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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 163 records · Page 9
All sourcesNASA NTRSDOE OSTI
DOE OSTI2025

SynopFrame: Multiscale time-dependent visual abstraction framework for analyzing DNA nanotechnology simulations

We present an open-source framework, SynopFrame, that allows DNA nanotechnology (DNA-nano) experts to analyze and understand molecular dynamics simulation trajectories of their designs. We use a multiscale multi-dimensional abstraction space, connect the representations to a projected conformational space plot of the structure’s temporal sequence, and thus enable experts to analyze the dynamics of their structural designs and, specifically, failure cases of the assembly. In addition, our time-dependent abstraction representation allows the biologists, for the first time in a smooth and structurally clear way, to identify and observe temporal transitions of a DNA-nano design from one configuration to another, and to highlight important periods of the simulation for further analysis. We realize SynopFrame as a dashboard of the different synchronized 3D spatial and 2D schematic visual representations, with a color overlay to show essential properties such as the status of hydrogen bonds. The linking of the spatial, schematic, and abstract views ensures that users can effectively analyze the high-frequency motion. We also categorize the status of the hydrogen bonds into a new format to allow us to color-encode it and overlay it on the representations. To demonstrate the utility of SynopFrame, we describe example usage scenarios and report user feedback.

Abstraction space↗
DOE OSTI2025

MODE: A Web Application for Interactive Visualization and Exploration of Omics Data

Studies generating transcriptomics, proteomics, lipidomics, and metabolomics (colloquially referred to as “omics”) data allow researchers to find biomarkers or molecular targets, or understand complex biological structures and functions by identifying changes in biomolecule abundance and expression between experimental conditions. Omics data is multi-dimensional and oftentimes summarization techniques such as principal component analysis (PCA) are used to identify high-level patterns in data. Though useful, these summaries don’t allow exploration of detailed patterns in omics data that may have biological relevance. The use of interactive HTML displays with plots allows researchers to interact with omics data at a detailed level, but building these displays requires significant coding expertise. To overcome this barrier, the software MODE was built to empower users to build their own interactive HTML displays to support scientific discovery. These displays are easily shareable, do not depend on a specific operating system, and allow users to effortlessly sort and filter plots by categorical or numerical variables. MODE allows users to build and share these displays with several options for plot design and meta selection. In conclusion, the MODE web application and its capabilities are presented and then demonstrated on lipidomics data from a leaf wounding study.

lipidomics↗
DOE OSTI2020

Revealing the Structural Evolution of Green Rust Synthesized in Ionic Liquids by In Situ Molecular Imaging

Abstract Ionic liquids are green solvents that have wide applications in material synthesis, catalysis, and separation. A model switchable ionic liquid (SWIL) consisting of 1,8‐diazabicycloundec‐7‐ene (DBU) and 1‐hexanol with carbon dioxide (CO 2 ) as the trigger gas is chosen to synthesize nanocrystalline green rust. Under anoxic conditions, by adding iron (II) acetate (Fe(C 2 H 3 O 2 ) 2 ) and methanol to the degassed SWIL, a nanoparticulate green rust with carbonate (nano‐GR) is synthesized. More importantly, the molecular structural change of the ionic liquid resulting in green rust crystallines is first characterized using in situ liquid using time‐of‐flight secondary ion mass spectrometry (ToF‐SIMS) coupled with the system for analysis at the liquid vacuum interface (SALVI), a vacuum compatible microfluidic reactor in this work. Dimers and ionic clusters consisting ferric and ferrous ions are identified in liquid ToF‐SIMS spectra. Spectral principal component analysis is used to confirm that these ion pairs including dimers and cluster ions are different from nonionic liquids. The results show that liquid ToF‐SIMS can be a useful tool to study complex liquids at the molecular level providing insights into predicative synthesis of nanomaterials using environmentally friendly green solvents and giving unique visualization of the evolving material interface due to nucleation.

