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Results for “molecular templating”

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 199 records · Page 11
All sourcesNASA NTRSDOE OSTI
DOE OSTI2025

Hydrodynamic characterization of the redox chemistry of crown-encapsulated uranyl complexes

The redox properties of actinide-containing species strongly influence their reactivity, speciation, and interfacial behavior, but the experimental quantification of the electrochemical characteristics of molecular actinide complexes in nonaqueous media has not received the attention it deserves. Here, results from hydrodynamic methods and electrochemical simulations of U(VI)/U(V) redox are reported, including quantification of heterogeneous electron-transfer kinetics and estimation of chemical reversibility of U(VI)/U(V) interconversion at electrodes in acetonitrile-based electrolyte. The complexes investigated are recently reported U(VI) and U(V) complexes in which the uranyl ion (UO 2 n+ ) is encapsulated in a macrocyclic 18-crown-6-like moiety templated by a Pt(II) center. These complexes feature the most positive value U VI /U V reduction potential yet reported and are thus particularly relevant to study of facile U(V) generation from U(VI) precursors as well as uranium electroanalysis. Rotating disk electrode (RDE) studies have been used to quantify the diffusion coefficients of the U(VI) and U(V) complexes, and standard heterogeneous electron transfer rate constants ( k 0 ) for the redox have been determined using a conventional Koutecký-Levich analysis. Rotating ring-disk electrode (RRDE) studies have been used to directly interrogate the chemical reversibility of U(VI)-U(V) interconversion, confirming that reduction of the U(VI) complex at an Au disk is associated with formation of the U(V) analogue that can be readily re-oxidized at a Pt ring under hydrodynamic (rotating) conditions. Because measurements of the type reported here are generally associated with current flows that are larger than those found in corresponding quiescent (unstirred) conditions, our findings suggest that hydrodynamic methods could be advantageous for design of electroanalytical approaches to detection of actinide species and study of their redox properties.

actinides↗
DOE OSTI2023

Metal-Mediated DNA Nanotechnology in 3D: Structural Library by Templated Diffraction

DNA double helices containing metal-mediated DNA (mmDNA) base pairs are constructed from Ag + and Hg 2+ ions between pyrimidine:pyrimidine pairs with the promise of nanoelectronics. Rational design of mmDNA nanomaterials is impractical without a complete lexical and structural description. Here, in this study, the programmability of structural DNA nanotechnology toward its founding mission of self-assembling a diffraction platform for biomolecular structure determination is explored. The tensegrity triangle is employed to build a comprehensive structural library of mmDNA pairs via X-ray diffraction and generalized design rules for mmDNA construction are elucidated. Two binding modes are uncovered: N3-dominant, centrosymmetric pairs and major groove binders driven by 5-position ring modifications. Energy gap calculations show additional levels in the lowest unoccupied molecular orbitals (LUMO) of mmDNA structures, rendering them attractive molecular electronic candidates.

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

Data-Driven and Multiscale Modeling of DNA-Templated Dye Aggregates

Dye aggregates are of interest for excitonic applications, including biomedical imaging, organic photovoltaics, and quantum information systems. Dyes with large transition dipole moments (μ) are necessary to optimize coupling within dye aggregates. Extinction coefficients (ε) can be used to determine the μ of dyes, and so dyes with a large ε (>150,000 M –1 cm –1 ) should be engineered or identified. However, dye properties leading to a large ε are not fully understood, and low-throughput methods of dye screening, such as experimental measurements or density functional theory (DFT) calculations, can be time-consuming. In order to screen large datasets of molecules for desirable properties (i.e., large ε and μ), a computational workflow was established using machine learning (ML), DFT, time-dependent (TD-) DFT, and molecular dynamics (MD). ML models were developed through training and validation on a dataset of 8802 dyes using structural features. A Classifier was developed with an accuracy of 97% and a Regressor was constructed with an R2 of above 0.9, comparing between experiment and ML prediction. Using the Regressor, the ε values of over 18,000 dyes were predicted. The top 100 dyes were further screened using DFT and TD-DFT to identify 15 dyes with a μ relative to a reference dye, pentamethine indocyanine dye Cy5. Two benchmark MD simulations were performed on Cy5 and Cy5.5 dimers, and it was found that MD could accurately capture experimental results. The results of this study exhibit that our computational workflow for identifying dyes with a large μ for excitonic applications is effective and can be used as a tool to develop new dyes for excitonic applications.

