Microbundles of zinc oxide nanorods: Assembly in ionic liquid [EMIM]{sup +}[BF{sub 4}]{sup -}, photoluminescence and photocatalytic properties

DOE Office of Scientific and Technical Information (OSTI.GOV)

Wang Li; Xu Shenzhi; Li Huijun

2011-03-15

A simple, efficient and low-temperature approach for the assembly of hierarchical Zinc oxide (ZnO) microstructures in ionic liquid [EMIM]{sup +}[BF{sub 4}]{sup -} is reported. The as-obtained ZnO superstructures are composed of microbundles of nanorods from the center points, with the diameter and length in the range of 100-150 nm and 2-4 {mu}m, which have been characterized by X-ray diffraction, scanning and transmission electron microscopy, and photoluminescence spectroscopy. The ZnO microstructures exhibit significant defect-related green-yellow emission and high photodegradation of dye Methyl Orange (5x10{sup -5} mol/L) under UV excitation within 80 min. -- Graphical abstract: Easy formation of microbundles of ZnOmore » nanorods were accomplished in low temperature with [EMIM]{sup +}[BF{sub 4}]{sup -} (1-ethyl-3-methylimidazolium tetrafluoroborate) ionic liquid, which exhibit significant green-yellow photoluminescence property and high photodegradation of Methyl Orange dye. Display Omitted Research highlights: {yields} Ionic liquid assisted solid-state route was introduced into synthesis of ZnO nanorods. {yields} The distinctive microbundles ZnO nanorod assembles was evidenced by SEM and TEM. {yields} ZnO nano-material exhibited high efficiency in photodegradation of Methyl Orange.« less

Surface-assisted DNA self-assembly: An enzyme-free strategy towards formation of branched DNA lattice

DOE Office of Scientific and Technical Information (OSTI.GOV)

Bhanjadeo, Madhabi M.; Academy of Scientific and Innovative Research; Nayak, Ashok K.

DNA based self-assembled nanostructures and DNA origami has proven useful for organizing nanomaterials with firm precision. However, for advanced applications like nanoelectronics and photonics, large-scale organization of self-assembled branched DNA (bDNA) into periodic lattices is desired. In this communication for the first time we report a facile method of self-assembly of Y-shaped bDNA nanostructures on the cationic surface of Aluminum (Al) foil to prepare periodic two dimensional (2D) bDNA lattice. Particularly those Y-shaped bDNA structures having smaller overhangs and unable to self-assemble in solution, they are easily assembled on the surface of Al foil in the absence of ligase. Fieldmore » emission scanning electron microscopy (FESEM) analysis shows homogenous distribution of two-dimensional bDNA lattices across the Al foil. When the assembled bDNA structures were recovered from the Al foil and electrophoresed in nPAGE only higher order polymeric bDNA structures were observed without a trace of monomeric structures which confirms the stability and high yield of the bDNA lattices. Therefore, this enzyme-free economic and efficient strategy for developing bDNA lattices can be utilized in assembling various nanomaterials for functional molecular components towards development of DNA based self-assembled nanodevices. - Highlights: • Al foil surface-assisted self-assembly of monomeric structures into larger branched DNA lattice. • FESEM study confirms the uniform distribution of two-dimensional bDNA lattice structures across the surface of Al foil. • Enzyme-free and economic strategy to prepare higher order structures from simpler DNA nanostructures have been confirmed by recovery assay. • Use of well proven sequences for the preparation of pure Y-shaped monomeric DNA nanostructure with high yield.« less

Directed self-assembly of mesoscopic components for led applications

NASA Astrophysics Data System (ADS)

Tkachenko, Anton

Light-emitting diodes (LEDs) constitute a rapidly evolving and fast growing technology that promises to replace incandescent bulbs and compact fluorescent lights in many illumination applications. Large-area LED luminaires have a capability to transform lighting by providing a venue for development of smart lighting systems with additional benefits, such as visible light communications, sensing, health and productivity improvement through color temperature control, capability of creating "virtual sky" ceiling, and many others. The objective of this work is to explore directed self-assembly (DSA) approaches suitable for cost-effective assembly of large amount of LEDs and other mesoscopic (i.e. millimeter and sub-millimeter) electronic components and thus to enable manufacturing of smart lighting luminaires. Existing alternative approaches for assembly of semiconductor dies are examined including transfer printing, laser-assisted die transfer, and various directed self-assembly approaches using shape-recognition, magnetic and capillary forces, etc. After comparing their advantages and limitations, we developed two approaches to magnetic force-assisted DSA of LEDs on a large-area substrate in liquid and air medium. The first approach involves pick-up of buoyant and magnetic dies from the liquid surface onto the flexible substrate in a roll-to-roll process. The possibility of high-speed assembly of LED dies is demonstrated, but with a low yield due to the influence of the capillary force of the carrier liquid and the difficulty in ensuring reliable supply of dies to the assembly interface. To overcome the aforementioned challenges this process was modified to assemble the dies by sinking them onto the receiving substrate with a stencil mask on top, demonstrating LED assembly with a very low error rate but at a lower speed. A solder-assisted self-alignment is used to further improve placement precision and to ensure the proper orientation of the dies. The second approach involves self-assembly of dies in an air medium by levitating them in a periodic magnetic field. Using only vibration in z-direction with properly selected waveforms, both high-yield and high-speed DSA was demonstrated. Magnetostatic simulations were used to demonstrate scaling of DSA process with the die size while a model based on a 2D random walk was used to show how the assembly time scales with the number of dies and how this scaling law can be improved. These results indicate that this process can scale well both with the die size and with the number of assembled dies. Through this thesis work, it was demonstrated that assembly in liquid using ferromagnetic dies can be done either with high speed or with high yield, but not with both at the same time. DSA using diamagnetic levitation offers a way to achieve both through a careful design of magnetic field, thickness and quality of diamagnetic material (graphite) as well as proper selection of vibration pattern. This DSA process can enable large-area parallel assembly of millimeter and sub-millimeter components for manufacturing of LED panels, displays and microcell photovoltaics.

Guiding the folding pathway of DNA origami

NASA Astrophysics Data System (ADS)

Dunn, Katherine E.; Dannenberg, Frits; Ouldridge, Thomas E.; Kwiatkowska, Marta; Turberfield, Andrew J.; Bath, Jonathan

2015-09-01

DNA origami is a robust assembly technique that folds a single-stranded DNA template into a target structure by annealing it with hundreds of short `staple' strands. Its guiding design principle is that the target structure is the single most stable configuration. The folding transition is cooperative and, as in the case of proteins, is governed by information encoded in the polymer sequence. A typical origami folds primarily into the desired shape, but misfolded structures can kinetically trap the system and reduce the yield. Although adjusting assembly conditions or following empirical design rules can improve yield, well-folded origami often need to be separated from misfolded structures. The problem could in principle be avoided if assembly pathway and kinetics were fully understood and then rationally optimized. To this end, here we present a DNA origami system with the unusual property of being able to form a small set of distinguishable and well-folded shapes that represent discrete and approximately degenerate energy minima in a vast folding landscape, thus allowing us to probe the assembly process. The obtained high yield of well-folded origami structures confirms the existence of efficient folding pathways, while the shape distribution provides information about individual trajectories through the folding landscape. We find that, similarly to protein folding, the assembly of DNA origami is highly cooperative; that reversible bond formation is important in recovering from transient misfoldings; and that the early formation of long-range connections can very effectively enforce particular folds. We use these insights to inform the design of the system so as to steer assembly towards desired structures. Expanding the rational design process to include the assembly pathway should thus enable more reproducible synthesis, particularly when targeting more complex structures. We anticipate that this expansion will be essential if DNA origami is to continue its rapid development and become a reliable manufacturing technology.

Guiding the folding pathway of DNA origami.

PubMed

Dunn, Katherine E; Dannenberg, Frits; Ouldridge, Thomas E; Kwiatkowska, Marta; Turberfield, Andrew J; Bath, Jonathan

2015-09-03

DNA origami is a robust assembly technique that folds a single-stranded DNA template into a target structure by annealing it with hundreds of short 'staple' strands. Its guiding design principle is that the target structure is the single most stable configuration. The folding transition is cooperative and, as in the case of proteins, is governed by information encoded in the polymer sequence. A typical origami folds primarily into the desired shape, but misfolded structures can kinetically trap the system and reduce the yield. Although adjusting assembly conditions or following empirical design rules can improve yield, well-folded origami often need to be separated from misfolded structures. The problem could in principle be avoided if assembly pathway and kinetics were fully understood and then rationally optimized. To this end, here we present a DNA origami system with the unusual property of being able to form a small set of distinguishable and well-folded shapes that represent discrete and approximately degenerate energy minima in a vast folding landscape, thus allowing us to probe the assembly process. The obtained high yield of well-folded origami structures confirms the existence of efficient folding pathways, while the shape distribution provides information about individual trajectories through the folding landscape. We find that, similarly to protein folding, the assembly of DNA origami is highly cooperative; that reversible bond formation is important in recovering from transient misfoldings; and that the early formation of long-range connections can very effectively enforce particular folds. We use these insights to inform the design of the system so as to steer assembly towards desired structures. Expanding the rational design process to include the assembly pathway should thus enable more reproducible synthesis, particularly when targeting more complex structures. We anticipate that this expansion will be essential if DNA origami is to continue its rapid development and become a reliable manufacturing technology.

Automated assembly of Gallium Arsenide and 50-micron thick silicon solar cell modules

NASA Technical Reports Server (NTRS)

Mesch, H. G.

1984-01-01

The TRW automated solar array assembly equipment was used for the module assembly of 300 GaAs solar cells and 300 50 micron thick silicon solar cells (2 x 4 cm in size). These cells were interconnected with silver plated Invar tabs by means of welding. The GaAs cells were bonded to Kapton graphite aluminum honeycomb graphite substrates and the thin silicon cells were bonded to 0.002 inch thick single layer Kapton substrates. The GaAs solar cell module assembly resulted in a yield of 86% and the thin cell assembly produced a yield of 46% due to intermittent sticking of weld electrodes during the front cell contact welding operation. (Previously assembled thin cell solar modules produced an overall assembly yield of greater than 80%).

Peptide-oligonucleotide conjugates as nanoscale building blocks for assembly of an artificial three-helix protein mimic

NASA Astrophysics Data System (ADS)

Lou, Chenguang; Martos-Maldonado, Manuel C.; Madsen, Charlotte S.; Thomsen, Rasmus P.; Midtgaard, Søren Roi; Christensen, Niels Johan; Kjems, Jørgen; Thulstrup, Peter W.; Wengel, Jesper; Jensen, Knud J.

2016-07-01

Peptide-based structures can be designed to yield artificial proteins with specific folding patterns and functions. Template-based assembly of peptide units is one design option, but the use of two orthogonal self-assembly principles, oligonucleotide triple helix and a coiled coil protein domain formation have never been realized for de novo protein design. Here, we show the applicability of peptide-oligonucleotide conjugates for self-assembly of higher-ordered protein-like structures. The resulting nano-assemblies were characterized by ultraviolet-melting, gel electrophoresis, circular dichroism (CD) spectroscopy, small-angle X-ray scattering and transmission electron microscopy. These studies revealed the formation of the desired triple helix and coiled coil domains at low concentrations, while a dimer of trimers was dominating at high concentration. CD spectroscopy showed an extraordinarily high degree of α-helicity for the peptide moieties in the assemblies. The results validate the use of orthogonal self-assembly principles as a paradigm for de novo protein design.

De novo transcriptome assembly for a non-model species, the blood-sucking bug Triatoma brasiliensis, a vector of Chagas disease.

PubMed

Marchant, A; Mougel, F; Almeida, C; Jacquin-Joly, E; Costa, J; Harry, M

2015-04-01

High throughput sequencing (HTS) provides new research opportunities for work on non-model organisms, such as differential expression studies between populations exposed to different environmental conditions. However, such transcriptomic studies first require the production of a reference assembly. The choice of sampling procedure, sequencing strategy and assembly workflow is crucial. To develop a reliable reference transcriptome for Triatoma brasiliensis, the major Chagas disease vector in Northeastern Brazil, different de novo assembly protocols were generated using various datasets and software. Both 454 and Illumina sequencing technologies were applied on RNA extracted from antennae and mouthparts from single or pooled individuals. The 454 library yielded 278 Mb. Fifteen Illumina libraries were constructed and yielded nearly 360 million RNA-seq single reads and 46 million RNA-seq paired-end reads for nearly 45 Gb. For the 454 reads, we used three assemblers, Newbler, CAP3 and/or MIRA and for the Illumina reads, the Trinity assembler. Ten assembly workflows were compared using these programs separately or in combination. To compare the assemblies obtained, quantitative and qualitative criteria were used, including contig length, N50, contig number and the percentage of chimeric contigs. Completeness of the assemblies was estimated using the CEGMA pipeline. The best assembly (57,657 contigs, completeness of 80 %, <1 % chimeric contigs) was a hybrid assembly leading to recommend the use of (1) a single individual with large representation of biological tissues, (2) merging both long reads and short paired-end Illumina reads, (3) several assemblers in order to combine the specific advantages of each.

Fine mapping of copy number variations on two cattle genome assemblies using high density SNP array

USDA-ARS?s Scientific Manuscript database

Btau_4.0 and UMD3.1 are two distinct cattle reference genome assemblies. In our previous study using the low density BovineSNP50 array, we reported a copy number variation (CNV) analysis on Btau_4.0 with 521 animals of 21 cattle breeds, yielding 682 CNV regions with a total length of 139.8 megabases...

Draft Assembly of Elite Inbred Line PH207 Provides Insights into Genomic and Transcriptome Diversity in Maize

DOE Office of Scientific and Technical Information (OSTI.GOV)

Hirsch, Candice N.; Hirsch, Cory D.; Brohammer, Alex B.

Intense artificial selection over the last 100 years has produced elite maize (Zea mays) inbred lines that combine to produce high-yielding hybrids. To further our understanding of how genome and transcriptome variation contribute to the production of high-yielding hybrids, we generated a draft genome assembly of the inbred line PH207 to complement and compare with the existing B73 reference sequence. B73 is a founder of the Stiff Stalk germplasm pool, while PH207 is a founder of Iodent germplasm, both of which have contributed substantially to the production of temperate commercial maize and are combined to make heterotic hybrids. Comparison ofmore » these two assemblies revealed over 2500 genes present in only one of the two genotypes and 136 gene families that have undergone extensive expansion or contraction. Transcriptome profiling revealed extensive expression variation, with as many as 10,564 differentially expressed transcripts and 7128 transcripts expressed in only one of the two genotypes in a single tissue. Genotype-specific genes were more likely to have tissue/condition-specific expression and lower transcript abundance. The availability of a high-quality genome assembly for the elite maize inbred PH207 expands our knowledge of the breadth of natural genome and transcriptome variation in elite maize inbred lines across heterotic pools.« less

Draft Assembly of Elite Inbred Line PH207 Provides Insights into Genomic and Transcriptome Diversity in Maize

DOE PAGES

Hirsch, Candice N.; Hirsch, Cory D.; Brohammer, Alex B.; ...

2016-11-01

Intense artificial selection over the last 100 years has produced elite maize (Zea mays) inbred lines that combine to produce high-yielding hybrids. To further our understanding of how genome and transcriptome variation contribute to the production of high-yielding hybrids, we generated a draft genome assembly of the inbred line PH207 to complement and compare with the existing B73 reference sequence. B73 is a founder of the Stiff Stalk germplasm pool, while PH207 is a founder of Iodent germplasm, both of which have contributed substantially to the production of temperate commercial maize and are combined to make heterotic hybrids. Comparison ofmore » these two assemblies revealed over 2500 genes present in only one of the two genotypes and 136 gene families that have undergone extensive expansion or contraction. Transcriptome profiling revealed extensive expression variation, with as many as 10,564 differentially expressed transcripts and 7128 transcripts expressed in only one of the two genotypes in a single tissue. Genotype-specific genes were more likely to have tissue/condition-specific expression and lower transcript abundance. The availability of a high-quality genome assembly for the elite maize inbred PH207 expands our knowledge of the breadth of natural genome and transcriptome variation in elite maize inbred lines across heterotic pools.« less

Draft Assembly of Elite Inbred Line PH207 Provides Insights into Genomic and Transcriptome Diversity in Maize[OPEN

PubMed Central

Soifer, Ilya; Barad, Omer; Shem-Tov, Doron; Baruch, Kobi; Lu, Fei; Hernandez, Alvaro G.; Wright, Chris L.; Koehler, Klaus; Buell, C. Robin; de Leon, Natalia

2016-01-01

Intense artificial selection over the last 100 years has produced elite maize (Zea mays) inbred lines that combine to produce high-yielding hybrids. To further our understanding of how genome and transcriptome variation contribute to the production of high-yielding hybrids, we generated a draft genome assembly of the inbred line PH207 to complement and compare with the existing B73 reference sequence. B73 is a founder of the Stiff Stalk germplasm pool, while PH207 is a founder of Iodent germplasm, both of which have contributed substantially to the production of temperate commercial maize and are combined to make heterotic hybrids. Comparison of these two assemblies revealed over 2500 genes present in only one of the two genotypes and 136 gene families that have undergone extensive expansion or contraction. Transcriptome profiling revealed extensive expression variation, with as many as 10,564 differentially expressed transcripts and 7128 transcripts expressed in only one of the two genotypes in a single tissue. Genotype-specific genes were more likely to have tissue/condition-specific expression and lower transcript abundance. The availability of a high-quality genome assembly for the elite maize inbred PH207 expands our knowledge of the breadth of natural genome and transcriptome variation in elite maize inbred lines across heterotic pools. PMID:27803309

A highly flexible platform for nanowire sensor assembly using a combination of optically induced and conventional dielectrophoresis.

PubMed

Lin, Yen-Heng; Ho, Kai-Siang; Yang, Chin-Tien; Wang, Jung-Hao; Lai, Chao-Sung

2014-06-02

The number and position of assembled nanowires cannot be controlled using most nanowire sensor assembling methods. In this paper, we demonstrate a high-yield, highly flexible platform for nanowire sensor assembly using a combination of optically induced dielectrophoresis (ODEP) and conventional dielectrophoresis (DEP). With the ODEP platform, optical images can be used as virtual electrodes to locally turn on a non-contact DEP force and manipulate a micron- or nano-scale substance suspended in fluid. Nanowires were first moved next to the previously deposited metal electrodes using optical images and, then, were attracted to and arranged in the gap between two electrodes through DEP forces generated by switching on alternating current signals to the metal electrodes. A single nanowire can be assembled within 24 seconds using this approach. In addition, the number of nanowires in a single nanowire sensor can be controlled, and the assembly of a single nanowire on each of the adjacent electrodes can also be achieved. The electrical properties of the assembled nanowires were characterized by IV curve measurement. Additionally, the contact resistance between the nanowires and electrodes and the stickiness between the nanowires and substrates were further investigated in this study.

High-Yield Excited Triplet States in Pentacene Self-Assembled Monolayers on Gold Nanoparticles through Singlet Exciton Fission.

PubMed

Kato, Daiki; Sakai, Hayato; Tkachenko, Nikolai V; Hasobe, Taku

2016-04-18

One of the major drawbacks of organic-dye-modified self-assembled monolayers on metal nanoparticles when employed for efficient use of light energy is the fact that singlet excited states on dye molecules can be easily deactivated by means of energy transfer to the metal surface. In this study, a series of 6,13-bis(triisopropylsilylethynyl)pentacene-alkanethiolate monolayer protected gold nanoparticles with different particle sizes and alkane chain lengths were successfully synthesized and were employed for the efficient generation of excited triplet states of the pentacene derivatives by singlet fission. Time-resolved transient absorption measurements revealed the formation of excited triplet states in high yield (172±26 %) by suppressing energy transfer to the gold surface. © 2016 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Highly luminescent colloidal nanoplates of perovskite cesium lead halide and their oriented assemblies

DOE PAGES

Bekenstein, Yehonadav; Koscher, Brent A.; Eaton, Samuel W.; ...

2015-12-15

Anisotropic colloidal quasi-two-dimensional nanoplates (NPLs) hold great promise as functional materials due to their combination of low dimensional optoelectronic properties and versatility through colloidal synthesis. Recently, lead-halide perovskites have emerged as important optoelectronic materials with excellent efficiencies in photovoltaic and light-emitting applications. Here we report the synthesis of quantum confined all inorganic cesium lead halide nanoplates in the perovskite crystal structure that are also highly luminescent (PLQY 84%). The controllable self-assembly of nanoplates either into stacked columnar phases or crystallographic-oriented thin-sheet structures is demonstrated. Furthermore, the broad accessible emission range, high native quantum yields, and ease of self-assembly make perovskitemore » NPLs an ideal platform for fundamental optoelectronic studies and the investigation of future devices.« less

De novo assembly of the Aedes aegypti genome using Hi-C yields chromosome-length scaffolds.

PubMed

Dudchenko, Olga; Batra, Sanjit S; Omer, Arina D; Nyquist, Sarah K; Hoeger, Marie; Durand, Neva C; Shamim, Muhammad S; Machol, Ido; Lander, Eric S; Aiden, Aviva Presser; Aiden, Erez Lieberman

2017-04-07

The Zika outbreak, spread by the Aedes aegypti mosquito, highlights the need to create high-quality assemblies of large genomes in a rapid and cost-effective way. Here we combine Hi-C data with existing draft assemblies to generate chromosome-length scaffolds. We validate this method by assembling a human genome, de novo, from short reads alone (67× coverage). We then combine our method with draft sequences to create genome assemblies of the mosquito disease vectors Ae aegypti and Culex quinquefasciatus , each consisting of three scaffolds corresponding to the three chromosomes in each species. These assemblies indicate that almost all genomic rearrangements among these species occur within, rather than between, chromosome arms. The genome assembly procedure we describe is fast, inexpensive, and accurate, and can be applied to many species. Copyright © 2017, American Association for the Advancement of Science.

Self-assembled hybrid polymer-TiO2 nanotube array heterojunction solar cells.

PubMed

Shankar, Karthik; Mor, Gopal K; Prakasam, Haripriya E; Varghese, Oomman K; Grimes, Craig A

2007-11-20

Films comprised of 4 microm long titanium dioxide nanotube arrays were fabricated by anodizing Ti foils in an ethylene glycol based electrolyte. A carboxylated polythiophene derivative was self-assembled onto the TiO2 nanotube arrays by immersing them in a solution of the polymer. The binding sites of the carboxylate moiety along the polymer chain provide multiple anchoring sites to the substrate, making for a stable rugged film. Backside illuminated liquid junction solar cells based on TiO2 nanotube films sensitized by the self-assembled polymeric layer showed a short-circuit current density of 5.5 mA cm-2, a 0.7 V open circuit potential, and a 0.55 fill factor yielding power conversion efficiencies of 2.1% under AM 1.5 sun. A backside illuminated single heterojunction solid state solar cell using the same self-assembled polymer was demonstrated and yielded a photocurrent density as high as 2.0 mA cm-2. When a double heterojunction was formed by infiltrating a blend of poly(3-hexylthiophene) (P3HT) and C60-methanofullerene into the self-assembled polymer coated nanotube arrays, a photocurrent as high as 6.5 mA cm-2 was obtained under AM 1.5 sun with a corresponding efficiency of 1%. The photocurrent action spectra showed a maximum incident photon-to-electron conversion efficiency (IPCE) of 53% for the liquid junction cells and 25% for the single heterojunction solid state solar cells.

Meshing complex macro-scale objects into self-assembling bricks

PubMed Central

Hacohen, Adar; Hanniel, Iddo; Nikulshin, Yasha; Wolfus, Shuki; Abu-Horowitz, Almogit; Bachelet, Ido

2015-01-01

Self-assembly provides an information-economical route to the fabrication of objects at virtually all scales. However, there is no known algorithm to program self-assembly in macro-scale, solid, complex 3D objects. Here such an algorithm is described, which is inspired by the molecular assembly of DNA, and based on bricks designed by tetrahedral meshing of arbitrary objects. Assembly rules are encoded by topographic cues imprinted on brick faces while attraction between bricks is provided by embedded magnets. The bricks can then be mixed in a container and agitated, leading to properly assembled objects at high yields and zero errors. The system and its assembly dynamics were characterized by video and audio analysis, enabling the precise time- and space-resolved characterization of its performance and accuracy. Improved designs inspired by our system could lead to successful implementation of self-assembly at the macro-scale, allowing rapid, on-demand fabrication of objects without the need for assembly lines. PMID:26226488

High-Rate Assembly of Nanomaterials on Insulating Surfaces Using Electro-Fluidic Directed Assembly.

