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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 325 records · Page 18
All sourcesNASA NTRSDOE OSTI
DOE OSTI2025

Scaling Field-Theoretic Simulation for Multicomponent Mixtures with Neural Operators

Multicomponent polymer mixtures are ubiquitous in biological self-organization but are notoriously difficult to study computationally. Plagued by both slow single molecule relaxation times and slow equilibration within dense mixtures, molecular dynamics simulations are typically infeasible at the spatial scales required to study the stability of mesophase structure. Polymer field theories offer an attractive alternative, but analytical calculations are only tractable for mean-field theories and nearby perturbations, constraints that become especially problematic for fluctuation-induced effects such as coacervation. Here, we show that a recently developed technique for obtaining numerical solutions to partial differential equations based on operator learning, neural operators, lends itself to a highly scalable training strategy by parallelizing per-species operator maps. We illustrate the efficacy of our approach on six-component mixtures with randomly selected compositions and that it significantly outperforms the state-of-the-art pseudospectral integrators for field-theoretic simulations, especially as polymer lengths become long.

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

Autonomous Molecular Structure Imaging with High-Resolution Atomic Force Microscopy for Molecular Mixture Discovery

Due to its single-molecule sensitivity, high-resolution atomic force microscopy (HR-AFM) has proved to be a valuable and uniquely advantageous tool to study complex molecular mixtures, which hold promise for developing clean energy and achieving environmental sustainability. However, significant challenges remain to achieve the full potential of the sophisticated and time-consuming experiments. Automation combined with machine learning (ML) and artificial intelligence (AI) is key to overcoming these challenges. Here we present Auto-HR-AFM, an AI tool to automatically collect HR-AFM images of petroleum-based mixtures. In this study, we trained an instance segmentation model to teach Auto-HR-AFM how to recognize features in HR-AFM images. Auto-HR-AFM then uses that information to optimize the imaging by adjusting the probe-molecule distance for each molecule in the run. Auto-HR-AFM is the initial tool that will lead to fully automated scanning probe microscopy (SPM) experiments, from start to finish. This automation will allow SPM to become a mainstream characterization technique for complex mixtures, an otherwise unattainable target.

36 MATERIALS SCIENCE↗
DOE OSTI2025

Toward a Better Understanding of Ni Coarsening in Solid Oxide Cells: NiH on Ni (111) Examined Using a Combined Theoretical Approach

The coarsening of the Ni particles in the hydrogen electrode of solid oxide cells (SOCs) is an important degradation mechanism. Here, in this paper, density-functional theory and kinetic Monte Carlo methods are used to explore our recent hypothesis that the surface diffusion of NiH may cause faster Ni coarsening in electrolysis cell mode under an overpotential. Using both methods, the diffusion constant or diffusivity of NiH on Ni (111) is determined as the product of the surface coverage and single-molecule diffusivity for the first time considering all possible diffusion paths. It is then determined versus overpotential at the triple-phase boundary of the hydrogen electrode assuming a typical operating temperature of the SOC. Under a significant overpotential, the diffusivity of NiH is found to be sufficiently large to support the above hypothesis that NiH may promote Ni coarsening. However, based on the adsorption configurations identified, the dissociation and reformation of NiH on Ni (111) could occur. Thus, more work is needed to develop a model of Ni coarsening considering both molecular and dissociated forms of NiH.

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

Excited-State Charge Distribution of a Donor–π–Acceptor Zn Porphyrin Probed by N K-Edge Transient Absorption Spectroscopy

Zinc porphyrin solar cell dyes with donor-π–acceptor architectures combine light absorber (π), electron-donor, and electron-acceptor moieties inside a single molecule with atomic precision. The donor-π–acceptor design promotes the separation of charge carriers following optical excitation. Here, we probe the excited-state electronic structure within such molecules by combining time-resolved X-ray absorption spectroscopy at the N K-edge with first-principles time-dependent density functional theory (TD-DFT) calculations. Furthermore, customized Zn porphyrins with strong-donor triphenylamine groups or weak-donor tri-tert-butylbenzene groups were synthesized. Energetically well-separated N K-edge absorption features simultaneously probe the excited-state electronic structure from the perspectives of the macrocycle and triphenylamine N atoms. New absorption transitions between the macrocycle N atoms and the excited-state HOMO vacancy are observed, and the triphenylamine associated absorption feature blue-shifts, consistent with partial oxidation of the donor groups in the excited state.