77 NANOSCIENCE AND NANOTECHNOLOGY↗
DOE OSTI2022

A human antibody reveals a conserved site on beta-coronavirus spike proteins and confers protection against SARS-CoV-2 infection

Broadly neutralizing antibodies (bnAbs) to coronaviruses (CoVs) are valuable in their own right as prophylactic and therapeutic reagents to treat diverse CoVs and as templates for rational pan-CoV vaccine design. We recently described a bnAb, CC40.8, from a CoV disease 2019 (COVID-19) convalescent donor that exhibits broad reactivity with human β-CoVs. Here, we showed that CC40.8 targets the conserved S2 stem helix region of the CoV spike fusion machinery. We determined a crystal structure of CC40.8 Fab with a SARS-CoV-2 S2 stem peptide at 1.6-Å resolution and found that the peptide adopted a mainly helical structure. Conserved residues in β-CoVs interacted with CC40.8 antibody, thereby providing a molecular basis for its broad reactivity. CC40.8 exhibited in vivo protective efficacy against SARS-CoV-2 challenge in two animal models. In both models, CC40.8-treated animals exhibited less weight loss and reduced lung viral titers compared to controls. Furthermore, we noted that CC40.8-like bnAbs are relatively rare in human COVID-19 infection, and therefore, their elicitation may require rational structure-based vaccine design strategies. Overall, our study describes a target on β-CoV spike proteins for protective antibodies that may facilitate the development of pan–β-CoV vaccines.

60 APPLIED LIFE SCIENCES↗
DOE OSTI2025

Genetic control of morphological transitions in a coacervating protein template

Nature routinely exploits liquid–liquid phase separation (LLPS) of proteins to control the assembly and mineralization of hybrid materials. Here, we show that fusion of the Car9 silica-binding peptide to an elastin-like polypeptide (ELP) yields temperature- and sequence-programmable soft matter templates for the synthesis of silicified architectures ranging in size from nanometers to micrometers. Specifically, we demonstrate unprecedented control over the diameter of silica nanoparticles (SiNP) in the 30–60 nm range with 4 nm precision, show that a single arginine residue (R4) in the Car9 sequence underpins the transition from micelles to proteinosomes, and find that substitutions in other basic residues modulate electrostatic repulsion and solvation to enable access to kinetically trapped species. These structures, which include interconnected micelles, small (∼200 nm) and large (>5 µm) vesicles, are readily visualized by SEM imaging following silicification. Molecular dynamics (MD) simulations and AlphaFold predictions reveal that mutations in positively charged residues alter interfacial packing, hydration, and conformational freedom of the silica-binding segments. Overall, our results establish sequence and thermal energy as synergistic levers for morphological control across length scales using solid-binding ELPs and establish mineralization as a powerful tool to visualize the structure of dynamic soft matter assemblies.

hierarchy↗
DOE OSTI2020

Printing 2D Conjugated Polymer Monolayers and Their Distinct Electronic Properties

Abstract Recently, 2D monolayer films of conjugated polymers have gained increasing attention owing to the preeminence of 2D inorganic films that exhibit unique optoelectronic and mechanical properties compared to their bulk analogs. Despite numerous efforts, crystallization of semiconducting polymers into highly ordered 2D monolayer films still remains challenging. Herein, a dynamic‐template‐assisted meniscus‐guided coating is utilized to fabricate continuous, highly ordered 2D monolayer films of conjugated polymers over a centimeter scale with enhanced backbone π–π stacking. In contrast, monolayer films printed on solid substrates confer upon the 1D fiber networks strong alkyl side‐chain stacking at the expense of backbone packing. From single‐layers to multilayers, the polymer π‐stacks change from edge‐on to bimodal orientation as the film thickness reaches ≈20 nm. Spectroscopic and cyclic voltammetry analysis reveals an abrupt increase in J‐aggregation and absorption coefficient and a decrease in bandgap and highest occupied molecular orbital level until critical thickness, possibly arising from the straightened polymer backbone. This is corroborated by an abrupt increase in hole mobility with film thickness, reaching a maximum of 0.7 cm 2 V −1 s −1 near the critical thickness. Finally, fabrication of chemical sensors incorporating polymer films of various thicknesses is demonstrated, and an ultrahigh sensitivity of the ≈7 nm thick ultrathin film (bilayers) to 1 ppb ammonia is shown.

