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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 37 records · Page 2
All sourcesNASA NTRSDOE OSTI
DOE OSTI2021

Laser-induced electron diffraction of the ultrafast umbrella motion in ammonia

Visualizing molecular transformations in real-time requires a structural retrieval method with Ångström spatial and femtosecond temporal atomic resolution. Imaging of hydrogen-containing molecules additionally requires an imaging method sensitive to the atomic positions of hydrogen nuclei, with most methods possessing relatively low sensitivity to hydrogen scattering. Laser-induced electron diffraction (LIED) is a table-top technique that can image ultrafast structural changes of gas-phase polyatomic molecules with sub-Ångström and femtosecond spatiotemporal resolution together with relatively high sensitivity to hydrogen scattering. Here, we image the umbrella motion of an isolated ammonia molecule (NH3) following its strong-field ionization. Upon ionization of a neutral ammonia molecule, the ammonia cation (NH3+) undergoes an ultrafast geometrical transformation from a pyramidal (ΦHNH=107°) to planar (ΦHNH=120°) structure in approximately 8 femtoseconds. Using LIED, we retrieve a near-planar (ΦHNH=117 ± 5°) field-dressed NH3+ molecular structure 7.8−9.8 femtoseconds after ionization. Our measured field-dressed NH3+ structure is in excellent agreement with our calculated equilibrium field-dressed structure using quantum chemical ab initio calculations.

71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗
DOE OSTI2025

A single-cell atlas of the bobtail squid visual and nervous system highlights molecular principles of convergent evolution

Abstract The cephalopod and vertebrate visual systems are a textbook example of convergent evolution with unknown molecular underpinnings. Here we characterize 98,537 single-cell transcriptomes in the bobtail squidEuprymna berryito understand how the cephalopod retina and optic lobes relate to the vertebrate retina. We confirm the overall relative simplicity of the cephalopod retina but identify two related photoreceptor cell subtypes expressing distinct r-opsins. By contrast, the adult optic lobe contains a diverse repertoire of neuronal and glial cell types, with a predominance of dopaminergic neurons. We show that cephalopod-specific gene duplicates probably contributed to this cell type diversification. Comparing neuronal cell population in the optic lobes of hatchlings and adults, we reveal a switch towards dopaminergic neurotransmitter usage with age, indicative of a maturation process. We further identify an FMRF-amide-based retrograde signal from the optic lobe towards the retina that supports the functional analogy of the cephalopod optic lobe cortex and the vertebrate inner retina in visual signal processing from a molecular standpoint. Finally, comparative analyses with vertebrate and arthropod cells suggest a scenario in which two photoreceptor types and two neuronal populations may have already been present in the eye of the bilaterian ancestor.

Environmental Sciences & Ecology↗
DOE OSTI2023

Simulation of Molecular Hydrogen Jets and Visualization of Associated Hydrodynamic Features [Slides]

A numerical method is presented for solving the Navier-Stokes equations to represent a steady-state hydrogen jet expanding into a vacuum chamber. This numerical method has been evaluated using three test problems with promising results. Simulations of the hydrogen jet indicate the presence of a low temperature region (less than 15 K) within the jet for the high flow rate case. The high flow rate case also gives rise to a large recirculation region within the jet. The conditions at the minimum temperature point within the jet approach the hydrogen sublimation line when the mass flow rate exceeds 2 g/s, which may allow for the formation of hydrogen ice crystals.

