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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 109 records · Page 6
All sourcesNASA NTRSDOE OSTI
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↗
DOE OSTI2025

Wavelength-dependent photodissociation of iodomethylbutane

Ultrashort XUV pulses of the Free-Electron-LASer in Hamburg (FLASH) were used to investigate laser-induced fragmentation patterns of the prototypical chiral molecule 1-iodo-2-methyl-butane (C 5 H 11 I) in a pump-probe scheme. Ion velocity-map images and mass spectra of optical-laser-induced fragmentation were obtained for subsequent FEL exposure with photon energies of 63 eV and 75 eV. These energies specifically address the iodine 4d edge of neutral and singly charged iodine, respectively. The presented ion spectra for two optical pump-laser wavelengths, i.e., 800 nm and 267 nm, reveal substantially different cationic fragment yields in dependence on the wavelength and intensity. For the case of 800-nm-initiated fragmentation, the molecule dissociates notably slower than for the 267 nm pump. The results underscore the importance of considering optical-laser wavelength and intensity in the dissociation dynamics of this prototypical chiral molecule that is a promising candidate for future studies of its asymmetric nature.

74 ATOMIC AND MOLECULAR PHYSICS↗
DOE OSTI2023

Single molecule insights into interfacial molecular recognition for model electrochemical DNA biosensors

Electrochemical sensors that use surface-immobilized DNA to bind analytes and transduce the binding into electrochemical signals, have the potential for rapid, specific, and sensitive detection of bioanalytes via a compact and portable platform. However, accessing the structure of these surfaces/interfaces at the relevant spatial scale (< 10 nm), which determines the interfacial interactions and ultimately sensing performance, remains an unsolved challenge. Here, we review studies that have used high resolution atomic force microscope imaging and spatial statistical analysis tools to understand crowding interactions between thiolated DNA probes immobilized on gold electrodes and how such interactions impact target binding. We also review related studies that attempt to control the nanoscale spatial arrangement of the immobilized recognition elements to optimize sensing performance. Furthermore, these efforts have led to new advances in understanding of the structure-function relationships of DNA-based electrochemical biosensors to move the field toward rational engineering of these biosensing interfaces.

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

Atomic Force Microscopy to Characterize Antimicrobial Peptide-Induced Defects in Model Supported Lipid Bilayers

Antimicrobial peptides (AMPs) interact with bacterial cell membranes through a variety of mechanisms, causing changes extending from nanopore formation to microscale membrane lysis, eventually leading to cell death. Several AMPs also disrupt mammalian cell membranes, despite their significantly different lipid composition and such collateral hemolytic damage hinders the potential therapeutic applicability of the AMP as an anti-microbial. Elucidating the mechanisms underlying the AMP–membrane interactions is challenging due to the variations in the chemical and structural features of the AMPs, the complex compositional variations of cell membranes and the inadequacy of any single experimental technique to comprehensively probe them. (1) Background: Atomic Force Microscopy (AFM) imaging can be used in combination with other techniques to help understand how AMPs alter the orientation and structural organization of the molecules within cell membranes exposed to AMPs. The structure, size, net charge, hydrophobicity and amphipathicity of the AMPs affect how they interact with cell membranes of differing lipid compositions. (2) Methods: Our study examined two different types of AMPs, a 20-amino acid, neutral, α-helical (amphipathic) peptide, alamethicin, and a 13-amino acid, non-α-helical cationic peptide, indolicidin (which intramolecularly folds, creating a hydrophobic core), for their interactions with supported lipid bilayers (SLBs). Robust SLB model membranes on quartz supports, incorporating predominantly anionic lipids representative of bacterial cells, are currently not available and remain to be developed. Therefore, the SLBs of zwitterionic egg phosphatidylcholine (PC), which represents the composition of a mammalian cell membrane, was utilized as the model membrane. This also allows for a comparison with the results obtained from the Quartz Crystal Microbalance with Dissipation (QCM-D) experiments conducted for these peptides interacting with the same zwitterionic SLBs. Further, in the case of alamethicin, because of its neutrality, the lipid charge may be less relevant for understanding its membrane interactions. (3) Results: Using AFM imaging and roughness analysis, we found that alamethicin produced large, unstable defects in the membrane at 5 µM concentrations, and completely removed the bilayer at 10 µM. Indolicidin produced smaller holes in the bilayer at 5 and 10 µM, although they were able to fill in over time. The root-mean-square (RMS) roughness values for the images showed that the surface roughness caused by visible defects peaked after peptide injection and gradually decreased over time. (4) Conclusions: AFM is useful for helping to uncover the dynamic interactions between different AMPs and cell membranes, which can facilitate the selection and design of more efficient AMPs for use in therapeutics and antimicrobial applications.

