demonstrate selective single Ba 2+ ion imaging inside a high-pressure xenon gas environment. Ba 2+ ions chelated with molecular chemosensors are resolved at the gas-solid interface using a diffraction-limited imaging system with scan area of 1 × 1 cm 2 located inside 10 bar of xenon gas. This form of microscopy represents key ingredient in the development of barium tagging for neutrinoless double beta decay searches in 136 Xe. This also provides a new tool for studying the photophysics of fluorescent molecules and chemosensors at the solid-gas interface to enable bottom-up design of catalysts and sensors.

46 INSTRUMENTATION RELATED TO NUCLEAR SCIENCE AND ↗
DOE OSTI2021

High-Resolution Momentum Imaging—From Stern’s Molecular Beam Method to the COLTRIMS Reaction Microscope [Book Chapter]

Multi-particle momentum imaging experiments are now capable of providing detailed information on the properties and the dynamics of quantum systems in Atomic, Molecular and Photon (AMO) physics. Historically, Otto Stern can be considered the pioneer of high-resolution momentum measurements of particles moving in a vacuum and he was the first to obtain sub-atomic unit (a.u.) momentum resolution (Schmidt-Böcking et al. in The precision limits in a single-event quantum measurement of electron momentum and position, these proceedings). A major contribution to modern experimental atomic and molecular physics was his so-called molecular beam method, which Stern developed and employed in his experiments. With this method he discovered several fundamental properties of atoms, molecules and nuclei. As corresponding particle detection techniques were lacking during his time, he was only able to observe the averaged footprints of large particle ensembles. Today it is routinely possible to measure the momenta of single particles, because of the tremendous progress in single particle detection and data acquisition electronics. A “state-of-the-art” COLTRIMS reaction microscope can measure, for example, the momenta of several particles ejected in the same quantum process in coincidence with sub-a.u. momentum resolution. Such setups can be used to visualize the dynamics of quantum reactions and image the entangled motion of electrons inside atoms and molecules. This review will briefly summarize Stern’s work and then present in longer detail the historic steps of the development of the COLTRIMS reaction microscope. Furthermore, some benchmark results are shown which initially paved the way for a broad acceptance of the COLTRIMS approach. Finally, a small selection of milestone work is presented which has been performed during the last two decades.

Jahnke, T.↗
DOE OSTI2020

Understanding the Interplay between the Nonvalence and Valence States of the Uracil Anion upon Monohydration

In this work we present an ab initio investigation into the effect of monohydration on the interaction of uracil with low energy electrons. Electron attachment and photodetachment experimental studies have previously shown dramatic changes in uracil upon solvation with even a single water molecule, due to an inversion of the character of the ground state of the anion. Here we explore the interplay between the nonvalence and valence states of the uracil anion, as a function of geometry and site of solvation. Our model provides unambiguous interpretation of previous photoelectron studies, reproducing the binding energies and photoelectron images for bare uracil and a single isomer of the U•(H 2 O) 1 cluster. Furthermore, the results of this study provide insight into how electrons may attach to hydrated nucleobases. These results lay the foundations for further investigations into the effect of microhydration on the electronic structure and electron capture dynamics of nucleobases.

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

Pump and ionizing-probe dynamics in a simultaneous treatment of electronic and nuclear motion in LiH

The dissociative single ionization of the LiH molecule using a two-color UV-UV pump-probe scheme is simulated in ab initio calculations demonstrating how the dynamics initiated on intermediate Rydberg states of diatomic molecules can be imaged by such experiments. The theoretical treatment combines nuclear motion with highly correlated descriptions of electronic continua and bound electronic states. Nuclear dynamics on Rydberg states are only weakly reflected by changes in photoelectron energies ejected by time-delayed ionizing pulses if the Rydberg potential curves parallel those of the ion states being produced. However, coincidence measurements guided by knowledge of the photoionization amplitudes as a function of internuclear distance can still reveal intermediate-state dynamics in pump-probe experiments.

74 ATOMIC AND MOLECULAR PHYSICS↗
DOE OSTI2021

Toward Å-fs-meV Resolution in Electron Microscopy: Systematic Simulation of the Temporal Spread of Single-Electron Packets

Though efforts to improve the temporal resolution of transmission electron microscopes (TEMs) have waxed and waned for decades, with relatively recent advances routinely reaching sub-picosecond scales, fundamental and practical challenges have hindered the advance of combined Å-fs-meV resolutions, particularly for core-loss spectroscopy and real-space imaging. This is due in no small part to the complexity of the approach required to access timescales upon which electrons, atoms, molecules, and materials first begin to respond and transform – attoseconds to picoseconds. Here we present part of a larger effort devoted to systematically mapping the instrument parameter space of a TEM modified to reach ultrafast timescales. With General Particle Tracer, we studied the statistical temporal distributions of single-electron packets as a function of various fs pulsed-laser parameters and electron-gun configurations and fields for the exact architecture and dimensions of a Thermo Fisher Tecnai Femto ultrafast electron microscope. We focused on easily-adjustable parameters, such as laser pulse duration, laser spot size, photon energy, Wehnelt aperture diameter, and photocathode size. In addition to establishing trends and dispersion behaviors, we identify regimes within which packet duration can be 100s of fs and approach the 300-fs laser limit employed here. Overall, the results provide a detailed picture of the temporal behavior of single-electron packets in the Tecnai Femto gun region, forming the initial contribution of a larger effort.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