PubMed

Yilmaz, Cihan; Sirman, Asli; Halder, Aditi; Busnaina, Ahmed

2017-08-22

Conductive or semiconducting nanomaterials-based applications such as electronics and sensors often require direct placement of such nanomaterials on insulating surfaces. Most fluidic-based directed assembly techniques on insulating surfaces utilize capillary force and evaporation but are diffusion limited and slow. Electrophoretic-based assembly, on the other hand, is fast but can only be utilized for assembly on a conductive surface. Here, we present a directed assembly technique that enables rapid assembly of nanomaterials on insulating surfaces. The approach leverages and combines fluidic and electrophoretic assembly by applying the electric field through an insulating surface via a conductive film underneath. The approach (called electro-fluidic) yields an assembly process that is 2 orders of magnitude faster compared to fluidic assembly. By understanding the forces on the assembly process, we have demonstrated the controlled assembly of various types of nanomaterials that are conducting, semiconducting, and insulating including nanoparticles and single-walled carbon nanotubes on insulating rigid and flexible substrates. The presented approach shows great promise for making practical devices in miniaturized sensors and flexible electronics.

Carbon-rich supramolecular metallacycles and metallacages

PubMed Central

Northrop, Brian H.; Chercka, Dennis; Stang, Peter J.

2008-01-01

Coordination-driven self-assembly via the directional-bonding approach utilizes rigid transition metal acceptors and electron-rich donors to allow for complex, nanoscale 2D polygons and 3D polyhedra to be prepared under mild conditions and in high yields. To ensure proper rigidity and directionality, many acceptor and donor precursors contain largely carbon-rich aromatic and/or acetylenic moieties. This article introduces self-assembly as an alternative means of synthesizing carbon-rich materials and discusses the development, design, synthesis, and applications of carbon-rich supramolecular metallacycles and metallacages as well as the self-assembly of new diastereomeric carbon-rich supramolecular triangles. PMID:20011029

Yield stress and scaling of polyelectrolyte multilayer modified suspensions: effect of polyelectrolyte conformation during multilayer assembly.

PubMed

Hess, Andreas; Aksel, Nuri

2013-09-10

The yield stress of polyelectrolyte multilayer modified suspensions exhibits a surprising dependence on the polyelectrolyte conformation of multilayer films. The rheological data scale onto a universal master curve for each polyelectrolyte conformation as the particle volume fraction, φ, and the ionic strength of the background fluid, I, are varied. It is shown that rough films with highly coiled, brushy polyelectrolytes significantly enhance the yield stress. Moreover, via the ionic strength I of the background fluid, the dynamic yield stress of brushy polyelectrolyte multilayers can be finely adjusted over 2 decades.

Testing and Analysis of NEXT Ion Engine Discharge Cathode Assembly Wear

NASA Technical Reports Server (NTRS)

Domonkos, Matthew T.; Foster, John E.; Soulas, George C.; Nakles, Michael

2003-01-01

Experimental and analytical investigations were conducted to predict the wear of the discharge cathode keeper in the NASA Evolutionary Xenon Thruster. The ion current to the keeper was found to be highly dependent upon the beam current, and the average beam current density was nearly identical to that of the NSTAR thruster for comparable beam current density. The ion current distribution was highly peaked toward the keeper orifice. A deterministic wear assessment predicted keeper orifice erosion to the same diameter as the cathode tube after processing 375 kg of xenon. A rough estimate of discharge cathode assembly life limit due to sputtering indicated that the current design exceeds the qualification goal of 405 kg. Probabilistic wear analysis showed that the plasma potential and the sputter yield contributed most to the uncertainty in the wear assessment. It was recommended that fundamental experimental and modeling efforts focus on accurately describing the plasma potential and the sputtering yield.

Nano-encrypted Morse code: a versatile approach to programmable and reversible nanoscale assembly and disassembly.

PubMed

Wong, Ngo Yin; Xing, Hang; Tan, Li Huey; Lu, Yi

2013-02-27

While much work has been devoted to nanoscale assembly of functional materials, selective reversible assembly of components in the nanoscale pattern at selective sites has received much less attention. Exerting such a reversible control of the assembly process will make it possible to fine-tune the functional properties of the assembly and to realize more complex designs. Herein, by taking advantage of different binding affinities of biotin and desthiobiotin toward streptavidin, we demonstrate selective and reversible decoration of DNA origami tiles with streptavidin, including revealing an encrypted Morse code "NANO" and reversible exchange of uppercase letter "I" with lowercase "i". The yields of the conjugations are high (>90%), and the process is reversible. We expect this versatile conjugation technique to be widely applicable with different nanomaterials and templates.

Ion-Specific Control of the Self-Assembly Dynamics of a Nanostructured Protein Lattice

DOE PAGES

Rad, Behzad; Haxton, Thomas K.; Shon, Albert; ...

2014-12-10

Self-assembling proteins offer a potential means of creating nanostructures with complex structure and function. However, using self-assembly to create nanostructures with long-range order whose size is tunable is challenging, because the kinetics and thermodynamics of protein interactions depend sensitively on solution conditions. Here we systematically investigate the impact of varying solution conditions on the self-assembly of SbpA, a surface-layer protein from Lysinibacillus sphaericus that forms two-dimensional nanosheets. Using high-throughput light scattering measurements, we mapped out diagrams that reveal the relative yield of self-assembly of nanosheets over a wide range of concentrations of SbpA and Ca 2+. These diagrams revealed amore » localized region of optimum yield of nanosheets at intermediate Ca 2+ concentration. Replacement of Mg 2+ or Ba 2+ for Ca 2+ indicates that Ca 2+ acts both as a specific ion that is required to induce self-assembly and as a general divalent cation. In addition, we use competitive titration experiments to find that 5 Ca 2+ bind to SbpA with an affinity of 67.1 ± 0.3 μM. Finally, we show via modeling that nanosheet assembly occurs by growth from a negligibly small critical nucleus. We also chart the dynamics of nanosheet size over a variety of conditions. In conclusion, our results demonstrate control of the dynamics and size of the self-assembly of a nanostructured lattice, the constituents of which are one of a class of building blocks able to form novel hybrid nanomaterials.« less

Synthesis and solution self-assembly of side-chain cobaltocenium-containing block copolymers.

PubMed

Ren, Lixia; Hardy, Christopher G; Tang, Chuanbing

2010-07-07

The synthesis of side-chain cobaltocenium-containing block copolymers and their self-assembly in solution was studied. Highly pure monocarboxycobaltocenium was prepared and subsequently attached to side chains of poly(tert-butyl acrylate)-block-poly(2-hydroxyethyl acrylate), yielding poly(tert-butyl acrylate)-block-poly(2-acryloyloxyethyl cobaltoceniumcarboxylate). The cobaltocenium block copolymers exhibited vesicle morphology in the mixture of acetone and water, while micelles of nanotubes were formed in the mixture of acetone and chloroform.

Strategies for optimizing BioNano and Dovetail explored through a second reference quality assembly for the legume model, Medicago truncatula.

PubMed

Moll, Karen M; Zhou, Peng; Ramaraj, Thiruvarangan; Fajardo, Diego; Devitt, Nicholas P; Sadowsky, Michael J; Stupar, Robert M; Tiffin, Peter; Miller, Jason R; Young, Nevin D; Silverstein, Kevin A T; Mudge, Joann

2017-08-04

Third generation sequencing technologies, with sequencing reads in the tens- of kilo-bases, facilitate genome assembly by spanning ambiguous regions and improving continuity. This has been critical for plant genomes, which are difficult to assemble due to high repeat content, gene family expansions, segmental and tandem duplications, and polyploidy. Recently, high-throughput mapping and scaffolding strategies have further improved continuity. Together, these long-range technologies enable quality draft assemblies of complex genomes in a cost-effective and timely manner. Here, we present high quality genome assemblies of the model legume plant, Medicago truncatula (R108) using PacBio, Dovetail Chicago (hereafter, Dovetail) and BioNano technologies. To test these technologies for plant genome assembly, we generated five assemblies using all possible combinations and ordering of these three technologies in the R108 assembly. While the BioNano and Dovetail joins overlapped, they also showed complementary gains in continuity and join numbers. Both technologies spanned repetitive regions that PacBio alone was unable to bridge. Combining technologies, particularly Dovetail followed by BioNano, resulted in notable improvements compared to Dovetail or BioNano alone. A combination of PacBio, Dovetail, and BioNano was used to generate a high quality draft assembly of R108, a M. truncatula accession widely used in studies of functional genomics. As a test for the usefulness of the resulting genome sequence, the new R108 assembly was used to pinpoint breakpoints and characterize flanking sequence of a previously identified translocation between chromosomes 4 and 8, identifying more than 22.7 Mb of novel sequence not present in the earlier A17 reference assembly. Adding Dovetail followed by BioNano data yielded complementary improvements in continuity over the original PacBio assembly. This strategy proved efficient and cost-effective for developing a quality draft assembly compared to traditional reference assemblies.

Nano-Encrypted Morse Code: A Versatile Approach to Programmable and Reversible Nanoscale Assembly and Disassembly

PubMed Central

Wong, Ngo Yin; Xing, Hang; Tan, Li Huey; Lu, Yi

2013-01-01

While much work has been devoted to nanoscale assembly of functional materials, selective reversible assembly of components in the nanoscale pattern at selective sites has received much less attention. Exerting such a reversible control of the assembly process will make it possible to fine-tune the functional properties of the assembly and to realize more complex designs. Herein, by taking advantage of different binding affinities of biotin and desthiobiotin toward streptavidin, we demonstrate selective and reversible decoration of DNA origami tiles with streptavidin, including revealing an encrypted Morse code “NANO” and reversible exchange of uppercase letter “I” with lowercase “i”. The yields of the conjugations are high (> 90%) and the process is reversible. We expect this versatile conjugation technique to be widely applicable with different nanomaterials and templates. PMID:23373425

Two unprecedented aromatic guanidines supramolecular chains self-assembled by hydrogen bonding interaction

NASA Astrophysics Data System (ADS)

Zhang, Yunshen; Huang, Yichao; Zhang, Jiangwei; Zhu, Li; Chen, Kun; Hao, Jian

2015-10-01

Two aromatic guanidine derivatives, C6H5N = C(NHCy)2 (1), (n-TBA)C6H5NHC(NHCy)2Mo2O7 (2) (Cy = cyclohexyl), were synthetized with high yields. Both of them self-assembled into supramolecules via H-bond interactions. Single crystal XRD indicated that crystal 1 showed helix chains combining pseudo four-fold and pseudo six-fold symmetries, while crystal 2 presented ladder chains with alternate ring structures. In this paper, a novel way to design ladder-like supramolecular chains from helix chains was presented, using POMs (polyoxometalates) to provide protons to help assembly.

Simulating Self-Assembly with Simple Models

NASA Astrophysics Data System (ADS)

Rapaport, D. C.

Results from recent molecular dynamics simulations of virus capsid self-assembly are described. The model is based on rigid trapezoidal particles designed to form polyhedral shells of size 60, together with an atomistic solvent. The underlying bonding process is fully reversible. More extensive computations are required than in previous work on icosahedral shells built from triangular particles, but the outcome is a high yield of closed shells. Intermediate clusters have a variety of forms, and bond counts provide a useful classification scheme

Characterization of the Caliban and Prospero Critical Assemblies Neutron Spectra for Integral Measurements Experiments

NASA Astrophysics Data System (ADS)

Casoli, P.; Authier, N.; Jacquet, X.; Cartier, J.

2014-04-01

Caliban and Prospero are two highly enriched uranium metallic core reactors operated on the CEA Center of Valduc. These critical assemblies are suitable for integral experiments, such as fission yields measurements or perturbation measurements, which have been carried out recently on the Caliban reactor. Different unfolding methods, based on activation foils and fission chambers measurements, are used to characterize the reactor spectra and especially the Caliban spectrum, which is very close to a pure fission spectrum.

Pathway-engineering for highly-aligned block copolymer arrays.

PubMed

Choo, Youngwoo; Majewski, Paweł W; Fukuto, Masafumi; Osuji, Chinedum O; Yager, Kevin G

2017-12-21

While the ultimate driving force in self-assembly is energy minimization and the corresponding evolution towards equilibrium, kinetic effects can also play a very strong role. These kinetic effects, such as trapping in metastable states, slow coarsening kinetics, and pathway-dependent assembly, are often viewed as complications to be overcome. Here, we instead exploit these effects to engineer a desired final nano-structure in a block copolymer thin film, by selecting a particular ordering pathway through the self-assembly energy landscape. In particular, we combine photothermal shearing with high-temperature annealing to yield hexagonal arrays of block copolymer cylinders that are aligned in a single prescribed direction over macroscopic sample dimensions. Photothermal shearing is first used to generate a highly-aligned horizontal cylinder state, with subsequent thermal processing used to reorient the morphology to the vertical cylinder state in a templated manner. Finally, we demonstrate the successful transfer of engineered morphologies into inorganic replicas.

Assembly of LiMnPO4 Nanoplates into Microclusters as a High-Performance Cathode in Lithium-Ion Batteries.

PubMed

Wang, Chao; Li, Shiheng; Han, Yuyao; Lu, Zhenda

2017-08-23

A novel structure of a carbon-coated LiMnPO 4 microcluster through emulsion-based self-assembly has been fabricated to yield a high-performance battery cathode. In this rational design, nanosized LiMnPO 4 plates are assembled into microclusters to achieve a dense packing and robust interparticle contact. In addition, the conductive carbon framework wrapping around these clusters functions as a fast electron highway, ensuring the high utilization of the active materials. The designed structure demonstrates enhanced specific capacity and cycling stability in lithium-ion batteries, delivering a discharge capacity of 120 mAh g -1 after 200 cycles at 0.2 C. It also shows a superior rate capability with discharge capacities of 139.7 mAh g -1 at 0.05 C, 131.7 mAh g -1 at 0.1 C, and 99.2 mAh g -1 at 1 C at room temperature.

High Throughput Engineering to Revitalize a Vestigial Electron Transfer Pathway in Bacterial Photosynthetic Reaction Centers*

PubMed Central

Faries, Kaitlyn M.; Kressel, Lucas L.; Wander, Marc J.; Holten, Dewey; Laible, Philip D.; Kirmaier, Christine; Hanson, Deborah K.

2012-01-01

Photosynthetic reaction centers convert light energy into chemical energy in a series of transmembrane electron transfer reactions, each with near 100% yield. The structures of reaction centers reveal two symmetry-related branches of cofactors (denoted A and B) that are functionally asymmetric; purple bacterial reaction centers use the A pathway exclusively. Previously, site-specific mutagenesis has yielded reaction centers capable of transmembrane charge separation solely via the B branch cofactors, but the best overall electron transfer yields are still low. In an attempt to better realize the architectural and energetic factors that underlie the directionality and yields of electron transfer, sites within the protein-cofactor complex were targeted in a directed molecular evolution strategy that implements streamlined mutagenesis and high throughput spectroscopic screening. The polycistronic approach enables efficient construction and expression of a large number of variants of a heteroligomeric complex that has two intimately regulated subunits with high sequence similarity, common features of many prokaryotic and eukaryotic transmembrane protein assemblies. The strategy has succeeded in the discovery of several mutant reaction centers with increased efficiency of the B pathway; they carry multiple substitutions that have not been explored or linked using traditional approaches. This work expands our understanding of the structure-function relationships that dictate the efficiency of biological energy-conversion reactions, concepts that will aid the design of bio-inspired assemblies capable of both efficient charge separation and charge stabilization. PMID:22247556

AFEAP cloning: a precise and efficient method for large DNA sequence assembly.

PubMed

Zeng, Fanli; Zang, Jinping; Zhang, Suhua; Hao, Zhimin; Dong, Jingao; Lin, Yibin

2017-11-14

Recent development of DNA assembly technologies has spurred myriad advances in synthetic biology, but new tools are always required for complicated scenarios. Here, we have developed an alternative DNA assembly method named AFEAP cloning (Assembly of Fragment Ends After PCR), which allows scarless, modular, and reliable construction of biological pathways and circuits from basic genetic parts. The AFEAP method requires two-round of PCRs followed by ligation of the sticky ends of DNA fragments. The first PCR yields linear DNA fragments and is followed by a second asymmetric (one primer) PCR and subsequent annealing that inserts overlapping overhangs at both sides of each DNA fragment. The overlapping overhangs of the neighboring DNA fragments annealed and the nick was sealed by T4 DNA ligase, followed by bacterial transformation to yield the desired plasmids. We characterized the capability and limitations of new developed AFEAP cloning and demonstrated its application to assemble DNA with varying scenarios. Under the optimized conditions, AFEAP cloning allows assembly of an 8 kb plasmid from 1-13 fragments with high accuracy (between 80 and 100%), and 8.0, 11.6, 19.6, 28, and 35.6 kb plasmids from five fragments at 91.67, 91.67, 88.33, 86.33, and 81.67% fidelity, respectively. AFEAP cloning also is capable to construct bacterial artificial chromosome (BAC, 200 kb) with a fidelity of 46.7%. AFEAP cloning provides a powerful, efficient, seamless, and sequence-independent DNA assembly tool for multiple fragments up to 13 and large DNA up to 200 kb that expands synthetic biologist's toolbox.

Synthesis and Primary Characterization of Self-Assembled Peptide-Based Hydrogels

PubMed Central

Nagarkar, Radhika P.; Schneider, Joel P.

2009-01-01

Summary Hydrogels based on peptide self-assembly form an important class of biomaterials that find application in tissue engineering and drug delivery. It is essential to prepare peptides with high purity to achieve batch-to-batch consistency affording hydrogels with reproducible properties. Automated solid-phase peptide synthesis coupled with optimized Fmoc (9-fluorenylmethoxycarbonyl) chemistry to obtain peptides in high yield and purity is discussed. Details of isolating a desired peptide from crude synthetic mixtures and assessment of the peptide’s final purity by high-performance liquid chromatography and mass spectrometry are provided. Beyond the practical importance of synthesis and primary characterization, techniques used to investigate the properties of hydrogels are briefly discussed. PMID:19031061

Printable semiconductor structures and related methods of making and assembling

DOEpatents

Nuzzo, Ralph G.; Rogers, John A.; Menard, Etienne; Lee, Keon Jae; Khang; , Dahl-Young; Sun, Yugang; Meitl, Matthew; Zhu, Zhengtao; Ko, Heung Cho; Mack, Shawn

2013-03-12

The present invention provides a high yield pathway for the fabrication, transfer and assembly of high quality printable semiconductor elements having selected physical dimensions, shapes, compositions and spatial orientations. The compositions and methods of the present invention provide high precision registered transfer and integration of arrays of microsized and/or nanosized semiconductor structures onto substrates, including large area substrates and/or flexible substrates. In addition, the present invention provides methods of making printable semiconductor elements from low cost bulk materials, such as bulk silicon wafers, and smart-materials processing strategies that enable a versatile and commercially attractive printing-based fabrication platform for making a broad range of functional semiconductor devices.

Printable semiconductor structures and related methods of making and assembling

DOEpatents

Nuzzo, Ralph G [Champaign, IL; Rogers, John A [Champaign, IL; Menard, Etienne [Durham, NC; Lee, Keon Jae [Tokyo, JP; Khang, Dahl-Young [Urbana, IL; Sun, Yugang [Westmont, IL; Meitl, Matthew [Raleigh, NC; Zhu, Zhengtao [Rapid City, SD; Ko, Heung Cho [Urbana, IL; Mack, Shawn [Goleta, CA

2011-10-18

The present invention provides a high yield pathway for the fabrication, transfer and assembly of high quality printable semiconductor elements having selected physical dimensions, shapes, compositions and spatial orientations. The compositions and methods of the present invention provide high precision registered transfer and integration of arrays of microsized and/or nanosized semiconductor structures onto substrates, including large area substrates and/or flexible substrates. In addition, the present invention provides methods of making printable semiconductor elements from low cost bulk materials, such as bulk silicon wafers, and smart-materials processing strategies that enable a versatile and commercially attractive printing-based fabrication platform for making a broad range of functional semiconductor devices.

Printable semiconductor structures and related methods of making and assembling

DOEpatents

Nuzzo, Ralph G.; Rogers, John A.; Menard, Etienne; Lee, Keon Jae; Khang, Dahl-Young; Sun, Yugang; Meitl, Matthew; Zhu, Zhengtao; Ko, Heung Cho; Mack, Shawn

2010-09-21

The present invention provides a high yield pathway for the fabrication, transfer and assembly of high quality printable semiconductor elements having selected physical dimensions, shapes, compositions and spatial orientations. The compositions and methods of the present invention provide high precision registered transfer and integration of arrays of microsized and/or nanosized semiconductor structures onto substrates, including large area substrates and/or flexible substrates. In addition, the present invention provides methods of making printable semiconductor elements from low cost bulk materials, such as bulk silicon wafers, and smart-materials processing strategies that enable a versatile and commercially attractive printing-based fabrication platform for making a broad range of functional semiconductor devices.

Rational Design of High-Number dsDNA Fragments Based on Thermodynamics for the Construction of Full-Length Genes in a Single Reaction.

PubMed

Birla, Bhagyashree S; Chou, Hui-Hsien

2015-01-01

Gene synthesis is frequently used in modern molecular biology research either to create novel genes or to obtain natural genes when the synthesis approach is more flexible and reliable than cloning. DNA chemical synthesis has limits on both its length and yield, thus full-length genes have to be hierarchically constructed from synthesized DNA fragments. Gibson Assembly and its derivatives are the simplest methods to assemble multiple double-stranded DNA fragments. Currently, up to 12 dsDNA fragments can be assembled at once with Gibson Assembly according to its vendor. In practice, the number of dsDNA fragments that can be assembled in a single reaction are much lower. We have developed a rational design method for gene construction that allows high-number dsDNA fragments to be assembled into full-length genes in a single reaction. Using this new design method and a modified version of the Gibson Assembly protocol, we have assembled 3 different genes from up to 45 dsDNA fragments at once. Our design method uses the thermodynamic analysis software Picky that identifies all unique junctions in a gene where consecutive DNA fragments are specifically made to connect to each other. Our novel method is generally applicable to most gene sequences, and can improve both the efficiency and cost of gene assembly.

Self-Assembly of Hierarchical DNA Nanotube Architectures with Well-Defined Geometries.

PubMed

Jorgenson, Tyler D; Mohammed, Abdul M; Agrawal, Deepak K; Schulman, Rebecca

2017-02-28

An essential motif for the assembly of biological materials such as actin at the scale of hundreds of nanometers and beyond is a network of one-dimensional fibers with well-defined geometry. Here, we demonstrate the programmed organization of DNA filaments into micron-scale architectures where component filaments are oriented at preprogrammed angles. We assemble L-, T-, and Y-shaped DNA origami junctions that nucleate two or three micron length DNA nanotubes at high yields. The angles between the nanotubes mirror the angles between the templates on the junctions, demonstrating that nanoscale structures can control precisely how micron-scale architectures form. The ability to precisely program filament orientation could allow the assembly of complex filament architectures in two and three dimensions, including circuit structures, bundles, and extended materials.

Chiral transcription in self-assembled tetrahedral Eu 4L 6 chiral cages displaying sizable circularly polarized luminescence

DOE PAGES

Yeung, Chi -Tung; Yim, King -Him; Wong, Ho -Yin; ...

2017-10-24

Predictable stereoselective formation of supramolecular assembly is generally believed to be an important but complicated process. Here, we show that point chirality of a ligand decisively influences its supramolecular assembly behavior. We designed three closely related chiral ligands with different point chiralities, and observe their self-assembly into europium (Eu) tetrametallic tetrahedral cages. One ligand exhibits a highly diastereoselective assembly into homochiral (either ΔΔΔΔ or ΛΛΛΛ) Eu tetrahedral cages whereas the two other ligands, with two different approaches of loosened point chirality, lead to a significant breakdown of the diastereoselectivity to generate a mixture of (ΔΔΔΔ and ΛΛΛΛ) isomers. The cagesmore » are highly emissive (luminescence quantum yields of 16(1) to 18(1)%) and exhibit impressive circularly polarized luminescence properties (|g lum |: up to 0.16). With in-depth studies, we present an example that correlates the nonlinear enhancement of the chiroptical response to the nonlinearity dependence on point chirality.« less

Functional Supramolecular Polymers*

PubMed Central

Aida, T.; Meijer, E.W.; Stupp, S.I.

2012-01-01

Supramolecular polymers can be random and entangled coils with the mechanical properties of plastics and elastomers, but with great capacity for processability, recycling, and self-healing due to their reversible monomer-to-polymer transitions. At the other extreme, supramolecular polymers can be formed by self-assembly among designed subunits to yield shape-persistent and highly ordered filaments. The use of strong and directional interactions among molecular subunits can achieve not only rich dynamic behavior but also high degrees of internal order that are not known in ordinary polymers. They can resemble, for example, the ordered and dynamic one-dimensional supramolecular assemblies of the cell cytoskeleton, and possess useful biological and electronic functions. PMID:22344437

Self-assembled nanostructures of linear arylacetylenes and their aza-substituted analogues

DOE Office of Scientific and Technical Information (OSTI.GOV)

Xu, Jia-Ju; Department of Physics and Materials Science and Centre of Super Diamond and Advanced Films; Yang, Xiong-Bo

2016-06-15

A series of linear phenylene ethynylene molecules have been synthesized, and aza-substitution has been used as a strategy to fine-tune the properties of the molecules. All the compounds exhibited pure blue emission both in solution and solid state, and fluorescence quantum yields as high as 0.66, 0.63 and 0.82 were found in chloroform solutions. The well-defined nanostructures such as quasi-cubes, cubes and rods were fabricated by self-assembly method from these compounds. The photophysical properties and aggregation behavior of self-assembled structures were analyzed in detail. The morphology as well as photophysical properties of these nanostructures have been tuned with selective requirements.

