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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 793 records · Page 44
All sourcesNASA NTRSDOE OSTI
DOE OSTI2022

Comprehensive view of microscopic interactions between DNA-coated colloids

Abstract The self-assembly of DNA-coated colloids into highly-ordered structures offers great promise for advanced optical materials. However, control of disorder, defects, melting, and crystal growth is hindered by the lack of a microscopic understanding of DNA-mediated colloidal interactions. Here we use total internal reflection microscopy to measure in situ the interaction potential between DNA-coated colloids with nanometer resolution and the macroscopic melting behavior. The range and strength of the interaction are measured and linked to key material design parameters, including DNA sequence, polymer length, grafting density, and complementary fraction. We present a first-principles model that screens and combines existing theories into one coherent framework and quantitatively reproduces our experimental data without fitting parameters over a wide range of DNA ligand designs. Our theory identifies a subtle competition between DNA binding and steric repulsion and accurately predicts adhesion and melting at a molecular level. Combining experimental and theoretical results, our work provides a quantitative and predictive approach for guiding material design with DNA-nanotechnology and can be further extended to a diversity of colloidal and biological systems.

71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗
DOE OSTI2022

Broad-spectrum CRISPR-mediated inhibition of SARS-CoV-2 variants and endemic coronaviruses in vitro

A major challenge in coronavirus vaccination and treatment is to counteract rapid viral evolution and mutations. Here we demonstrate that CRISPR-Cas13d offers a broad-spectrum antiviral (BSA) to inhibit many SARS-CoV-2 variants and diverse human coronavirus strains with >99% reduction of the viral titer. We show that Cas13d-mediated coronavirus inhibition is dependent on the crRNA cellular spatial colocalization with Cas13d and target viral RNA. Cas13d can significantly enhance the therapeutic effects of diverse small molecule drugs against coronaviruses for prophylaxis or treatment purposes, and the best combination reduced viral titer by over four orders of magnitude. Using lipid nanoparticle-mediated RNA delivery, we demonstrate that the Cas13d system can effectively treat infection from multiple variants of coronavirus, including Omicron SARS-CoV-2, in human primary airway epithelium air-liquid interface (ALI) cultures. Our study establishes CRISPR-Cas13 as a BSA which is highly complementary to existing vaccination and antiviral treatment strategies.

60 APPLIED LIFE SCIENCES↗
DOE OSTI2022

Emergence of distinct electronic states in epitaxially-fused PbSe quantum dot superlattices

Abstract Quantum coupling in arrayed nanostructures can produce novel mesoscale properties such as electronic minibands to improve the performance of optoelectronic devices, including ultra-efficient solar cells and infrared photodetectors. Colloidal PbSe quantum dots (QDs) that self-assemble into epitaxially-fused superlattices (epi-SLs) are predicted to exhibit such collective phenomena. Here, we show the emergence of distinct local electronic states induced by crystalline necks that connect individual PbSe QDs and modulate the bandgap energy across the epi-SL. Multi-probe scanning tunneling spectroscopy shows bandgap modulation from 0.7 eV in the QDs to 1.1 eV at their necks. Complementary monochromated electron energy-loss spectroscopy demonstrates bandgap modulation in spectral mapping, confirming the presence of these distinct energy states from necking. The results show the modification of the electronic structure of a precision-made nanoscale superlattice, which may be leveraged in new optoelectronic applications.

