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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 271 records · Page 15
All sourcesNASA NTRSDOE OSTI
DOE OSTI2022

Fast optical transport of ultracold molecules over long distances

Abstract Optically trapped laser-cooled polar molecules hold promise for new science and technology in quantum information and quantum simulation. Large numerical aperture optical access and long trap lifetimes are needed for many studies, but these requirements are challenging to achieve in a magneto-optical trap (MOT) vacuum chamber that is connected to a cryogenic buffer gas beam source, as is the case for all molecule laser cooling experiments so far. Long distance transport of molecules greatly eases fulfilling these requirements as molecules are placed into a region separate from the MOT chamber. We realize a fast transport method for ultracold molecules based on an electronically focus-tunable lens combined with an optical lattice. The high transport speed is achieved by the 1D red-detuned optical lattice, which is generated by interference of a focus-tunable laser beam and a focus-fixed laser beam. Efficiency of 48(8)% is realized in the transport of ultracold calcium monofluoride (CaF) molecules over 46 cm distance in 50 ms, with a moderate heating from 32(2) μ K to 53(4) μ K. Positional stability of the molecular cloud allows for stable loading of an optical tweezer array with single molecules.

74 ATOMIC AND MOLECULAR PHYSICS↗
DOE OSTI2024

Targeted protein degradation systems to enhance Wnt signaling

Molecules that facilitate targeted protein degradation (TPD) offer great promise as novel therapeutics. The human hepatic lectin asialoglycoprotein receptor (ASGR) is selectively expressed on hepatocytes. We have previously engineered an anti-ASGR1 antibody-mutant RSPO2 (RSPO2RA) fusion protein (called SWEETS) to drive tissue-specific degradation of ZNRF3/RNF43 E3 ubiquitin ligases, which achieved hepatocyte-specific enhanced Wnt signaling, proliferation, and restored liver function in mouse models, and an antibody–RSPO2RA fusion molecule is currently in human clinical trials. In the current study, we identified two new ASGR1- and ASGR1/2-specific antibodies, 8M24 and 8G8. High-resolution crystal structures of ASGR1:8M24 and ASGR2:8G8 complexes revealed that these antibodies bind to distinct epitopes on opposing sides of ASGR, away from the substrate-binding site. Both antibodies enhanced Wnt activity when assembled as SWEETS molecules with RSPO2RA through specific effects sequestering E3 ligases. In addition, 8M24-RSPO2RA and 8G8-RSPO2RA efficiently downregulate ASGR1 through TPD mechanisms. These results demonstrate the possibility of combining different therapeutic effects and degradation mechanisms in a single molecule.

59 BASIC BIOLOGICAL SCIENCES↗
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 OSTI2026

Unraveling the Dynamics of Nucleosome Arrays

The organization of genomic DNA into chromatin is a fundamental determinant of genome stability, regulation, and cellular function. Nucleosomes, the basic repeating units of chromatin, assemble into higher-order structures whose organization and heterogeneity remain difficult to characterize using conventional ensemble-averaged techniques. A key need in the field is the development of experimental approaches capable of directly visualizing nucleosome assemblies and their structural variability at the single-molecule level. This LDRD Lab-Wide project focused on establishing and evaluating atomic force microscopy (AFM)–based approaches for the characterization of nucleosome assemblies. The work emphasized experimental workflows for preparing, imaging, and assessing multi-nucleosome systems, rather than isolated single nucleosomes. Through method development and exploratory measurements, the project demonstrated the feasibility of applying scanning probe microscopy to investigate chromatin-relevant assemblies and provided preliminary insight into the strengths and limitations of this approach for future quantitative studies. Results and lessons learned from this effort were disseminated to the broader scientific community through multiple national conference presentations, helping to position LLNL for continued work in chromatin and genome organization research.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2025

Effect of tert -Butyl Substitution on the Interactions of Cobalt Phthalocyanine with a Carbon Monoxide-Functionalized Tip