A TinyOS-enabled MICA2-based wireless neural interface.

PubMed

Farshchi, Shahin; Nuyujukian, Paul H; Pesterev, Aleksey; Mody, Istvan; Judy, Jack W

2006-07-01

Existing approaches used to develop compact low-power multichannel wireless neural recording systems range from creating custom-integrated circuits to assembling commercial-off-the-shelf (COTS) PC-based components. Custom-integrated-circuit designs yield extremely compact and low-power devices at the expense of high development and upgrade costs and turn-around times, while assembling COTS-PC-technology yields high performance at the expense of large system size and increased power consumption. To achieve a balance between implementing an ultra-compact custom-fabricated neural transceiver and assembling COTS-PC-technology, an overlay of a neural interface upon the TinyOS-based MICA2 platform is described. The system amplifies, digitally encodes, and transmits neural signals real-time at a rate of 9.6 kbps, while consuming less than 66 mW of power. The neural signals are received and forwarded to a client PC over a serial connection. This data rate can be divided for recording on up to 6 channels, with a resolution of 8 bits/sample. This work demonstrates the strengths and limitations of the TinyOS-based sensor technology as a foundation for chronic remote biological monitoring applications and, thus, provides an opportunity to create a system that can leverage from the frequent networking and communications advancements being made by the global TinyOS-development community.

Lock and Key Colloids through Polymerization-Induced Buckling of Monodispersed Silicon Oil Droplets

NASA Astrophysics Data System (ADS)

Sacanna, Stefano; Irvine, William T. M.; Chaikin, Paul M.; Pine, David J.

2010-03-01

Colloidal particles can spontaneously associate into larger structured aggregates when driven by selective and directional interactions. Colloidal organization can be programmed by engineering shapes and interactions of basic building blocks in a manner similar to molecular self-assembly. Examples of successful strategies that allow non-trivial assembly of particles include template-directed patterning, capillary forces and, most commonly, the functionalization of the particle surfaces with ``sticky patches'' of biological or synthetic molecules. The level of complexity of the realizable assemblies, increases when particles with well defined shape anisotropies are used. In particular depletion forces and specific surface treatments in combination with non spherical particles have proven to be powerful tools to self-assembly complex microstructures. We describe a simple, high yield, synthetic pathway to fabricate monodisperse hybrid silica spheres with well defined cavities. Because the particle morphologies are reproducible and tunable with precision, the resulting particles can be used as basic building blocks in the assembly of larger monodisperse clusters. This is demonstrated using depletion to drive the self-assembly.

Fabrication of five-level ultraplanar micromirror arrays by flip-chip assembly

NASA Astrophysics Data System (ADS)

Michalicek, M. Adrian; Bright, Victor M.

2001-10-01

This paper reports a detailed study of the fabrication of various piston, torsion, and cantilever style micromirror arrays using a novel, simple, and inexpensive flip-chip assembly technique. Several rectangular and polar arrays were commercially prefabricated in the MUMPs process and then flip-chip bonded to form advanced micromirror arrays where adverse effects typically associated with surface micromachining were removed. These arrays were bonded by directly fusing the MUMPs gold layers with no complex preprocessing. The modules were assembled using a computer-controlled, custom-built flip-chip bonding machine. Topographically opposed bond pads were designed to correct for slight misalignment errors during bonding and typically result in less than 2 micrometers of lateral alignment error. Although flip-chip micromirror performance is briefly discussed, the means used to create these arrays is the focus of the paper. A detailed study of flip-chip process yield is presented which describes the primary failure mechanisms for flip-chip bonding. Studies of alignment tolerance, bonding force, stress concentration, module planarity, bonding machine calibration techniques, prefabrication errors, and release procedures are presented in relation to specific observations in process yield. Ultimately, the standard thermo-compression flip-chip assembly process remains a viable technique to develop highly complex prototypes of advanced micromirror arrays.

Intrinsically disordered proteins drive enamel formation via an evolutionarily conserved self-assembly motif.

PubMed

Wald, Tomas; Spoutil, Frantisek; Osickova, Adriana; Prochazkova, Michaela; Benada, Oldrich; Kasparek, Petr; Bumba, Ladislav; Klein, Ophir D; Sedlacek, Radislav; Sebo, Peter; Prochazka, Jan; Osicka, Radim

2017-02-28

The formation of mineralized tissues is governed by extracellular matrix proteins that assemble into a 3D organic matrix directing the deposition of hydroxyapatite. Although the formation of bones and dentin depends on the self-assembly of type I collagen via the Gly-X-Y motif, the molecular mechanism by which enamel matrix proteins (EMPs) assemble into the organic matrix remains poorly understood. Here we identified a Y/F-x-x-Y/L/F-x-Y/F motif, evolutionarily conserved from the first tetrapods to man, that is crucial for higher order structure self-assembly of the key intrinsically disordered EMPs, ameloblastin and amelogenin. Using targeted mutations in mice and high-resolution imaging, we show that impairment of ameloblastin self-assembly causes disorganization of the enamel organic matrix and yields enamel with disordered hydroxyapatite crystallites. These findings define a paradigm for the molecular mechanism by which the EMPs self-assemble into supramolecular structures and demonstrate that this process is crucial for organization of the organic matrix and formation of properly structured enamel.

Pyramiding genes and alleles for improving energy cane biomass yield

DOE Office of Scientific and Technical Information (OSTI.GOV)

Ming, Ray; Nagai, Chifumi; Yu, Qingyi

The overall goal of this project is to identify genes and gene interaction networks contributed to the extreme segregants with 30 folds biomass yield difference in sugarcane F2 populations. Towards achieving this goal, yield trials of 108 F2 extreme segregants from S. officinarum LA Purple and S. robustum MOL5829 (LM population) were carried out in two locations in three years. A yield trial of the second F2 population from S. officinarum LA Purple and S. spontaneum US56-14-4 (LU population) was installed in the summer of 2014 and the first set of yield component data was collected. For genotyping, transcriptomes frommore » leaves and stalks of 70 extreme segregants of the LM F2 population and 119 individuals of the LU F2 populations were sequenced. The genomes of 91 F1 individuals from the LM populations are being sequenced to construct ultra-high density genetic maps for each of the two parents for both assisting the LA Purple genome assembling and for testing a hypothesis of female restitution. The genomes of 110 F2 individuals from single F1 in the LU population, a different set from the 119 F2 individuals used for transcriptome sequencing, are being sequenced for mapping genes and QTLs affecting biomass yield and for testing a hypothesis of female restitution. Gene expression analysis between extreme segregants of high and low biomass yield showed up-regulation of cellulose synthase, cellulose, and xylan synthase in high biomass yield segregants among 3,274 genes differentially expressed between the two extremes. Our transcriptome results revealed not only the increment of cell wall biosynthesis pathway is essential, but the rapid turnover of certain cell wall polymers as well as carbohydrate partitioning are also important for recycling and energy conservation during rapid cell growth in high biomass sugarcane. Seventeen differentially expressed genes in auxin, one in ethylene and one in gibberellin related signaling and biosynthesis pathways were identified, which could potentially regulate biomass yield. Differentially expressed genes, PIF3 and EIL5, involved in gibberellin and ethylene pathway could play an important role in biomass accumulation. Differential gene expression analysis was also carried out on the LU population. High-biomass yield was mainly determined by assimilation of carbon in source tissues. The high-level expression of fermentative genes in the low-biomass group was likely induced by their low-energy status. The haploid (tetraploid) genome of S. spontanium AP85-441 was sequenced with chromosome level assembly and allele defined annotation. This reference genome along with the upcoming S. officinarum genome will allow us to identify genes and alleles contributed to biomass yield.« less

Kerosene space heaters--combustion technology and kerosene characteristics

DOE Office of Scientific and Technical Information (OSTI.GOV)

Kubayashi, k.; I Wasaki, N.

1984-07-01

This paper describes kerosene combustion technology. Unvented wick-type kerosene space heaters are very popular in Japan because of their economy and convenience. In recent years new vaporized kerosene burners having premixed combustion systems have been developed to solve some of the problems encountered in the older portable type. Some of the features of the new burners are instantaneous ignition, no vaporizing deposit on the burner and a wide range heating capacity. These new kerosene heaters have four major components: an air supply fan, a fuel supply assembly, a burner assembly and a control assembly. These heaters are designed to bemore » highly reliable, have stable combustion characteristics, yield minimum carbon deposit. Finally, they are simple and inexpensive to operate.« less

Self-assembled lipid--polymer hybrid nanoparticles: a robust drug delivery platform.

PubMed

Zhang, Liangfang; Chan, Juliana M; Gu, Frank X; Rhee, June-Wha; Wang, Andrew Z; Radovic-Moreno, Aleksandar F; Alexis, Frank; Langer, Robert; Farokhzad, Omid C

2008-08-01

We report the engineering of a novel lipid-polymer hybrid nanoparticle (NP) as a robust drug delivery platform, with high drug encapsulation yield, tunable and sustained drug release profile, excellent serum stability, and potential for differential targeting of cells or tissues. The NP comprises three distinct functional components: (i) a hydrophobic polymeric core where poorly water-soluble drugs can be encapsulated; (ii) a hydrophilic polymeric shell with antibiofouling properties to enhance NP stability and systemic circulation half-life; and (iii) a lipid monolayer at the interface of the core and the shell that acts as a molecular fence to promote drug retention inside the polymeric core, thereby enhancing drug encapsulation efficiency, increasing drug loading yield, and controlling drug release. The NP is prepared by self-assembly through a single-step nanoprecipitation method in a reproducible and predictable manner, making it potentially suitable for scale-up.

Microwave Assisted-Method for the Synthesis of Perylene Ester Imides as a Gateway towards Unsymmetrical Perylene Bisimides.

PubMed

Gupta, Ravindra Kumar; Achalkumar, Ammathnadu Sudhakar

2018-05-18

A high yielding microwave-assisted synthetic method to obtain unsymmetrical perylene diester monoimide (PEI), by treating the perylene tetrester (PTE) with requisite amine is reported. Perylene-based molecules are widely used in the construction of self-assembled supramolecular structures because of their propensity to aggregate under various conditions. In comparison to perylene bisimides (PBIs), PEIs are less studied in organic electronics/self-assembly due to the synthetic difficulty and low yields in their preparation. PEIs are less electron deficient and have an unsymmetric structure in comparison to PBIs. Further, the PEIs got higher solubility than PBIs. The present method is applicable with a wide range of substrates like aliphatic, aromatic, benzyl amines, PTEs and bay-annulated PTEs. This method provides a tuning handle for the optical/electronic properties of perylene derivatives and also provides an easy access to unsymmetrical PBIs from the PEIs.

Self-Assembled Lipid-Polymer Hybrid Nanoparticles: A Robust Drug Delivery Platform

PubMed Central

Zhang, Liangfang; Chan, Juliana M; Gu, Frank X; Rhee, June-Wha; Wang, Andrew Z; Radovic-Moreno, Aleksandar F; Alexis, Frank; Langer, Robert; Farokhzad, Omid C

2014-01-01

We report the engineering of a novel lipid-polymer hybrid nanoparticle (NP) as a robust drug delivery platform, with high drug encapsulation yield, tunable and sustained drug release profile, excellent serum stability, and potential for differential targeting of cells or tissues. The NP is comprised of three distinct functional components: i) a hydrophobic polymeric core where poorly water-soluble drugs can be encapsulated; ii) a hydrophilic polymeric shell with anti-biofouling properties to enhance NP stability and systemic circulation half-life; and iii) a lipid monolayer at the interface of the core and the shell that acts as a molecular fence to promote drug retention inside the polymeric core, thereby enhancing drug encapsulation efficiency, increasing drug loading yield, and controlling drug release. The NP is prepared by self-assembly through a single-step nanoprecipitation method in a reproducible and predictable manner, making it potentially suitable for scale-up PMID:19206374

The Rhodium(II) Carbenoid Cyclization-Cycloaddition Cascade of α-Diazo Dihydroindolinones for the Synthesis of Novel Azapolycyclic Ring Systems‡

PubMed Central

England, Dylan B.; Eagan, James M.; Merey, Gokce; Anac, Olcay; Padwa, Albert

2008-01-01

Tandem carbonyl ylide formation-1,3-dipolar cycloaddition of α-diazo N-acetyl-tetrahydro-β-carbolin-1-one derivatives occur efficiently in the presence of a dirhodium catalyst to afford bimolecular cycloadducts in high yield. The Rh(II)-catalyzed reaction also takes place intramolecularly to give products derived from trapping of the carbonyl ylide dipole with a tethered alkene. The power of the intramolecular cascade sequence is that it rapidly assembles a pentacyclic ring system containing three new stereocenters and two adjacent quaternary centers stereospecifically in a single step and in high yield. PMID:18437248

Self-Assembly through Noncovalent Preorganization of Reactants: Explaining the Formation of a Polyfluoroxometalate.

PubMed

Schreiber, Roy E; Avram, Liat; Neumann, Ronny

2018-01-09

High-order elementary reactions in homogeneous solutions involving more than two molecules are statistically improbable and very slow to proceed. They are not generally considered in classical transition-state or collision theories. Yet, rather selective, high-yield product formation is common in self-assembly processes that require many reaction steps. On the basis of recent observations of crystallization as well as reactions in dense phases, it is shown that self-assembly can occur by preorganization of reactants in a noncovalent supramolecular assembly, whereby directing forces can lead to an apparent one-step transformation of multiple reactants. A simple and general kinetic model for multiple reactant transformation in a dense phase that can account for many-bodied transformations was developed. Furthermore, the self-assembly of polyfluoroxometalate anion [H 2 F 6 NaW 18 O 56 ] 7- from simple tungstate Na 2 WO 2 F 4 was demonstrated by using 2D 19 F- 19 F NOESY, 2D 19 F- 19 F COSY NMR spectroscopy, a new 2D 19 F{ 183 W} NMR technique, as well as ESI-MS and diffusion NMR spectroscopy, and the crucial involvement of a supramolecular assembly was found. The deterministic kinetic reaction model explains the reaction in a dense phase and supports the suggested self-assembly mechanism. Reactions in dense phases may be of general importance in understanding other self-assembly reactions. © 2018 Wiley-VCH Verlag GmbH & Co. KGaA, Weinheim.

Effects of subtle differences in ligand constitution and conformation in metallo-supramolecular self-assembled polygons.

PubMed

Brusilowskij, Boris; Dzyuba, Egor V; Troff, Ralf W; Schalley, Christoph A

2011-12-07

3,3'-Bis(pyridin-[n]-ylethynyl)biphenyl (n = 3, 4) and the corresponding 2,2'-bipyridines assemble with (dppp)Pt(II) triflate into metallo-supramolecular polygons. Depending on the position of the terminal pyridine N atoms, the assembly reaction leads to different equilibrium products. With the slow ligand exchange on Pt(II) complexes, the equilibrium is reached on a many-hour time-scale. During the assembly process, larger polygons form under kinetic control. This was confirmed by time-dependent (1)H and (31)P NMR spectroscopy in line with complementary ESI mass spectrometric experiments. The constitutional difference in the pyridine N-atom position is reflected in the tandem mass spectra of the complex ions. In addition, a highly specific fragmentation process of mass-selected M(3)L(3) ions was observed, which proceeds through a ring contraction yielding smaller M(2)L(2) ions.

Aeroelastic modal characteristics of mistuned blade assemblies: Mode localization and loss of eigenstructure

NASA Technical Reports Server (NTRS)

Pierre, Christophe; Murthy, Durbha V.

1991-01-01

An investigation of the effects of small mistuning on the aeroelastic modes of bladed disk assemblies with aerodynamic coupling between blades is presented. The cornerstone of the approach is the use and development of perturbation methods that exhibit the crucial role of the interblade coupling and yield general findings regarding mistuning effects. It is shown that blade assemblies with weak aerodynamic interblade coupling are highly sensitive to small blade mistuning, and that their dynamics is quantitatively altered in the following ways: the regular pattern that characterizes the root locus of the tuned aeroelastic eigenvalues in the complex plane is totally lost; the aeroelastic mode shapes becomes severely localized to only a few blades of the assembly and lose their constant interblade phase angle feature; and curve veering phenomena take place when the eigenvalues are plotted versus a mistuning parameter.

Layer-by-layer assembled polyaniline nanofiber/multiwall carbon nanotube thin film electrodes for high-power and high-energy storage applications.

PubMed

Hyder, Md Nasim; Lee, Seung Woo; Cebeci, Fevzi Ç; Schmidt, Daniel J; Shao-Horn, Yang; Hammond, Paula T

2011-11-22

Thin film electrodes of polyaniline (PANi) nanofibers and functionalized multiwall carbon nanotubes (MWNTs) are created by layer-by-layer (LbL) assembly for microbatteries or -electrochemical capacitors. Highly stable cationic PANi nanofibers, synthesized from the rapid aqueous phase polymerization of aniline, are assembled with carboxylic acid functionalized MWNT into LbL films. The pH-dependent surface charge of PANi nanofibers and MWNTs allows the system to behave like weak polyelectrolytes with controllable LbL film thickness and morphology by varying the number of bilayers. The LbL-PANi/MWNT films consist of a nanoscale interpenetrating network structure with well developed nanopores that yield excellent electrochemical performance for energy storage applications. These LbL-PANi/MWNT films in lithium cell can store high volumetric capacitance (~238 ± 32 F/cm(3)) and high volumetric capacity (~210 mAh/cm(3)). In addition, rate-dependent galvanostatic tests show LbL-PANi/MWNT films can deliver both high power and high energy density (~220 Wh/L(electrode) at ~100 kW/L(electrode)) and could be promising positive electrode materials for thin film microbatteries or electrochemical capacitors. © 2011 American Chemical Society

Polythiophene-block-poly(γ-benzyl L-glutamate): Synthesis and study of a new rod-rod block copolymer

DOE Office of Scientific and Technical Information (OSTI.GOV)

Wu, Zong-Quan; Ono, Robert J.; Chen, Zheng

2011-01-01

Coupling of ethynyl terminated poly(3-hexylthiophene) with azide terminated poly(γ-benzyl L-glutamate) afforded the respective block copolymer in good yield and high purity; this material was found to self assemble into hierarchal structures in solution and in the solid state.

Electron mobility of self-assembled and dislocation free InN nanorods grown on GaN nano wall network template

DOE Office of Scientific and Technical Information (OSTI.GOV)

Tangi, Malleswararao; De, Arpan; Ghatak, Jay

2016-05-28

A kinetically controlled two-step growth process for the formation of an array of dislocation free high mobility InN nanorods (NRs) on GaN nanowall network (NWN) by Molecular Beam Epitaxy is demonstrated here. The epitaxial GaN NWN is formed on c-sapphire under nitrogen rich conditions, and then changing the source from Ga to In at appropriate substrate temperature yields the nucleation of a self assembled spontaneous m-plane side faceted-InN NR. By HRTEM, the NRs are shown to be dislocation-free and have a low band gap value of 0.65 eV. Hall measurements are carried out on a single InN NR along with J-Vmore » measurements that yield mobility values as high as ≈4453 cm{sup 2}/V s and the carrier concentration of ≈1.1 × 10{sup 17} cm{sup −3}, which are unprecedented in the literature for comparable InN NR diameters.« less

Surface-assisted DNA self-assembly: An enzyme-free strategy towards formation of branched DNA lattice.

PubMed

Bhanjadeo, Madhabi M; Nayak, Ashok K; Subudhi, Umakanta

2017-04-01

DNA based self-assembled nanostructures and DNA origami has proven useful for organizing nanomaterials with firm precision. However, for advanced applications like nanoelectronics and photonics, large-scale organization of self-assembled branched DNA (bDNA) into periodic lattices is desired. In this communication for the first time we report a facile method of self-assembly of Y-shaped bDNA nanostructures on the cationic surface of Aluminum (Al) foil to prepare periodic two dimensional (2D) bDNA lattice. Particularly those Y-shaped bDNA structures having smaller overhangs and unable to self-assemble in solution, they are easily assembled on the surface of Al foil in the absence of ligase. Field emission scanning electron microscopy (FESEM) analysis shows homogenous distribution of two-dimensional bDNA lattices across the Al foil. When the assembled bDNA structures were recovered from the Al foil and electrophoresed in nPAGE only higher order polymeric bDNA structures were observed without a trace of monomeric structures which confirms the stability and high yield of the bDNA lattices. Therefore, this enzyme-free economic and efficient strategy for developing bDNA lattices can be utilized in assembling various nanomaterials for functional molecular components towards development of DNA based self-assembled nanodevices. Copyright © 2017 Elsevier Inc. All rights reserved.

DOE Office of Scientific and Technical Information (OSTI.GOV)

Chen, Zhe; Cao, Minhua, E-mail: caomh@bit.edu.cn; Key Laboratory of Cluster Science, Ministry of Education of China, Department of Chemistry, Beijing Institute of Technology, Beijing 100081

Research highlights: {yields} Novel Bi{sub 2}S{sub 3} hierarchical nanostructures self-assembled by nanorods are successfully synthesized in mild benzyl alcohol system under hydrothermal conditions. {yields} The hierarchical nanostructures exhibit a flower-like shape. {yields} PVP plays an important role for the formation of the hierarchical nanostructures. {yields} Bi{sub 2}S{sub 3} film prepared from the flower-like hierarchical nanostructures exhibits good hydrophobic properties. -- Abstract: Novel Bi{sub 2}S{sub 3} hierarchical nanostructures self-assembled by nanorods are successfully synthesized in mild benzyl alcohol system under hydrothermal conditions. The hierarchical nanostructures exhibit a flower-like shape. X-ray diffraction (XRD), X-ray photoelectron spectra (XPS), scanning electron microscopy (SEM), transmissionmore » electron microscopy (TEM), high-resolution transmission electron microscopy (HRTEM), and selected area electron diffraction (SAED) were used to characterize the as-synthesized samples. Meanwhile, the effect of various experimental parameters including the concentration of reagents and reaction time on final product has been investigated. In our experiment, PVP plays an important role for the formation of the hierarchical nanostructures and the possible mechanism was proposed. In addition, Bi{sub 2}S{sub 3} film prepared from the flower-like hierarchical nanostructures exhibits good hydrophobic properties, which may bring nontrivial functionalities and may have some promising applications in the future.« less

Thermophilic Ferritin 24mer Assembly and Nanoparticle Encapsulation Modulated by Interdimer Electrostatic Repulsion.

PubMed

Pulsipher, Katherine W; Villegas, Jose A; Roose, Benjamin W; Hicks, Tacey L; Yoon, Jennifer; Saven, Jeffery G; Dmochowski, Ivan J

2017-07-18

Protein cage self-assembly enables encapsulation and sequestration of small molecules, macromolecules, and nanomaterials for many applications in bionanotechnology. Notably, wild-type thermophilic ferritin from Archaeoglobus fulgidus (AfFtn) exists as a stable dimer of four-helix bundle proteins at a low ionic strength, and the protein forms a hollow assembly of 24 protomers at a high ionic strength (∼800 mM NaCl). This assembly process can also be initiated by highly charged gold nanoparticles (AuNPs) in solution, leading to encapsulation. These data suggest that salt solutions or charged AuNPs can shield unfavorable electrostatic interactions at AfFtn dimer-dimer interfaces, but specific "hot-spot" residues controlling assembly have not been identified. To investigate this further, we computationally designed three AfFtn mutants (E65R, D138K, and A127R) that introduce a single positive charge at sites along the dimer-dimer interface. These proteins exhibited different assembly kinetics and thermodynamics, which were ranked in order of increasing 24mer propensity: A127R < wild type < D138K ≪ E65R. E65R assembled into the 24mer across a wide range of ionic strengths (0-800 mM NaCl), and the dissociation temperature for the 24mer was 98 °C. X-ray crystal structure analysis of the E65R mutant identified a more compact, closed-pore cage geometry. A127R and D138K mutants exhibited wild-type ability to encapsulate and stabilize 5 nm AuNPs, whereas E65R did not encapsulate AuNPs at the same high yields. This work illustrates designed protein cages with distinct assembly and encapsulation properties.

Expression, stabilization and purification of membrane proteins via diverse protein synthesis systems and detergents involving cell-free associated with self-assembly peptide surfactants.

PubMed

Zheng, Xuan; Dong, Shuangshuang; Zheng, Jie; Li, Duanhua; Li, Feng; Luo, Zhongli

2014-01-01

G-protein coupled receptors (GPCRs) are involved in regulating most of physiological actions and metabolism in the bodies, which have become most frequently addressed therapeutic targets for various disorders and diseases. Purified GPCR-based drug discoveries have become routine that approaches to structural study, novel biophysical and biochemical function analyses. However, several bottlenecks that GPCR-directed drugs need to conquer the problems including overexpression, solubilization, and purification as well as stabilization. The breakthroughs are to obtain efficient protein yield and stabilize their functional conformation which are both urgently requiring of effective protein synthesis system methods and optimal surfactants. Cell-free protein synthesis system is superior to the high yields and post-translation modifications, and early signs of self-assembly peptide detergents also emerged to superiority in purification of membrane proteins. We herein focus several predominant protein synthesis systems and surfactants involving the novel peptide detergents, and uncover the advantages of cell-free protein synthesis system with self-assembling peptide detergents in purification of functional GPCRs. This review is useful to further study in membrane proteins as well as the new drug exploration. Copyright © 2014 Elsevier Inc. All rights reserved.