36 MATERIALS SCIENCE↗
DOE OSTI2022

Prediction of inter-chain distance maps of protein complexes with 2D attention-based deep neural networks

Residue-residue distance information is useful for predicting tertiary structures of protein monomers or quaternary structures of protein complexes. Many deep learning methods have been developed to predict intra-chain residue-residue distances of monomers accurately, but few methods can accurately predict inter-chain residue-residue distances of complexes. We develop a deep learning method CDPred (i.e., Complex Distance Prediction) based on the 2D attention-powered residual network to address the gap. Tested on two homodimer datasets, CDPred achieves the precision of 60.94% and 42.93% for top L/5 inter-chain contact predictions (L: length of the monomer in homodimer), respectively, substantially higher than DeepHomo’s 37.40% and 23.08% and GLINTER’s 48.09% and 36.74%. Tested on the two heterodimer datasets, the top Ls/5 inter-chain contact prediction precision (Ls: length of the shorter monomer in heterodimer) of CDPred is 47.59% and 22.87% respectively, surpassing GLINTER’s 23.24% and 13.49%. Moreover, the prediction of CDPred is complementary with that of AlphaFold2-multimer.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2023

Silver nanoparticle enhanced metal-organic matrix with interface-engineering for efficient photocatalytic hydrogen evolution

Integrating plasmonic nanoparticles into the photoactive metal-organic matrix is highly desirable due to the plasmonic near field enhancement, complementary light absorption, and accelerated separation of photogenerated charge carriers at the junction interface. The construction of a well-defined, intimate interface is vital for efficient charge carrier separation, however, it remains a challenge in synthesis. Here we synthesize a junction bearing intimate interface, composed of plasmonic Ag nanoparticles and matrix with silver node via a facile one-step approach. The plasmonic effect of Ag nanoparticles on the matrix is visualized through electron energy loss mapping. Moreover, charge carrier transfer from the plasmonic nanoparticles to the matrix is verified through ultrafast transient absorption spectroscopy and in-situ photoelectron spectroscopy. The system delivers highly efficient visible-light photocatalytic H 2 generation, surpassing most reported metal-organic framework-based photocatalytic systems. This work sheds light on effective electronic and energy bridging between plasmonic nanoparticles and organic semiconductors.

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

Previously uncharacterized rectangular bacterial structures in the dolphin mouth

Much remains to be explored regarding the diversity of uncultured, host-associated microbes. Here, we describe rectangular bacterial structures (RBSs) in the mouths of bottlenose dolphins. DNA staining revealed multiple paired bands within RBSs, suggesting the presence of cells dividing along the longitudinal axis. Cryogenic transmission electron microscopy and tomography showed parallel membrane-bound segments that are likely cells, encapsulated by an S-layer-like periodic surface covering. RBSs displayed unusual pilus-like appendages with bundles of threads splayed at the tips. We present multiple lines of evidence, including genomic DNA sequencing of micromanipulated RBSs, 16S rRNA gene sequencing, and fluorescence in situ hybridization, suggesting that RBSs are bacterial and distinct from the genera Simonsiella and Conchiformibius (family Neisseriaceae), with which they share similar morphology and division patterning. Our findings highlight the diversity of novel microbial forms and lifestyles that await characterization using tools complementary to genomics such as microscopy.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2023

Enhancing reactivity of SiO + ions by controlled excitation to extreme rotational states

Optical pumping of molecules provides unique opportunities for control of chemical reactions at a wide range of rotational energies. This work reports a chemical reaction with extreme rotational excitation of a reactant and its kinetic characterization. We investigate the chemical reactivity for the hydrogen abstraction reaction SiO + + H 2 → SiOH + + H in an ion trap. The SiO + cations are prepared in a narrow rotational state distribution, including super-rotor states with rotational quantum number ( j ) as high as 170, using a broad-band optical pumping method. We show that the super-rotor states of SiO + substantially enhance the reaction rate, a trend reproduced by complementary theoretical studies. We reveal the mechanism for the rotational enhancement of the reactivity to be a strong coupling of the SiO + rotational mode with the reaction coordinate at the transition state on the dominant dynamical pathway.