Supported cobalt phthalocyanines (CoPc) are promising catalysts for CO 2 reduction, a critical process for mitigating greenhouse gas emissions. Enhancing the catalytic performance of CoPc involves modifying the interaction between the cobalt center and intermediate species. This study focuses on the effects of tert-butyl substitution on CoPc using (tert-butyl) 4 CoPc, where the substitution can both directly alter the molecule’s intramolecular electronic structure and indirectly alter it by the bulky group weakening the interaction with the support. Toward this end, we investigated the structural and chemical properties of (tert-butyl) 4 CoPc on a Ag(111) surface at the single-molecule level using three-dimensional atomic force microscopy (AFM) with a CO-terminated tip and discussed them in comparison with data for unmodified CoPc and amino-substituted CoPc. Notably, distance-dependent force measurements revealed anomalies in the tert-butyl groups’ force curves, attributed to their rotational flexibility. The tert-butyl (t-butyl) groups were also observed to increase the attraction of the central Co atom to CO, but this effect was attributed largely to enhanced interactions of the back of the tip with the peripheral t-butyl groups. In conclusion, while this longer-range interaction would not be expected to impact the interaction of small molecules with the catalytic center, the results reveal the ability of AFM to characterize longer range environmental interactions that can enhance adsorption and subsequent reactions of larger molecules, as well as the role side chains that offer configurational adaptability may play in these interactions.

77 NANOSCIENCE AND NANOTECHNOLOGY↗
DOE OSTI2021

Visualization and modeling of inhibition of IL-1β and TNF-α mRNA transcription at the single-cell level

Abstract IL-1β and TNF-α are canonical immune response mediators that play key regulatory roles in a wide range of inflammatory responses to both chronic and acute conditions. Here we employ an automated microscopy platform for the analysis of messenger RNA (mRNA) expression of IL-1β and TNF-α at the single-cell level. The amount of IL-1β and TNF-α mRNA expressed in a human monocytic leukemia cell line (THP-1) is visualized and counted using single-molecule fluorescent in-situ hybridization (smFISH) following exposure of the cells to lipopolysaccharide (LPS), an outer-membrane component of Gram-negative bacteria. We show that the small molecule inhibitors MG132 (a 26S proteasome inhibitor used to block NF-κB signaling) and U0126 (a MAPK Kinase inhibitor used to block CCAAT-enhancer-binding proteins C/EBP) successfully block IL-1β and TNF-α mRNA expression. Based upon this single-cell mRNA expression data, we screened 36 different mathematical models of gene expression, and found two similar models that capture the effects by which the drugs U0126 and MG132 affect the rates at which the genes transition into highly activated states. When their parameters were informed by the action of each drug independently, both models were able to predict the effects of the combined drug treatment. From our data and models, we postulate that IL-1β is activated by both NF-κB and C/EBP, while TNF-α is predominantly activated by NF-κB. Our combined single-cell experimental and modeling efforts show the interconnection between these two genes and demonstrates how the single-cell responses, including the distribution shapes, mean expression, and kinetics of gene expression, change with inhibition.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2022

Observation of Collective Molecular Dynamics in a Chalcogenide Glass: Results from X-ray Photon Correlation Spectroscopy

The structural relaxation processes in a Ge 3 As 52 S 45 molecular chalcogenide glass sample were directly studied by X-ray photon correlation spectroscopy (XPCS). XPCS was conducted at the first sharp diffraction peak at q = 1.16 Å -1 at temperatures ranging from 123 K to above the glass transition at 328 K, and the results showed two different dynamical regimes. At a low temperature, the observed glass dynamics are slow and dominated by X-ray-photon-induced effects, which are temperature independent. At a higher temperature, we observed a dramatic decrease in the fluctuation timescales, indicating that the dynamics were mainly due to the intermolecular correlation of the As 4 S 3 molecule in the glass. The timescales in this high-temperature range agree well with those determined from measurements of the Newtonian viscosity. Here our XPCS studies suggest an extended length scale of the relaxation process in glassy Ge 3 As 52 S 45 from the single molecule to the intermolecular range across the glass transition, providing a unique direct probe of the dynamics beyond the length scales of the individual molecule.