71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗
DOE OSTI2021

Rapid Automated Annotation and Analysis of N-Glycan Mass Spectrometry Imaging Data Sets Using NGlycDB in METASPACE

Imaging N-glycan spatial distribution in tissues using mass spectrometry imaging (MSI) is emerging as a promising tool in biological and clinical applications. However, there is currently no high throughput tool for visualization and molecular annotation of N-glycans in MSI data, which significantly slows down data processing and hampers the applicability of this approach. In this work, we present how METASPACE, an open-source cloud engine for molecular annotation of MSI data, can be used to automatically annotate, visualize, analyze, and interpret high-resolution mass spectrometry-based spatial N-glycomics data. METASPACE is an emerging tool in spatial metabolomics, but the lack of compatible glycan databases has limited its application for comprehensive N-glycan annotations from MSI datasets. We created NGlycDB, a public database of N-glycans, by adapting available glycan databases. We demonstrate the applicability of NGlycDB in METASPACE by analyzing MALDI-MSI data from formalin-fixed paraffin-embedded (FFPE) human kidney and mouse lung tissue sections. We added NGlycDB to METASPACE for public use, thus facilitating applications of MSI in glycobiology.

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

Bringing chemical structures to life with augmented reality, machine learning, and quantum chemistry

Visualizing 3D molecular structures is crucial to understanding and predicting their chemical behavior. However, static 2D hand-drawn skeletal structures remain the preferred method of chemical communication. Here, we combine cutting-edge technologies in augmented reality (AR), machine learning, and computational chemistry to develop MolAR, an open-source mobile application for visualizing molecules in AR directly from their hand-drawn chemical structures. Users can also visualize any molecule or protein directly from its name or protein data bank ID and compute chemical properties in real time via quantum chemistry cloud computing. MolAR provides an easily accessible platform for the scientific community to visualize and interact with 3D molecular structures in an immersive and engaging way.

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

Visualizing biomolecular electrostatics in virtual reality with UnityMol-APBS

The APBS software was developed to solve the equations of continuum electrostatics for large biomolecular assemblages. APBS has enjoyed widespread adoption throughout the biomedical community and is used in numerous applications involving biomolecular structures. However, visualization of complex biomolecular electrostatic properties can be challenging for two-dimensional graphics systems. Therefore, advanced visualization and manipulation capabilities have been incorporated. In particular, APBS tools have been integrated with the UnityMolX virtual reality platform to provide an immersive experience for preparing biomolecular systems for calculations as well as visualizing and comparing calculated results.

electrostatics, molecular visualization, solvation↗
DOE OSTI2021

A Multi-modal Approach to Understanding Degradation of Organic Photovoltaic Materials

State-of-the-art organic photovoltaic (OPV) materials are composed of complex, chemically diverse polymeric and molecular structures that form highly intricate solid-state interactions, collectively yielding exceptional tunability in performance and aesthetics. These properties are especially attractive for semitransparent power-generating windows or shades in living environments, greenhouses, or other architectural integrations. However, before such a future is realized, a broader and deeper understanding of property stability must be acquired. Stability during operating and environmental conditions is critical, namely, material color steadfastness, optoelectronic performance retention, morphological rigidity, and chemical robustness. To date, no single investigation encompasses all four distinct, yet interconnected, metrics. Here, we present a multimodal strategy that captures a dynamic and interconnected evolution of each property during the course of an accelerated photobleaching experiment. We demonstrate this approach across relevant length scales (from molecular to visual macroscale) using X-ray photoelectron spectroscopy, grazing-incidence X-ray scattering, microwave conductivity, and time-dependent photobleaching spectroscopies for two high-performance semitransparent OPV blends—PDPP4T:PC 60 BM and PDPP4T:IEICO-4F, with comparisons to the stabilities of the individual components. We present direct evidence that specific molecular acceptor (fullerene vs nonfullerene) designs and the resulting donor–acceptor interactions lead to distinctly different mechanistic routes that ultimately arrive at what is termed “OPV degradation.” We directly observe a chemical oxidation of the cyano endcaps of the IEICO-4F that coincides with a morphological change and large loss in photoconductivity while the fullerene acceptor-containing blend demonstrates a significantly greater fraction of oxygen uptake but retains 55% of the photoconductivity. Finally, this experimental roadmap provides meaningful guidance for future high-throughput, multimodal studies, benchmarking the sensitivity of the different analytical techniques for assessing stability in printable active layers, independent of complete device architectures.