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

Tuning the zeolite acidity enables selectivity control by suppressing ketene formation in lignin catalytic pyrolysis

Unveiling catalytic mechanisms at a molecular level aids rational catalyst design and selectivity control for process optimization. In this study, we find that the Brønsted acid site density of the zeolite catalyst efficiently controls the guaiacol catalytic pyrolysis mechanism. Guaiacol demethylation to catechol initiates the reaction, as evidenced by the detected methyl radicals. The mechanism branches to form either fulvenone (c-C 5 H 4 = C = O), a reactive ketene intermediate, by catechol dehydration, or phenol by acid-catalyzed dehydroxylation. At high Brønsted acid site density, fulvenone formation is inhibited due to surface coordination configuration of its precursor, catechol. By quantifying reactive intermediates and products utilizing operando photoelectron photoion coincidence spectroscopy, we find evidence that ketene suppression is responsible for the fivefold phenol selectivity increase. Complementary fulvenone reaction pathway calculations, along with 29 Si NMR-MAS spectroscopy results corroborate the mechanism. The proposed, flexible operando approach is applicable to a broad variety of heterogeneous catalytic reactions.

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

Visualizing moiré ferroelectricity via plasmons and nano-photocurrent in graphene/twisted-WSe2 structures

Abstract Ferroelectricity, a spontaneous and reversible electric polarization, is found in certain classes of van der Waals (vdW) materials. The discovery of ferroelectricity in twisted vdW layers provides new opportunities to engineer spatially dependent electric and optical properties associated with the configuration of moiré superlattice domains and the network of domain walls. Here, we employ near-field infrared nano-imaging and nano-photocurrent measurements to study ferroelectricity in minimally twisted WSe 2 . The ferroelectric domains are visualized through the imaging of the plasmonic response in a graphene monolayer adjacent to the moiré WSe 2 bilayers. Specifically, we find that the ferroelectric polarization in moiré domains is imprinted on the plasmonic response of the graphene. Complementary nano-photocurrent measurements demonstrate that the optoelectronic properties of graphene are also modulated by the proximal ferroelectric domains. Our approach represents an alternative strategy for studying moiré ferroelectricity at native length scales and opens promising prospects for (opto)electronic devices.

42 ENGINEERING↗
DOE OSTI2023

Structures of the DarR transcription regulator reveal unique modes of second messenger and DNA binding

The mycobacterial repressor, DarR, a TetR family regulator (TFR), was the first transcription regulator shown to bind c-di-AMP. However, the molecular basis for this interaction and the mechanism involved in DNA binding by DarR remain unknown. Here we describe DarR-c-di-AMP and DarR-DNA structures and complementary biochemical assays. The DarR-c-di-AMP structure reveals a unique effector binding site for a TFR, located between DarR dimer subunits. Strikingly, we show this motif also binds cAMP. The location of the adenine nucleotide binding site between subunits suggests this interaction may facilitate dimerization and hence DNA binding. Indeed, biochemical assays show cAMP enhances DarR DNA binding. Finally, DarR-DNA structures reveal a distinct TFR DNA-binding mechanism involving two interacting dimers on the DNA. Thus, the combined data unveil a newly described second messenger binding motif and DNA binding mode for this important family of regulators.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2024

Intermediate soil acidification induces highest nitrous oxide emissions

Global potent greenhouse gas nitrous oxide (N 2 O) emissions from soil are accelerating, with increases in the proportion of reactive nitrogen emitted as N 2 O, i.e., N 2 O emission factor (EF). Yet, the primary controls and underlying mechanisms of EFs remain unresolved. Based on two independent but complementary global syntheses, and three field studies determining effects of acidity on N 2 O EFs and soil denitrifying microorganisms, we show that soil pH predominantly controls N 2 O EFs and emissions by affecting the denitrifier community composition. Analysis of 5438 paired data points of N 2 O emission fluxes revealed a hump-shaped relationship between soil pH and EFs, with the highest EFs occurring in moderately acidic soils that favored N 2 O-producing over N 2 O-consuming microorganisms, and induced high N 2 O emissions. Our results illustrate that soil pH has a unimodal relationship with soil denitrifiers and EFs, and the net N 2 O emission depends on both the N 2 O/(N 2 O + N 2 ) ratio and overall denitrification rate. These findings can inform strategies to predict and mitigate soil N 2 O emissions under future nitrogen input scenarios.

