Search NASA⌕ Search

SEARCH · Search NASA

Results for “molecular junctions”

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.

Quote a phrase for an exact phrase match. Source license links do not imply unrestricted reuse.

At least 109 records · Page 6
All sourcesNASA NTRSDOE OSTI
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 OSTI2024

Self-assembled complex micelle phase stability in ABA-type triblock copolymers and related core-shell bottlebrushes

We report the synthesis and temperature-dependent morphologies of a series of polylactide--poly (-decalactone)--polylactide (LDL) triblock copolymers with M n = 16.0 – 18.1 kg / mol and volume fractions f L = 0.27 – 0.31 and associated core-shell bottlebrush (csBB) polymers, which derive from enchaining LDL triblocks through a polymerizable midchain functionality. While the LDL triblocks form micellar Frank-Kasper A15 and phases due to the conformational asymmetry of this monomer pair, the csBB morphologies sensitively depend on the backbone degree of polymerization ( N bb ). At low N bb values, micellar Frank-Kasper phases with the brush backbone situated in the matrix domain are stable, albeit with a modest reduction in the mean interfacial curvature evidenced by a to A15 order-to-order transition. However, larger N bb values drive csBBs to form hexagonally packed cylinders phases. This N bb -dependent phase behavior is rationalized in terms of a star-to-bottlebrush transition. At low N bb values, the csBBs are akin to star polymers with pointlike junctions that can support complex micelle packings. As N bb increases, the csBBs adopt cylindrical molecular geometries with extended backbones situated in the matrix domain that prefer hexagonally packed cylinders morphologies. Published by the American Physical Society 2024

Materials Science↗
DOE OSTI2022

Photocrosslinking Probes Proximity of Thymine Modifiers Tethering Excitonically Coupled Dye Aggregates to DNA Holliday Junction

A DNA Holliday junction (HJ) has been used as a versatile scaffold to create a variety of covalently templated molecular dye aggregates exhibiting strong excitonic coupling. In these dye-DNA constructs, one way to attach dyes to DNA is to tether them via single long linkers to thymine modifiers incorporated in the core of the HJ. Here, using photoinduced [2 + 2] cycloaddition (photocrosslinking) between thymines, we investigated the relative positions of squaraine-labeled thymine modifiers in the core of the HJ, and whether the proximity of thymine modifiers correlated with the excitonic coupling strength in squaraine dimers. Photocrosslinking between squaraine-labeled thymine modifiers was carried out in two distinct types of configurations: adjacent dimer and transverse dimer. The outcomes of the reactions in terms of relative photocrosslinking yields were evaluated by denaturing polyacrylamide electrophoresis. We found that for photocrosslinking to occur at a high yield, a synergetic combination of three parameters was necessary: adjacent dimer configuration, strong attractive dye–dye interactions that led to excitonic coupling, and an A-T neighboring base pair. The insight into the proximity of dye-labeled thymines in adjacent and transverse configurations correlated with the strength of excitonic coupling in the corresponding dimers. To demonstrate a utility of photocrosslinking, we created a squaraine tetramer templated by a doubly crosslinked HJ with increased thermal stability. These findings provide guidance for the design of HJ-templated dye aggregates exhibiting strong excitonic coupling for exciton-based applications such as organic optoelectronics and quantum computing.

77 NANOSCIENCE AND NANOTECHNOLOGY↗
DOE OSTI2022

Determinants of synapse diversity revealed by super-resolution quantal transmission and active zone imaging

Neural circuit function depends on the pattern of synaptic connections between neurons and the strength of those connections. Synaptic strength is determined by both postsynaptic sensitivity to neurotransmitter and the presynaptic probability of action potential evoked transmitter release (P r ). Whereas morphology and neurotransmitter receptor number indicate postsynaptic sensitivity, presynaptic indicators and the mechanism that sets P r remain to be defined. To address this, we developed QuaSOR, a super-resolution method for determining P r from quantal synaptic transmission imaging at hundreds of glutamatergic synapses at a time. We mapped the P r onto super-resolution 3D molecular reconstructions of the presynaptic active zones (AZs) of the same synapses at the Drosophila larval neuromuscular junction (NMJ). We find that P r varies greatly between synapses made by a single axon, quantify the contribution of key AZ proteins to P r diversity and find that one of these, Complexin, suppresses spontaneous and evoked transmission differentially, thereby generating a spatial and quantitative mismatch between release modes. Transmission is thus regulated by the balance and nanoscale distribution of release-enhancing and suppressing presynaptic proteins to generate high signal-to-noise evoked transmission.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2025