14 SOLAR ENERGY↗
DOE OSTI2022

AIMSim : An accessible cheminformatics platform for similarity operations on chemicals datasets

The recent advances in deep learning, generative modeling, and statistical learning have ushered in a renewed interest in traditional cheminformatics tools and methods. Quantifying molecular similarity is essential in molecular generative modeling, exploratory molecular synthesis campaigns, and drug-discovery applications to assess how new molecules differ from existing ones. Further, most tools target advanced users and lack general implementations accessible to the larger community. In this work, we introduce Artificial Intelligence Molecular Similarity (AIMSim), an accessible cheminformatics platform for performing similarity operations on collections of molecules called molecular datasets. AIMSim provides a unified platform to perform similarity-based tasks on molecular datasets, such as diversity quantification, outlier and novelty analysis, clustering, dimensionality reduction, and inter-molecular comparisons. AIMSim implements all major binary similarity metrics and molecular fingerprints and is provided as a Python package that includes support for command-line use as well as a Graphical User Interface for code-free utilization with fully interactive plots.

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

Toward Intelligent Multimodal Holography for Real-Time Chemical Imaging of Dynamic Ion Separation

Molecular-level visualization of ion transport and separation dynamics in complex environments is crucial for advancing energy systems, water purification, and critical materials recovery. Achieving this requires imaging platforms that combine structural sensitivity, chemical specificity, and real-time operation. Digital off-axis holography (DOAH) provides high-throughput, label-free quantitative phase imaging but inherently lacks chemical selectivity. Integrating DOAH with complementary spectroscopic channels such as fluorescence or hyperspectral imaging introduces the needed molecular specificity, while also creating challenges in multimodal data fusion, synchronization, and computational throughput. Artificial intelligence offers a powerful route to address these limitations by uniting physics-based reconstruction with data-driven interpretation. In this Perspective, we outline a framework for intelligent multimodal holography and demonstrate its potential using a preliminary AI-driven test case. Raw DOAH holograms of lanthanide solutions subjected to magnetic field gradients were analyzed using multi-agent AI workflows that autonomously selected reconstruction tools, extracted NMF components, and generated scientific claims consistent with true paramagnetic and diamagnetic behavior. This demonstration shows how AI-enabled reasoning can deliver real-time chemical–structural interpretation directly from raw holograms. Together, these advances define a path toward adaptive, intelligent holography platforms capable of supporting in situ chemical separations, dynamic ion transport analysis, and next-generation interfacial science.

Ricchiuti, Giovanna↗
DOE OSTI2023

Fungal organic acid uptake of mineral-derived K is dependent on distance from carbon hotspot

Fungal mineral weathering regulates the bioavailability of inorganic nutrients from mineral surfaces to organic matter and increase the bioavailable fraction of nutrients. Such weathering strategies are classified as biomechanical or biochemical. In the case of fungal uptake of mineral nutrients through biochemical weathering, it is widely hypothesized that uptake of inorganic nutrients occurs through organic acid chelation, but such processes have not been directly visualized. This is in part due to challenges in probing the complex and heterogeneous soil environment. Here, using an epoxy-based, mineral-doped soil micromodel platform, which emulates soil mineralogy and porosity, we visualize the molecular mechanisms of mineral weathering. Mass spectrometry imaging revealed differences in the distribution of fungal exudates, citric acid, and tartaric acid on the soil micromodels in presence of minerals. Citric acid was detected closer to the nutrient-rich inoculation point, whereas tartaric acid was highly abundant away from inoculation point. This suggested that the organic acid exuded by the fungi depended on the proximity from the carbon-rich organic substrate at the point of inoculation. Using a combination of X-ray fluorescence and X-ray near edge structure analysis, we identified citric acid- and tartaric acid-bound K within fungal hyphae networks grown in the presence of minerals. Combined, our results provide direct evidence that fungi uptake and transport mineral derived nutrient organic acid chelation. The results of this study provided unprecedented visualization of fungal uptake and transport of K + , while resolving the indirect weathering mechanism of fungal K uptake from mineral interfaces.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2024