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

Uncovering translation roadblocks during the development of a synthetic tRNA

Ribosomes are remarkable in their malleability to accept diverse aminoacyl-tRNA substrates from both the same organism and other organisms or domains of life. This is a critical feature of the ribosome that allows the use of orthogonal translation systems for genetic code expansion. Optimization of these orthogonal translation systems generally involves focusing on the compatibility of the tRNA, aminoacyl-tRNA synthetase, and a non-canonical amino acid with each other. As we expand the diversity of tRNAs used to include non-canonical structures, the question arises as to the tRNA suitability on the ribosome. Specifically, we investigated the ribosomal translation of allo-tRNA UTu1 , a uniquely shaped (9/3) tRNA exploited for site-specific selenocysteine insertion, using single-molecule fluorescence. With this technique we identified ribosomal disassembly occurring from translocation of allo-tRNA UTu1 from the A to the P site. Using cryo-EM to capture the tRNA on the ribosome, we pinpointed a distinct tertiary interaction preventing fluid translocation. Through a single nucleotide mutation, we disrupted this tertiary interaction and relieved the translation roadblock. With the continued diversification of genetic code expansion, our work highlights a targeted approach to optimize translation by distinct tRNAs as they move through the ribosome.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2022

A scanning-to-incision switch in TFIIH-XPG induced by DNA damage licenses nucleotide excision repair

Nucleotide excision repair (NER) is critical for removing bulky DNA base lesions and avoiding diseases. NER couples lesion recognition by XPC to strand separation by XPB and XPD ATPases, followed by lesion excision by XPF and XPG nucleases. Here, we describe key regulatory mechanisms and roles of XPG for and beyond its cleavage activity. Strikingly, by combing single-molecule imaging and bulk cleavage assays, we found that XPG binding to the 7-subunit TFIIH core (coreTFIIH) stimulates coreTFIIH-dependent double-strand (ds)DNA unwinding 10-fold, and XPG-dependent DNA cleavage by up to 700-fold. Simultaneous monitoring of rates for coreTFIIH single-stranded (ss)DNA translocation and dsDNA unwinding showed XPG acts by switching ssDNA translocation to dsDNA unwinding as a likely committed step. Pertinent to the NER pathway regulation, XPG incision activity is suppressed during coreTFIIH translocation on DNA but is licensed when coreTFIIH stalls at the lesion or when ATP hydrolysis is blocked. Moreover, ≥15 nucleotides of 5'-ssDNA is a prerequisite for efficient translocation and incision. Our results unveil a paired coordination mechanism in which key lesion scanning and DNA incision steps are sequentially coordinated, and damaged patch removal is only licensed after generation of ≥15 nucleotides of 5'-ssDNA, ensuring the correct ssDNA bubble size before cleavage.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2026

Carbon-Based Quantum Information Science with Symmetry Protected Topological States (Final Report, DOE-BES award DE-SC0023105)

This research program established the scientific foundation for the rational, bottom-up design, synthesis, isolation, and investigation of symmetry-protected topological (SPT) electron spin qubits embedded in graphene nanoribbons (GNRs). The work focused on integrating atomically precise low-dimensional carbon nanostructures with emerging quantum logic architectures, providing a pathway toward scalable quantum materials for next-generation computing and sensing technologies. A central component of the program was the elucidation of fundamental relationships between real-space molecular architecture, local spin density distributions, electronic band dispersion, and energy level alignment in atomically precise GNR systems. These correlations define key operational parameters of SPT qubits and were systematically investigated to establish quantitative benchmarks against established molecular and solid-state spin qubit platforms. Attention was given to properties critical for quantum device performance, e.g. decoherence times, spectral sharpness of energy transitions, and tunable exchange interactions between spin states. The research demonstrated that these parameters can be engineered with atomic precision through scalable bottom-up synthetic strategies. Theory-guided design played a central role in identifying candidate structures hosting topologically protected spin states. Experimental validation was performed using both ensemble measurements and single-molecule characterization. In addition to advances in quantum materials synthesis, the program developed and applied spin-sensitive scanning probe microscopy techniques capable of directly probing quantum states and dynamic processes with atomic-scale spatial resolution. These capabilities enabled direct observation and characterization of quantum structures at the single-atom level. While the research activities were primarily hypothesis-driven fundamental investigations, the program adopted a comprehensive materials-by-design framework aimed at translating scientific discoveries into technological concepts compatible with scalable and intelligent manufacturing approaches.