Structures of a synthetic antibody selected against and bound to the C‐terminal domain of Clostridium perfringens enterotoxin

Abstract Clostridium perfringensenterotoxin (CpE) causes cytotoxic gastrointestinal disease in mammalian epithelium by binding membrane protein receptors called claudins. Claudins direct the formation of cell/cell tight junctions through oligomerization and govern the transport of molecules between individual cells. CpE binds claudins through its C‐terminal domain (cCpE) and induces cytotoxicity through its N‐terminal domain. The non‐toxic cCpE is a useful tool to study claudins, tight junctions, and for translational applications, such as increasing the permeability of restrictive tissues like the blood–brain barrier or selective targeting of claudin overexpressing cancers. Conversely, there are no specialized molecular tools to study CpE or cCpE, or to modulate or inhibit their functions. We previously reported the development of synthetic antigen‐binding fragments (sFabs) that bind cCpE, and low‐resolution structures of them bound to claudin/cCpE complexes. Here, we determine high‐resolution structures of sFab COP‐2 bound to cCpE using X‐ray crystallography and cryogenic electron microscopy. The structures and biophysical findings provide the mechanism of COP‐2 binding to cCpE and the molecular determinants driving their interactions. These insights can advance the design of new antibody‐based tools from our COP‐2 scaffold to study or alter cCpE function and give rise to a “Trojan horse” strategy that exploits cCpE's tight junction barrier disrupting function to selectively deliver conjugated therapeutics through normally impermeable tissues.

Biochemistry & Molecular Biology↗
DOE OSTI2021

Grain size dependencies of intergranular solute segregation in nanocrystalline materials

Grain boundary segregation is of increasing importance for stabilizing nanocrystalline alloys, and while segregation is typically modeled as a scale-independent phenomenon, at the finest nanocrystalline grain sizes there are several sources of grain size dependence. Here we provide quantitative detail on two grain size dependencies not previously elaborated, both of which arise from the spectrality of intergranular segregation sites. The first of these arises because a change in grain size affects which portions of the segregation spectrum are occupied by the solutes, with no change in the shape or nature of the spectrum itself. The second of these arises from the presence of higher-order grain junctions, which have unique segregation behaviors and an increasing relative presence at finer grain sizes. This paper uses molecular statics to quantify these size dependencies in detail for the case of an Al(Mg) binary alloy. Together, these two effects combined have a significant effect on the effective McLean segregation energy of more than 6 kJ/mol (from approximately -18.5 kJ/mol at 5 nm to -12.5 kJ/mol at more than 40 nm), with the majority of grain size dependence arising from the spectrality of segregation sites.

36 MATERIALS SCIENCE↗
DOE OSTI2022

Efficient Intermolecular Charge Transport in π-Stacked Pyridinium Dimers Using Cucurbit[8]uril Supramolecular Complexes

Intermolecular charge transport through π-conjugated molecules plays an essential role in biochemical redox processes and energy storage applications. In this work, we observe highly efficient intermolecular charge transport upon dimerization of pyridinium molecules in the cavity of a synthetic host (cucurbit[8]uril, CB[8]). Stable, homoternary complexes are formed between pyridinium molecules and CB[8] with high binding affinity, resulting in an offset stacked geometry of two pyridiniums inside the host cavity. The charge transport properties of free and dimerized pyridiniums are characterized using a scanning tunneling microscope-break junction (STM-BJ) technique. Our results show that π-stacked pyridinium dimers exhibit comparable molecular conductance to isolated, single pyridinium molecules, despite a longer transport pathway and a switch from intra- to intermolecular charge transport. Control experiments using a CB[8] homologue (cucurbit[7]uril, CB[7]) show that the synthetic host primarily serves to facilitate dimer formation and plays a minimal role on molecular conductance. Molecular modeling using density functional theory (DFT) reveals that pyridinium molecules are planarized upon dimerization inside the host cavity, which facilitates charge transport. In addition, the π-stacked pyridinium dimers possess large intermolecular LUMO–LUMO couplings, leading to enhanced intermolecular charge transport. Altogether, this work demonstrates that supramolecular assembly can be used to control intermolecular charge transport in π-stacked molecules.