Cavity-Type DNA Origami-Based Plasmonic Nanostructures for Raman Enhancement.

PubMed

Zhao, Mengzhen; Wang, Xu; Ren, Shaokang; Xing, Yikang; Wang, Jun; Teng, Nan; Zhao, Dongxia; Liu, Wei; Zhu, Dan; Su, Shao; Shi, Jiye; Song, Shiping; Wang, Lihua; Chao, Jie; Wang, Lianhui

2017-07-05

DNA origami has been established as addressable templates for site-specific anchoring of gold nanoparticles (AuNPs). Given that AuNPs are assembled by charged DNA oligonucleotides, it is important to reduce the charge repulsion between AuNPs-DNA and the template to realize high yields. Herein, we developed a cavity-type DNA origami as templates to organize 30 nm AuNPs, which formed dimer and tetramer plasmonic nanostructures. Transmission electron microscopy images showed that high yields of dimer and tetramer plasmonic nanostructures were obtained by using the cavity-type DNA origami as the template. More importantly, we observed significant Raman signal enhancement from molecules covalently attached to the plasmonic nanostructures, which provides a new way to high-sensitivity Raman sensing.

Self-assembly of Archimedean tilings with enthalpically and entropically patchy polygons.

PubMed

Millan, Jaime A; Ortiz, Daniel; van Anders, Greg; Glotzer, Sharon C

2014-03-25

Considerable progress in the synthesis of anisotropic patchy nanoplates (nanoplatelets) promises a rich variety of highly ordered two-dimensional superlattices. Recent experiments of superlattices assembled from nanoplates confirm the accessibility of exotic phases and motivate the need for a better understanding of the underlying self-assembly mechanisms. Here, we present experimentally accessible, rational design rules for the self-assembly of the Archimedean tilings from polygonal nanoplates. The Archimedean tilings represent a model set of target patterns that (i) contain both simple and complex patterns, (ii) are comprised of simple regular shapes, and (iii) contain patterns with potentially interesting materials properties. Via Monte Carlo simulations, we propose a set of design rules with general applicability to one- and two-component systems of polygons. These design rules, specified by increasing levels of patchiness, correspond to a reduced set of anisotropy dimensions for robust self-assembly of the Archimedean tilings. We show for which tilings entropic patches alone are sufficient for assembly and when short-range enthalpic interactions are required. For the latter, we show how patchy these interactions should be for optimal yield. This study provides a minimal set of guidelines for the design of anisostropic patchy particles that can self-assemble all 11 Archimedean tilings.

High-temperature geothermal cableheads

NASA Astrophysics Data System (ADS)

Coquat, J. A.; Eifert, R. W.

1981-11-01

Two high temperature, corrosion resistant logging cable heads which use metal seals and a stable fluid to achieve proper electrical terminations and cable sonde interfacings are described. A tensile bar provides a calibrated yield point, and a cone assembly anchors the cable armor to the head. Electrical problems of the sort generally ascribable to the cable sonde interface were absent during demonstration hostile environment loggings in which these cable heads were used.

Highly Tunable Aptasensing Microarrays with Graphene Oxide Multilayers

NASA Astrophysics Data System (ADS)

Jung, Yun Kyung; Lee, Taemin; Shin, Eeseul; Kim, Byeong-Su

2013-11-01

A highly tunable layer-by-layer (LbL)-assembled graphene oxide (GO) array has been devised for high-throughput multiplex protein sensing. In this array, the fluorescence of different target-bound aptamers labeled with dye is efficiently quenched by GO through fluorescence resonance energy transfer (FRET), and simultaneous multiplex target detection is performed by recovering the quenched fluorescence caused by specific binding between an aptamer and a protein. Thin GO films consisting of 10 bilayers displayed a high quenching ability, yielding over 85% fluorescence quenching with the addition of a 2 μM dye-labeled aptamer. The limit for human thrombin detection in the 6- and 10-bilayered GO array is estimated to be 0.1 and 0.001 nM, respectively, indicating highly tunable nature of LbL assembled GO multilayers in controlling the sensitivity of graphene-based FRET aptasensor. Furthermore, the GO chip could be reused up to four times simply by cleaning it with distilled water.

Molecular Engineering of Self-assembled Nanoreactors

DTIC Science & Technology

2014-08-15

substrate diffusion. We demonstrated spatial control of the GOx/HRP cascade organized by DNA origami structures. As shown in Figure 13, the...quantify the level of protein assembly on the DNA origami tiles - assembled enzymes exhibited higher surface landscapes than the underlying origami ... origami tiles with assembled Gox/HRP pairs with inter-enzyme distances ranging from 10 nm to 65 nm. GOx/HRP co-assembly yields were determined from AFM

Hyper-Assembly of Self-Assembled Glycoclusters Mediated by Specific Carbohydrate-Carbohydrate Interactions.

PubMed

Yan, Gengwei; Yamaguchi, Takumi; Suzuki, Tatsuya; Yanaka, Saeko; Sato, Sota; Fujita, Makoto; Kato, Koichi

2017-05-04

Hybridization of a self-assembled, spherical complex with oligosaccharides containing Lewis X, a functional trisaccharide displayed on various cell surfaces, yielded well-defined glycoclusters. The self-assembled glycoclusters exhibited homophilic hyper-assembly in aqueous solution in a Ca 2+ -dependent manner through specific carbohydrate-carbohydrate interactions, offering a structural scaffold for functional biomimetic systems. © 2017 Wiley-VCH Verlag GmbH & Co. KGaA, Weinheim.

Self-assembly of noble metal nanoparticles into sub-100 nm colloidosomes with collective optical and catalytic properties† †Electronic supplementary information (ESI) available: Additional experimental details, TEM images, FTIR spectra, size distributions, FDTD simulations, SERS analysis, electrochemical measurements, extension of the self-assembly approach to other metals and comparison of the FAOR results with those from the literature. See DOI: 10.1039/c7sc01841j

PubMed Central

Zhang, Lei; Fan, Qikui; Sha, Xiao; Zhong, Ping; Zhang, Jie; Yin, Yadong

2017-01-01

Self-assembly at the nanoscale represents a powerful tool for creating materials with new structures and intriguing collective properties. Here, we report a novel strategy to synthesize nanoscale colloidosomes of noble metals by assembling primary metal nanoparticles at the interface of emulsion droplets formed by their capping agent. This strategy produces noble metal colloidosomes of unprecedentedly small sizes (<100 nm) in high yield and uniformity, which is highly desirable for practical applications. In addition, it enables the high tunability of the composition, producing a diversity of monometallic and bimetallic alloy colloidosomes. The colloidosomes exhibit interesting collective properties that are different from those of individual colloidal nanoparticles. Specifically, we demonstrate Au colloidosomes with well-controlled interparticle plasmon coupling and Au–Pd alloy colloidosomes with superior electrocatalytic performance, both thanks to the special structural features that arise from the assembly. We believe this strategy provides a general platform for producing a rich class of miniature colloidosomes that may have fascinating collective properties for a broad range of applications. PMID:29619198

High-coverage sequencing and annotated assembly of the genome of the Australian dragon lizard Pogona vitticeps.

PubMed

Georges, Arthur; Li, Qiye; Lian, Jinmin; O'Meally, Denis; Deakin, Janine; Wang, Zongji; Zhang, Pei; Fujita, Matthew; Patel, Hardip R; Holleley, Clare E; Zhou, Yang; Zhang, Xiuwen; Matsubara, Kazumi; Waters, Paul; Graves, Jennifer A Marshall; Sarre, Stephen D; Zhang, Guojie

2015-01-01

The lizards of the family Agamidae are one of the most prominent elements of the Australian reptile fauna. Here, we present a genomic resource built on the basis of a wild-caught male ZZ central bearded dragon Pogona vitticeps. The genomic sequence for P. vitticeps, generated on the Illumina HiSeq 2000 platform, comprised 317 Gbp (179X raw read depth) from 13 insert libraries ranging from 250 bp to 40 kbp. After filtering for low-quality and duplicated reads, 146 Gbp of data (83X) was available for assembly. Exceptionally high levels of heterozygosity (0.85 % of single nucleotide polymorphisms plus sequence insertions or deletions) complicated assembly; nevertheless, 96.4 % of reads mapped back to the assembled scaffolds, indicating that the assembly included most of the sequenced genome. Length of the assembly was 1.8 Gbp in 545,310 scaffolds (69,852 longer than 300 bp), the longest being 14.68 Mbp. N50 was 2.29 Mbp. Genes were annotated on the basis of de novo prediction, similarity to the green anole Anolis carolinensis, Gallus gallus and Homo sapiens proteins, and P. vitticeps transcriptome sequence assemblies, to yield 19,406 protein-coding genes in the assembly, 63 % of which had intact open reading frames. Our assembly captured 99 % (246 of 248) of core CEGMA genes, with 93 % (231) being complete. The quality of the P. vitticeps assembly is comparable or superior to that of other published squamate genomes, and the annotated P. vitticeps genome can be accessed through a genome browser available at https://genomics.canberra.edu.au.

Communication: Theoretical prediction of free-energy landscapes for complex self-assembly

DOE Office of Scientific and Technical Information (OSTI.GOV)

Jacobs, William M.; Reinhardt, Aleks; Frenkel, Daan

2015-01-14

We present a technique for calculating free-energy profiles for the nucleation of multicomponent structures that contain as many species as building blocks. We find that a key factor is the topology of the graph describing the connectivity of the target assembly. By considering the designed interactions separately from weaker, incidental interactions, our approach yields predictions for the equilibrium yield and nucleation barriers. These predictions are in good agreement with corresponding Monte Carlo simulations. We show that a few fundamental properties of the connectivity graph determine the most prominent features of the assembly thermodynamics. Surprisingly, we find that polydispersity in themore » strengths of the designed interactions stabilizes intermediate structures and can be used to sculpt the free-energy landscape for self-assembly. Finally, we demonstrate that weak incidental interactions can preclude assembly at equilibrium due to the combinatorial possibilities for incorrect association.« less

Precise Placement of Metallic Nanowires on a Substrate by Localized Electric Fields and Inter-Nanowire Electrostatic Interaction

PubMed Central

2017-01-01

Placing nanowires at the predetermined locations on a substrate represents one of the significant hurdles to be tackled for realization of heterogeneous nanowire systems. Here, we demonstrate spatially-controlled assembly of a single nanowire at the photolithographically recessed region at the electrode gap with high integration yield (~90%). Two popular routes, such as protruding electrode tips and recessed wells, for spatially-controlled nanowire alignment, are compared to investigate long-range dielectrophoretic nanowire attraction and short-range nanowire-nanowire electrostatic interaction for determining the final alignment of attracted nanowires. Furthermore, the post-assembly process has been developed and tested to make a robust electrical contact to the assembled nanowires, which removes any misaligned ones and connects the nanowires to the underlying electrodes of circuit. PMID:29048363

One ligand in dual roles: self-assembly of a bis-rhomboidal-shaped, three-dimensional molecular wheel.

PubMed

Lu, Xiaocun; Li, Xiaopeng; Guo, Kai; Wang, Jing; Huang, Mingjun; Wang, Jin-Liang; Xie, Ting-Zheng; Moorefield, Charles N; Cheng, Stephen Z D; Wesdemiotis, Chrys; Newkome, George R

2014-10-06

A facile high yield, self-assembly process that leads to a terpyridine-based, three-dimensional, bis-rhomboidal-shaped, molecular wheel is reported. The desired coordination-driven supramolecular wheel involves eight structurally distorted tristerpyridine (tpy) ligands possessing a 60° angle between the adjacent tpy units and twelve Zn(2+) ions. The tpy ligand plays dual roles in the self-assembly process: two are staggered at 180° to create the internal hub, while six produce the external rim. The wheel can be readily generated by mixing the tpy ligand and Zn(2+) in a stoichiometric ratio of 2:3; full characterization is provided by ESI-MS, NMR spectroscopy, and TEM imaging. © 2014 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Lightweight concentrator module with 30 percent AM0 efficient GaAs/GaSb tandem cells

NASA Technical Reports Server (NTRS)

Avery, J. E.; Fraas, L. M.; Sundaram, V. S.; Mansoori, N.; Yerkes, J. W.; Brinker, D. J.; Curtis, H. B.; O'Neill, M. J.

1990-01-01

A concept is presented for an aerospace concentrator module with lightweight domed lenses and 30 percent AM0 efficient GaAs/GaSb tandem solar cell circuits. The performance of transparent GaAs cells is reviewed. NASA's high-altitude jet flight calibration data for recent GaSb cells assembled with bulk GaAs filters are reported, along with subsequent Boeing and NASA measurements of GaSb I-V performance at various light levels and temperatures. The expected performance of a basic two-terminal tandem concentrator circuit with three-to-one voltage matching is discussed. All of the necessary components being developed to assemble complete flight test coupons are shown. Straightforward interconnect and assembly techniques yield voltage matched circuits with near-optimum performance over a wide temperature range.

Robotically Assembled Aerospace Structures: Digital Material Assembly using a Gantry-Type Assembler

NASA Technical Reports Server (NTRS)

Trinh, Greenfield; Copplestone, Grace; O'Connor, Molly; Hu, Steven; Nowak, Sebastian; Cheung, Kenneth; Jenett, Benjamin; Cellucci, Daniel

2017-01-01

This paper evaluates the development of automated assembly techniques for discrete lattice structures using a multi-axis gantry type CNC machine. These lattices are made of discrete components called digital materials. We present the development of a specialized end effector that works in conjunction with the CNC machine to assemble these lattices. With this configuration we are able to place voxels at a rate of 1.5 per minute. The scalability of digital material structures due to the incremental modular assembly is one of its key traits and an important metric of interest. We investigate the build times of a 5x5 beam structure on the scale of 1 meter (325 parts), 10 meters (3,250 parts), and 30 meters (9,750 parts). Utilizing the current configuration with a single end effector, performing serial assembly with a globally fixed feed station at the edge of the build volume, the build time increases according to a scaling law of n4, where n is the build scale. Build times can be reduced significantly by integrating feed systems into the gantry itself, resulting in a scaling law of n3. A completely serial assembly process will encounter time limitations as build scale increases. Automated assembly for digital materials can assemble high performance structures from discrete parts, and techniques such as built in feed systems, parallelization, and optimization of the fastening process will yield much higher throughput.

Robotically Assembled Aerospace Structures: Digital Material Assembly using a Gantry-Type Assembler

NASA Technical Reports Server (NTRS)

Trinh, Greenfield; Copplestone, Grace; O'Connor, Molly; Hu, Steven; Nowak, Sebastian; Cheung, Kenneth; Jenett, Benjamin; Cellucci, Daniel

2017-01-01

This paper evaluates the development of automated assembly techniques for discrete lattice structures using a multi-axis gantry type CNC machine. These lattices are made of discrete components called "digital materials." We present the development of a specialized end effector that works in conjunction with the CNC machine to assemble these lattices. With this configuration we are able to place voxels at a rate of 1.5 per minute. The scalability of digital material structures due to the incremental modular assembly is one of its key traits and an important metric of interest. We investigate the build times of a 5x5 beam structure on the scale of 1 meter (325 parts), 10 meters (3,250 parts), and 30 meters (9,750 parts). Utilizing the current configuration with a single end effector, performing serial assembly with a globally fixed feed station at the edge of the build volume, the build time increases according to a scaling law of n4, where n is the build scale. Build times can be reduced significantly by integrating feed systems into the gantry itself, resulting in a scaling law of n3. A completely serial assembly process will encounter time limitations as build scale increases. Automated assembly for digital materials can assemble high performance structures from discrete parts, and techniques such as built in feed systems, parallelization, and optimization of the fastening process will yield much higher throughput.

Efficient high-throughput sequencing of a laser microdissected chromosome arm

PubMed Central

2013-01-01

Background Genomic sequence assemblies are key tools for a broad range of gene function and evolutionary studies. The diploid amphibian Xenopus tropicalis plays a pivotal role in these fields due to its combination of experimental flexibility, diploid genome, and early-branching tetrapod taxonomic position, having diverged from the amniote lineage ~360 million years ago. A genome assembly and a genetic linkage map have recently been made available. Unfortunately, large gaps in the linkage map attenuate long-range integrity of the genome assembly. Results We laser dissected the short arm of X. tropicalis chromosome 7 for next generation sequencing and computational mapping to the reference genome. This arm is of particular interest as it encodes the sex determination locus, but its genetic map contains large gaps which undermine available genome assemblies. Whole genome amplification of 15 laser-microdissected 7p arms followed by next generation sequencing yielded ~35 million reads, over four million of which uniquely mapped to the X. tropicalis genome. Our analysis placed more than 200 previously unmapped scaffolds on the analyzed chromosome arm, providing valuable low-resolution physical map information for de novo genome assembly. Conclusion We present a new approach for improving and validating genetic maps and sequence assemblies. Whole genome amplification of 15 microdissected chromosome arms provided sufficient high-quality material for localizing previously unmapped scaffolds and genes as well as recognizing mislocalized scaffolds. PMID:23714049

Formation of hexagonal boron nitride nanoscrolls induced by inclusion and exclusion of self-assembling molecules in solution process

NASA Astrophysics Data System (ADS)

Hwang, Da Young; Suh, Dong Hack

2014-05-01

Unlike nanoscrolls of 2D graphene, those of 2D h-BN have not been demonstrated, except for only a few experimental reports. Nanoscrolls of h-BN with high yields and reproducibility are first synthesized by a simple solution process. Inner-tube diameters of BNSs including LCAs, N-(2-aminoethyl)-3α-hydroxy-5β-cholan-24-amide, a bile acid derivative and self-assembling material, can be controlled by adjusting the diameter of the LCA fiber which is grown by self-assembly. TEM and SEM images show that BNSs have a tube-like morphology and the inner-tube diameter of BNSs can be controlled in the range from 20 to 60 nm for a smaller diameter, up to 300 nm for a larger diameter by LCA fiber growth inside the BNSs. Finally, open cylindrical BNSs with hollow cores were obtained by dissolving LCAs inside BNSs.Unlike nanoscrolls of 2D graphene, those of 2D h-BN have not been demonstrated, except for only a few experimental reports. Nanoscrolls of h-BN with high yields and reproducibility are first synthesized by a simple solution process. Inner-tube diameters of BNSs including LCAs, N-(2-aminoethyl)-3α-hydroxy-5β-cholan-24-amide, a bile acid derivative and self-assembling material, can be controlled by adjusting the diameter of the LCA fiber which is grown by self-assembly. TEM and SEM images show that BNSs have a tube-like morphology and the inner-tube diameter of BNSs can be controlled in the range from 20 to 60 nm for a smaller diameter, up to 300 nm for a larger diameter by LCA fiber growth inside the BNSs. Finally, open cylindrical BNSs with hollow cores were obtained by dissolving LCAs inside BNSs. Electronic supplementary information (ESI) available. See DOI: 10.1039/c4nr00897a

Expanding the genetic code for site-specific labelling of tobacco mosaic virus coat protein and building biotin-functionalized virus-like particles.

PubMed

Wu, F C; Zhang, H; Zhou, Q; Wu, M; Ballard, Z; Tian, Y; Wang, J Y; Niu, Z W; Huang, Y

2014-04-18

A method for site-specific and high yield modification of tobacco mosaic virus coat protein (TMVCP) utilizing a genetic code expanding technology and copper free cycloaddition reaction has been established, and biotin-functionalized virus-like particles were built by the self-assembly of the protein monomers.

Nanomechanical properties of distinct fibrillar polymorphs of the protein α-synuclein.

PubMed

Makky, Ali; Bousset, Luc; Polesel-Maris, Jérôme; Melki, Ronald

2016-11-30

Alpha-synuclein (α-Syn) is a small presynaptic protein of 140 amino acids. Its pathologic intracellular aggregation within the central nervous system yields protein fibrillar inclusions named Lewy bodies that are the hallmarks of Parkinson's disease (PD). In solution, pure α-Syn adopts an intrinsically disordered structure and assembles into fibrils that exhibit considerable morphological heterogeneity depending on their assembly conditions. We recently established tightly controlled experimental conditions allowing the assembly of α-Syn into highly homogeneous and pure polymorphs. The latter exhibited differences in their shape, their structure but also in their functional properties. We have conducted an AFM study at high resolution and performed a statistical analysis of fibrillar α-Syn shape and thermal fluctuations to calculate the persistence length to further assess the nanomechanical properties of α-Syn polymorphs. Herein, we demonstrated quantitatively that distinct polymorphs made of the same protein (wild-type α-Syn) show significant differences in their morphology (height, width and periodicity) and physical properties (persistence length, bending rigidity and axial Young's modulus).

Nanomechanical properties of distinct fibrillar polymorphs of the protein α-synuclein

NASA Astrophysics Data System (ADS)

Makky, Ali; Bousset, Luc; Polesel-Maris, Jérôme; Melki, Ronald

2016-11-01

Alpha-synuclein (α-Syn) is a small presynaptic protein of 140 amino acids. Its pathologic intracellular aggregation within the central nervous system yields protein fibrillar inclusions named Lewy bodies that are the hallmarks of Parkinson’s disease (PD). In solution, pure α-Syn adopts an intrinsically disordered structure and assembles into fibrils that exhibit considerable morphological heterogeneity depending on their assembly conditions. We recently established tightly controlled experimental conditions allowing the assembly of α-Syn into highly homogeneous and pure polymorphs. The latter exhibited differences in their shape, their structure but also in their functional properties. We have conducted an AFM study at high resolution and performed a statistical analysis of fibrillar α-Syn shape and thermal fluctuations to calculate the persistence length to further assess the nanomechanical properties of α-Syn polymorphs. Herein, we demonstrated quantitatively that distinct polymorphs made of the same protein (wild-type α-Syn) show significant differences in their morphology (height, width and periodicity) and physical properties (persistence length, bending rigidity and axial Young’s modulus).

Molecular basis of cooperativity in pH-triggered supramolecular self-assembly

NASA Astrophysics Data System (ADS)

Li, Yang; Zhao, Tian; Wang, Chensu; Lin, Zhiqiang; Huang, Gang; Sumer, Baran D.; Gao, Jinming

2016-10-01

Supramolecular self-assembly offers a powerful strategy to produce high-performance, stimuli-responsive nanomaterials. However, lack of molecular understanding of stimulated responses frequently hampers our ability to rationally design nanomaterials with sharp responses. Here we elucidated the molecular pathway of pH-triggered supramolecular self-assembly of a series of ultra-pH sensitive (UPS) block copolymers. Hydrophobic micellization drove divergent proton distribution in either highly protonated unimer or neutral micelle states along the majority of the titration coordinate unlike conventional small molecular or polymeric bases. This all-or-nothing two-state solution is a hallmark of positive cooperativity. Integrated modelling and experimental validation yielded a Hill coefficient of 51 in pH cooperativity for a representative UPS block copolymer, by far the largest reported in the literature. These data suggest hydrophobic micellization and resulting positive cooperativity offer a versatile strategy to convert responsive nanomaterials into binary on/off switchable systems for chemical and biological sensing, as demonstrated in an additional anion sensing model.

Nanoscale superstructures assembled by polymerase chain reaction (PCR): programmable construction, structural diversity, and emerging applications.

PubMed

Kuang, Hua; Ma, Wei; Xu, Liguang; Wang, Libing; Xu, Chuanlai

2013-11-19

Polymerase chain reaction (PCR) is an essential tool in biotechnology laboratories and is becoming increasingly important in other areas of research. Extensive data obtained over the last 12 years has shown that the combination of PCR with nanoscale dispersions can resolve issues in the preparation DNA-based materials that include both inorganic and organic nanoscale components. Unlike conventional DNA hybridization and antibody-antigen complexes, PCR provides a new, effective assembly platform that both increases the yield of DNA-based nanomaterials and allows researchers to program and control assembly with predesigned parameters including those assisted and automated by computers. As a result, this method allows researchers to optimize to the combinatorial selection of the DNA strands for their nanoparticle conjugates. We have developed a PCR approach for producing various nanoscale assemblies including organic motifs such as small molecules, macromolecules, and inorganic building blocks, such as nanorods (NRs), metal, semiconductor, and magnetic nanoparticles (NPs). We start with a nanoscale primer and then modify that building block using the automated steps of PCR-based assembly including initialization, denaturation, annealing, extension, final elongation, and final hold. The intermediate steps of denaturation, annealing, and extension are cyclic, and we use computer control so that the assembled superstructures reach their predetermined complexity. The structures assembled using a small number of PCR cycles show a lower polydispersity than similar discrete structures obtained by direct hybridization between the nanoscale building blocks. Using different building blocks, we assembled the following structural motifs by PCR: (1) discrete nanostructures (NP dimers, NP multimers including trimers, pyramids, tetramers or hexamers, etc.), (2) branched NP superstructures and heterochains, (3) NP satellite-like superstructures, (4) Y-shaped nanostructures and DNA networks, (5) protein-DNA co-assembly structures, and (6) DNA block copolymers including trimers and pentamers. These results affirm that this method can produce a variety of chemical structures and in yields that are tunable. Using PCR-based preparation of DNA-bridged nanostructures, we can program the assembly of the nanoscale blocks through the adjustment of the primer intensity on the assembled units, the number of PCR cycles, or both. The resulting structures are highly complex and diverse and have interesting dynamics and collective properties. Potential applications of these materials include chirooptical materials, probe fabrication, and environmental and biomedical sensors.