36 MATERIALS SCIENCE↗
DOE OSTI2021

A Nitroxide Containing Organic Molecule in a Deep Eutectic Solvent for Flow Battery Applications

The nitroxide radical redox organic molecule, 2-phenyl-4,4,5,5-tetrame- thylimidazoline-1-oxyl-3-oxide (PTIO), was investigated for the first time in a deep eutectic solvent (DES)-like system consisting of a 1:4 molar ratio of choline chloride and ethylene glycol(Ch1EG4) as a redox flow battery electrolyte. PTIO is a single molecule with three oxidation states, and can provide both positive and negative redox couples for a flow battery. A flow battery using the PTIO/Ch1EG4 electrolyte demonstrated nearly 50% roundtrip efficiency with an approximately 1 V open circuit potential. Inefficiencies were primarily due to membrane resistance which can be significantly lowered with increased temperature. While PTIO appears stable over short periods (hours), the oxidized form is not stable in the DES-like electrolyte over longer times. Molecular modeling was performed to investigate the relative stability of PTIO in DES as compared to the previously studied 4-hydroxy-TEMPO (4HT). It was found that the oxoammonium cation 4HT + exhibits a noticeably larger nucleophilic reactive cloud as compared to PTIO + , indicating a higher reactivity. This method to predict stability of the oxoammonium cation shows promise to inform the design and synthesis of promising redox systems based on nitroxide radicals in DES electrolytes to identify new chemistries for large scale energy storage.

25 ENERGY STORAGE↗
DOE OSTI2021

Light–matter interaction of a molecule in a dissipative cavity from first principles

Cavity-mediated light–matter coupling can dramatically alter opto-electronic and physico-chemical properties of a molecule. Ab initio theoretical predictions of these systems need to combine non-perturbative, many-body electronic structure theory-based methods with cavity quantum electrodynamics and theories of open-quantum systems. Here, we generalize quantum-electrodynamical density functional theory to account for dissipative dynamics of the cavity and describe coupled cavity–single molecule interactions in the weak-to-strong-coupling regimes. Specifically, to establish this generalized technique, we study excited-state dynamics and spectral responses of benzene and toluene under weak-to-strong light–matter coupling. By tuning the coupling, we achieve cavity-mediated energy transfer between electronically excited states. This generalized ab initio quantum-electrodynamical density functional theory treatment can be naturally extended to describe cavity-mediated interactions in arbitrary electromagnetic environments, accessing correlated light–matter observables and thereby closing the gap between electronic structure theory, quantum optics, and nanophotonics.

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

Long-term super-resolution inner mitochondrial membrane imaging with a lipid probe

The inner mitochondrial membrane (IMM) generates power to drive cell function, and its dynamics control mitochondrial health and cellular homeostasis. Here, we describe the cell-permeant, lipid-like small molecule MAO-N 3 and use it to assemble high-density environmentally sensitive (HIDE) probes that selectively label and image the IMM in live cells and multiple cell states. MAO-N 3 pairs with strain-promoted azide–alkyne click chemistry-reactive fluorophores to support HIDE imaging using confocal, structured illumination, single-molecule localization and stimulated emission depletion microscopy, all with significantly improved resistance to photobleaching. These probes generate images with excellent spatial and temporal resolution, require no genetic manipulations, are non-toxic in model cell lines and primary cardiomyocytes (even under conditions that amplify the effects of mitochondrial toxins) and can visualize mitochondrial dynamics for 12.5 h. This probe will enable comprehensive studies of IMM dynamics with high temporal and spatial resolution.

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

Extremely Bright, Near-IR Emitting Spontaneously Blinking Fluorophores Enable Ratiometric Multicolor Nanoscopy in Live Cells

New bright, photostable, emission-orthogonal fluorophores that blink without toxic additives are needed to enable multicolor, live-cell, single-molecule localization microscopy (SMLM). Here we report the design, synthesis, and biological evaluation of Yale676sb, a photostable, near-IR-emitting fluorophore that achieves these goals in the context of an exceptional quantum yield (0.59). When used alongside HMSiR, Yale676sb enables simultaneous, live-cell, two-color SMLM of two intracellular organelles (ER + mitochondria) with only a single laser and no chemical additives.