Secondary structure determines electron transport in peptides

Proteins play a key role in biological electron transport, but the structure–function relationships governing the electronic properties of peptides are not fully understood. Despite recent progress, understanding the link between peptide conformational flexibility, hierarchical structures, and electron transport pathways has been challenging. Here, we use single-molecule experiments, molecular dynamics (MD) simulations, nonequilibrium Green’s function-density functional theory (NEGF-DFT), and unsupervised machine learning to understand the role of secondary structure on electron transport in peptides. Our results reveal a two-state molecular conductance behavior for peptides across several different amino acid sequences. MD simulations and Gaussian mixture modeling are used to show that this two-state molecular conductance behavior arises due to the conformational flexibility of peptide backbones, with a high-conductance state arising due to a more defined secondary structure (beta turn or 3 10 helices) and a low-conductance state occurring for extended peptide structures. These results highlight the importance of helical conformations on electron transport in peptides. Conformer selection for the peptide structures is rationalized using principal component analysis of intramolecular hydrogen bonding distances along peptide backbones. Molecular conformations from MD simulations are used to model charge transport in NEGF-DFT calculations, and the results are in reasonable qualitative agreement with experiments. Projected density of states calculations and molecular orbital visualizations are further used to understand the role of amino acid side chains on transport. Overall, our results show that secondary structure plays a key role in electron transport in peptides, which provides broad avenues for understanding the electronic properties of proteins.

Science & Technology - Other Topics↗
DOE OSTI2025

Visualizing the strong field–induced molecular breakup of C 60 via x-ray diffraction

Laser-driven dynamics in polyatomic molecules poses a complex many-body problem. Understanding intense light-matter interaction is crucial for steering intramolecular quantum dynamical processes. Here, we record time-resolved x-ray diffraction images of C 60 molecules during and after their interaction with intense near-infrared fields, giving direct access to structural changes of the molecules and their fragmentation in real time. Tuning the intensity of the excitation pulses, we uncover a transition from a weak-field regime of excited but stable molecules to a high-field regime dominated by Coulomb explosion. In the transition region, the molecules expand by up to 50% of their initial size within just 140 fs, with major fragmentation only setting in afterward. This work demonstrates that x-ray diffractive imaging is capable of retrieving time-resolved structural information of large molecules reshaped by intense laser fields. Laser-driven fragmentation is a first step toward observing molecular processes modified by laser fields of increasing intensity.

Schnorr, Kirsten [Paul Scherrer Inst. (PSI), Villi↗
DOE OSTI2020

UnityMol-APBS

Virtual reality for biomolecular electrostatics UnityMol-APBS (NIH iEdison No. 0685901-19-0009, Grant No. GM069702) Visualization of molecular electrostatics on a two-dimensional screen greatly diminishes the associated depth component. Using a virtual world to explore molecular electrostatics allows researchers to be immersed within their data.

Baker, Nathan↗
DOE OSTI2024

Single-molecule imaging of lignocellulose deconstruction by SCATTIRSTORM microscopy

The goal of this project is to build a multimodal optical microscope to measure the binding, processive degradation, and pausing behaviors of cellulases as they interact with and degrade both synthetic and naturally occurring lignocellulosic walls. To achieve this, we will use high spatio-temporal single-molecule imaging to track cellulases, while visualizing specific molecular components of cellulose, lignin and hemicellulose, that make up their lignocellulose substrate. The microscope will combine Interferometric Scattering (iSCAT), which provides unprecedented spatiotemporal resolution; Total Internal Reflection Fluorescence (TIRF), which provides single-molecule resolution of multiple fluorophore-labeled molecules; and Stochastic Reconstruction (STORM), which allows for three-dimensional super-resolution imaging of intact plant cell walls during degradation. Initial studies will investigate cellulase dynamics on in vitro-assembled cell wall analogs, and later work will progress to using native plant cell walls.