Swana, Kathleen W.↗
NASA NTRS2003

Quantifying clustered DNA damage induction and repair by gel electrophoresis, electronic imaging and number average length analysis

Assessing DNA damage induction, repair and consequences of such damages requires measurement of specific DNA lesions by methods that are independent of biological responses to such lesions. Lesions affecting one DNA strand (altered bases, abasic sites, single strand breaks (SSB)) as well as damages affecting both strands (clustered damages, double strand breaks) can be quantified by direct measurement of DNA using gel electrophoresis, gel imaging and number average length analysis. Damage frequencies as low as a few sites per gigabase pair (10(9)bp) can be quantified by this approach in about 50ng of non-radioactive DNA, and single molecule methods may allow such measurements in DNA from single cells. This review presents the theoretical basis, biochemical requirements and practical aspects of this approach, and shows examples of their applications in identification and quantitation of complex clustered damages.

NASA Program Biological Systems Research↗
DOE OSTI2024

Atomic-Scale Imaging of Condensed Counterions

Here, the functioning of a wide variety of charged macromolecules, from DNA to fuel cell membranes, is dependent on how the counterions surrounding them are arranged. In order to decrease Coulombic repulsion, some of the fixed charges on these molecules are neutralized by a fraction of the counterions-this phenomenon is called counterion condensation. The nature of counterion condensation can be only be inferred indirectly from traditional experiments such as X-ray scattering and modern experiments such as single molecule electrometry. The prevalent conclusion in the literature, based on both theory and experiment, is that the distribution of counterions is peaked right next to the macromolecule, i.e., condensation results in the formation of contact ion pairs. In this study, cryogenic electron microscopy (cryo-EM) was used to study the arrangement of condensed halide counterions near a positively charged polypeptoid nanofiber. The locations of both condensed and fixed charges were determined directly from atomic-scale images. Our experimentally determined counterion distributions were peaked at distances of about 5 Å away from the fixed positive charge, indicating the presence of a layer of water molecules between condensed ion pairs. We posit that this distribution is driven by the entropy of the condensed ions.

36 MATERIALS SCIENCE↗
DOE OSTI2020

Thermodynamics and Mechanism of a Photocatalyzed Stereoselective [2 + 2] Cycloaddition on a CdSe Quantum Dot

Colloidal quantum dots (QDs) have shown promise over the last few decades for a range of applications including single photon emission, in vivo imaging and photocatalysis. Recent experiments demonstrated that QDs impart stereoselectivity to triplet excited-state [2+2] cycloaddition reactions of alkenes photocatalyzed by the QD through self-assembly of the reagent molecules on the QD surface, but these experiments did not reveal the precise geometries of surface-bound molecules or their interactions with surface atoms. Here, a theoretical mechanistic approach is used to study such interactions for [2+2] cycloadditions of 4-vinylbenzoic acid derivatives on CdSe QDs. Spin-polarized periodic density functional theory (DFT) and non-periodic DFT calculations are deployed to determine the origin of the selectivity for the syn diastereomer of the resultant tetrasubstituted cyclobutane product via atomistic modelling of the CdSe surface and substrates, and determination of the thermodynamic energies of reactions for each step, the intermolecular interactions between the substrates, and the triplet state reaction paths. The calculations indicate that reaction selectivity arises from preferred binding of pairs through intermolecular interactions of substrate molecules on the QD surface in a syn-precursor structure followed by dimerization after triplet excitation. Further, these mechanisms are generalizable to other metal-enriched QD surfaces that have a similar surface structure to CdSe, such as InSe or CdTe. Design principles for anti diastereomer derivatives are also discussed.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
NASA NTRS2006