Shen, Yanjie↗
DOE OSTI2025

Nanopolysaccharide Builder: A User-Friendly Tool for Atomistic Models of Polysaccharide-Based Nanostructures

Here, we introduce Nanopolysaccharide Builder (NPB), a user-friendly software tool designed to construct polysaccharide nanostructures─mainly those based on cellulose, chitin, and chitosan─using experimental data or user-defined parameters. NPB enables the generation of cellulose and chitin allomorphs with customizable biochemical topologies and also facilitates the construction of large bundles that replicate nanostructures found in biological support systems, including plant cell walls and arthropod cuticles. The software outputs atomic Cartesian coordinates in Protein Data Bank (PDB) format and also provides atom connectivity files in PSF and PARM formats, ensuring seamless integration with major molecular dynamics (MD) engines such as NAMD, CHARMM, GROMACS, AMBER, OpenMM, and LAMMPS. Built on an interactive visualization framework, NPB features a graphical user interface (GUI) and supports both macOS and Linux operating systems. By enabling detailed atomic-scale studies of polysaccharide evolution in extracellular matrices and cell walls of algae, bacteria, fungi, and plants, NPB is poised to advance AI-guided research in sustainable chemical development and biomass utilization.

Wan, Zhangmin [Univ. of British Columbia, Vancouve↗
DOE OSTI2023

Manipulating single excess electrons in monolayer transition metal dihalide

Polarons are entities of excess electrons dressed with local response of lattices, whose atomic-scale characterization is essential for understanding the many body physics arising from the electron-lattice entanglement, yet difficult to achieve. Here, using scanning tunneling microscopy and spectroscopy (STM/STS), we show the visualization and manipulation of single polarons in monolayer CoCl 2 , that are grown on HOPG substrate via molecular beam epitaxy. Two types of polarons are identified, both inducing upward local band bending, but exhibiting distinct appearances, lattice occupations and polaronic states. First principles calculations unveil origin of polarons that are stabilized by cooperative electron-electron and electron-phonon interactions. Both types of polarons can be created, moved, erased, and moreover interconverted individually by the STM tip, as driven by tip electric field and inelastic electron tunneling effect. This finding identifies the rich category of polarons in CoCl 2 and their feasibility of precise control unprecedently, which can be generalized to other transition metal halides.

71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗
DOE OSTI2020

Laser-Plasma Spatiotemporal Cyanide Spectroscopy and Applications

This article reports new measurements of laser-induced plasma hypersonic expansion measurements of diatomic molecular cyanide (CN). Focused, high-peak-power 1064 nm Q-switched radiation of the order of 1 TW/cm 2 generated optical breakdown plasma in a cell containing a 1:1 molar gas mixture of N 2 and CO 2 at a fixed pressure of 1.1 × 10 5 Pascal and in a 100 mL/min flow of the mixture. Line-of-sight (LOS) analysis of recorded molecular spectra indicated the outgoing shockwave at expansion speeds well in excess of Mach 5. Spectra of atomic carbon confirmed increased electron density near the shockwave, and, equally, molecular CN spectra revealed higher excitation temperature near the shockwave. Results were consistent with corresponding high-speed shadowgraphs obtained by visualization with an effective shutter speed of 5 nanoseconds. In addition, LOS analysis and the application of integral inversion techniques allow inferences about the spatiotemporal plasma distribution.