Kafle, Prapti↗
DOE OSTI2020

Lipid membrane templated misfolding and self-assembly of intrinsically disordered tau protein

The aggregation of the intrinsically disordered tau protein into highly ordered β-sheet-rich fibrils is implicated in the pathogenesis of a range of neurodegenerative disorders. The mechanism of tau fibrillogenesis remains unresolved, particularly early events that trigger the misfolding and assembly of the otherwise soluble and stable tau. We investigated the role the lipid membrane plays in modulating the aggregation of three tau variants, the largest isoform hTau40, the truncated construct K18, and a hyperphosphorylation-mimicking mutant hTau40/3Epi. Despite being charged and soluble, the tau proteins were also highly surface active and favorably interacted with anionic lipid monolayers at the air/water interface. Membrane binding of tau also led to the formation of a macroscopic, gelatinous layer at the air/water interface, possibly related to tau phase separation. At the molecular level, tau assembled into oligomers composed of ~ 40 proteins misfolded in a β-sheet conformation at the membrane surface, as detected by in situ synchrotron grazing-incidence X-ray diffraction. Concomitantly, membrane morphology and lipid packing became disrupted. Our findings support a general tau aggregation mechanism wherein tau’s inherent surface activity and favorable interactions with anionic lipids drive tau-membrane association, inducing misfolding and self-assembly of the disordered tau into β-sheet-rich oligomers that subsequently seed fibrillation and deposition into diseased tissues.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2020

Rational Construction of Porous Metal–Organic Frameworks for Uranium(VI) Extraction: The Strong Periodic Tendency with a Metal Node

Although metal-organic frameworks (MOFs) have been reported as important porous materials for the potential utility in metal ion separation, coordinating the functionality, structure, and component of MOFs remains a great challenge. Herein, a series of anionic rare earth MOFs (RE-MOFs) were synthesized via a solvothermal template reaction and for the first time explored for uranium(VI) capture from an acidic medium. The unusually high extraction capacity of UO2 2 + (e.g., 538 mg U per g of Y-MOF) was achieved through ion-exchange with the concomitant release of Me 2 NH 2 + , during which the uranium(VI) extraction in the series of isostructural RE-MOFs was found to be highly sensitive to the ionic radii of the metal nodes. That is, the uranium(VI) adsorption capacities continuously increased as the ionic radii decreased. Finally, in-depth mechanism insight was obtained from molecular dynamics simulations, suggesting that both the accessible pore volume of the MOFs and hydrogen-bonding interactions contribute to the strong periodic tendency of uranium(VI) extraction.

36 MATERIALS SCIENCE↗
NASA NTRS1994

Continuous in vitro evolution of bacteriophage RNA polymerase promoters

Rapid in vitro evolution of bacteriophage T7, T3, and SP6 RNA polymerase promoters was achieved by a method that allows continuous enrichment of DNAs that contain functional promoter elements. This method exploits the ability of a special class of nucleic acid molecules to replicate continuously in the presence of both a reverse transcriptase and a DNA-dependent RNA polymerase. Replication involves the synthesis of both RNA and cDNA intermediates. The cDNA strand contains an embedded promoter sequence, which becomes converted to a functional double-stranded promoter element, leading to the production of RNA transcripts. Synthetic cDNAs, including those that contain randomized promoter sequences, can be used to initiate the amplification cycle. However, only those cDNAs that contain functional promoter sequences are able to produce RNA transcripts. Furthermore, each RNA transcript encodes the RNA polymerase promoter sequence that was responsible for initiation of its own transcription. Thus, the population of amplifying molecules quickly becomes enriched for those templates that encode functional promoters. Optimal promoter sequences for phage T7, T3, and SP6 RNA polymerase were identified after a 2-h amplification reaction, initiated in each case with a pool of synthetic cDNAs encoding greater than 10(10) promoter sequence variants.