54 ENVIRONMENTAL SCIENCES↗
DOE OSTI2024

Kinetically controlled metal-elastomer nanophases for environmentally resilient stretchable electronics

Nanophase mixtures, leveraging the complementary strengths of each component, are vital for composites to overcome limitations posed by single elemental materials. Among these, metal-elastomer nanophases are particularly important, holding various practical applications for stretchable electronics. However, the methodology and understanding of nanophase mixing metals and elastomers are limited due to difficulties in blending caused by thermodynamic incompatibility. Here, we present a controlled method using kinetics to mix metal atoms with elastomeric chains on the nanoscale. We find that the chain migration flux and metal deposition rate are key factors, allowing the formation of reticular nanophases when kinetically in-phase. Moreover, we observe spontaneous structural evolution, resulting in gyrified structures akin to the human brain. The hybridized gyrified reticular nanophases exhibit strain-invariant metallic electrical conductivity up to 156% areal strain, unparalleled durability in organic solvents and aqueous environments with pH 2–13, and high mechanical robustness, a prerequisite for environmentally resilient devices.

36 MATERIALS SCIENCE↗
DOE OSTI2024

A hemoprotein with a zinc-mirror heme site ties heme availability to carbon metabolism in cyanobacteria

Abstract Heme has a critical role in the chemical framework of the cell as an essential protein cofactor and signaling molecule that controls diverse processes and molecular interactions. Using a phylogenomics-based approach and complementary structural techniques, we identify a family of dimeric hemoproteins comprising a domain of unknown function DUF2470. The heme iron is axially coordinated by two zinc-bound histidine residues, forming a distinct two-fold symmetric zinc-histidine-iron-histidine-zinc site. Together with structure-guided in vitro and in vivo experiments, we further demonstrate the existence of a functional link between heme binding by Dri1 (Domain related to iron 1, formerly ssr1698) and post-translational regulation of succinate dehydrogenase in the cyanobacterium Synechocystis , suggesting an iron-dependent regulatory link between photosynthesis and respiration. Given the ubiquity of proteins containing homologous domains and connections to heme metabolism across eukaryotes and prokaryotes, we propose that DRI (Domain Related to Iron; formerly DUF2470) functions at the molecular level as a heme-dependent regulatory domain.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2024

Johnson-noise-limited cancellation-free microwave impedance microscopy with monolithic silicon cantilever probes

Abstract Microwave impedance microscopy (MIM) is an emerging scanning probe technique for nanoscale complex permittivity mapping and has made significant impacts in diverse fields. To date, the most significant hurdles that limit its widespread use are the requirements of specialized microwave probes and high-precision cancellation circuits. Here, we show that forgoing both elements not only is feasible but also enhances performance. Using monolithic silicon cantilever probes and a cancellation-free architecture, we demonstrate Johnson-noise-limited, drift-free MIM operation with 15 nm spatial resolution, minimal topography crosstalk, and an unprecedented sensitivity of 0.26 zF/ √ Hz. We accomplish this by taking advantage of the high mechanical resonant frequency and spatial resolution of silicon probes, the inherent common-mode phase noise rejection of self-referenced homodyne detection, and the exceptional stability of the streamlined architecture. Our approach makes MIM drastically more accessible and paves the way for advanced operation modes as well as integration with complementary techniques.