36 MATERIALS SCIENCE↗
DOE OSTI2022

PDB‐101: Molecular Explorations through Biology and Medicine

PDB‐101 is an online portal for teachers, students, and the general public to promote exploration of the structural biology of proteins and nucleic acids ( pdb101.rcsb.org ). Learning about the diverse shapes and functions of these biological macromolecules helps to understand all aspects of biomedicine and agriculture, from protein synthesis to health and disease to biological energy. Why PDB‐101? Researchers around the world are studying these molecules at the atomic level. These 3D structures are freely available at the Protein Data Bank (PDB), the central storehouse of biomolecular structures. This website builds introductory materials to help beginners get started in the basics of biomolecular structure and function (“101”, as in an entry level course) as well as resources for extended learning. Since 2011, PDB‐101 has been developed by the RCSB PDB , a global resource for the advancement of research and education in biology and medicine. Along with our Worldwide PDB collaborators, RCSB PDB curates, annotates, and makes publicly available the PDB data deposited by scientists around the globe. The RCSB PDB then provides a window to these data through a rich online resource with powerful searching, reporting, and visualization tools for researchers. This information is then streamlined for students and teachers at PDB‐101. Features include the ongoing Molecule of the Month series, educational materials such as paper models, posters, molecular animations, educational curricula and more. The section “Guide to Understanding PDB Data” is a primer for detailed PDB‐specific information: PDB Data, Visualizing Structures, Reading Coordinate Files, scientific methods for structure determination, and more. PDB‐101 also runs annual Video Challenges for high school students. Participants create short videos that tell molecular stories that connect structural biology and medicine. Previous topics have included HIV/AIDS, diabetes, and antimicrobial resistance. The 2022 challenge will focus on Molecular Mechanisms of Cancer. PDB‐101 activities are evaluated using user surveys, feedback from in‐person activities, and website analytics. In 2020, PDB‐101 hosted >850,000 users and >2.6 million page views.

Zardecki, Christine↗
DOE OSTI2023

Dynamics of multilayer Rayleigh–Taylor instability at moderately high Atwood numbers

This paper investigates the multilayer Rayleigh–Taylor instability (RTI) using statistically stationary experiments conducted in a gas tunnel. Employing diagnostics such as particle image velocimetry (PIV) and planar laser induced fluorescence (PLIF), we make simultaneous velocity–density measurements to study how dynamics and mixing are linked in this variable density flow. Experiments are conducted in a newly built, blow-down three-layer gas tunnel facility. Mixing between three gas streams is studied, where the top and bottom streams are comprised of air, and the middle stream is an air–helium mixture. Shear is minimized between these streams by matching their inlet velocities. The four experimental conditions investigated here consist of two different density ratios (Atwood numbers 0.3 and 0.6), each investigated at two instability development times (or equivalently, two streamwise locations), and all experiments are with the same middle stream thickness of 3 cm. The growth of the middle layer is measured using laser-based planar Mie scattering visualization. The mixing width is found to grow linearly with time at late times. Various quantitative measures of molecular mixing indicate a very high degree of molecular mixing at late times in the multilayer RTI flow. The vertical turbulent mass flux $a_y$ is calculated. In addition to mostly negative values of $a_y$ , typical of buoyancy-dominated flows due to negative correlation between velocity and density fluctuations, positive regions are also observed in profiles of $a_y$ due to entrainment and erosion at the lower edge of the mixing region. Global energy budgets are calculated for the multilayer RTI flow at late times and it is found that the majority of potential energy released has been dissipated due to viscous effects, and a large value of mixing efficiency ( $\sim$ 60 %) is observed.

Mechanics↗
DOE OSTI2022

LigninGraphs: lignin structure determination with multiscale graph modeling

Lignin is an aromatic biopolymer found in ubiquitous sources of woody biomass. Designing and optimizing lignin valorization processes requires a fundamental understanding of lignin structures. Experimental characterization techniques, such as 2D-heteronuclear single quantum coherence (HSQC) nuclear magnetic resonance (NMR) spectra, could elucidate the global properties of the polymer molecules. Computer models could extend the resolution of experiments by representing structures at the molecular and atomistic scales. We introduce a graph-based multiscale modeling framework for lignin structure generation and visualization. The framework employs accelerated rejection-free polymerization and hierarchical Metropolis Monte Carlo optimization algorithms. We obtain structure libraries for various lignin feedstocks based on literature and new experimental NMR data for poplar wood, pinewood, and herbaceous lignin. The framework could guide researchers towards feasible lignin structures, efficient space exploration, and future kinetics modeling. Its software implementation in Python, LigninGraphs, is open-source and available on GitHub.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
NASA NTRS1988

Application of Hoffman modulation contrast microscopy coupled with three-wavelength two-beam interferometry to the in situ direct observation of the growth process of a crystal in microgravity

Direct visualization of three dimensional transfer process of both heat and mass around a growing crystal and mono-molecular growth layers on the surface is possible in situ by means of high resolution Hoffman modulation contrast microscopy coupled with three wavelength two beam Mach-Zehnder interferometry. This in situ observation is very suitable for the verification of the growth mechanism of a crystal in a solution or a melt in microgravity.