09 BIOMASS FUELS↗
DOE OSTI2020

Short-wavelength-sensitive 2 (Sws2) visual photopigment models combined with atomistic molecular simulations to predict spectral peaks of absorbance

For many species, vision is one of the most important sensory modalities for mediating essential tasks that include navigation, predation and foraging, predator avoidance, and numerous social behaviors. The vertebrate visual process begins when photons of the light interact with rod and cone photoreceptors that are present in the neural retina. Vertebrate visual photopigments are housed within these photoreceptor cells and are sensitive to a wide range of wavelengths that peak within the light spectrum, the latter of which is a function of the type of chromophore used and how it interacts with specific amino acid residues found within the opsin protein sequence. Minor differences in the amino acid sequences of the opsins are known to lead to large differences in the spectral peak of absorbance (i.e. the λ max value). In our prior studies, we developed a new approach that combined homology modeling and molecular dynamics simulations to gather structural information associated with chromophore conformation, then used it to generate statistical models for the accurate prediction of λ max values for photopigments derived from Rh1 and Rh2 amino acid sequences. In the present study, we test our novel approach to predict the λ max of phylogenetically distant Sws2 cone opsins. To build a model that can predict the λ max using our approach presented in our prior studies, we selected a spectrally-diverse set of 11 teleost Sws2 photopigments for which both amino acid sequence information and experimentally measured λ max values are known. The final first-order regression model, consisting of three terms associated with chromophore conformation, was sufficient to predict the λ max of Sws2 photopigments with high accuracy. This study further highlights the breadth of our approach in reliably predicting λ max values of Sws2 cone photopigments, evolutionary-more distant from template bovine RH1, and provided mechanistic insights into the role of known spectral tuning sites.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2023

Molecular-gas-dynamics simulations of turbulent Couette flow over a mean-free-path-scale permeable substrate

Here we report flow statistics and visualizations from molecular-gas-dynamics simulations using the direct simulation Monte Carlo (DSMC) method for turbulent Couette flow in a minimal domain where the lower wall is replaced by an idealized permeable fibrous substrate representative of thermal-protection-system materials for which the Knudsen number is O(10 -1 ). Comparisons are made with smooth-wall DSMC simulations and smooth-wall direct numerical simulations (DNS) of the Navier-Stokes equations for the same conditions. Roughness, permeability, and noncontinuum effects are assessed. In the range of Reynolds numbers considered herein, the scalings of the skin friction on the permeable substrate and of the mean flow within the substrate suggest that they are dominated by viscous effects. While the regenerative cycle characteristic of smooth-wall turbulence remains intact for all cases considered, we observe that the near-wall velocity fluctuations are modulated by the permeable substrate with a wavelength equal to the pore spacing. Additionally, the flow within the substrate shows significant rarefaction effects, resulting in an apparent permeability that is 13% larger than the intrinsic permeability. In contrast, the smooth-wall DSMC and DNS simulations exhibit remarkably good agreement for the statistics examined, despite the Knudsen number based on the viscous length scale being as large as O(10 -1 ). This latter result is at variance with classical estimates for the breakdown of the continuum assumption and calls for further investigations into the interaction of noncontinuum effects and turbulence.

42 ENGINEERING↗
DOE OSTI2023

Direct Observation of Twin van der Waals Molecular Chains

The van der Waals (vdW) assemblies are the most common structures of materials. However, directly mapping intermolecular electron clouds of a vdW assembly has never been obtained, even though the intramolecular electron clouds were visualized by atomic-resolution techniques. In this report, we unprecedently mapped the intermolecular electron cloud of the assembles of ethanol molecules via ethyl groups with noncontact atomic force microscopy at 5 K, leading to the first visualization of vdW molecular chains, in which ethanol molecules assemble into twin vdW molecular chains in a reverse parallel configuration on Ag(111) plane. Furthermore, spontaneous order-disorder transitions in the chain were dynamically observed, suggesting its unusual properties different from 2D vdW materials. In conclusion, these findings provide an "eye" to see the atomic world of vdW materials.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