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

Tying the knot in the tetrahydrofolate (THF) riboswitch: A molecular basis for gene regulation

Effective gene regulation by the tetrahydrofolate riboswitch depends not only on ligand affinity but also on the kinetics of ligand association, which involves two cooperative binding sites. Here, we have determined a 1.9-Å resolution crystal structure of the ligand-free THF riboswitch aptamer. The pseudoknot binding site ‘unwinds’ in the absence of ligand, whereby the adjacent helical domains (P1, P2, and P3) become disjointed, resulting in rotation and misalignment of the gene-regulatory P1 helix with respect to P3. In contrast, the second binding site at the three-way junction, which is the first to fold, is structurally conserved between apo and holo forms. This suggests a kinetic role for this site, in which binding of the first ligand molecule to the stably folded three-way junction promotes formation of the regulatory pseudoknot site and subsequent binding of the second molecule. As such, these findings provide a molecular basis for both conformational switching and kinetic control.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2024

Tunneling magnetoresistance in MgO tunnel junctions with Fe-based leads in empirically corrected density functional theory

The minority-spin Fe/MgO interface states are at the Fermi level in density functional theory (DFT), but experimental evidence and GW calculations place them slightly higher in energy. This small shift can strongly influence tunneling magnetoresistance (TMR) in junctions with a thin MgO barrier and its dependence on the concentration of Co in the electrodes. Here, in this study, an empirical potential correction to DFT is introduced to shift the interface states up to match the tunnel spectroscopy data. With this shift, TMR in Fe/MgO/Fe junctions exceeds 800% and 3000% at 3 and 4 monolayers (ML) of MgO, respectively. We further consider the effect of alloying of the Fe electrodes with up to 30% Co or 10% V, treating them in the coherent potential approximation (CPA). Alloying with Co broadens the interface states and brings a large incoherent minority-spin spectral weight to the Fermi level. Alloying with V brings the minority-spin resonant states close to the Fermi level. However, in both cases the minority-spin spectral weight at the Fermi level resides primarily at the periphery of the Brillouin zone, which is favorable for spin filtering. Using convolutions of k II -resolved barrier densities of states calculated in CPA, it is found that TMR is strongly reduced by alloying with Co or V but still remains above 500% at 4 ML of MgO up to 30% of Co or 5% V. At 5 ML, the TMR increases above 1000% in all systems considered. However, while TMR declines sharply with increasing bias up to 0.2 eV in the tunnel junctions with pure Fe leads, it remains almost constant up to 0.5 eV if leads are alloyed with Co.

74 ATOMIC AND MOLECULAR PHYSICS↗
DOE OSTI2020

Thermal conductance enhanced via inelastic phonon transport by atomic vacancies at Cu/Si interfaces

Understanding and controlling heat transfer across interfaces has become an important issue for the performance of micro- and nanoscale electronics, as well as achieving a high figure of merit for thermoelectrics. Intrinsic and extrinsic defects can have a significant impact on thermal transport in bulk materials and across interfaces, but the mechanism is not well understood. Here, nonequilibrium molecular dynamics simulations are used to determine the impact of interfacial atomic vacancies on thermal transport across a Cu/Si junction. In contrast to the reduction in thermal transport typically seen with bulk defects, we find that by introducing atomic vacancies at a concentration of 6.3% near the interface in either or both materials, the interfacial thermal conductance can be increased by up to 76%. By controlling the initial positions of the vacancies and keeping track of their movements and population, we find that interfacial thermal transport is dependent on temperature, vacancy concentration, and distribution, and a positive correlation between the conductance and point defect activities (extent of vacancy migration, rate of Frenkel defect creation and annihilation) is observed. Further calculations based on the phonon density of states and normal mode decomposition reveal that the increase in interfacial thermal conductance originates primarily from high-frequency phonons, supported by enhanced inelastic phonon transport which contributes to more than 60% of the increase. Our findings suggest a practical way to manipulate inelastic phonon conversion through the presence of defects, which provides an alternative perspective on improving thermal transport between materials with a large lattice mismatch.

75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗
DOE OSTI2026

Microphase Separation of Randomly Linked Branched Polystyrene/Polylactic Acid for Formation of Cocontinuous Nanostructures