Tsukamoto, Katsuo↗
NASA NTRS1989

Star formation and the interstellar medium in two peculiar, nonspiral galaxies - NGC 1569 and NGC 3593

This paper discusses far-IR and optical observations aimed at investigating the far-IR energy distribution of two peculiar galaxies without spiral arms which are actively forming stars: NGC 1569, a Magellanic irregular galaxy, and NGC 3593, a dusty S0/a galaxy. The data are used to determine the characteristic temperatures of the dust and to infer dust and molecular gas masses which are combined with other data to explore the characteristics of the interstellar media. Visual-wavelength continuum and H-alpha images are presented and used to estimate current and past star formation rates and the efficiency of stellar creation.

Hunter, Deidre A.↗
NASA NTRS1991

Characterization of selected LDEF polymer matrix resin composite materials

The characterization of selected graphite fiber reinforced epoxy (934 and 5208) and polysulfone (P1700) matrix resin composite materials which received 5 years and 10 months of exposure to the LEO environment on the Long Duration Exposure Facility is reported. Resin loss and a decrease in mechanical performance as well as dramatic visual effects were observed. However, chemical characterization including infrared, thermal, and selected solution property measurements showed that the molecular structure of the polymeric matrix had not changed significantly in response to this exposure. The potential effect of a silicon-containing molecular contamination of these specimens is addressed.

Young, Philip R.↗
NASA NTRS2013

Further Analysis of Materials Exposed on MISSE-6 and-7B

Materials samples were exposed to the low Earth orbit (LEO) environment as part of the MISSE- 6 and -7B flight experiments. Optical properties, thickness/mass loss, surface elemental analysis, visual and microscopic analysis for surface change are some of the techniques employed in this investigation. Effects of molecular contamination are discussed. Where possible, the MISSE-6 and -7B results are compared to analyses from other LEO experiments.

Finckenor, Miria↗
NASA NTRS1984

NGC 2024: Far-infrared and radio molecular observations

Far infrared continuum and millimeter wave molecular observations are presented for the infrared and radio source NGC 2024. The measurements are obtained at relatively high angular resolution, enabling a description of the source energetics and mass distribution in greater detail than previously reported. The object appears to be dominated by a dense ridge of material, extended in the north/south direction and centered on the dark lane that is seen in visual photographs. Maps of the source using the high density molecules CS and HCN confirm this picture and allow a description of the core structure and molecular abundances. The radio molecular and infrared observations support the idea that an important exciting star in NGC 2024 has yet to be identified and is centered on the dense ridge about 1' south of the bright mid infrared source IRS 2. The data presented here allows a presentation of a model for the source.

Thronson, H. A., Jr.↗
DOE OSTI2023

Facile hermetic TEM grid preparation for molecular imaging of hydrated biological samples at room temperature

Abstract Although structures of vitrified supramolecular complexes have been determined at near-atomic resolution, elucidating in situ molecular structure in living cells remains a challenge. Here, we report a straightforward liquid cell technique, originally developed for real-time visualization of dynamics at a liquid-gas interface using transmission electron microscopy, to image wet biological samples. Due to the scattering effects from the liquid phase, the micrographs display an amplitude contrast comparable to that observed in negatively stained samples. We succeed in resolving subunits within the protein complex GroEL imaged in a buffer solution at room temperature. Additionally, we capture various stages of virus cell entry, a process for which only sparse structural data exists due to their transient nature. To scrutinize the morphological details further, we used individual particle electron tomography for 3D reconstruction of each virus. These findings showcase this approach potential as an efficient, cost-effective complement to other microscopy technique in addressing biological questions at the molecular level.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2021