Patchy particles made by colloidal fusion

NASA Astrophysics Data System (ADS)

Gong, Zhe; Hueckel, Theodore; Yi, Gi-Ra; Sacanna, Stefano

2017-10-01

Patches on the surfaces of colloidal particles provide directional information that enables the self-assembly of the particles into higher-order structures. Although computational tools can make quantitative predictions and can generate design rules that link the patch motif of a particle to its internal microstructure and to the emergent properties of the self-assembled materials, the experimental realization of model systems of particles with surface patches (or `patchy' particles) remains a challenge. Synthetic patchy colloidal particles are often poor geometric approximations of the digital building blocks used in simulations and can only rarely be manufactured in sufficiently high yields to be routinely used as experimental model systems. Here we introduce a method, which we refer to as colloidal fusion, for fabricating functional patchy particles in a tunable and scalable manner. Using coordination dynamics and wetting forces, we engineer hybrid liquid-solid clusters that evolve into particles with a range of patchy surface morphologies on addition of a plasticizer. We are able to predict and control the evolutionary pathway by considering surface-energy minimization, leading to two main branches of product: first, spherical particles with liquid surface patches, capable of forming curable bonds with neighbouring particles to assemble robust supracolloidal structures; and second, particles with a faceted liquid compartment, which can be cured and purified to yield colloidal polyhedra. These findings outline a scalable strategy for the synthesis of patchy particles, first by designing their surface patterns by computer simulation, and then by recreating them in the laboratory with high fidelity.

Smart assembly of polymer fibers: lessons from major ampullate spider silk

NASA Astrophysics Data System (ADS)

Viney, Christopher

1996-02-01

Studies of major ampullate silk (MAS), especially the secretions and fibers produced by the spider Nephila clavipes (golden orb weaver), have yielded several results of potential value to the materials scientist/engineer. There are lessons to be learned about synthesis, processing and microstructural design of high-tensile polymer fibers. The 'smart' aspect of silk production in nature concerns the ability of the spider to rapidly process a concentrated, viscous aqueous solution of silk protein (stored in the gland) into water-insoluble fiber on demand. This process centers on the assembly of a shear-sensitive supramolecular liquid crystalline phase by aggregation of the solubilized globular protein molecules.

Fabrication of circular assemblies with DNA tetrahedrons: from static structures to a dynamic rotary motor

PubMed Central

Wang, Liying; Meng, Zhenyu; Martina, Felicia; Shao, Huilin

2017-01-01

Abstract DNA tetrahedron as the simplest 3D DNA nanostructure has been applied widely in biomedicine and biosensing. Herein, we design and fabricate a series of circular assemblies of DNA tetrahedron with high purity and decent yields. These circular nanostructures are confirmed by endonuclease digestion, gel electrophoresis and atomic force microscopy. Inspired by rotary protein motor, we demonstrate these circular architectures can serve as a stator for a rotary DNA motor to achieve the circular rotation. The DNA motor can rotate on the stators for several cycles, and the locomotion of the motor is monitored by the real-time fluorescent measurements. PMID:29126166

A Kinematic, Kevlar(registered) Suspension System for an ADR

NASA Technical Reports Server (NTRS)

Voellmer, George M.; Jackson, Michael L.; Shirron, Peter J.; Tuttle, James G.

2003-01-01

The High Resolution Airborne Wideband Camera (HAWC) and the Submillimeter And Far Infrared Experiment (SAFIRE) will use identical Adiabatic Demagnetization Refrigerators (ADR) to cool their bolometer detectors to 200mK and 100mK, respectively. In order to minimize thermal loads on the salt pill, a Kevlar@ suspension system is used to hold it in place. An innovative, kinematic suspension system is presented. The suspension system is unique in that it consists or two parts that can be assembled and tensioned offline, and later bolted onto the salt pill. The resulting assembly constrains each degree of freedom only once, yielding a kinematic, tensile structure.

Eco-friendly microwave-assisted protocol to prepare hyaluronan-fatty acid conjugates and to induce their self-assembly process.

PubMed

Calce, Enrica; Mercurio, Flavia Anna; Leone, Marilisa; Saviano, Michele; De Luca, Stefania

2016-06-05

An environmentally sustainable and energy-efficient synthetic process has been developed to prepare hyaluronan-based nano-sized material. It consists in a microwave-promoted acylation of the hydroxyl function of the polysaccharide with natural fatty acids, performed under solvent-free conditions. The efficient interaction of the solid reagents with the MW radiation accounts for the obtained high yielded products. The self-assembly process of the obtained compounds very fast occurred in an aqueous medium under MW-radiation, thus allowing the development of a green protocol for the nano-particles preparation. Copyright © 2016 Elsevier Ltd. All rights reserved.

Self-assembling semiconducting polymers--rods and gels from electronic materials.

PubMed

Clark, Andrew P-Z; Shi, Chenjun; Ng, Benny C; Wilking, James N; Ayzner, Alexander L; Stieg, Adam Z; Schwartz, Benjamin J; Mason, Thomas G; Rubin, Yves; Tolbert, Sarah H

2013-02-26

In an effort to favor the formation of straight polymer chains without crystalline grain boundaries, we have synthesized an amphiphilic conjugated polyelectrolyte, poly(fluorene-alt-thiophene) (PFT), which self-assembles in aqueous solutions to form cylindrical micelles. In contrast to many diblock copolymer assemblies, the semiconducting backbone runs parallel, not perpendicular, to the long axis of the cylindrical micelle. Solution-phase micelle formation is observed by X-ray and visible light scattering. The micelles can be cast as thin films, and the cylindrical morphology is preserved in the solid state. The effects of self-assembly are also observed through spectral shifts in optical absorption and photoluminescence. Solutions of higher-molecular-weight PFT micelles form gel networks at sufficiently high aqueous concentrations. Rheological characterization of the PFT gels reveals solid-like behavior and strain hardening below the yield point, properties similar to those found in entangled gels formed from surfactant-based micelles. Finally, electrical measurements on diode test structures indicate that, despite a complete lack of crystallinity in these self-assembled polymers, they effectively conduct electricity.

Self‐Assembled Graphene‐Based Architectures and Their Applications

PubMed Central

Yuan, Zhongke; Xiao, Xiaofen; Li, Jing; Zhao, Zhe

2017-01-01

Abstract Due to unique planar structures and remarkable thermal, electronic, and mechanical properties, chemically modified graphenes (CMGs) such as graphene oxides, reduced graphene oxides, and the related derivatives are recognized as the attractive building blocks for “bottom‐up” nanotechnology, while self‐assembly of CMGs has emerged as one of the most promising approaches to construct advanced functional materials/systems based on graphene. By virtue of a variety of noncovalent forces like hydrogen bonding, van der Waals interaction, metal‐to‐ligand bonds, electrostatic attraction, hydrophobic–hydrophilic interactions, and π–π interactions, the CMGs bearing various functional groups are highly desirable for the assemblies with themselves and a variety of organic and/or inorganic species which can yield various hierarchical nanostructures and macroscopic composites endowed with unique structures, properties, and functions for widespread technological applications such as electronics, optoelectronics, electrocatalysis/photocatalysis, environment, and energy storage and conversion. In this review, significant recent advances concerning the self‐assembly of CMGs are summarized, and the broad applications of self‐assembled graphene‐based materials as well as some future opportunities and challenges in this vibrant area are elucidated. PMID:29619311

Primers of glycosaminoglycan biosynthesis from Peruvian rain forest plants.

PubMed

Taylor, W H; Sinha, A; Khan, I A; McDaniel, S T; Esko, J D

1998-08-28

We have developed a rapid, high throughput screening assay for compounds that alter the assembly of glycosaminoglycan chains in Chinese hamster ovary cells. The assay uses autoradiography to measure the binding of newly synthesized [35S]proteoglycans and [35S]glycosaminoglycans to a positively charged membrane. Screening over 1000 extracts from a random plant collection obtained from the Amazon rain forest yielded five plants that stimulated glycosaminoglycan assembly in both wild-type cells and a mutant cell line defective in xylosyltransferase (the first committed enzyme involved in glycosaminoglycan biosynthesis). Fractionation of an extract of Maieta guianensis by silica gel and reverse-phase chromatography yielded two pure compounds with stimulatory activity. Spectroscopic analysis by NMR and mass spectrometry revealed that the active principles were xylosides of dimethylated ellagic acid. One of the compounds also contained a galloyl group at C-3 of the xylose moiety. These findings suggest that plants and other natural products may be a source of agents that can potentially alter glycosaminoglycan and proteoglycan formation in animal cells.

Transcriptome analysis of Capsicum annuum varieties Mandarin and Blackcluster: assembly, annotation and molecular marker discovery.

PubMed

Ahn, Yul-Kyun; Tripathi, Swati; Kim, Jeong-Ho; Cho, Young-Il; Lee, Hye-Eun; Kim, Do-Sun; Woo, Jong-Gyu; Cho, Myeong-Cheoul

2014-01-10

Next generation sequencing technologies have proven to be a rapid and cost-effective means to assemble and characterize gene content and identify molecular markers in various organisms. Pepper (Capsicum annuum L., Solanaceae) is a major staple vegetable crop, which is economically important and has worldwide distribution. High-throughput transcriptome profiling of two pepper cultivars, Mandarin and Blackcluster, using 454 GS-FLX pyrosequencing yielded 279,221 and 316,357 sequenced reads with a total 120.44 and 142.54Mb of sequence data (average read length of 431 and 450 nucleotides). These reads resulted from 17,525 and 16,341 'isogroups' and were assembled into 19,388 and 18,057 isotigs, and 22,217 and 13,153 singletons for both the cultivars, respectively. Assembled sequences were annotated functionally based on homology to genes in multiple public databases. Detailed sequence variant analysis identified a total of 9701 and 12,741 potential SNPs which eventually resulted in 1025 and 1059 genotype specific SNPs, for both the varieties, respectively, after examining SNP frequency distribution for each mapped unigenes. These markers for pepper will be highly valuable for marker-assisted breeding and other genetic studies. © 2013 Elsevier B.V. All rights reserved.

Time lapse microscopy of temperature control during self-assembly of 3D DNA crystals

NASA Astrophysics Data System (ADS)

Conn, Fiona W.; Jong, Michael Alexander; Tan, Andre; Tseng, Robert; Park, Eunice; Ohayon, Yoel P.; Sha, Ruojie; Mao, Chengde; Seeman, Nadrian C.

2017-10-01

DNA nanostructures are created by exploiting the high fidelity base-pairing interactions of double-stranded branched DNA molecules. These structures present a convenient medium for the self-assembly of macroscopic 3D crystals. In some self-assemblies in this system, crystals can be formed by lowering the temperature, and they can be dissolved by raising it. The ability to monitor the formation and melting of these crystals yields information that can be used to monitor crystal formation and growth. Here, we describe the development of an inexpensive tool that enables direct observation of the crystal growth process as a function of both time and temperature. Using the hanging-drop crystallization of the well-characterized 2-turn DNA tensegrity triangle motif for our model system, its response to temperature has been characterized visually.

Stepwise Synthesis of Giant Unilamellar Vesicles on a Microfluidic Assembly Line

PubMed Central

2011-01-01

Among the molecular milieu of the cell, the membrane bilayer stands out as a complex and elusive synthetic target. We report a microfluidic assembly line that produces uniform cellular compartments from droplet, lipid, and oil/water interface starting materials. Droplets form in a lipid-containing oil flow and travel to a junction where the confluence of oil and extracellular aqueous media establishes a flow-patterned interface that is both stable and reproducible. A triangular post mediates phase transfer bilayer assembly by deflecting droplets from oil, through the interface, and into the extracellular aqueous phase to yield a continuous stream of unilamellar phospholipid vesicles with uniform and tunable size. The size of the droplet precursor dictates vesicle size, encapsulation of small-molecule cargo is highly efficient, and the single bilayer promotes functional insertion of a bacterial transmembrane pore. PMID:21309555

The Bicycle Assembly Line Game

ERIC Educational Resources Information Center

Klotz, Dorothy

2011-01-01

"The Bicycle Assembly Line Game" is a team-based, in-class activity that helps students develop a basic understanding of continuously operating processes. Each team of 7-10 students selects one of seven prefigured bicycle assembly lines to operate. The lines are run in real-time, and the team that operates the line that yields the…

A Nonconventional Approach to Patterned Nanoarrays of DNA Strands for Template-Assisted Assembly of Polyfluorene Nanowires.

PubMed

Bae, Dong Geun; Jeong, Ji-Eun; Kang, Seok Hee; Byun, Myunghwan; Han, Dong-Wook; Lin, Zhiqun; Woo, Han Young; Hong, Suck Won

2016-08-01

DNA molecules have been widely recognized as promising building blocks for constructing functional nanostructures with two main features, that is, self-assembly and rich chemical functionality. The intrinsic feature size of DNA makes it attractive for creating versatile nanostructures. Moreover, the ease of access to tune the surface of DNA by chemical functionalization offers numerous opportunities for many applications. Herein, a simple yet robust strategy is developed to yield the self-assembly of DNA by exploiting controlled evaporative assembly of DNA solution in a unique confined geometry. Intriguingly, depending on the concentration of DNA solution, highly aligned nanostructured fibrillar-like arrays and well-positioned concentric ring-like superstructures composed of DNAs are formed. Subsequently, the ring-like negatively charged DNA superstructures are employed as template to produce conductive organic nanowires on a silicon substrate by complexing with a positively charged conjugated polyelectrolyte poly[9,9-bis(6'-N,N,N-trimethylammoniumhexyl)fluorene dibromide] (PF2) through the strong electrostatic interaction. Finally, a monolithic integration of aligned arrays of DNA-templated PF2 nanowires to yield two DNA/PF2-based devices is demonstrated. It is envisioned that this strategy can be readily extended to pattern other biomolecules and may render a broad range of potential applications from the nucleotide sequence and hybridization as recognition events to transducing elements in chemical sensors. © 2016 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Genovo: De Novo Assembly for Metagenomes

NASA Astrophysics Data System (ADS)

Laserson, Jonathan; Jojic, Vladimir; Koller, Daphne

Next-generation sequencing technologies produce a large number of noisy reads from the DNA in a sample. Metagenomics and population sequencing aim to recover the genomic sequences of the species in the sample, which could be of high diversity. Methods geared towards single sequence reconstruction are not sensitive enough when applied in this setting. We introduce a generative probabilistic model of read generation from environmental samples and present Genovo, a novel de novo sequence assembler that discovers likely sequence reconstructions under the model. A Chinese restaurant process prior accounts for the unknown number of genomes in the sample. Inference is made by applying a series of hill-climbing steps iteratively until convergence. We compare the performance of Genovo to three other short read assembly programs across one synthetic dataset and eight metagenomic datasets created using the 454 platform, the largest of which has 311k reads. Genovo's reconstructions cover more bases and recover more genes than the other methods, and yield a higher assembly score.

DOE Office of Scientific and Technical Information (OSTI.GOV)

Metz, Lori A.; Friese, Judah I.; Finn, Erin C.

Critical assemblies provide one method of achieving a fast neutron spectrum that is close to a 235U fission-energy neutron spectrum for nuclear data measurements. Previous work has demonstrated the use of a natural boron carbide capsule for spectral-tailoring in a mixed spectrum reactor as an alternate and complementary method for performing fission-energy neutron experiments. Previous fission products measurements showed that the neutron spectrum achievable with natural boron carbide was not as hard as what can be achieved with critical assemblies. New measurements performed with the Washington State University TRIGA reactor using a boron carbide capsule 96% enriched in 10B formore » irradiations resulted in a neutron spectrum very similar to a critical assembly and a pure 235U fission spectrum. The current work describes an experiment involving a highly-enriched uranium target irradiated under the new 10B4C capsule. Fission product yields were measured following radiochemical separations and are presented here. Reactor dosimetry measurements for characterizing neutron spectra and fluence for the enriched boron carbide capsule and critical assemblies are also discussed.« less

Supramolecular self-assembly of heterobimetallic complexes: a new N,P-based, selective heteroditopic ligand.

PubMed

Hutchinson, Daniel John; Clauss, Reike; Sárosi, Menyhárt-Botond; Hey-Hawkins, Evamarie

2018-01-23

Pyrimidine-hydrazone and phosphole architectures have been combined to create a new heteroditopic ligand capable of forming heterobimetallic Zn II /Pd II , Pb II /Pd II and Cu II /Pd II complexes in high yielding stepwise or one pot reactions. The catalytic activity of these complexes in Heck coupling and Miyaura borylation reactions was investigated.

Common drive unit

NASA Technical Reports Server (NTRS)

Ellis, R. C.; Fink, R. A.; Moore, E. A.

1987-01-01

The Common Drive Unit (CDU) is a high reliability rotary actuator with many versatile applications in mechanism designs. The CDU incorporates a set of redundant motor-brake assemblies driving a single output shaft through differential. Tachometers provide speed information in the AC version. Operation of both motors, as compared to the operation of one motor, will yield the same output torque with twice the output speed.

Efficiency, error and yield in light-directed maskless synthesis of DNA microarrays

PubMed Central

2011-01-01

Background Light-directed in situ synthesis of DNA microarrays using computer-controlled projection from a digital micromirror device--maskless array synthesis (MAS)--has proved to be successful at both commercial and laboratory scales. The chemical synthetic cycle in MAS is quite similar to that of conventional solid-phase synthesis of oligonucleotides, but the complexity of microarrays and unique synthesis kinetics on the glass substrate require a careful tuning of parameters and unique modifications to the synthesis cycle to obtain optimal deprotection and phosphoramidite coupling. In addition, unintended deprotection due to scattering and diffraction introduce insertion errors that contribute significantly to the overall error rate. Results Stepwise phosphoramidite coupling yields have been greatly improved and are now comparable to those obtained in solid phase synthesis of oligonucleotides. Extended chemical exposure in the synthesis of complex, long oligonucleotide arrays result in lower--but still high--final average yields which approach 99%. The new synthesis chemistry includes elimination of the standard oxidation until the final step, and improved coupling and light deprotection. Coupling Insertions due to stray light are the limiting factor in sequence quality for oligonucleotide synthesis for gene assembly. Diffraction and local flare are by far the largest contributors to loss of optical contrast. Conclusions Maskless array synthesis is an efficient and versatile method for synthesizing high density arrays of long oligonucleotides for hybridization- and other molecular binding-based experiments. For applications requiring high sequence purity, such as gene assembly, diffraction and flare remain significant obstacles, but can be significantly reduced with straightforward experimental strategies. PMID:22152062

Degradation of FEP thermal control materials returned from the Hubble Space Telescope

NASA Technical Reports Server (NTRS)

Zuby, Thomas M.; Degroh, Kim K.; Smith, Daniela C.

1995-01-01

After an initial 3.6 years of space flight, the Hubble Space Telescope was serviced through a joint effort with the NASA and the European Space Agency. Multi-layer insulation (MLI) was retrieved from the electronics boxes of the two magnetic sensing systems (MSS), also called the magnetometers, and from the returned solar array (SA-I) drive arm assembly. The top layer of each MLI assembly is fluorinated ethylene propylene (FEP, a type of Teflon). Dramatic changes in material properties were observed when comparing areas of high solar fluence to areas of low solar fluence. Cross sectional analysis shows atomic oxygen (AO) erosion values up to 25.4 mu m (1 mil). Greater occurrences of through-thickness cracking and surface microcracking were observed in areas of high solar exposure. Atomic force microscopy (AFM) showed increases in surface microhardness measurements with increasing solar exposure. Decreases in FEP tensile strength and elongation were measured when compared to non-flight material. Erosion yield and tensile results are compared with FEP data from the Long Duration Exposure Facility. AO erosion yield data, solar fluence values, contamination, micrometeoroid or debris impact sites, and optical properties are presented.

Design of a flexible organometallic tecton: host-guest chemistry with picric acid and self-assembly of platinum macrocycles.

PubMed

Jana, Achintya; Bhowmick, Sourav; Kaur, Supreet; Kashyap, Hemant K; Das, Neeladri

2017-02-14

The synthesis and characterization of a new pyrazine-based "flexible" and ditopic platinum(ii) organometallic molecule (3) is being reported. Flexibility in this molecule is due to the presence of ether functional groups that bridge the rigid core and periphery. Due to the presence of square planar Pt(ii) centers at the two ends, the molecule's potential to act as an acceptor building block in the construction of metallamacrocycles was tested. Upon reaction of 3 with various dicarboxylates in a 1 : 1 stoichiometric ratio, [2 + 2] self-assembled neutral metallacycles (M1-M3) were obtained in high yields. M1-M3 were characterized using multinuclear NMR, high resolution mass spectrometry and elemental analyses. The shape and dimensions of these supramolecular structures were also confirmed by optimizing the geometry using the density functional theory (DFT) approach. Computational studies suggest that M1-M3 are nanoscalar macrocyles. Furthermore, using isothermal titration calorimetry (ITC), it was shown that 3 can bind with picric acid (PA) to yield a 3·(PA) 2 host-guest complex. The magnitude of the binding constant indicates that 3 has significant affinity for PA.

Purification of High Molecular Weight Genomic DNA from Powdery Mildew for Long-Read Sequencing.

PubMed

Feehan, Joanna M; Scheibel, Katherine E; Bourras, Salim; Underwood, William; Keller, Beat; Somerville, Shauna C

2017-03-31

The powdery mildew fungi are a group of economically important fungal plant pathogens. Relatively little is known about the molecular biology and genetics of these pathogens, in part due to a lack of well-developed genetic and genomic resources. These organisms have large, repetitive genomes, which have made genome sequencing and assembly prohibitively difficult. Here, we describe methods for the collection, extraction, purification and quality control assessment of high molecular weight genomic DNA from one powdery mildew species, Golovinomyces cichoracearum. The protocol described includes mechanical disruption of spores followed by an optimized phenol/chloroform genomic DNA extraction. A typical yield was 7 µg DNA per 150 mg conidia. The genomic DNA that is isolated using this procedure is suitable for long-read sequencing (i.e., > 48.5 kbp). Quality control measures to ensure the size, yield, and purity of the genomic DNA are also described in this method. Sequencing of the genomic DNA of the quality described here will allow for the assembly and comparison of multiple powdery mildew genomes, which in turn will lead to a better understanding and improved control of this agricultural pathogen.

Bacterium Escherichia coli- and phage P22-templated synthesis of semiconductor nanostructures

NASA Astrophysics Data System (ADS)

Shen, Liming

The properties of inorganic materials in the nanoscale are found to be size- and shape-dependent due to quantum confinement effects, and thereby nanomaterials possess properties very different from those of single molecules as well as those of bulk materials. Assembling monodispersed nanoparticles into highly ordered hierarchical architectures is expected to generate novel collective properties for potential applications in catalysis, energy, biomedicine, etc. The major challenge in the assembly of nanoparticles lies in the development of controllable synthetic strategies that enable the growth and assembly of nanoparticles with high selectivity and good controllability. Biological matter possesses robust and precisely ordered structures that exist in a large variety of shapes and sizes, providing an ideal platform for synthesizing high-performance nanostructures. The primary goal of this thesis work has been to develop rational synthetic strategies for high-performance nanostructured materials using biological templates, which are difficult to achieve through traditional chemical synthetic methods. These approaches can serve as general bio-inspired approaches for synthesizing nanoparticle assemblies with desired components and architectures. CdS- and TiO2-binding peptides have been identified using phage display biopanning technique and the mechanism behind the specific affinity between the selected peptides and inorganic substrates are analyzed. The ZnS- and CdS-binding peptides, identified by the phage display biopanning, are utilized for the selective nucleation and growth of sulfides over self-assembled genetically engineered P22 coat proteins, resulting in ordered nanostructures of sulfide nanocrystal assemblies. The synthetic strategy can be extended to the fabrication of a variety of other nanostructures. A simple sonochemical route for the synthesis and assembly of CdS nanostructures with high yield under ambient conditions has been developed by exploiting the chemical characteristics and structure of permeabilized E. coli bacteria. The crystal phase, morphology, micro/nanostructure, optical absorption, and photocatalytic properties of the CdS nanostructures are tailored over a wide range by merely changing the synthetic conditions. Photoanodes fabricated using the nanoporous hollow CdS microrods exhibit excellent performance for the photocatalytic hydrogen production. This facile approach has been extended to the synthesis and assembly of other semiconducting sulfides, including PbS, ZnS, and HgS.