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

Super-resolution Imaging of Plasmonic Near-Fields: Overcoming Emitter Mislocalizations

Plasmonic nano-objects have shown great potential in enhancing applications like biological/chemical sensing, light harvesting and energy transfer, and optical/quantum computing. Therefore, an extensive effort has been vested in optimizing plasmonic systems and exploiting their field enhancement properties. Super-resolution imaging with quantum dots (QDs) is a promising method to probe plasmonic near-fields but is hindered by the distortion of the QD radiation pattern. Here, we investigate the interaction between QDs and “L-shaped” gold nanoantennas and demonstrate both theoretically and experimentally that this strong interaction can induce polarization-dependent modifications to the apparent QD emission intensity, polarization, and localization. Based on FDTD simulations and polarization-modulated single-molecule microscopy, we show that the displacement of the emitter’s localization is due to the position-dependent interference between the emitter and the induced dipole, and can be up to 100 nm. Our results help pave a pathway for higher precision plasmonic near-field mapping and its underlying applications.

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

Using Hyperoptimized Tensor Networks and First-Principles Electronic Structure to Simulate the Experimental Properties of the Giant {Mn 84 } Torus

The single-molecule magnet {Mn 84 } is a challenge to theory because of its high nuclearity. Here, we directly compute two experimentally accessible observables, the field-dependent magnetization up to 75 T and the temperature-dependent heat capacity, using parameter-free theory. In particular, we use first-principles calculations to derive short- and long-range exchange interactions and compute the exact partition function of the resulting classical Potts and Ising spin models for all 84 Mn S = 2 spins to obtain observables. The latter computation is made possible by using hyperoptimized tensor network contractions, a technique developed to simulate quantum supremacy circuits. We also synthesize the magnet and measure its heat capacity and magnetization, observing qualitative agreement between theory and experiment and identifying an unusual bump in the heat capacity and a plateau in the magnetization. Our work also identifies some limitations of current theoretical modeling in large magnets, such as sensitivity to small, long-range exchange couplings.

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

Trap-Filling Magnetoconductance as an Initialization and Readout Mechanism of Triplet Exciton Spins

Photoexcited triplet states are promising candidates for hybrid qubit systems, as they can be used as a controlling gate for nuclear spins. But microwave readout schemes do not generally offer the sensitivity needed to approach the single-molecule limit or the scope to integrate such systems into devices. In this report we demonstrate the possibility of electrical readout of triplet spins at room temperature through a specific mechanism of magnetoconductance (MC) in polycrystalline pentacene. We show that hole-only pentacene devices exhibit a positive photoinduced MC response that is consistent with a trap-filling mechanism. Spin and magnetic-field-dependent quenching of photogenerated triplets by holes quantitatively explains the MC response we observe. These results are distinct in both sign and proposed mechanism compared to previous reports on polyacene materials and provide clear design rules for future spintronic devices based on this spin-sensing mechanism.

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

LHCSR1 Functions as a Dimmer Switch for Light Harvesting

In oxygenic photosynthesis, high light leads to a set of photoprotective processes, known as nonphotochemical quenching, that are required for fitness. In moss and algae, the pigment−protein complex, light-harvesting stress-related (LHCSR), is crucial for photoprotection. Acidification of the thylakoid lumen under high light triggers the activation of LHCSR and the conversion of the xanthophyll violaxanthin into zeaxanthin, which is found within LHCSR. These interrelated molecular components combine to turn on a safety valve that dissipates excess energy as heat. Previous studies of detergent-solubilized LHCSR1 found that pH and zeaxanthin regulate distinct quenching sites via the protein conformation. However, protein function in the native membrane environment can be significantly different. In this work, we applied single-molecule fluorescence spectroscopy to LHCSR1 in membrane nanodiscs. The membrane environment enhanced total quenching, regardless of pH or zeaxanthin-binding. pH-dependent quenching was still observed whereas zeaxanthin-dependent quenching was suppressed. Conformational changes also increased in the membrane, establishing that the local environment can change the nature of the equilibrium between light harvesting and photoprotection.