Synergistic foam stabilization and transport improvement in simulated fractures with polyelectrolyte complex nanoparticles: Microscale observation using laser etched glass micromodels

Inaccessibility to direct pore scale observation in hydrocarbon recovery of tight shale formations poses a great challenge to water-energy nexus initiatives and necessitates the use of high throughput technologies to emulate environmentally friendly processes. Herein, we employ a precise glass micromodel fabrication and visualization method to isolate the supercritical CO 2 bubbles surrounded by CO 2 -water lamella prepared in saline produced water stabilized with molecular complexation of zwitterionic surfactants (ZS) and polyelectrolyte complex nanoparticles (PECNP). The Selective Laser Enhanced Etching (SLE) technique was selected for micromodel simulation of high-pressure flow. Two representative designs, (1) fracture/micro-crack network 28 and (2) fracture/matrix were etched on fused silica glass with a laser printing machine and scCO 2 foam was injected to study the foamability, propagation, stability, and fluid loss properties. The highly monodispersed and uniformly distributed array of scCO 2 bubbles were detected in flow of scCO 2 foam in highly saline brine containing ionic complexes of positively charged PECNPs and ZS, whereas foam flow with the lamella containing ZS in fractures offered a noticeably large and polydisperse array of scCO 2 bubbles. scCO 2 bubble motion and deformation were traced, and local description of foam flow was visually examined. The confined array of scCO 2 bubbles stabilized by ZS in microcracks was affected by bubble growth and coalescence, whereas the super-populated array of monodispersed scC O2 bubbles with lamella containing complexes of PECNP and ZS were able to fill the channels with stable configurations within the timeframe of comparative stability measurements. The ability of complex fluid to prevent the formation damage was evaluated through fluid loss visualization in micromodels. Probing scCO 2 foam transport in homogenous porous media revealed smaller volume leak-off for scCO 2 foam containing PECNP-ZS ionic complexes.

04 OIL SHALES AND TAR SANDS↗
DOE OSTI2021

Visualizing defects and pore connectivity within metal–organic frameworks by X-ray transmission tomography

Metal–Organic Frameworks (MOFs) have the potential to change the landscape of molecular separations in chemical processes owing to their ability of selectively binding molecules. Their molecular sorting properties generally rely on the micro- and meso-pore structure, as well as on the presence of coordinatively unsaturated sites that interact with the different chemical species present in the feed. In this work, we show a first-of-its-kind tomographic imaging of the crystal morphology of a metal– organic framework by means of transmission X-ray microscopy (TXM), including a detailed data reconstruction and processing approach. Corroboration with Focused Ion Beam-Scanning Electron Microscopy (FIB-SEM) images shows the potential of this strategy for further (non-destructively) assessing the inner architecture of MOF crystals. By doing this, we have unraveled the presence of large voids in the internal structure of a MIL-47(V) crystal, which are typically thought of as rather homogeneous lattices. This challenges the established opinion that hydrothermal syntheses yield relatively defect-free material and sheds further light on the internal morphology of crystals.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
NASA NTRS1984

NGC 2024 - Far-infrared and radio molecular observations

New far-infrared continuum and millimeter-wave molecular observations of NGC 2024 are presented. The measurements were obtained at relatively high angular resolution making it possible to describe the source energetics and mass distribution in greater detail than previously reported. The object appears to be dominated by a dense ridge of material, extended in the north-south direction and centered on the dark lane that is seen in visual photographs. The maps of the source using the 'high-density' molecules CS and HCN confirm this picture and makes it possible to describe the core structure and molecular abundances. The radio molecular and infrared observations support the idea that an important exciting star in NGC 2024 has yet to be identified and is centered on the dense ridge about 1 arcmin south of the bright mid-infrared source IRS 2. The data presented here, along with other observations, make it possible to describe a model for the source.

Thronson, H. A., Jr.↗