Non-NASA Center↗
DOE OSTI2021

van der Waals Epitaxy Growth of Bi 2 Se 3 on a Freestanding Monolayer Graphene Membrane: Implications for Layered Materials and Heterostructures

Research on two-dimensional and layered materials has expanded over the past 2 decades because of their unique properties and application potential. The key hurdles in realizing this potential are the challenges in controlling their atomic structure and their incompatibility with existing semiconductor nanofabrication techniques. Here we report on high-quality van der Waals epitaxial growth and characterization of a layered topological insulator on freestanding monolayer graphene transferred to different mechanical supports. This “templated” synthesis approach enables direct interrogation of the interfacial atomic structure of the as-grown materials and opens a route toward creating device structures with more traditional semiconductor nanofabrication techniques.

36 MATERIALS SCIENCE↗
DOE OSTI2023

Green Needle Coke Production from Pyrolysis Biocrude toward Bio-based Anode Material Manufacture: Biochar Fines Addition Effect as “Physical Template” on the Crystalline Order

Here, a new method for producing green needle coke (GNC) is developed by replacing the “heavy fraction” of petroleum pitch delayed coking with fast pyrolysis biocrude. A series of alternative biocrude distillation, carbonization, and calcination conditions were investigated to determine the influence of these processing parameters onto the crystalline structure of the resulting graphitized material. For the first time, the addition of biochar fines was found to serve as a “physical template” to increase the graphitic nature of the final product. During the initial biocrude carbonization (350–450 °C), volatile compounds are released, and aromatics in pyrolysis biocrude experience condensation, resulting in GNC solids with carbon contents above 95 wt % and some early lamellar structure. In the second stage of the thermal process (25–1500 °C), there are additional thermal decomposition reactions with an increase in the aromatic nature of the graphitized solid. It was found that systematic addition of biochar fines induces a nucleating effect during the GNC development. Thermogravimetric analysis suggests that biochar fines promote polycondensation reactions by modifying the biopitch structure and molecular weight, while elemental analysis (CHN) shows a reduction in both H/C and O/C ratios which are consistent with the increase in aromaticity and removal of oxygenated compounds as thermal treatment evolves. The effects of different bio-based pitch materials (after distillation) and GNC intermediates were evaluated by pyrolysis-gas chromatography mass spectrometry and Fourier transform infrared, displaying slight changes on product yields and quality. X-ray diffraction patterns taken after graphitization evidence an increase in the graphitic order with the addition of biochar fines. Transmittance electron microscopy depicts an improvement on graphitic morphology as biochar fine content increases. The use of biochar fines showed a significant increase in graphitic ordering at addition levels above 0.01 wt %. These results show that thermally treated biocrude/biochar fine systems can produce graphitic structures (hard carbon-like) that might be suitable for the manufacture of sodium-ion batteries.

09 BIOMASS FUELS↗
NASA NTRS2017

Single Object & Time Series Spectroscopy with JWST NIRCam

JWST will enable high signal-to-noise spectroscopic observations of the atmospheres of transiting planets with high sensitivity at wavelengths that are inaccessible with HST or other existing facilities. We plan to exploit this by measuring abundances, chemical compositions, cloud properties, and temperature-pressure parameters of a set of mostly warm (T 600 - 1200 K) and low mass (14 -200 Earth mass) planets in our guaranteed time program. These planets are expected to have significant molecular absorptions of H2O, CH4, CO2, CO, and other molecules that are key for determining these parameters and illuminating how and where the planets formed. We describe how we will use the NIRCam grisms to observe slitless transmission and emission spectra of these planets over 2.4 - 5.0 microns wavelength and how well these observations can measure our desired parameters. This will include how we set integration times, exposure parameters, and obtain simultaneous shorter wavelength images to track telescope pointing and stellar variability. We will illustrate this with specific examples showing model spectra, simulated observations, expected information retrieval results, completed Astronomer's Proposal Tools observing templates, target visibility, and other considerations.