Hoffmann, Madeline P. [Massachusetts Inst. of Tech↗
DOE OSTI2021

Topological Frustration as a New Parameter to Tune Morphology Revealed through Exploring the Continuum between A-B-C 3-Arm Star and Linear Triblock Polymers

Block polymers assemble into a variety of phase-separated morphologies based on volume fraction (φ) and interactions (χ) of the respective blocks. The arrangement of three different polymer blocks could either be a 3-arm star, with each block having one terminus attached to a common junction point or a linear A-B-C architecture. A versatile strategy is reported to synthesize a series of well-defined graft polymers that lie along the unexplored continuum between a 3-arm star and an A-B-C linear triblock polymer architecture. Using the technique of single-molecule insertion, precise control over the position of graft arm C along the B chain was achieved. A series of discrete graft polymers (PMMA-b-PS-g-PEO) with fixed φ and prescribed ω values that lie on the continuum between a 3-arm star (ω = 0) and linear triblock polymer (ω = 1) were synthesized. Morphological studies using small-angle X-ray scattering and conventional and energy-filtered transmission electron microscopy reveal the transition between lamellae, perforated lamellae, and cylindrical morphologies with systematic variation in the ω values, a trend attributed to the topological frustration and the associated χ values between the three blocks. Molecular dynamic simulations of coarse-grained models were found to predict phase diagrams that are consistent with the experimentally observed morphologies. Furthermore, our results suggest that changes in ω lead to topological frustration which is an important additional new design parameter that can be used to tune the morphology of multiblock polymers in addition to φ and χ.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2024

Engineering Small HOMO–LUMO Gaps in Polycyclic Aromatic Hydrocarbons with Topologically Protected States

Topological phases in laterally confined low-dimensional nanographenes have emerged as versatile design tools that can imbue otherwise unremarkable materials with exotic band structures ranging from topological semiconductors and quantum dots to intrinsically metallic bands. The periodic boundary conditions that define the topology of a given lattice have thus far prevented the translation of this technology to the quasi-zero-dimensional (0D) domain of small molecular structures. Here, we describe the synthesis of a polycyclic aromatic hydrocarbon (PAH) featuring two localized zero modes (ZMs) formed by the topological junction interface between a trivial and nontrivial phase within a single molecule. First-principles density functional theory calculations predict a strong hybridization between adjacent ZMs that gives rise to an exceptionally small HOMO–LUMO gap. Scanning tunneling microscopy and spectroscopy corroborate the molecular structure of 9/7/9-double quantum dots and reveal an experimental quasiparticle gap of 0.16 eV, corresponding to a carbon-based small molecule long-wavelength infrared (LWIR) absorber.

77 NANOSCIENCE AND NANOTECHNOLOGY↗
DOE OSTI2025

Molecular-Scale Insights into the Heterogeneous Interactions between an m -Terphenyl Isocyanide Ligand and Noble Metal Nanoparticles

The structural and chemical properties of metal nanoparticles are often dictated by their interactions with molecular ligand shells. These interactions are highly material-specific and can vary significantly even among elements within the same group or materials with similar crystal structure. In this study, we surveyed the heterogeneous interactions between an m-terphenyl isocyanide ligand and Au and Ag nanoparticles (NPs) at the single-molecule limit. Specifically, we found that the ligation behavior with this molecule differs significantly between that of Au and AgNPs. Surface-enhanced Raman spectroscopy measurements revealed unique enhancement factors for two molecular vibrational modes between two metal surfaces, indicating different ligand binding geometries. Molecular-level characterization using scanning tunneling microscopy allowed us to directly visualize these variations between Ag and Au surfaces, which we assign as two distinct binding mechanisms. This molecular-scale visualization provides clear insights into the different ligand–metal interactions as well as the chemical behavior and spectroscopic characteristics of isocyanide-functionalized NPs.

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

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

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

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2022

Stressing Halide Perovskites with Light and Electric Fields

Understanding the light and electric field-induced effects underlying the local changes in optoelectronic properties in lead halide perovskites is crucial to establish a detailed structure–function relationship. Here, in this study, we use single-molecule absorption scanning tunneling microscopy (SMA-STM) to probe the local surface inhomogeneity of a mixed A-site cation/mixed halide perovskite under pulsed 532 nm photoexcitation to gain insight into the varying grain-to-grain absorption behavior at the nanoscale and reduction in the electronic bandgap under illumination. To correlate the observed changes in the absorption signal to structural ones, we utilize synchrotron X-ray STM (SX-STM) where we find that photoexcitation induces changes in the X-ray absorption spectral signatures. Lastly, using pump–probe time-resolved wide-angle X-ray scattering, we show the presence of nonthermal lattice deformations upon photoexcitation which indicate that the excited photocarriers distort the perovskite lattice, corroborating the local electronic changes observed by our STM measurements.