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

Theory of Photoluminescence Spectral Line Shapes of Semiconductor Nanocrystals

Single-molecule photoluminescence (PL) spectroscopy of semiconductor nanocrystals (NCs) reveals the nature of exciton–phonon interactions in NCs. Understanding the homogeneous spectral line shapes and their temperature dependence remains an open problem. Here, we develop an atomistic model to describe the PL spectrum of NCs, accounting for excitonic effects, phonon dispersion relations, and exciton–phonon couplings. We validate our model using single-NC measurements on CdSe/CdS NCs from T = 4 to 290 K, and we find that the slightly asymmetric main peak at low temperatures is comprised of a narrow zero-phonon line (ZPL) and acoustic phonon sidebands. Furthermore, we identify the specific phonon modes that give rise to the optical phonon sidebands. At temperatures above 200 K, the spectral line width shows a stronger dependence upon the temperature, which we demonstrate to be correlated with higher order exciton–phonon couplings. We also identify the line width dependence upon reorganization energy, NC core sizes, and shell thicknesses.

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

A Generalized Transformer-Based Pulse Detection Algorithm

Pulse-like signals are ubiquitous in the field of single molecule analysis, e.g., electrical or optical pulses caused by analyte translocations in nanopores. The primary challenge in processing pulse-like signals is to capture the pulses in noisy backgrounds, but current methods are subjectively based on a user-defined threshold for pulse recognition. Here, we propose a generalized machine-learning based method, named pulse detection transformer (PETR), for pulse detection. PETR determines the start and end time points of individual pulses, thereby singling out pulse segments in a time-sequential trace. It is objective without needing to specify any threshold. It provides a generalized interface for downstream algorithms for specific application scenarios. PETR is validated using both simulated and experimental nanopore translocation data. It returns a competitive performance in detecting pulses through assessing them with several standard metrics. Finally, the generalization nature of the PETR output is demonstrated using two representative algorithms for feature extraction.

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

Charge Transport Characteristics of Molecular Electronic Junctions Studied by Transition Voltage Spectroscopy

The field of molecular electronics is prompted by tremendous opportunities for using a single-molecule and molecular monolayers as active components in integrated circuits. Until now, a wide range of molecular devices exhibiting characteristic functions, such as diodes, transistors, switches, and memory, have been demonstrated. However, a full understanding of the crucial factors that affect charge transport through molecular electronic junctions should yet be accomplished. Remarkably, recent advances in transition voltage spectroscopy (TVS) elucidate that it can provide key quantities for probing the transport characteristics of the junctions, including, for example, the position of the frontier molecular orbital energy relative to the electrode Fermi level and the strength of the molecule–electrode interactions. These parameters are known to be highly associated with charge transport behaviors in molecular systems and can then be used in the design of molecule-based devices with rationally tuned electronic properties. This article highlights the fundamental principle of TVS and then demonstrates its major applications to study the charge transport properties of molecular electronic junctions.

36 MATERIALS SCIENCE↗
DOE OSTI2024

SISGR: The regulation of carbon fixation in plant and green algae: Rubisco activase and the origin of heat inactivation of CO 2 assimilation

Rubisco activase (Rca) is a critical AAA+ ATPase protein complex that remodels and promotes the Rubisco enzyme, a key player in photosynthetic performance and carbon fixation. The assembly and function of the Rca protein complex are regulated by a range of factors, including subunit concentration, nucleotide-binding states, thermal conditions, metal-ion coordination, and post-translational modifications, such as phosphorylation. Despite its importance in photosynthesis, the detailed molecular mechanisms underlying the regulation of plant Rca and how it activates Rubisco remain elusive. This project aims to bridge this knowledge gap by integrating sophisticated enzymology tools with single-molecule methods and high-resolution electron microscopy to elucidate the structure and function of plant Rca. Through these multiple approaches, we have systematically investigated how the activity of plant Rca is impacted by various factors, such as phosphorylation and metal-ion coordination. The Rca complex assembly/disassembly dynamics were captured using anti-Brownian electrokinetic (ABEL) trap-based measurements, providing unprecedented insight into its structural flexibility and diverse assembly states. Furthermore, the structural analysis of Rca through electron crystallography and single-particle cryogenic electron microscopy (cryo-EM) reveals novel assembly states of the spinach Rca, providing insight into the mechanistic action for Rubisco remodeling. By combining cutting-edge tools and approaches, this work uncovers critical aspects of Rca’s regulation and assembly, paving the way for a deeper understanding of its role in photosynthetic efficiency and the potential for enhancing carbon fixation in crops.

59 BASIC BIOLOGICAL SCIENCES↗