Peptide tessellation yields micrometre-scale collagen triple helices

NASA Astrophysics Data System (ADS)

Tanrikulu, I. Caglar; Forticaux, Audrey; Jin, Song; Raines, Ronald T.

2016-11-01

Sticky-ended DNA duplexes can associate spontaneously into long double helices; however, such self-assembly is much less developed with proteins. Collagen is the most prevalent component of the extracellular matrix and a common clinical biomaterial. As for natural DNA, the ~103-residue triple helices (~300 nm) of natural collagen are recalcitrant to chemical synthesis. Here we show how the self-assembly of short collagen-mimetic peptides (CMPs) can enable the fabrication of synthetic collagen triple helices that are nearly a micrometre in length. Inspired by the mathematics of tessellations, we derive rules for the design of single CMPs that self-assemble into long triple helices with perfect symmetry. Sticky ends thus created are uniform across the assembly and drive its growth. Enacting this design yields individual triple helices that, in length, match or exceed those in natural collagen and are remarkably thermostable, despite the absence of higher-order association. The symmetric assembly of CMPs provides an enabling platform for the development of advanced materials for medicine and nanotechnology.

De novo transcriptome assembly and identification of genes associated with feed conversion ratio and breast muscle yield in domestic ducks.

PubMed

Zhu, Feng; Yuan, Jian-Ming; Zhang, Zhen-He; Hao, Jin-Ping; Yang, Yu-Ze; Hu, Shen-Qiang; Yang, Fang-Xi; Qu, Lu-Jiang; Hou, Zhuo-Cheng

2015-12-01

Breast muscle yield and feed conversion efficiency are the major breeding aims in duck breeding. Understanding the role of specific transcripts in the muscle and small intestine might lead to the elucidation of interrelated biological processes. In this study, we obtained jejunum and breast muscle samples from two strains of Peking ducks that were sorted by feed conversion ratio (FCR) and breast muscle percentage into two-tailed populations. Ten RNA-Seq libraries were developed from the pooled samples and sequenced using the Hiseq2000 platform. We created a reference duck transcript database using de novo assembly methods, which included 16 663 irredundant contigs with an N50 length of 1530 bp. This new duck reference cDNA dataset significantly improved the mapping rate for RNA-Seq data, from 50% to 70%. Mapping and annotation were followed by Gene Ontology analysis, which showed that numerous genes were differentially expressed between the low and high FCR groups. The differentially expressed genes in the jejunum were enriched in biological processes related to immune response and immune response activation, whereas those in the breast muscle were significantly enriched in biological processes related to muscle cell differentiation and organ development. We identified new candidate genes, that is, PCK1, for improving the FCR and breast muscle yield of ducks and obtained much better reference duck transcripts. This study suggested that de novo assembly is essential when applying transcriptome analysis to a species with an incomplete genome. © 2015 Stichting International Foundation for Animal Genetics.

Reiterative Recombination for the in vivo assembly of libraries of multigene pathways.

PubMed

Wingler, Laura M; Cornish, Virginia W

2011-09-13

The increasing sophistication of synthetic biology is creating a demand for robust, broadly accessible methodology for constructing multigene pathways inside of the cell. Due to the difficulty of rationally designing pathways that function as desired in vivo, there is a further need to assemble libraries of pathways in parallel, in order to facilitate the combinatorial optimization of performance. While some in vitro DNA assembly methods can theoretically make libraries of pathways, these techniques are resource intensive and inherently require additional techniques to move the DNA back into cells. All previously reported in vivo assembly techniques have been low yielding, generating only tens to hundreds of constructs at a time. Here, we develop "Reiterative Recombination," a robust method for building multigene pathways directly in the yeast chromosome. Due to its use of endonuclease-induced homologous recombination in conjunction with recyclable markers, Reiterative Recombination provides a highly efficient, technically simple strategy for sequentially assembling an indefinite number of DNA constructs at a defined locus. In this work, we describe the design and construction of the first Reiterative Recombination system in Saccharomyces cerevisiae, and we show that it can be used to assemble multigene constructs. We further demonstrate that Reiterative Recombination can construct large mock libraries of at least 10(4) biosynthetic pathways. We anticipate that our system's simplicity and high efficiency will make it a broadly accessible technology for pathway construction and render it a valuable tool for optimizing pathways in vivo.

Reiterative Recombination for the in vivo assembly of libraries of multigene pathways

PubMed Central

Wingler, Laura M.; Cornish, Virginia W.

2011-01-01

The increasing sophistication of synthetic biology is creating a demand for robust, broadly accessible methodology for constructing multigene pathways inside of the cell. Due to the difficulty of rationally designing pathways that function as desired in vivo, there is a further need to assemble libraries of pathways in parallel, in order to facilitate the combinatorial optimization of performance. While some in vitro DNA assembly methods can theoretically make libraries of pathways, these techniques are resource intensive and inherently require additional techniques to move the DNA back into cells. All previously reported in vivo assembly techniques have been low yielding, generating only tens to hundreds of constructs at a time. Here, we develop “Reiterative Recombination,” a robust method for building multigene pathways directly in the yeast chromosome. Due to its use of endonuclease-induced homologous recombination in conjunction with recyclable markers, Reiterative Recombination provides a highly efficient, technically simple strategy for sequentially assembling an indefinite number of DNA constructs at a defined locus. In this work, we describe the design and construction of the first Reiterative Recombination system in Saccharomyces cerevisiae, and we show that it can be used to assemble multigene constructs. We further demonstrate that Reiterative Recombination can construct large mock libraries of at least 104 biosynthetic pathways. We anticipate that our system’s simplicity and high efficiency will make it a broadly accessible technology for pathway construction and render it a valuable tool for optimizing pathways in vivo. PMID:21876185

Characterization of assembled MEMS

NASA Astrophysics Data System (ADS)

Jandric, Zoran; Randall, John N.; Saini, Rahul; Nolan, Michael; Skidmore, George

2004-12-01

Zyvex is developing a low-cost high-precision method for manufacturing MEMS-based three-dimensional structures/assemblies. The assembly process relies on compliant properties of the interconnecting components. The sockets and connectors are designed to benefit from their compliant nature by allowing the mechanical component to self-align, i.e. reposition themselves to their designed, stable position, independent of the initial placement of the part by the external robot. Thus, the self-aligning property guarantees the precision of the assembled structure to be very close to, or the same, as the precision of the lithography process itself. A three-dimensional (3D) structure is achieved by inserting the connectors into the sockets through the use of a passive end-effector. We have developed the automated, high-yield, assembly procedure which permits connectors to be picked up from any location within the same die, or a separate die. This general procedure allows for the possibility to assemble parts of dissimilar materials. We have built many 3D MEMS structures, including several 3D MEMS devices such as a scanning electron microscope (SEM) micro column, mass-spectrometer column, variable optical attenuator. For these 3D MEMS structures we characterize their mechanical strength through finite element simulation, dynamic properties by finite-element analysis and experimentally with UMECH"s MEMS motion analyzer (MMA), alignment accuracy by using an in-house developed dihedral angle measurement laser autocollimator, and impact properties by performing drop tests. The details of the experimental set-ups, the measurement procedures, and the experimental data are presented in this paper.

Characterization of assembled MEMS

NASA Astrophysics Data System (ADS)

Jandric, Zoran; Randall, John N.; Saini, Rahul; Nolan, Michael; Skidmore, George

2005-01-01

Zyvex is developing a low-cost high-precision method for manufacturing MEMS-based three-dimensional structures/assemblies. The assembly process relies on compliant properties of the interconnecting components. The sockets and connectors are designed to benefit from their compliant nature by allowing the mechanical component to self-align, i.e. reposition themselves to their designed, stable position, independent of the initial placement of the part by the external robot. Thus, the self-aligning property guarantees the precision of the assembled structure to be very close to, or the same, as the precision of the lithography process itself. A three-dimensional (3D) structure is achieved by inserting the connectors into the sockets through the use of a passive end-effector. We have developed the automated, high-yield, assembly procedure which permits connectors to be picked up from any location within the same die, or a separate die. This general procedure allows for the possibility to assemble parts of dissimilar materials. We have built many 3D MEMS structures, including several 3D MEMS devices such as a scanning electron microscope (SEM) micro column, mass-spectrometer column, variable optical attenuator. For these 3D MEMS structures we characterize their mechanical strength through finite element simulation, dynamic properties by finite-element analysis and experimentally with UMECH"s MEMS motion analyzer (MMA), alignment accuracy by using an in-house developed dihedral angle measurement laser autocollimator, and impact properties by performing drop tests. The details of the experimental set-ups, the measurement procedures, and the experimental data are presented in this paper.

Bacteriophage M13 gene 2 protein. Increasing its yield in infected cells, and identification and localization

DOE Office of Scientific and Technical Information (OSTI.GOV)

Lin, Norm S. -C.; Pratt, David

M13 gene 2 protein, implicated in the introduction of single-strand nicks into double-stranded closed circular (RFI) DNA molecules, was previously found in only very small quantities in infected cells. We now find that the gene 2 protein can be readily identified and its yield can be increased manyfold if infections are carried out at high temperature with either a gene 2 temperature- sensitive mutant or with wild type M13. Mechanisms are suggested by which the increased yield could result from subnormal function of the protein in these infections. Under conditions of high yield, the gene 2 protein is found largelymore » in a rapidly sedimenting particulate fraction of unknown nature, where it constitutes as much as 36 percent of the leucine-labeled protein. The gene 2 protein can be readily solubilized from this particulate fraction with the ionic detergent sodium dodecyl sulfate (SDS) but no satisfactory solubilization method was found which keeps the protein in its native state. Attempts to demonstrate in vitro activity of the gene 2 protein, that is, nicking of M13 RFI DNA, were not successful. On the basis of SDS-polyacrylamide gel electrophoresis, we estimate that the gene 2 polypeptide has a molecular weight of approximately 40,000. In the course of the experiments on gene 2 protein, it was observed that the gene 3, as well as the gene 8, virion protein molecules were found predominantly in the cell inner membrane, supporting the idea that virion assembly is carried out there. The gene 4, nonvirion, protein also proved to be in the inner membrane, as would be expected if this protein plays a role in virion assembly.« less

Mapping quantum yield for (Fe-Zn-Sn-Ti)Ox photoabsorbers using a high throughput photoelectrochemical screening system.

PubMed

Xiang, Chengxiang; Haber, Joel; Marcin, Martin; Mitrovic, Slobodan; Jin, Jian; Gregoire, John M

2014-03-10

Combinatorial synthesis and screening of light absorbers are critical to material discoveries for photovoltaic and photoelectrochemical applications. One of the most effective ways to evaluate the energy-conversion properties of a semiconducting light absorber is to form an asymmetric junction and investigate the photogeneration, transport and recombination processes at the semiconductor interface. This standard photoelectrochemical measurement is readily made on a semiconductor sample with a back-side metallic contact (working electrode) and front-side solution contact. In a typical combinatorial material library, each sample shares a common back contact, requiring novel instrumentation to provide spatially resolved and thus sample-resolved measurements. We developed a multiplexing counter electrode with a thin layer assembly, in which a rectifying semiconductor/liquid junction was formed and the short-circuit photocurrent was measured under chopped illumination for each sample in a material library. The multiplexing counter electrode assembly demonstrated a photocurrent sensitivity of sub-10 μA cm(-2) with an external quantum yield sensitivity of 0.5% for each semiconductor sample under a monochromatic ultraviolet illumination source. The combination of cell architecture and multiplexing allows high-throughput modes of operation, including both fast-serial and parallel measurements. To demonstrate the performance of the instrument, the external quantum yields of 1819 different compositions from a pseudoquaternary metal oxide library, (Fe-Zn-Sn-Ti)Ox, at 385 nm were collected in scanning serial mode with a throughput of as fast as 1 s per sample. Preliminary screening results identified a promising ternary composition region centered at Fe0.894Sn0.103Ti0.0034Ox, with an external quantum yield of 6.7% at 385 nm.

Engineering of Novel Biocolloid Suspensions

NASA Technical Reports Server (NTRS)

Hammer, D. A.; Rodges, S.; Hiddessen, A.; Weitz, D. A.

1999-01-01

Colloidal suspensions are materials with a variety of uses from cleaners and lubricants to food, cosmetics, and coatings. In addition, they can be used as a tool for testing the fundamental tenets of statistical physics. Colloidal suspensions can be synthesized from a wide variety of materials, and in the form of monodisperse particles, which can self-assemble into highly ordered colloidal crystal structures. As such they can also be used as templates for the construction of highly ordered materials. Materials design of colloids has, to date, relied on entropic self-assembly, where crystals form as result of lower free energy due to a transition to order. Here, our goal is to develop a completely new method for materials fabrication using colloidal precursors, in which the self-assembly of the ordered colloidal structures is driven by a highly controllable, attractive interaction. This will greatly increase the range of potential structures that can be fabricated with colloidal particles. In this work, we demonstrate that colloidal suspensions can be crosslinked through highly specific biological crosslinking reactions. In particular, the molecules we use are protein-carbohydrate interactions derived from the immune system. This different driving force for self-assembly will yield different and novel suspensions structures. Because the biological interactions are heterotypic (A binding to B), this chemical system can be used to make binary alloys in which the two colloid subpopulations vary in some property - size, density, volume fraction, magnetic susceptibility, etc. An additional feature of these molecules which is unique - even within the realm of biological recognition - is that the molecules bind reversibly on reasonable time-scales, which will enable the suspension to sample different configurations, and allow us to manipulate and measure the size of the suspension dynamically. Because of the wide variety of structures that can be made from these novel colloids, and because the suspension structure can be altered dynamically, we believe this biocolloid system will yield a novel set of materials with many technological applications, including sensors (both biological and non-biological), optical filters and separation media.

The design and fabrication of supramolecular semiconductor nanowires formed by benzothienobenzothiophene (BTBT)-conjugated peptides.

PubMed

Khalily, Mohammad Aref; Usta, Hakan; Ozdemir, Mehmet; Bakan, Gokhan; Dikecoglu, F Begum; Edwards-Gayle, Charlotte; Hutchinson, Jessica A; Hamley, Ian W; Dana, Aykutlu; Guler, Mustafa O

2018-05-31

π-Conjugated small molecules based on a [1]benzothieno[3,2-b]benzothiophene (BTBT) unit are of great research interest in the development of solution-processable semiconducting materials owing to their excellent charge-transport characteristics. However, the BTBT π-core has yet to be demonstrated in the form of electro-active one-dimensional (1D) nanowires that are self-assembled in aqueous media for potential use in bioelectronics and tissue engineering. Here we report the design, synthesis, and self-assembly of benzothienobenzothiophene (BTBT)-peptide conjugates, the BTBT-peptide (BTBT-C3-COHN-Ahx-VVAGKK-Am) and the C8-BTBT-peptide (C8-BTBT-C3-COHN-Ahx-VVAGKK-Am), as β-sheet forming amphiphilic molecules, which self-assemble into highly uniform nanofibers in water with diameters of 11-13(±1) nm and micron-size lengths. Spectroscopic characterization studies demonstrate the J-type π-π interactions among the BTBT molecules within the hydrophobic core of the self-assembled nanofibers yielding an electrical conductivity as high as 6.0 × 10-6 S cm-1. The BTBT π-core is demonstrated, for the first time, in the formation of self-assembled peptide 1D nanostructures in aqueous media for potential use in tissue engineering, bioelectronics and (opto)electronics. The conductivity achieved here is one of the highest reported to date in a non-doped state.

Solvent-Assisted Surface Engineering for High-Performance All-Inorganic Perovskite Nanocrystal Light-Emitting Diodes.

PubMed

Wang, Lin; Liu, Baiquan; Zhao, Xin; Demir, Hilmi Volkan; Gu, Haoshuang; Sun, Handong

2018-06-13

All-inorganic cesium halide perovskite nanocrystals have attracted much interest in optoelectronic applications for the sake of the readily adjustable band gaps, high photoluminescence quantum yield, pure color emission, and affordable cost. However, because of the ineluctable utilization of organic surfactants during the synthesis, the structural and optical properties of CsPbBr 3 nanocrystals degrade upon transforming from colloidal solutions to solid thin films, which plagues the device operation. Here, we develop a novel solvent-assisted surface engineering strategy, producing high-quality CsPbBr 3 thin films for device applications. A good solvent is first introduced as an assembly trigger to conduct assembly in a one-dimensional direction, which is then interrupted by adding a nonsolvent. The nonsolvent drives the adjacent nanoparticles connecting in a two-dimensional direction. Assembled CsPbBr 3 nanocrystal thin films are densely packed and very smooth with a surface roughness of ∼4.8 nm, which is highly desirable for carrier transport in a light-emitting diode (LED) device. Meanwhile, the film stability is apparently improved. Benefiting from this facile and reliable strategy, we have achieved remarkably improved performance of CsPbBr 3 nanocrystal-based LEDs. Our results not only enrich the methods of nanocrystal surface engineering but also shed light on developing high-performance LEDs.

Identification and characterization of protein interactions in the mammalian mRNA processing body using a novel two-hybrid assay

DOE Office of Scientific and Technical Information (OSTI.GOV)

Bloch, Donald B., E-mail: bloch@helix.mgh.harvard.edu; Nobre, Rita A.; Bernstein, Gillian A.

2011-09-10

Components of the mRNA processing body (P-body) regulate critical steps in mRNA storage, transport, translation and degradation. At the core of the P-body is the decapping complex, which removes the 5' cap from de-adenylated mRNAs and mediates an irreversible step in mRNA degradation. The assembly of P-bodies in Saccharomyces cerevisiae, Arabidopsis thaliana and Drosophila melanogaster has been previously described. Less is known about the assembly of mammalian P-bodies. To investigate the interactions that occur between components of mammalian P-bodies, we developed a fluorescence-based, two-hybrid assay system. The assay depends on the ability of one P-body component, fused to an exogenousmore » nuclear localization sequence (NLS), to recruit other P-body components to the nucleus. The assay was used to investigate interactions between P-body components Ge-1, DCP2, DCP1, EDC3, RAP55, and RCK. The results of this study show that the modified two-hybrid assay can be used to identify protein interactions that occur in a macromolecular complex. The assay can also be used to efficiently detect protein interaction domains. The results provide important insights into mammalian P-body assembly and demonstrate similarities, and critical differences, between P-body assembly in mammalian cells compared with that of other species. -- Research highlights: {yields} A two-hybrid assay was developed to study interactions in macromolecular complexes. {yields} The assay was applied to interactions between components of mRNA P-bodies. {yields} The assay effectively and efficiently identified protein interaction domains. {yields} P-body assembly in mammalian cells differs from that in other species.« less

Genome-Wide Identification of Differentially Expressed Genes Associated with the High Yielding of Oleoresin in Secondary Xylem of Masson Pine (Pinus massoniana Lamb) by Transcriptomic Analysis

PubMed Central

Liu, Qinghua; Zhou, Zhichun; Wei, Yongcheng; Shen, Danyu; Feng, Zhongping; Hong, Shanping

2015-01-01

Masson pine is an important timber and resource for oleoresin in South China. Increasing yield of oleoresin in stems can raise economic benefits and enhance the resistance to bark beetles. However, the genetic mechanisms for regulating the yield of oleoresin were still unknown. Here, high-throughput sequencing technology was used to investigate the transcriptome and compare the gene expression profiles of high and low oleoresin-yielding genotypes. A total of 40,690,540 reads were obtained and assembled into 137,499 transcripts from the secondary xylem tissues. We identified 84,842 candidate unigenes based on sequence annotation using various databases and 96 unigenes were candidates for terpenoid backbone biosynthesis in pine. By comparing the expression profiles of high and low oleoresin-yielding genotypes, 649 differentially expressed genes (DEGs) were identified. GO enrichment analysis of DEGs revealed that multiple pathways were related to high yield of oleoresin. Nine candidate genes were validated by QPCR analysis. Among them, the candidate genes encoding geranylgeranyl diphosphate synthase (GGPS) and (-)-alpha/beta-pinene synthase were up-regulated in the high oleoresin-yielding genotype, while tricyclene synthase revealed lower expression level, which was in good agreement with the GC/MS result. In addition, DEG encoding ABC transporters, pathogenesis-related proteins (PR5 and PR9), phosphomethylpyrimidine synthase, non-specific lipid-transfer protein-like protein and ethylene responsive transcription factors (ERFs) were also confirmed to be critical for the biosynthesis of oleoresin. The next-generation sequencing strategy used in this study has proven to be a powerful means for analyzing transcriptome variation related to the yield of oleoresin in masson pine. The candidate genes encoding GGPS, (-)-alpha/beta-pinene, tricyclene synthase, ABC transporters, non-specific lipid-transfer protein-like protein, phosphomethylpyrimidine synthase, ERFs and pathogen responses may play important roles in regulating the yield of oleoresin. These DEGs are worthy of special attention in future studies. PMID:26167875

Probabilistic Analysis of Pattern Formation in Monotonic Self-Assembly

PubMed Central

Moore, Tyler G.; Garzon, Max H.; Deaton, Russell J.

2015-01-01

Inspired by biological systems, self-assembly aims to construct complex structures. It functions through piece-wise, local interactions among component parts and has the potential to produce novel materials and devices at the nanoscale. Algorithmic self-assembly models the product of self-assembly as the output of some computational process, and attempts to control the process of assembly algorithmically. Though providing fundamental insights, these computational models have yet to fully account for the randomness that is inherent in experimental realizations, which tend to be based on trial and error methods. In order to develop a method of analysis that addresses experimental parameters, such as error and yield, this work focuses on the capability of assembly systems to produce a pre-determined set of target patterns, either accurately or perhaps only approximately. Self-assembly systems that assemble patterns that are similar to the targets in a significant percentage are “strong” assemblers. In addition, assemblers should predominantly produce target patterns, with a small percentage of errors or junk. These definitions approximate notions of yield and purity in chemistry and manufacturing. By combining these definitions, a criterion for efficient assembly is developed that can be used to compare the ability of different assembly systems to produce a given target set. Efficiency is a composite measure of the accuracy and purity of an assembler. Typical examples in algorithmic assembly are assessed in the context of these metrics. In addition to validating the method, they also provide some insight that might be used to guide experimentation. Finally, some general results are established that, for efficient assembly, imply that every target pattern is guaranteed to be assembled with a minimum common positive probability, regardless of its size, and that a trichotomy exists to characterize the global behavior of typical efficient, monotonic self-assembly systems in the literature. PMID:26421616

Ensemble brightening and enhanced quantum yield in size-purified silicon nanocrystals

DOE PAGES

Miller, Joseph B.; Van Sickle, Austin R.; Anthony, Rebecca J.; ...

2012-07-18

Here, we report on the quantum yield, photoluminescence (PL) lifetime and ensemble photoluminescent stability of highly monodisperse plasma-synthesized silicon nanocrystals (SiNCs) prepared though density-gradient ultracentrifugation in mixed organic solvents. Improved size uniformity leads to a reduction in PL line width and the emergence of entropic order in dry nanocrystal films. We find excellent agreement with the anticipated trends of quantum confinement in nanocrystalline silicon, with a solution quantum yield that is independent of nanocrystal size for the larger fractions but decreases dramatically with size for the smaller fractions. We also find a significant PL enhancement in films assembled from themore » fractions, and we use a combination of measurement, simulation and modeling to link this ‘brightening’ to a temporally enhanced quantum yield arising from SiNC interactions in ordered ensembles of monodisperse nanocrystals. Using an appropriate excitation scheme, we exploit this enhancement to achieve photostable emission.« less

Formation of hexagonal boron nitride nanoscrolls induced by inclusion and exclusion of self-assembling molecules in solution process.

PubMed

Hwang, Da Young; Suh, Dong Hack

2014-06-07

Unlike nanoscrolls of 2D graphene, those of 2D h-BN have not been demonstrated, except for only a few experimental reports. Nanoscrolls of h-BN with high yields and reproducibility are first synthesized by a simple solution process. Inner-tube diameters of BNSs including LCAs, N-(2-aminoethyl)-3α-hydroxy-5β-cholan-24-amide, a bile acid derivative and self-assembling material, can be controlled by adjusting the diameter of the LCA fiber which is grown by self-assembly. TEM and SEM images show that BNSs have a tube-like morphology and the inner-tube diameter of BNSs can be controlled in the range from 20 to 60 nm for a smaller diameter, up to 300 nm for a larger diameter by LCA fiber growth inside the BNSs. Finally, open cylindrical BNSs with hollow cores were obtained by dissolving LCAs inside BNSs.

Allylic aminations with hindered secondary amine nucleophiles catalyzed by heterobimetallic Pd-Ti complexes.

PubMed

Walker, Whitney K; Anderson, Diana L; Stokes, Ryjul W; Smith, Stacey J; Michaelis, David J

2015-02-06

Phosphinoamide-scaffolded heterobimetallic palladium-titanium complexes are highly effective catalysts for allylic aminations of allylic chlorides with hindered secondary amine nucleophiles. Three titanium-containing ligands are shown to assemble active catalysts in situ and enable catalysis at room temperature. A variety of sterically bulky secondary amines are efficiently allylated in high yields with as little as 1 mol % palladium catalyst. Piperidine and pyrrolidine products are also efficiently generated via intramolecular aminations with hindered amine nucleophiles.