NIRCam↗
DOE OSTI2024

SEC ‐ SAXS / MC Ensemble Structural Studies of the Microtubule Binding Protein Cdt1 Show Monomeric, Folded‐Over Conformations

ABSTRACT Cdt1 is a mixed folded protein critical for DNA replication licensing and it also has a “moonlighting” role at the kinetochore via direct binding to microtubules and the Ndc80 complex. However, it is unknown how the structure and conformations of Cdt1 could allow it to participate in these multiple, unique sets of protein complexes. While robust methods exist to study entirely folded or unfolded proteins, structure–function studies of combined, mixed folded/disordered proteins remain challenging. In this work, we employ orthogonal biophysical and computational techniques to provide structural characterization of mitosis‐competent human Cdt1. Thermal stability analyses shows that both folded winged helix domains1 are unstable. CD and NMR show that the N‐terminal and linker regions are intrinsically disordered. DLS shows that Cdt1 is monomeric and polydisperse, while SEC‐MALS confirms that it is monomeric at high concentrations, but without any apparent inter‐molecular self‐association. SEC‐SAXS enabled computational modeling of the protein structures. Using the program SASSIE, we performed rigid body Monte Carlo simulations to generate a conformational ensemble of structures. We observe that neither fully extended nor extremely compact Cdt1 conformations are consistent with SAXS. The best‐fit models have the N‐terminal and linker disordered regions extended into the solution and the two folded domains close to each other in apparent “folded over” conformations. We hypothesize the best‐fit Cdt1 conformations could be consistent with a function as a scaffold protein that may be sterically blocked without binding partners. Our study also provides a template for combining experimental and computational techniques to study mixed‐folded proteins.

Cell Biology↗
NASA NTRS1995

Insights to primitive replication derived from structures of small oligonucleotides

Available information on the structure of small oligonucleotides is surveyed. It is observed that even small oligomers typically exhibit defined structures over a wide range of pH and temperature. These structures rely on a plethora of non-standard base-base interactions in addition to the traditional Watson-Crick pairings. Stable duplexes, though typically antiparallel, can be parallel or staggered and perfect complementarity is not essential. These results imply that primitive template directed reactions do not require high fidelity. Hence, the extensive use of Watson-Crick complementarity in genes rather than being a direct consequence of the primitive condensation process, may instead reflect subsequent selection based on the advantage of accuracy in maintaining the primitive genetic machinery once it arose.

Review↗
NASA NTRS2017

Successful Validation of RNA Purification and Quantitative Real-Time PCR Analysis of Gene Expression on the International Space Station

The NASA Ames WetLab-2 system was developed to offer new on-orbit gene expression analysis capabilities to ISS researchers and can be used to conduct on-orbit RNA isolation and quantitative real time PCR (RT-qPCR) analysis of gene expression from a wide range of biological samples ranging from microbes to mammalian tissues. On orbit validation included three quantitative PCR (qPCR) runs using an E. coli genomic DNA template pre-loaded at three different concentrations. The flight Ct values for the DNA standards showed no statistically significant differences relative to ground controls although there was increased noise in Ct curves, likely due to microgravity-related bubble retention in the optical windows. RNA was successfully purified from both E. coli and mouse liver samples and successfully generated singleplex, duplex and triplex data although with higher standard deviations than ground controls, also likely due to bubbles. Using volunteer science activities, a potential bubble reduction strategy was tested and resulted in smooth amplification curves and tighter Cts between replicates. The WetLab-2 validation experiment demonstrates a novel molecular biology workbench on ISS which allows scientists to purify and stabilize RNA, and to conduct RT-qPCR analyses on-orbit with rapid results. This novel ability is an important step towards utilizing ISS as a National Laboratory facility with the capability to conduct and adjust science experiments in real time without sample return, and opens new possibilities for rapid medical diagnostics and biological environmental monitoring on ISS.