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

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

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

multiscale imaging↗
DOE OSTI2024

Discovery of Multiple Light-Harvesting States of the Photosynthetic Protein PE545

Cryptophytes are photosynthetic microalga that flourish in a remarkable diversity of natural environments by using pigment-containing proteins with absorption maxima tuned to each ecological niche. While this diversity in the absorption has been well established, the subsequent photophysics is highly sensitive to the local protein environment and so may exhibit similar variation. Thermal fluctuations of the protein conformation are expected to introduce photophysical heterogeneity of the pigments that may have evolved important functional properties in a manner similar to that of the absorption. However, such heterogeneity is averaged out in ensemble measurements and, therefore, has not yet been probed. Here, we report single-molecule measurements of phycoerythrin 545 (PE545), the prototypical cryptophyte antenna protein, in its native dimeric form. A conformational ensemble was resolved consisting of distinct photophysical states with different light-harvesting properties. Proteins that did not quench, partially quenched, or fully quenched absorbed light were observed. Light intensity increased the quenched-state population of the dimer, potentially as a mechanism to deal with the extreme light intensities found in aqueous environments. Cross-linking, which mimics local interactions, introduces this light-dependent functionality while also suppressing other conformational dynamics. The cellular organization can, therefore, actively modulate the protein conformation and dynamics, selecting for distinct levels of light harvesting. Furthermore, the complex conformational equilibrium provides an additional mechanism for cryptophytes and likely other photosynthetic organisms to optimize solar energy capture and conversion.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2024

Observation of a single protein by ultrafast X-ray diffraction

The idea of using ultrashort X-ray pulses to obtain images of single proteins frozen in time has fascinated and inspired many. It was one of the arguments for building X-ray free-electron lasers. According to theory, the extremely intense pulses provide sufficient signal to dispense with using crystals as an amplifier, and the ultrashort pulse duration permits capturing the diffraction data before the sample inevitably explodes. This was first demonstrated on biological samples a decade ago on the giant mimivirus. Since then, a large collaboration has been pushing the limit of the smallest sample that can be imaged. The ability to capture snapshots on the timescale of atomic vibrations, while keeping the sample at room temperature, may allow probing the entire conformational phase space of macromolecules. Here we show the first observation of an X-ray diffraction pattern from a single protein, that of Escherichia coli GroEL which at 14 nm in diameter is the smallest biological sample ever imaged by X-rays, and demonstrate that the concept of diffraction before destruction extends to single proteins. From the pattern, it is possible to determine the approximate orientation of the protein. Our experiment demonstrates the feasibility of ultrafast imaging of single proteins, opening the way to single-molecule time-resolved studies on the femtosecond timescale.

71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗
DOE OSTI2020

X-ray structure of LeuT in an inward-facing occluded conformation reveals mechanism of substrate release

Neurotransmitter:sodium symporters (NSS) are conserved from bacteria to man and serve as targets for drugs, including antidepressants and psychostimulants. Here we report the X-ray structure of the prokaryotic NSS member, LeuT, in a Na+/substrate-bound, inward-facing occluded conformation. To obtain this structure, we were guided by findings from single-molecule fluorescence spectroscopy and molecular dynamics simulations indicating that L-Phe binding and mutation of the conserved N-terminal Trp8 to Ala both promote an inward-facing state. Compared to the outward-facing occluded conformation, our structure reveals a major tilting of the cytoplasmic end of transmembrane segment (TM) 5, which, together with release of the N-terminus but without coupled movement of TM1, opens a wide cavity towards the second Na + binding site. The structure of this key intermediate in the LeuT transport cycle, in the context of other NSS structures, leads to the proposal of an intracellular release mechanism of substrate and ions in NSS proteins.

Science & Technology - Other Topics↗
DOE OSTI2020

Molecular design principles of Lysine-DOPA wet adhesion

The mussel byssus has long been a source of inspiration for the adhesion community. Recently, adhesive synergy between flanking lysine (Lys, K) and 3,4-Dihydroxyphenylalanine (DOPA, Y ) residues in the mussel foot proteins (Mfps) has been highlighted. However, the complex topological relationship of DOPA and Lys as well as the interfacial adhesive roles of other amino acids have been understudied. Herein, we study adhesion of Lys and DOPA-containing peptides to organic and inorganic substrates using single-molecule force spectroscopy (SMFS). We show that a modest increase in peptide length, from K Y to (K Y ) 3 , increases adhesion strength to TiO 2. Surprisingly, further increase in peptide length offers no additional benefit. Additionally, comparison of adhesion of dipeptides containing Lys and either DOPA (K Y ) or phenylalanine (KF) shows that DOPA is stronger and more versatile. We furthermore demonstrate that incorporating a nonadhesive spacer between (K Y ) repeats can mimic the hidden length in the Mfp and act as an effective strategy to dissipate energy.

59 BASIC BIOLOGICAL SCIENCES↗