Electron Microscopic Visualization of Protein Assemblies on Flattened DNA Origami.

PubMed

Mallik, Leena; Dhakal, Soma; Nichols, Joseph; Mahoney, Jacob; Dosey, Anne M; Jiang, Shuoxing; Sunahara, Roger K; Skiniotis, Georgios; Walter, Nils G

2015-07-28

DNA provides an ideal substrate for the engineering of versatile nanostructures due to its reliable Watson-Crick base pairing and well-characterized conformation. One of the most promising applications of DNA nanostructures arises from the site-directed spatial arrangement with nanometer precision of guest components such as proteins, metal nanoparticles, and small molecules. Two-dimensional DNA origami architectures, in particular, offer a simple design, high yield of assembly, and large surface area for use as a nanoplatform. However, such single-layer DNA origami were recently found to be structurally polymorphous due to their high flexibility, leading to the development of conformationally restrained multilayered origami that lack some of the advantages of the single-layer designs. Here we monitored single-layer DNA origami by transmission electron microscopy (EM) and discovered that their conformational heterogeneity is dramatically reduced in the presence of a low concentration of dimethyl sulfoxide, allowing for an efficient flattening onto the carbon support of an EM grid. We further demonstrated that streptavidin and a biotinylated target protein (cocaine esterase, CocE) can be captured at predesignated sites on these flattened origami while maintaining their functional integrity. Our demonstration that protein assemblies can be constructed with high spatial precision (within ∼2 nm of their predicted position on the platforms) by using strategically flattened single-layer origami paves the way for exploiting well-defined guest molecule assemblies for biochemistry and nanotechnology applications.

DOE Office of Scientific and Technical Information (OSTI.GOV)

Wang, Xiaoming; Nan, Zhaodong, E-mail: zdnan@yzu.edu.cn

Graphical abstract: Glass-slices were used as a template to induce formation and assembly of aragonite. Different morphologies, such as hemisphere, twinborn hemisphere and flower-shaped particles, were produced by direction of the glass-slices. Highlights: {yields} Glass-slices were used as a template to induce formation and assembly of aragonite. {yields} Hemisphere, twinborn hemisphere and flower-shaped particles were produced by direction of the glass-slices. {yields} Planes were always appeared in these as-synthesized samples. {yields} Thermodynamic theory was applied to explain the production of the aragonite. -- Abstract: A glass-slice was used as a template to induce formation and assembly of aragonite. Thermodynamic theorymore » was applied to explain the production of the aragonite. Transformation of three-dimensional nucleation to template-based two-dimensional surface nucleation caused the production of aragonite. Hemisphere, twinborn hemisphere and flower-shaped particles were produced by direction of the glass-slices. Planes were always appeared in these as-synthesized samples because the nucleation and the growth of these samples were adsorbed at the surfaces of the glass-slices. The formation mechanism of the as-formed sample was proposed. Compared with organic template, the present study provides a facile method to apply inorganic template to prepare functional materials.« less

Failure Investigation & Design Optimization of a Photo-Multiplier Tube Assembly Under Thermal Loading

NASA Technical Reports Server (NTRS)

Dahya, Kevin

2004-01-01

Analysis of GLAST ACD Photo-Multiplier Tube (PMT) assembly under thermal loading demonstrates that the glass tube experiences high stresses due to Coefficient of Thermal Expansion mismatch, as well as increased stress due to high stiffness and incompressibility of potting compound. Further investigation shows adverse loading effects due to the magnetic shield, a thin piece of steel wrapped around the PMT. This steel, Mu Metal, contained an overlap region that directly attributed to crack propagation in the outside surface of the tube. Sensitivities to different configurations were studied to reduce the stress and provide a more uniform loading throughout the PMT to ensure mission success. Studies indicate substituting a softer and more compressible potting compound and moving the Mu metal from the glass tube to the outside wall of the aluminum housing yields lower stress.

Molecular transport through nanoporous silicon nitride membranes produced from self-assembling block copolymers.

PubMed

Montagne, Franck; Blondiaux, Nicolas; Bojko, Alexandre; Pugin, Raphaël

2012-09-28

To achieve fast and selective molecular filtration, membrane materials must ideally exhibit a thin porous skin and a high density of pores with a narrow size distribution. Here, we report the fabrication of nanoporous silicon nitride membranes (NSiMs) at the full wafer scale using a versatile process combining block copolymer (BCP) self-assembly and conventional photolithography/etching techniques. In our method, self-assembled BCP micelles are used as templates for creating sub-100 nm nanopores in a thin low-stress silicon nitride layer, which is then released from the underlying silicon wafer by etching. The process yields 100 nm thick free-standing NSiMs of various lateral dimensions (up to a few mm(2)). We show that the membranes exhibit a high pore density, while still retaining excellent mechanical strength. Permeation experiments reveal that the molecular transport rate across NSiMs is up to 16-fold faster than that of commercial polymeric membranes. Moreover, using dextran molecules of various molecular weights, we also demonstrate that size-based separation can be achieved with a very good selectivity. These new silicon nanosieves offer a relevant technological alternative to commercially available ultra- and microfiltration membranes for conducting high resolution biomolecular separations at small scales.

Nanomechanical properties of distinct fibrillar polymorphs of the protein α-synuclein

PubMed Central

Makky, Ali; Bousset, Luc; Polesel-Maris, Jérôme; Melki, Ronald

2016-01-01

Alpha-synuclein (α-Syn) is a small presynaptic protein of 140 amino acids. Its pathologic intracellular aggregation within the central nervous system yields protein fibrillar inclusions named Lewy bodies that are the hallmarks of Parkinson’s disease (PD). In solution, pure α-Syn adopts an intrinsically disordered structure and assembles into fibrils that exhibit considerable morphological heterogeneity depending on their assembly conditions. We recently established tightly controlled experimental conditions allowing the assembly of α-Syn into highly homogeneous and pure polymorphs. The latter exhibited differences in their shape, their structure but also in their functional properties. We have conducted an AFM study at high resolution and performed a statistical analysis of fibrillar α-Syn shape and thermal fluctuations to calculate the persistence length to further assess the nanomechanical properties of α-Syn polymorphs. Herein, we demonstrated quantitatively that distinct polymorphs made of the same protein (wild-type α-Syn) show significant differences in their morphology (height, width and periodicity) and physical properties (persistence length, bending rigidity and axial Young’s modulus). PMID:27901068

Optimization of De Novo Short Read Assembly of Seabuckthorn (Hippophae rhamnoides L.) Transcriptome

PubMed Central

Ghangal, Rajesh; Chaudhary, Saurabh; Jain, Mukesh; Purty, Ram Singh; Chand Sharma, Prakash

2013-01-01

Seabuckthorn ( Hippophae rhamnoides L.) is known for its medicinal, nutritional and environmental importance since ancient times. However, very limited efforts have been made to characterize the genome and transcriptome of this wonder plant. Here, we report the use of next generation massive parallel sequencing technology (Illumina platform) and de novo assembly to gain a comprehensive view of the seabuckthorn transcriptome. We assembled 86,253,874 high quality short reads using six assembly tools. At our hand, assembly of non-redundant short reads following a two-step procedure was found to be the best considering various assembly quality parameters. Initially, ABySS tool was used following an additive k-mer approach. The assembled transcripts were subsequently subjected to TGICL suite. Finally, de novo short read assembly yielded 88,297 transcripts (> 100 bp), representing about 53 Mb of seabuckthorn transcriptome. The average length of transcripts was 610 bp, N50 length 1198 BP and 91% of the short reads uniquely mapped back to seabuckthorn transcriptome. A total of 41,340 (46.8%) transcripts showed significant similarity with sequences present in nr protein databases of NCBI (E-value < 1E-06). We also screened the assembled transcripts for the presence of transcription factors and simple sequence repeats. Our strategy involving the use of short read assembler (ABySS) followed by TGICL will be useful for the researchers working with a non-model organism’s transcriptome in terms of saving time and reducing complexity in data management. The seabuckthorn transcriptome data generated here provide a valuable resource for gene discovery and development of functional molecular markers. PMID:23991119

Photo-Induced Assembly of a Luminescent Tetraruthenium Square.

PubMed

Laramée-Milette, Baptiste; Nastasi, Francesco; Puntoriero, Fausto; Campagna, Sebastiano; Hanan, Garry S

2017-11-21

Self-assembly is a powerful synthetic tool that has led to the development of one-, two- and three-dimensional architectures. From MOFs to molecular flasks, self-assembled materials have proven to be of great interest to the scientific community. Here we describe a strategy for the construction and de-construction of a supramolecular structure through unprecedented photo-induced assembly and dis-assembly. The combination of two approaches, a [n×1]-directional bonding strategy and a ligand photo-dissociation strategy, allows the photo-induced assembly of a polypyridyl Ru II precursor into a discrete molecular square. Diffusion-ordered NMR spectroscopy confirmed the synthesis of a higher volume species, while the identity of the species was established by high-resolution mass spectrometry and single-crystal X-ray diffraction studies. The self-assembled square is not obtained by classical thermal techniques in similar conditions, but is obtained only by light-irradiation. The tetraruthenium square has an excited-state lifetime (135 ns), 40 times that of its mononuclear precursor and its luminescence quantum yield (1.0 %) is three orders of magnitude higher. These remarkable luminescence properties are closely related to the relatively rigid square structure of the tetraruthenium assembly, as suggested by slow radiationless decay and transient absorption spectroscopy. The results described herein are a rare example of photo-induced assembly and dis-assembly processes, and can open the way to a new avenue in supramolecular chemistry, leading to the preparation of structurally organized supermolecules by photochemical techniques. © 2017 Wiley-VCH Verlag GmbH & Co. KGaA, Weinheim.

Impact of physicochemical parameters on in vitro assembly and disassembly kinetics of recombinant triple-layered rotavirus-like particles.

PubMed

Mellado, Maria Candida M; Mena, Jimmy A; Lopes, António; Ramírez, Octavio T; Carrondo, Manuel J T; Palomares, Laura A; Alves, Paula M

2009-11-01

Virus-like particles constitute potentially relevant vaccine candidates. Nevertheless, their behavior in vitro and assembly process needs to be understood in order to improve their yield and quality. In this study we aimed at addressing these issues and for that purpose triple- and double-layered rotavirus-like particles (TLP 2/6/7 and DLP 2/6, respectively) size and zeta potential were measured using dynamic light scattering at different physicochemical conditions, namely pH, ionic strength, and temperature. Both TLP and DLP were stable within a pH range of 3-7 and at 5-25 degrees C. Aggregation occurred at 35-45 degrees C and their disassembly became evident at 65 degrees C. The isoelectric points of TLP and DLP were 3.0 and 3.8, respectively. In vitro kinetics of TLP disassembly was monitored. Ionic strength, temperature, and the chelating agent employed determined disassembly kinetics. Glycerol (10%) stabilized TLP by preventing its disassembly. Disassembled TLP was able to reassemble by dialysis at high calcium conditions. VP7 monomers were added to DLP in the presence of calcium to follow in vitro TLP assembly kinetics; its assembly rate being mostly affected by pH. Finally, DLP and TLP were found to coexist under certain conditions as determined from all reaction products analyzed by capillary electrophoresis. Overall, these results contribute to the design of new strategies for the improvement of TLP yield and quality by reducing the VP7 detachment from TLP. Copyright 2009 Wiley Periodicals, Inc.

SOFI of GABAB neurotransmitter receptors in hippocampal neurons elucidates intracellular receptor trafficking and assembly

NASA Astrophysics Data System (ADS)

Huss, Anja; Ramírez, Omar; Santibáñez, Felipe; Couve, Andrés.; Härtel, Steffen; Enderlein, Jörg

2013-02-01

The synaptic efficacy of neurons depends on the number of neurotransmitter receptors in the plasma membrane. The availability of these receptors is controlled by their specific intracellular trafficking routes. γ-Aminobutyric acid type B receptors (GABABRs) are heteromeric proteins consisting of GABABR1 and GABABR2 subunits. These receptors are found at the plasma membrane of somatodendritic postsynaptic sites and in axons. It is unknown whether the assembly of the subunits occurs directly in the somatic endoplasmic reticulum (ER) followed by vesicular transport, or whether the assembly occurs after the separate transport of the subunits to the dendritic ER compartment. To address this question we have studied the assembly of the GABABRs in hippocampal neurons with dual-color, 3D super-resolution optical fluctuation imaging (SOFI). SOFI is a fluorescence imaging modality which yields superresolved spatial resolution, 3D-sectioning and high image contrast. We will use the SOFI images to quantify the distribution of the GABABR subunits in the plasma membrane and in the dendritic intracellular compartments. Finally, we want to apply quantitative co-localization analysis to determine the compartments in which the assembly of the GABABR subunits occurs.

Mind the gap; seven reasons to close fragmented genome assemblies.

PubMed

Thomma, Bart P H J; Seidl, Michael F; Shi-Kunne, Xiaoqian; Cook, David E; Bolton, Melvin D; van Kan, Jan A L; Faino, Luigi

2016-05-01

Like other domains of life, research into the biology of filamentous microbes has greatly benefited from the advent of whole-genome sequencing. Next-generation sequencing (NGS) technologies have revolutionized sequencing, making genomic sciences accessible to many academic laboratories including those that study non-model organisms. Thus, hundreds of fungal genomes have been sequenced and are publically available today, although these initiatives have typically yielded considerably fragmented genome assemblies that often lack large contiguous genomic regions. Many important genomic features are contained in intergenic DNA that is often missing in current genome assemblies, and recent studies underscore the significance of non-coding regions and repetitive elements for the life style, adaptability and evolution of many organisms. The study of particular types of genetic elements, such as telomeres, centromeres, repetitive elements, effectors, and clusters of co-regulated genes, but also of phenomena such as structural rearrangements, genome compartmentalization and epigenetics, greatly benefits from having a contiguous and high-quality, preferably even complete and gapless, genome assembly. Here we discuss a number of important reasons to produce gapless, finished, genome assemblies to help answer important biological questions. Copyright © 2015 Elsevier Inc. All rights reserved.

Optimization of a vacuum chamber for vibration measurements.

PubMed

Danyluk, Mike; Dhingra, Anoop

2011-10-01

A 200 °C high vacuum chamber has been built to improve vibration measurement sensitivity. The optimized design addresses two significant issues: (i) vibration measurements under high vacuum conditions and (ii) use of design optimization tools to reduce operating costs. A test rig consisting of a cylindrical vessel with one access port has been constructed with a welded-bellows assembly used to seal the vessel and enable vibration measurements in high vacuum that are comparable with measurements in air. The welded-bellows assembly provides a force transmissibility of 0.1 or better at 15 Hz excitation under high vacuum conditions. Numerical results based on design optimization of a larger diameter chamber are presented. The general constraints on the new design include material yield stress, chamber first natural frequency, vibration isolation performance, and forced convection heat transfer capabilities over the exterior of the vessel access ports. Operating costs of the new chamber are reduced by 50% compared to a preexisting chamber of similar size and function.

The effect of 17-4PH stainless steel on the lifetime of a Pennzane lubricated Microwave Limb Sounder Antenna Actuator Assembly ball screw for the AURA spacecraft

NASA Astrophysics Data System (ADS)

Jones, William R., Jr.; Jansen, Mark J.; Chen, Gun-Shing; Lam, Jonathan; Balzer, Mark; Lo, John; Anderson, Mark; Schepis, Joseph P.

2005-07-01

During ground based life testing of a Microwave Limb Sounder (MLS) Antenna Actuator Assembly (AAA) ball-screw assembly, lubricant darkening and loss were noted when approximately 10% of required lifetime was completed. The MLS-AAA ball screw and nut are made from 17-4 PH steel, the nut has 440C stainless steel balls, and the assembly is lubricated with a Pennzane formulation containing a three weight percent lead naphthenate additive. Life tests were done in dry nitrogen at 50°C. To investigate the MLS-AAA life test anomaly, Spiral Orbit Tribometer (SOT) accelerated tests were performed. SOT results indicated greatly reduced relative lifetimes of Pennzane formulations in contact with 17-4 PH steel compared to 440C stainless steel. Also, dry nitrogen tests yielded longer relative lifetimes than comparable ultrahigh vacuum tests. Generally, oxidized Pennzane formulations yielded shorter lifetimes than non-oxidized lubricant. This study emphasizes surface chemistry effects on the lubricated lifetime of moving mechanical assemblies.

The Effect of 17-4 PH Stainless Steel on the Lifetime of a Pennzane(Trademark) Lubricated Microwave Limb Sounder Antenna Actuator Assembly Ball Screw for the AURA Spacecraft

NASA Technical Reports Server (NTRS)

Jones, William R., Jr.; Jansen, Mark J.; Chen, Gun-Shing; Lam, Jonathan; Balzer, Mark; Anderson, Mark; Lo, John; Schepis, Joseph P.

2005-01-01

During ground based life testing of a Microwave Limb Sounder (MLS) Antenna Actuator Assembly (AAA) ball-screw assembly, lubricant darkening and loss were noted when approximately 10 percent of required lifetime was completed. The MLS-AAA ball screw and nut are made from 17-4 PH steel, the nut has 440C stainless steel balls, and the assembly is lubricated with a Pennzane formulation containing a three weight percent lead naphthenate additive. Life tests were done in dry nitrogen at 50 C. To investigate the MLS-AAA life test anomaly, Spiral Orbit Tribometer (SOT) accelerated tests were performed. SOT results indicated greatly reduced relative lifetimes of Pennzane formulations in contact with 17-4 PH steel compared to 440C stainless steel. Also, dry nitrogen tests yielded longer relative lifetimes than comparable ultrahigh vacuum tests. Generally, oxidized Pennzane formulations yielded shorter lifetimes than non-oxidized lubricant. This study emphasizes surface chemistry effects on the lubricated lifetime of moving mechanical assemblies.

Hydrogen Bonding Stabilized Self-Assembly of Inorganic Nanoparticles: Mechanism and Collective Properties.

PubMed

Yue, Mingli; Li, Yanchun; Hou, Ying; Cao, Wenxin; Zhu, Jiaqi; Han, Jiecai; Lu, Zhongyuan; Yang, Ming

2015-06-23

Developing a simple and efficient method to organize nanoscale building blocks into ordered superstructures, understanding the mechanism for self-assembly and revealing the essential collective properties are crucial steps toward the practical use of nanostructures in nanotechnology-based applications. In this study, we showed that the high-yield formation of ZnO nanoparticle chains with micrometer length can be readily achieved by the variation of solvents from methanol to water. Spectroscopic studies confirmed the solvent effect on the surface properties of ZnO nanoparticles, which were found to be critical for the formation of anisotropic assemblies. Quantum mechanical calculations and all atom molecular dynamic simulations indicated the contribution of hydrogen bonding for stabilizing the structure in water. Dissipative particle dynamics further revealed the importance of solvent-nanoparticle interactions for promoting one-dimensional self-assembly. The branching of chains was found upon aging, resulting in the size increase of the ensembles and network formation. Steady-state and time-resolved luminescent spectroscopes, which probed the variation of defect-related emission, revealed stronger Forster resonance energy transfer (FRET) between nanoparticles when the chain networks were formed. The high efficiency of FRET quenching can be ascribed to the presence of multiple energy transfer channels, as well as the short internanoparticle distances and the dipole alignment.

Self-assembly of microscopic chiplets at a liquid–liquid–solid interface forming a flexible segmented monocrystalline solar cell

PubMed Central

Knuesel, Robert J.; Jacobs, Heiko O.

2010-01-01

This paper introduces a method for self-assembling and electrically connecting small (20–60 micrometer) semiconductor chiplets at predetermined locations on flexible substrates with high speed (62500 chips/45 s), accuracy (0.9 micrometer, 0.14°), and yield (> 98%). The process takes place at the triple interface between silicone oil, water, and a penetrating solder-patterned substrate. The assembly is driven by a stepwise reduction of interfacial free energy where chips are first collected and preoriented at an oil-water interface before they assemble on a solder-patterned substrate that is pulled through the interface. Patterned transfer occurs in a progressing linear front as the liquid layers recede. The process eliminates the dependency on gravity and sedimentation of prior methods, thereby extending the minimal chip size to the sub-100 micrometer scale. It provides a new route for the field of printable electronics to enable the integration of microscopic high performance inorganic semiconductors on foreign substrates with the freedom to choose target location, pitch, and integration density. As an example we demonstrate a fault-tolerant segmented flexible monocrystalline silicon solar cell, reducing the amount of Si that is used when compared to conventional rigid cells. PMID:20080682

High Speed, Low Cost Fabrication of Gas Diffusion Electrodes for Membrane Electrode Assemblies

DOE Office of Scientific and Technical Information (OSTI.GOV)

DeCastro, Emory S.; Tsou, Yu-Min; Liu, Zhenyu

Fabrication of membrane electrode assemblies (MEAs) depends on creating inks or pastes of catalyst and binder, and applying this suspension to either the membrane (catalyst coated membrane) or gas diffusion media (gas diffusion electrode) and respectively laminating either gas diffusion media or gas diffusion electrodes (GDEs) to the membrane. One barrier to cost effective fabrication for either of these approaches is the development of stable and consistent suspensions. This program investigated the fundamental forces that destabilize the suspensions and developed innovative approaches to create new, highly stable formulations. These more concentrated formulations needed fewer application passes, could be coated overmore » longer and wider substrates, and resulted in significantly lower coating defects. In March of 2012 BASF Fuel Cell released a new high temperature product based on these advances, whereby our customers received higher performing, more uniform MEAs resulting in higher stack build yields. Furthermore, these new materials resulted in an “instant” increase in capacity due to higher product yields and material throughput. Although not part of the original scope of this program, these new formulations have also led us to materials that demonstrate equivalent performance with 30% less precious metal in the anode. This program has achieved two key milestones in DOE’s Manufacturing R&D program: demonstration of processes for direct coating of electrodes and continuous in-line measurement for component fabrication.« less

Self-assembly of gibberellic amide assemblies and their applications in the growth and fabrication of ordered gold nanoparticles

NASA Astrophysics Data System (ADS)

Smoak, Evan M.; Carlo, Andrew D.; Fowles, Catherine C.; Banerjee, Ipsita A.

2010-01-01

Gibberellins are a group of naturally occurring diterpenoid based phytohormones that play a vital role in plant growth and development. In this work, we have studied the self-assembly of gibberellic acid, a phytohormone, which belongs to the family of gibberellins, and designed amide derivatives of gibberellic acid (GA3) for the facile, green synthesis of gold nanoparticles. It was found that the derivatives self-assembled into nanofibers and nanoribbons in aqueous solutions at varying pH. Further, upon incubation with tetrachloroaurate, the self-assembled GA3-amide derivatives efficiently nucleated and formed gold nanoparticles when heated to 60 °C. Energy dispersive x-ray spectroscopy, transmission electron microscopy and scanning electron microscopy analyses revealed that uniform coatings of gold nanoparticles in the 10-20 nm range were obtained at low pH on the nanowire surfaces without the assistance of additional reducing agents. This simple method for the development of morphology controlled gold nanoparticles using a plant hormone derivative opens doors for a new class of plant biomaterials which can efficiently yield gold nanoparticles in an environmentally friendly manner. The gold encrusted nanowires formed using biomimetic methods may lead on to the formation of conductive nanowires, which may be useful for a wide range of applications such as in optoelectronics and sensors. Further, the spontaneous formation of highly organized nanostructures obtained from plant phytohormone derivatives such as gibberellic acid is of particular interest as it might help in further understanding the supramolecular assembly mechanism of more highly organized biological structures.

Rapid high-yield expression of full-size IgG antibodies in plants coinfected with noncompeting viral vectors

PubMed Central

Giritch, Anatoli; Marillonnet, Sylvestre; Engler, Carola; van Eldik, Gerben; Botterman, Johan; Klimyuk, Victor; Gleba, Yuri

2006-01-01

Plant viral vectors allow expression of heterologous proteins at high yields, but so far, they have been unable to express heterooligomeric proteins efficiently. We describe here a rapid and indefinitely scalable process for high-level expression of functional full-size mAbs of the IgG class in plants. The process relies on synchronous coinfection and coreplication of two viral vectors, each expressing a separate antibody chain. The two vectors are derived from two different plant viruses that were found to be noncompeting. Unlike vectors derived from the same virus, noncompeting vectors effectively coexpress the heavy and light chains in the same cell throughout the plant body, resulting in yields of up to 0.5 g of assembled mAbs per kg of fresh-leaf biomass. This technology allows production of gram quantities of mAbs for research purposes in just several days, and the same protocol can be used on an industrial scale in situations requiring rapid response, such as pandemic or terrorism events. PMID:16973752

pH-directed self-assembling helical peptide conformation

USDA-ARS?s Scientific Manuscript database

The beta-sheet and alpha-helix peptide conformation are two of the most fundamentally ordered secondary structures found in proteins and peptides. They also give rise to self-assembling motifs that form macromolecular channels and nanostructures. Through design these conformations can yield enhance...