Cocontinuous polymeric nanomaterials have gained attention for their ability to preserve distinct properties of constituent microphases within a single material. Randomly linked copolymer networks have shown very wide stability windows for disordered cocontinuous phases (extending over ≈ 30 wt % in composition), but the reliance on a network architecture prevents subsequent solution- or melt-processing. Furthermore, the key factors contributing to cocontinuity have remained unclear. We recently found that randomly linked star copolymers (RSCs) can exhibit a cocontinuous window as wide as 25 wt % in the case of 4-arm stars, suggesting that while a network architecture is not essential for the formation of disordered cocontinuous phases, the presence of random elastic forces in such architectures may indeed facilitate their formation. In addition, the behavior was found to be highly sensitive to arm number, with 6-arm RSCs exhibiting almost no cocontinuous phase. These results raised a key mechanistic question regarding the contribution of random elastic forces, originating from strands that bridge between junctions, in stabilizing disordered cocontinuous phases. In the current study, we synthesized randomly linked branched copolymers (RBCs) of polystyrene (PS) and poly(D,L-lactic acid) (PLA), which represent an intermediate architecture between networks and stars. This approach allows for the introduction of elastic contributions from strands bridging between different junctions, while still maintaining the processability advantages of a non-network architecture. The cocontinuous regions of the PS/PLA RBCs, with varying polymer and linker functionalities (f p and f l , respectively), were characterized by small-angle X-ray scattering, gravimetry, and scanning electron microscopy. We found that the cocontinuous windows of RBCs typically expanded with increasing elastic contributions and exhibited reduced sensitivity to junction-functionality compared to RSCs. Notably, RBCs with f p = 1.50 and f l = 3, which had large molecular weights due to proximity to the gel point, achieved a cocontinuous window of ≈ 34 wt %, which is almost twice as wide as analogous 3-arm RSCs and comparable to randomly linked networks. Leveraging this robust cocontinuity and solution-processability, we fabricated a film of interconnected nanoporous PS.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2025

Diffusion and Deformation Mechanism Maps in Li Metal from Atomistic Simulations

The rate of Li transport in the Li metal anode is important for the operation of Li metal-solid state batteries. Here, transport rates due to diffusion and creep are predicted in Li using atomistic simulations. First, molecular dynamics is used to estimate the rate of Li diffusion along dislocations and in grain boundary triple junctions. By combining this data with that from a prior study of grain boundary diffusion the dominant mechanisms and rates of self-diffusion in Li polycrystals are predicted as a function of grain size, grain shape, dislocation density, and temperature. Second, the dominant creep mechanisms are predicted and used to estimate critical current densities and void annihilation times. Grain boundary sliding and coble creep are the dominant mechanisms for micron-sized grains. Lastly, a continuum model for interfacial contact loss reveals that high dislocation densities of ∼10 12 /cm 2 enable achieving battery performance targets for Li grain sizes of ∼10 μm.

Batteries↗
DOE OSTI2021

Cell transdifferentiation in ocular disease: Potential role for connexin channels

Highlights: • Cell transdifferentiation including EMT and EndMT is a pathological process in a number of ocular diseases. • Gap junction channels and connexin hemichannels play a role in cell transdifferentiation in ocular diseases. • Connexin-blocking therapies demonstrate efficacy in ocular disease models. • Future studies could explore connexin-based therapies for prevention and treatment of pathological transdifferentiation. Cell transdifferentiation is the conversion of a cell type to another without requiring passage through a pluripotent cell state, and encompasses epithelial- and endothelial-mesenchymal transition (EMT and EndMT). EMT and EndMT are well defined processes characterized by a loss of epithelial/endothelial phenotype and gain in mesenchymal spindle shaped morphology, which results in increased cell migration and decreased apoptosis and cellular senescence. Such cells often develop invasive properties. Physiologically, these processes may occur during embryonic development and can resurface, for example, to promote wound healing in later life. However, they can also be a pathological process. In the eye, EMT, EndMT and cell transdifferentiation have all been implicated in development, homeostasis, and multiple diseases affecting different parts of the eye. Connexins, constituents of connexin hemichannels and intercellular gap junctions, have been implicated in many of these processes. In this review, we firstly provide an overview of the molecular mechanisms induced by transdifferentiation (including EMT and EndMT) and its involvement in eye diseases. We then review the literature for the role of connexins in transdifferentiation in the eye and eye diseases. The evidence presented in this review supports the need for more studies into the therapeutic potential for connexin modulators in prevention and treatment of transdifferentiation related eye diseases, but does indicate that connexin channel modulation may be an upstream and unifying approach for regulating these otherwise complex processes.

60 APPLIED LIFE SCIENCES↗
DOE OSTI2024

Engineering tertiary chirality in helical biopolymers

Tertiary chirality describes the handedness of supramolecular assemblies and relies not only on the primary and secondary structures of the building blocks but also on topological driving forces that have been sparsely characterized. Helical biopolymers, especially DNA, have been extensively investigated as they possess intrinsic chirality that determines the optical, mechanical, and physical properties of the ensuing material. Here, we employ the DNA tensegrity triangle as a model system to locate the tipping points in chirality inversion at the tertiary level by X-ray diffraction. We engineer tensegrity triangle crystals with incremental rotational steps between immobile junctions from 3 to 28 base pairs (bp). We construct a mathematical model that accurately predicts and explains the molecular configurations in both this work and previous studies. Our design framework is extendable to other supramolecular assemblies of helical biopolymers and can be used in the design of chiral nanomaterials, optically active molecules, and mesoporous frameworks, all of which are of interest to physical, biological, and chemical nanoscience.