Visualization of a Capsule Entry Vehicle Reaction-Control System (RCS) Thruster

Planar laser-induced fluorescence (PLIF) was used to visualize the reaction control system (RCS) jet flow emanating from the aft-body of an Apollo-geometry capsule test article in the NASA Langley Research Center 31-Inch Mach 10 Air wind tunnel. The RCS jet was oriented normal to the aft surface of the model and had a nominal Mach number of 2.94. The composition of the jet gas by mass was 95% nitrogen (N2) and 5% nitric oxide (NO). The RCS jet flowrate varied between zero and 0.5 standard liters per minute and the angle of attack and tunnel stagnation pressure were also varied. PLIF was used to excite the NO molecules for flow visualization. These flow visualization images were processed to determine the trajectory and to quantify the flapping of the RCS jet. The spatial resolution of the jet trajectory measurement was about 1 mm and the single-shot precision of the measurement was estimated to be 0.02 mm in the far field of the jet plume. The jet flapping, measured by the standard deviation of the jet centerline position was as large as 0.9 mm, while the jet was 1.5-4 mm in diameter (full width at half maximum). Schlieren flow visualization images were obtained for comparison with the PLIF. Surface pressures were also measured and presented. Virtual Diagnostics Interface (VIDI) technology developed at NASA Langley was used to superimpose and visualize the data sets. The measurements demonstrate some of the capabilities of the PLIF method while providing a test case for computational fluid dynamics (CFD) validation.

Danehy, P. M.↗
DOE OSTI2024

A Deep Multimodal Representation Learning Framework for Accurate Molecular Properties Prediction

Drug discovery is a complex and challenging process, requiring the optimization of candidate compounds to identify those with the potential to become safe and effective drugs. Predicting molecular properties is an indispensable step in the drug discovery pipeline. Traditionally, this process is costly and time-intensive, involving multiple rounds of experiments and clinical trials, rendering it impractical for every candidate compound. Deep learning techniques have emerged as a promising approach to drug discovery to reduce the cost and time required to identify novel drugs. However, prevalent research in deep learning models focused on predicting molecular properties has primarily fixated on single-modal models, which utilize a single modality of data, neglecting the potential benefits of combining different data modalities. To overcome this limitation, we introduce MRL-Mol: a deep \textbf{M}ultimodal \textbf{R}epresentation \textbf{L}earning framework for accurate \textbf{Mol}ecular properties prediction. MRL-Mol harnesses three data modalities: sequence, graph, and image, augmenting the depth of comprehension. Leveraging a large-scale unlabeled dataset~($\sim$1M unique molecules), we pretrain MRL-Mol to extract inter- and intra-modal information. Our study demonstrates the superior performance of MRL-Mol in predicting molecular properties across six benchmark datasets, including both classification and regression tasks. Notably, MRL-Mol outperforms other state-of-the-art molecular properties prediction models. These findings suggest that by combining information from multiple data modalities, MRL-Mol can comprehend molecules better than single-modal deep learning models and identify molecular properties with better accuracy.

Yang, Yuxin↗
DOE OSTI2025

Characterizing Absolute Orientations in DNA Self-Assembly of Single Molecules

DNA self-assembly of single molecules (i.e., dyes) with deterministic orientations is a powerful approach for engineering mo-lecular excitons. However, current determination methods of the dye orientation relative to DNA do not account for the orien-tation of the dye plane, which is a missing degree of freedom needed to define absolute three-dimensional orientations. In this work, we combine fluorescence-detected linear dichroism, defocused dipole imaging, and DNA points accumulation for imaging in nanoscale topography (DNA-PAINT) super-resolution microscopy to determine the absolute three-dimensional orientations of single Cy5 dyes relative to host DNA duplexes which includes the dye plane orientation. The data revealed that the absorption and emission dipoles are perpendicular to the DNA duplex, and the mean dye plane is parallel to the DNA bases, which supports the notion that Cy5 dyes intercalate between DNA base pairs. The presented methodology will inspire the investigation of the dye plane orientation for controlling dye arrangement configurations beyond spontaneous π-stacking between dyes as well as achieving novel dye-DNA arrangements.

36 MATERIALS SCIENCE↗