microgravity↗
NASA NTRS2005

Making Macroscopic Assemblies of Aligned Carbon Nanotubes

A method of aligning and assembling single-wall carbon nanotubes (SWNTs) to fabricate macroscopic structures has been invented. The method entails suspending SWNTs in a fluid, orienting the SWNTs by use of a magnetic and/or electric field, and then removing the aligned SWNTs from suspension in such a way as to assemble them while maintaining the alignment. SWNTs are essentially tubular extensions of fullerene molecules. It is desirable to assemble aligned SWNTs into macroscopic structures because the common alignment of the SWNTs in such a structure makes it possible to exploit, on a macroscopic scale, the unique mechanical, chemical, and electrical properties that individual oriented SWNTs exhibit at the molecular level. Because of their small size and high electrical conductivity, carbon nanotubes, and especially SWNTs, are useful for making electrical connectors in integrated circuits. Carbon nanotubes can be used as antennas at optical frequencies, and as probes in scanning tunneling microscopes, atomic-force microscopes, and the like. Carbon nanotubes can be used with or instead of carbon black in tires. Carbon nanotubes are useful as supports for catalysts. Ropes of SWNTs are metallic and, as such, are potentially useful in some applications in which electrical conductors are needed - for example, they could be used as additives in formulating electrically conductive paints. Finally, macroscopic assemblies of aligned SWNTs can serve as templates for the growth of more and larger structures of the same type. The great variety of tubular fullerene molecules and of the structures that could be formed by assembling them in various ways precludes a complete description of the present method within the limits of this article. It must suffice to present a typical example of the use of one of many possible variants of the method to form a membrane comprising SWNTs aligned substantially parallel to each other in the membrane plane. The apparatus used in this variant of the method (see figure) includes a reservoir containing SWNTs dispersed in a suspending agent (for example, dimethylformamide) and a reservoir containing a suitable solvent (for example, water mixed with a surfactant). By use of either pressurized gas supplied from upstream or suction from downstream, the suspension of SWNTs and the solvent are forced to mix and flow into a tank. A filter inside the tank contains pores small enough to prevent the passage of most SWNTs, but large enough to allow the passage of molecules of the solvent and suspending agent. The filter is oriented perpendicular to the flow path. A magnetic field parallel to the plane of the filter is applied. The success of the method is based on the tendency of SWNTs to become aligned with their longitudinal axes parallel to an applied magnetic field. The alignment energy of an SWNT increases with the length of the SWNT and the magnetic-field strength. In order to obtain an acceptably small degree of statistical deviation of SWNTs of a given length from alignment with a magnetic field, one must make the field strong enough so that the thermal energy associated with rotation of an SWNT away from alignment is less than the alignment energy.

Smalley, Richard E.↗
NASA NTRS2011

Post-Fragmentation Whole Genome Amplification-Based Method

This innovation is derived from a proprietary amplification scheme that is based upon random fragmentation of the genome into a series of short, overlapping templates. The resulting shorter DNA strands (<400 bp) constitute a library of DNA fragments with defined 3 and 5 termini. Specific primers to these termini are then used to isothermally amplify this library into potentially unlimited quantities that can be used immediately for multiple downstream applications including gel eletrophoresis, quantitative polymerase chain reaction (QPCR), comparative genomic hybridization microarray, SNP analysis, and sequencing. The standard reaction can be performed with minimal hands-on time, and can produce amplified DNA in as little as three hours. Post-fragmentation whole genome amplification-based technology provides a robust and accurate method of amplifying femtogram levels of starting material into microgram yields with no detectable allele bias. The amplified DNA also facilitates the preservation of samples (spacecraft samples) by amplifying scarce amounts of template DNA into microgram concentrations in just a few hours. Based on further optimization of this technology, this could be a feasible technology to use in sample preservation for potential future sample return missions. The research and technology development described here can be pivotal in dealing with backward/forward biological contamination from planetary missions. Such efforts rely heavily on an increasing understanding of the burden and diversity of microorganisms present on spacecraft surfaces throughout assembly and testing. The development and implementation of these technologies could significantly improve the comprehensiveness and resolving power of spacecraft-associated microbial population censuses, and are important to the continued evolution and advancement of planetary protection capabilities. Current molecular procedures for assaying spacecraft-associated microbial burden and diversity have inherent sample loss issues at practically every step, particularly nucleic acid extraction. In engineering a molecular means of amplifying nucleic acids directly from single cells in their native state within the sample matrix, this innovation has circumvented entirely the need for DNA extraction regimes in the sample processing scheme.

Benardini, James↗