Science & Technology - Other Topics↗
DOE OSTI2023

Enhanced Photo-Cross-Linking of Thymines in DNA Holliday Junction-Templated Squaraine Dimers

Programmable self-assembly of dyes using DNA templates to promote exciton delocalization in dye aggregates is gaining considerable interest. New methods to improve the rigidity of the DNA scaffold and thus the stability of the molecular dye aggregates to encourage exciton delocalization are desired. In these dye–DNA constructs, one potential way to increase the stability of the aggregates is to create an additional covalent bond via photo-cross-linking reactions between thymines in the DNA scaffold. Specifically, we report an approach to increase the yield of photo-cross-linking reaction between thymines in the core of a DNA Holliday junction while limiting the damage from UV irradiation to DNA. We investigated the effect of the distance between thymines on the photo-cross-linking reaction yields by using linkers with different lengths to tether the dyes to the DNA templates. By comprehensively evaluating the photo-cross-linking reaction yields of dye–DNA aggregates using linkers with different lengths, we conclude that interstrand thymines tend to photo-cross-link more efficiently with short linkers. A higher cross-linking yield was achieved due to the shorter intermolecular distance between thymines influenced by strong dye–dye interactions. Furthermore, our method establishes the possibility of improving the stability of DNA-scaffolded dye aggregates, thereby expanding their use in exciton-based applications such as light harvesting, nanoscale computing, quantum computing, and optoelectronics.

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

Methods to Create Novel La 2- x Sr x CuO 4 Devices with Multiple Atomically Sharp Interfaces

We present methods to create devices that utilize the high-temperature superconductor La 2-x Sr x CuO 4 grown by atomic layer-by-layer molecular beam epitaxy (ALL-MBE). The ALL-MBE synthesis technique provides atomically precise interfaces necessary for the tunnel junctions, Josephson junctions, and dyon detection devices that will be considered. A series of microfabrication processing steps using established techniques are given for each device, and their details are discussed. These procedures are easily extended to generate more complex designs and could be suitable for a wider variety of materials.

75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗
DOE OSTI2020

Local Environment Affects the Activity of Enzymes on a 3D Molecular Scaffold

The ability to coordinate and confine enzymes presents an opportunity to affect their performance and to create chemically active materials. Recent studies show that polymers and biopolymers can be used to scaffold enzymes, and that can lead to the modulated biocatalytic efficiency. In this work, we investigated the role of microenvironments on enzyme activity using a well-defined molecular scaffold. An enzyme, glucose oxidase (GO x ), was positioned at different locations of a three-dimensional (3D) octahedral DNA scaffold (OS), allowing the enzyme’s polyanionic environments to be altered. Using electrical sensing, based on a bipolar junction transistor, we measured directly and in real-time the enzyme’s proton generation at these different microenvironments. We found a 200% enhancement of immobilized enzyme over free GOx and about a 30% increase in catalytic rates when the enzyme was moved on the same molecular scaffold to a microenvironment with a higher local concentration of polyanions, which suggests a role of local pH on the enzymatic activity.

77 NANOSCIENCE AND NANOTECHNOLOGY↗
DOE OSTI2023

Probing DNA structural heterogeneity by identifying conformational subensembles of a bicovalently bound cyanine dye

DNA is a re-configurable, biological information-storage unit, and much remains to be learned about its heterogeneous structural dynamics. For example, while it is known that molecular dyes templated onto DNA exhibit increased photostability, the mechanism by which the structural dynamics of DNA affect the dye photophysics remains unknown. Here, we use femtosecond, two-dimensional electronic spectroscopy measurements of a cyanine dye, Cy5, to probe local conformations in samples of single-stranded DNA (ssDNA–Cy5), double-stranded DNA (dsDNA–Cy5), and Holliday junction DNA (HJ–DNA–Cy5). A line shape analysis of the 2D spectra reveals a strong excitation–emission correlation present in only the dsDNA–Cy5 complex, which is a signature of inhomogeneous broadening. Molecular dynamics simulations support the conclusion that this inhomogeneous broadening arises from a nearly degenerate conformer found only in the dsDNA–Cy5 complex. These insights will support future studies on DNA’s structural heterogeneity.

77 NANOSCIENCE AND NANOTECHNOLOGY↗