47 OTHER INSTRUMENTATION↗
DOE OSTI2024

Global protein turnover quantification in Escherichia coli reveals cytoplasmic recycling under nitrogen limitation

Protein turnover is critical for proteostasis, but turnover quantification is challenging, and even in well-studied E. coli, proteome-wide measurements remain scarce. Here, we quantify the turnover rates of ~3200 E. coli proteins under 13 conditions by combining heavy isotope labeling with complement reporter ion quantification and find that cytoplasmic proteins are recycled when nitrogen is limited. We use knockout experiments to assign substrates to the known cytoplasmic ATP-dependent proteases. Surprisingly, none of these proteases are responsible for the observed cytoplasmic protein degradation in nitrogen limitation, suggesting that a major proteolysis pathway in E. coli remains to be discovered. Lastly, we show that protein degradation rates are generally independent of cell division rates. Thus, we present broadly applicable technology for protein turnover measurements and provide a rich resource for protein half-lives and protease substrates in E. coli, complementary to genomics data, that will allow researchers to study the control of proteostasis.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2024

Unidirectional ray polaritons in twisted asymmetric stacks

Abstract The vast repository of van der Waals (vdW) materials supporting polaritons offers numerous possibilities to tailor electromagnetic waves at the nanoscale. The development of twistoptics—the modulation of the optical properties by twisting stacks of vdW materials—enables directional propagation of phonon polaritons (PhPs) along a single spatial direction, known as canalization. Here we demonstrate a complementary type of directional propagation of polaritons by reporting the visualization of unidirectional ray polaritons (URPs). They arise naturally in twisted hyperbolic stacks with very different thicknesses of their constituents, demonstrated for homostructures of$$\alpha$$ α -MoO 3 and heterostructures of$$\alpha$$ α -MoO 3 and$$\beta$$ β -Ga 2 O 3 . Importantly, their ray-like propagation, characterized by large momenta and constant phase, is tunable by both the twist angle and the illumination frequency. Apart from their fundamental importance, our findings introduce twisted asymmetric stacks as efficient platforms for nanoscale directional polariton propagation, opening the door for applications in nanoimaging, (bio)-sensing, or polaritonic thermal management.

Science & Technology - Other Topics↗
DOE OSTI2024

Highly multiplexed design of an allosteric transcription factor to sense new ligands

Allosteric transcription factors (aTF) regulate gene expression through conformational changes induced by small molecule binding. Although widely used as biosensors, aTFs have proven challenging to design for detecting new molecules because mutation of ligand-binding residues often disrupts allostery. Here, we develop Sensor-seq, a high-throughput platform to design and identify aTF biosensors that bind to non-native ligands. We screen a library of 17,737 variants of the aTF TtgR, a regulator of a multidrug exporter, against six non-native ligands of diverse chemical structures – four derivatives of the cancer therapeutic tamoxifen, the antimalarial drug quinine, and the opiate analog naltrexone – as well as two native flavonoid ligands, naringenin and phloretin. Sensor-seq identifies biosensors for each of these ligands with high dynamic range and diverse specificity profiles. The structure of a naltrexone-bound design shows shape-complementary methionine-aromatic interactions driving ligand specificity. To demonstrate practical utility, we develop cell-free detection systems for naltrexone and quinine. Sensor-seq enables rapid and scalable design of new biosensors, overcoming constraints of natural biosensors.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2024

Direct observation of ultrafast cluster dynamics in supercritical carbon dioxide using X-ray Photon Correlation Spectroscopy

Supercritical fluids exhibit distinct thermodynamic and transport properties, making them of particular interest for a wide range of scientific and engineering applications. These anomalous properties emerge from structural heterogeneities due to the formation of molecular clusters at conditions above the critical point. While the static behavior of these clusters and their effects on the thermodynamic response functions have been recognized, the relation between the ultrafast cluster dynamics and transport properties remains elusive. By measuring the intermediate scattering function in carbon dioxide at conditions near the critical point with X-ray photon correlation spectroscopy, we directly capture the cross-over dynamics between 4 and 13 picoseconds, revealing the transition between ballistic and diffusive motion. Complementary analysis using large-scale molecular dynamics simulations reveals that this behavior arises from collisions between unbound molecules and clusters. This study provides direct evidence of the ultrafast momentum exchange between clusters, which has significant impact on transport properties, solvation processes, and reaction kinetics in supercritical fluids.

carbon capture and storage↗