High-level rapid production of full-size monoclonal antibodies in plants by a single-vector DNA replicon system

PubMed Central

Huang, Zhong; Phoolcharoen, Waranyoo; Lai, Huafang; Piensook, Khanrat; Cardineau, Guy; Zeitlin, Larry; Whaley, Kevin J.; Arntzen, Charles J.

2010-01-01

Plant viral vectors have great potential in rapid production of important pharmaceutical proteins. However, high-yield production of heterooligomeric proteins that require the expression and assembly of two or more protein subunits often suffers problems due to the “competing” nature of viral vectors derived from the same virus. Previously we reported that a bean yellow dwarf virus (BeYDV)-derived, three-component DNA replicon system allows rapid production of single recombinant proteins in plants (Huang et al. 2009). In this article, we report further development of this expression system for its application in high-yield production of oligomeric protein complexes including monoclonal antibodies (mAbs) in plants. We showed that the BeYDV replicon system permits simultaneous efficient replication of two DNA replicons and thus, high-level accumulation of two recombinant proteins in the same plant cell. We also demonstrated that a single vector that contains multiple replicon cassettes was as efficient as the three-component system in driving the expression of two distinct proteins. Using either the non-competing, three-vector system or the multi-replicon single vector, we produced both the heavy and light chain subunits of a protective IgG mAb 6D8 against Ebola virus GP1 (Wilson et al. 2000) at 0.5 mg of mAb per gram leaf fresh weight within 4 days post infiltration of Nicotiana benthamiana leaves. We further demonstrated that full-size tetrameric IgG complex containing two heavy and two light chains was efficiently assembled and readily purified, and retained its functionality in specific binding to inactivated Ebola virus. Thus, our single-vector replicon system provides high-yield production capacity for heterooligomeric proteins, yet eliminates the difficult task of identifying non-competing virus and the need for co-infection of multiple expression modules. The multi-replicon vector represents a significant advance in transient expression technology for antibody production in plants. PMID:20047189

Toughening of Epoxies: Novel Self-Assembling Block Copolymers Versus Traditional Telechelic Oligomers

NASA Astrophysics Data System (ADS)

Bacigalupo, Lauren N.

Epoxy resins are commonly utilized because of their adhesive capacity and high strength. However, epoxies are inherently brittle; so much research has been dedicated to improving their fracture toughness. This study will focus on a comparing a traditional telechelic oligomer, CTBN, and a novel self-assembling block copolymer, SBM, as it relates to improving the fracture toughness of a lightly crosslinked epoxy system. After characterizing the modified systems for fracture toughness, mechanical and thermal properties, namely yield stress and the glass transition, will be determined in order to discern the impact these modifiers have on the overall properties of the blend. TEM, SEM and TOM techniques will be utilized for characterizing morphology, fractography and subsurface damage, respectively. Once this was accomplished, it was deduced that the toughening mechanisms of CTBN and SBM-modified epoxies are very similar. The main difference between the two is that the inherent structure of SBM allows the SBM-modified epoxy to retain its compressive yield strength. This, consequently, makes SBM ideal for thin bondline applications in the industrial adhesive and/or electronics industry.

Frictional response of fatty acids on steel.

PubMed

Sahoo, Rashmi R; Biswas, S K

2009-05-15

Self-assembled monolayers of fatty acids were formed on stainless steel by room-temperature solution deposition. The acids are covalently bound to the surface as carboxylate in a bidentate manner. To explore the effect of saturation in the carbon backbone on friction in sliding tribology, we study the response of saturated stearic acid (SA) and unsaturated linoleic acid (LA) as self-assembled monolayers using lateral force microscopy and nanotribometry and when the molecules are dispersed in hexadecane, using pin-on-disc tribometry. Over a very wide range (10 MPa-2.5 GPa) of contact pressures it is consistently demonstrated that the unsaturated linoleic acid molecules yield friction which is significantly lower than that of the saturated stearic acid. It is argued, using density functional theory predictions and XPS of slid track, that when the molecular backbone of unsaturated fatty acids are tilted and pressed strongly by a probe, in tribological contact, the high charge density of the double bond region of the backbone allows coupling with the steel substrate. The interaction yields a low friction carboxylate soap film on the substrate. The saturated fatty acid does not show this effect.

Vesicle-mediated growth of tubular branches and centimeter-long microtubes from a single molecule.

PubMed

Abbas, Abdennour; Brimer, Andrew; Tian, Limei; d'Avignon, D André; Hameed, Abdulrahman Shahul; Vittal, Jagadese J; Singamaneni, Srikanth

2013-08-12

The mechanism by which small molecules assemble into microscale tubular structures in aqueous solution remains poorly understood, particularly when the initial building blocks are non-amphiphilic molecules and no surfactant is used. It is here shown how a subnanometric molecule, namely p-aminothiophenol (p-ATP), prepared in normal water with a small amount of ethanol, spontaneously assembles into a new class of nanovesicle. Due to Brownian motion, these nanostructures rapidly grow into micrometric vesicles and start budding to yield macroscale tubular branches with a remarkable growth rate of ∼20 μm s⁻¹. A real-time visualization by optical microscopy reveals that tubular growth proceeds by vesicle walk and fusion on the apex (growth cone) and sides of the branches and ultimately leads to the generation of centimeter-long microtubes. This unprecedented growth mechanism is triggered by a pH-activated proton switch and maintained by hydrogen bonding. The vesicle fusion-mediated synthesis suggests that functional microtubes with biological properties can be efficiently prepared with a mixture of appropriate diaminophenyl blocks and the desired macromolecule. The reversibility, timescale, and very high yield (90%) of this synthetic approach make it a valuable model for the investigation of hierarchical and structural transition between organized assemblies with different size scales and morphologies. Copyright © 2013 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Quantitative Single-Molecule Surface-Enhanced Raman Scattering by Optothermal Tuning of DNA Origami-Assembled Plasmonic Nanoantennas.

PubMed

Simoncelli, Sabrina; Roller, Eva-Maria; Urban, Patrick; Schreiber, Robert; Turberfield, Andrew J; Liedl, Tim; Lohmüller, Theobald

2016-11-22

DNA origami is a powerful approach for assembling plasmonic nanoparticle dimers and Raman dyes with high yields and excellent positioning control. Here we show how optothermal-induced shrinking of a DNA origami template can be employed to control the gap sizes between two 40 nm gold nanoparticles in a range from 1 to 2 nm. The high field confinement achieved with this optothermal approach was demonstrated by detection of surface-enhanced Raman spectroscopy (SERS) signals from single molecules that are precisely placed within the DNA origami template that spans the nanoparticle gap. By comparing the SERS intensity with respect to the field enhancement in the plasmonic hot-spot region, we found good agreement between measurement and theory. Our straightforward approach for the fabrication of addressable plasmonic nanosensors by DNA origami demonstrates a path toward future sensing applications with single-molecule resolution.

Polymersome magneto-valves for reversible capture and release of nanoparticles

PubMed Central

van Rhee, P.G.; Rikken, R.S.M.; Abdelmohsen, L.K.E.A.; Maan, J.C.; Nolte, R.J.M.; van Hest, J.C.M.; Christianen, P.C.M.; Wilson, D.A.

2014-01-01

Stomatocytes are polymersomes with an infolded bowl-shaped architecture. This internal cavity is connected to the outside environment via a small ‘mouth’ region. Stomatocytes are assembled from diamagnetic amphiphilic block-copolymers with a highly anisotropic magnetic susceptibility, which permits to magnetically align and deform the polymeric self-assemblies. Here we show the reversible opening and closing of the mouth region of stomatocytes in homogeneous magnetic fields. The control over the size of the opening yields magneto-responsive supramolecular valves that are able to reversibly capture and release cargo. Furthermore, the increase in the size of the opening is gradual and starts at fields below 10 T, which opens the possibility of using these structures for delivery and nanoreactor applications. PMID:25248402

The Self-Assembly of DNA Nanostructures for use as Organizing Templates

NASA Astrophysics Data System (ADS)

Samec, Timothy; Cholewinski, Mitchell; Reamer, Nickalas; Reardon, Michael; Ford, Arlene

There is growing interest in the self-assembling capabilities of DNA to create functional nanodevices for use in cancer detection and treatment. One important reason for this interest is that DNA nanostructures are highly programmable molecules. This means that these structures allow for increased stability and control when designing biomacromolecules via adhesion of plasmonic nanoparticles and other similar materials. Our current work reports on the procedure and construction of hexagonal two-dimensional DNA lattice structures using three specific DNA single strands. We also reflect on several barriers that were presented during fabrication as well as the adaptations made to overcome the aforementioned barriers by improving the quality, reproducibility, and yield of the hexagonal two-dimensional DNA lattice as organizing templates.

A setup for active neutron analysis of the fissile material content in fuel assemblies of nuclear reactors

NASA Astrophysics Data System (ADS)

Bushuev, A. V.; Kozhin, A. F.; Aleeva, T. B.; Zubarev, V. N.; Petrova, E. V.; Smirnov, V. E.

2016-12-01

An active neutron method for measuring the residual mass of 235U in spent fuel assemblies (FAs) of the IRT MEPhI research reactor is presented. The special measuring stand design and uniform irradiation of the fuel with neutrons along the entire length of the active part of the FA provide high accuracy of determination of the residual 235U content. AmLi neutron sources yield a higher effect/background ratio than other types of sources and do not induce the fission of 238U. The proposed method of transfer of the isotope source in accordance with a given algorithm may be used in experiments where the studied object needs to be irradiated with a uniform fluence.

Fabrication of circular assemblies with DNA tetrahedrons: from static structures to a dynamic rotary motor.

PubMed

Wang, Liying; Meng, Zhenyu; Martina, Felicia; Shao, Huilin; Shao, Fangwei

2017-12-01

DNA tetrahedron as the simplest 3D DNA nanostructure has been applied widely in biomedicine and biosensing. Herein, we design and fabricate a series of circular assemblies of DNA tetrahedron with high purity and decent yields. These circular nanostructures are confirmed by endonuclease digestion, gel electrophoresis and atomic force microscopy. Inspired by rotary protein motor, we demonstrate these circular architectures can serve as a stator for a rotary DNA motor to achieve the circular rotation. The DNA motor can rotate on the stators for several cycles, and the locomotion of the motor is monitored by the real-time fluorescent measurements. © The Author(s) 2017. Published by Oxford University Press on behalf of Nucleic Acids Research.

Neutron temporal diagnostic for high-yield deuterium-tritium cryogenic implosions on OMEGA

DOE PAGES

Stoeckl, C.; Boni, R.; Ehrne, F.; ...

2016-05-10

A next-generation neutron temporal diagnostic (NTD) capable of recording high-quality data for the highest anticipated yield cryogenic DT implosion experiments was recently installed at the Omega Laser Facility. A high-quality measurement of the neutron production width is required to determine the hot-spot pressure achieved in inertial confinement fusion experiments—a key metric in assessing the quality of these implosions. The design of this NTD is based on a fast-rise-time plastic scintillator, which converts the neutron kinetic energy to 350- to 450-nm-wavelength light. The light from the scintillator inside the nose-cone assembly is relayed ~16 m to a streak camera in amore » well-shielded location. An ~200× reduction in neutron background was observed during the first high-yield DT cryogenic implosions compared to the current NTD installation on OMEGA. An impulse response of ~40±10 ps was measured in a dedicated experiment using hard x rays from a planar target irradiated with a 10-ps short pulse from the OMEGA EP laser. Furthermore, the measured instrument response includes contributions from the scintillator rise time, optical relay, and streak camera.« less

Neutron temporal diagnostic for high-yield deuterium–tritium cryogenic implosions on OMEGA

DOE Office of Scientific and Technical Information (OSTI.GOV)

Stoeckl, C.; Boni, R.; Ehrne, F.

A next-generation neutron temporal diagnostic (NTD) capable of recording high-quality data for the highest anticipated yield cryogenic deuterium–tritium (DT) implosion experiments was recently installed at the Omega Laser Facility. A high-quality measurement of the neutron production width is required to determine the hot-spot pressure achieved in inertial confinement fusion experiments—a key metric in assessing the quality of these implosions. The design of this NTD is based on a fast-rise-time plastic scintillator, which converts the neutron kinetic energy to 350- to 450-nm-wavelength light. The light from the scintillator inside the nose-cone assembly is relayed ∼16 m to a streak camera inmore » a well-shielded location. An ∼200× reduction in neutron background was observed during the first high-yield DT cryogenic implosions compared to the current NTD installation on OMEGA. An impulse response of ∼40 ± 10 ps was measured in a dedicated experiment using hard x-rays from a planar target irradiated with a 10-ps short pulse from the OMEGA EP laser. The measured instrument response includes contributions from the scintillator rise time, optical relay, and streak camera.« less

Neutron temporal diagnostic for high-yield deuterium-tritium cryogenic implosions on OMEGA

DOE Office of Scientific and Technical Information (OSTI.GOV)

Stoeckl, C.; Boni, R.; Ehrne, F.

A next-generation neutron temporal diagnostic (NTD) capable of recording high-quality data for the highest anticipated yield cryogenic DT implosion experiments was recently installed at the Omega Laser Facility. A high-quality measurement of the neutron production width is required to determine the hot-spot pressure achieved in inertial confinement fusion experiments—a key metric in assessing the quality of these implosions. The design of this NTD is based on a fast-rise-time plastic scintillator, which converts the neutron kinetic energy to 350- to 450-nm-wavelength light. The light from the scintillator inside the nose-cone assembly is relayed ~16 m to a streak camera in amore » well-shielded location. An ~200× reduction in neutron background was observed during the first high-yield DT cryogenic implosions compared to the current NTD installation on OMEGA. An impulse response of ~40±10 ps was measured in a dedicated experiment using hard x rays from a planar target irradiated with a 10-ps short pulse from the OMEGA EP laser. Furthermore, the measured instrument response includes contributions from the scintillator rise time, optical relay, and streak camera.« less

Gigadalton-scale shape-programmable DNA assemblies

NASA Astrophysics Data System (ADS)

Wagenbauer, Klaus F.; Sigl, Christian; Dietz, Hendrik

2017-12-01

Natural biomolecular assemblies such as molecular motors, enzymes, viruses and subcellular structures often form by self-limiting hierarchical oligomerization of multiple subunits. Large structures can also assemble efficiently from a few components by combining hierarchical assembly and symmetry, a strategy exemplified by viral capsids. De novo protein design and RNA and DNA nanotechnology aim to mimic these capabilities, but the bottom-up construction of artificial structures with the dimensions and complexity of viruses and other subcellular components remains challenging. Here we show that natural assembly principles can be combined with the methods of DNA origami to produce gigadalton-scale structures with controlled sizes. DNA sequence information is used to encode the shapes of individual DNA origami building blocks, and the geometry and details of the interactions between these building blocks then control their copy numbers, positions and orientations within higher-order assemblies. We illustrate this strategy by creating planar rings of up to 350 nanometres in diameter and with atomic masses of up to 330 megadaltons, micrometre-long, thick tubes commensurate in size to some bacilli, and three-dimensional polyhedral assemblies with sizes of up to 1.2 gigadaltons and 450 nanometres in diameter. We achieve efficient assembly, with yields of up to 90 per cent, by using building blocks with validated structure and sufficient rigidity, and an accurate design with interaction motifs that ensure that hierarchical assembly is self-limiting and able to proceed in equilibrium to allow for error correction. We expect that our method, which enables the self-assembly of structures with sizes approaching that of viruses and cellular organelles, can readily be used to create a range of other complex structures with well defined sizes, by exploiting the modularity and high degree of addressability of the DNA origami building blocks used.

Gigadalton-scale shape-programmable DNA assemblies.

PubMed

Wagenbauer, Klaus F; Sigl, Christian; Dietz, Hendrik

2017-12-06

Natural biomolecular assemblies such as molecular motors, enzymes, viruses and subcellular structures often form by self-limiting hierarchical oligomerization of multiple subunits. Large structures can also assemble efficiently from a few components by combining hierarchical assembly and symmetry, a strategy exemplified by viral capsids. De novo protein design and RNA and DNA nanotechnology aim to mimic these capabilities, but the bottom-up construction of artificial structures with the dimensions and complexity of viruses and other subcellular components remains challenging. Here we show that natural assembly principles can be combined with the methods of DNA origami to produce gigadalton-scale structures with controlled sizes. DNA sequence information is used to encode the shapes of individual DNA origami building blocks, and the geometry and details of the interactions between these building blocks then control their copy numbers, positions and orientations within higher-order assemblies. We illustrate this strategy by creating planar rings of up to 350 nanometres in diameter and with atomic masses of up to 330 megadaltons, micrometre-long, thick tubes commensurate in size to some bacilli, and three-dimensional polyhedral assemblies with sizes of up to 1.2 gigadaltons and 450 nanometres in diameter. We achieve efficient assembly, with yields of up to 90 per cent, by using building blocks with validated structure and sufficient rigidity, and an accurate design with interaction motifs that ensure that hierarchical assembly is self-limiting and able to proceed in equilibrium to allow for error correction. We expect that our method, which enables the self-assembly of structures with sizes approaching that of viruses and cellular organelles, can readily be used to create a range of other complex structures with well defined sizes, by exploiting the modularity and high degree of addressability of the DNA origami building blocks used.

High-density sub-100-nm peptide-gold nanoparticle complexes improve vaccine presentation by dendritic cells in vitro.

PubMed

Lin, Adam Yuh; Lunsford, Jessica; Bear, Adham Sean; Young, Joseph Keith; Eckels, Phillip; Luo, Laureen; Foster, Aaron Edward; Drezek, Rebekah Anna

2013-02-12

Nanocarriers have been explored to improve the delivery of tumor antigens to dendritic cells (DCs). Gold nanoparticles are attractive nanocarriers because they are inert, non-toxic, and can be readily endocytosed by DCs. Here, we designed novel gold-based nanovaccines (AuNVs) using a simple self-assembling bottom-up conjugation method to generate high-peptide density delivery and effective immune responses with limited toxicity. AuNVs were synthesized using a self-assembling conjugation method and optimized using DC-to-splenocyte interferon-γ enzyme-linked immunosorbent spot assays. The AuNV design has shown successful peptide conjugation with approximately 90% yield while remaining smaller than 80 nm in diameter. DCs uptake AuNVs with minimal toxicity and are able to process the vaccine peptides on the particles to stimulate cytotoxic T lymphocytes (CTLs). These high-peptide density AuNVs can stimulate CTLs better than free peptides and have great potential as carriers for various vaccine types.

Poly(methyl methacrylate) as a self-assembled gate dielectric for graphene field-effect transistors

DOE Office of Scientific and Technical Information (OSTI.GOV)

Sanne, A.; Movva, H. C. P.; Kang, S.

We investigate poly(methyl methacrylate) (PMMA) as a low thermal budget organic gate dielectric for graphene field effect-transistors (GFETs) based on a simple process flow. We show that high temperature baking steps above the glass transition temperature (∼130 °C) can leave a self-assembled, thin PMMA film on graphene, where we get a gate dielectric almost for “free” without additional atomic layer deposition type steps. Electrical characterization of GFETs with PMMA as a gate dielectric yields a dielectric constant of k = 3.0. GFETs with thinner PMMA dielectrics have a lower dielectric constant due to decreased polarization arising from neutralization of dipoles and charged carriersmore » as baking temperatures increase. The leakage through PMMA gate dielectric increases with decreasing dielectric thickness and increasing electric field. Unlike conventional high-k gate dielectrics, such low-k organic gate dielectrics are potentially attractive for devices such as the proposed Bilayer pseudoSpin Field-Effect Transistor or flexible high speed graphene electronics.« less

High-density sub-100-nm peptide-gold nanoparticle complexes improve vaccine presentation by dendritic cells in vitro

NASA Astrophysics Data System (ADS)

Lin, Adam Yuh; Lunsford, Jessica; Bear, Adham Sean; Young, Joseph Keith; Eckels, Phillip; Luo, Laureen; Foster, Aaron Edward; Drezek, Rebekah Anna

2013-02-01

Nanocarriers have been explored to improve the delivery of tumor antigens to dendritic cells (DCs). Gold nanoparticles are attractive nanocarriers because they are inert, non-toxic, and can be readily endocytosed by DCs. Here, we designed novel gold-based nanovaccines (AuNVs) using a simple self-assembling bottom-up conjugation method to generate high-peptide density delivery and effective immune responses with limited toxicity. AuNVs were synthesized using a self-assembling conjugation method and optimized using DC-to-splenocyte interferon-γ enzyme-linked immunosorbent spot assays. The AuNV design has shown successful peptide conjugation with approximately 90% yield while remaining smaller than 80 nm in diameter. DCs uptake AuNVs with minimal toxicity and are able to process the vaccine peptides on the particles to stimulate cytotoxic T lymphocytes (CTLs). These high-peptide density AuNVs can stimulate CTLs better than free peptides and have great potential as carriers for various vaccine types.

Combining independent de novo assemblies optimizes the coding transcriptome for nonconventional model eukaryotic organisms.

PubMed

Cerveau, Nicolas; Jackson, Daniel J

2016-12-09

Next-generation sequencing (NGS) technologies are arguably the most revolutionary technical development to join the list of tools available to molecular biologists since PCR. For researchers working with nonconventional model organisms one major problem with the currently dominant NGS platform (Illumina) stems from the obligatory fragmentation of nucleic acid material that occurs prior to sequencing during library preparation. This step creates a significant bioinformatic challenge for accurate de novo assembly of novel transcriptome data. This challenge becomes apparent when a variety of modern assembly tools (of which there is no shortage) are applied to the same raw NGS dataset. With the same assembly parameters these tools can generate markedly different assembly outputs. In this study we present an approach that generates an optimized consensus de novo assembly of eukaryotic coding transcriptomes. This approach does not represent a new assembler, rather it combines the outputs of a variety of established assembly packages, and removes redundancy via a series of clustering steps. We test and validate our approach using Illumina datasets from six phylogenetically diverse eukaryotes (three metazoans, two plants and a yeast) and two simulated datasets derived from metazoan reference genome annotations. All of these datasets were assembled using three currently popular assembly packages (CLC, Trinity and IDBA-tran). In addition, we experimentally demonstrate that transcripts unique to one particular assembly package are likely to be bioinformatic artefacts. For all eight datasets our pipeline generates more concise transcriptomes that in fact possess more unique annotatable protein domains than any of the three individual assemblers we employed. Another measure of assembly completeness (using the purpose built BUSCO databases) also confirmed that our approach yields more information. Our approach yields coding transcriptome assemblies that are more likely to be closer to biological reality than any of the three individual assembly packages we investigated. This approach (freely available as a simple perl script) will be of use to researchers working with species for which there is little or no reference data against which the assembly of a transcriptome can be performed.

Automated solar cell assembly team process research

NASA Astrophysics Data System (ADS)

Nowlan, M. J.; Hogan, S. J.; Darkazalli, G.; Breen, W. F.; Murach, J. M.; Sutherland, S. F.; Patterson, J. S.

1994-06-01

This report describes work done under the Photovoltaic Manufacturing Technology (PVMaT) project, Phase 3A, which addresses problems that are generic to the photovoltaic (PV) industry. Spire's objective during Phase 3A was to use its light soldering technology and experience to design and fabricate solar cell tabbing and interconnecting equipment to develop new, high-yield, high-throughput, fully automated processes for tabbing and interconnecting thin cells. Areas that were addressed include processing rates, process control, yield, throughput, material utilization efficiency, and increased use of automation. Spire teamed with Solec International, a PV module manufacturer, and the University of Massachusetts at Lowell's Center for Productivity Enhancement (CPE), automation specialists, who are lower-tier subcontractors. A number of other PV manufacturers, including Siemens Solar, Mobil Solar, Solar Web, and Texas instruments, agreed to evaluate the processes developed under this program.

Polyoxometalate-based Supramolecular Gel

PubMed Central

He, Peilei; Xu, Biao; Liu, Huiling; He, Su; Saleem, Faisal; Wang, Xun

2013-01-01

Self-assemblyings of surfactant-encapsulated Wells-Dawson polyoxometalates (SEPs) nanobuilding blocks in butanone and esters yielded supramolecular gels showing thermo and photo responsive properties. The gels can be further polymerized if unsaturated esters were used and subsequently electrospinned into nanowires and non-woven mats. The as-prepared non-woven mats have a Young's modulus as high as 542.55 MPa. It is believed that this supramolecular gel is a good platform for polyoxometalates processing. PMID:23666013

CAPRRESI: Chimera Assembly by Plasmid Recovery and Restriction Enzyme Site Insertion.

PubMed

Santillán, Orlando; Ramírez-Romero, Miguel A; Dávila, Guillermo

2017-06-25

Here, we present chimera assembly by plasmid recovery and restriction enzyme site insertion (CAPRRESI). CAPRRESI benefits from many strengths of the original plasmid recovery method and introduces restriction enzyme digestion to ease DNA ligation reactions (required for chimera assembly). For this protocol, users clone wildtype genes into the same plasmid (pUC18 or pUC19). After the in silico selection of amino acid sequence regions where chimeras should be assembled, users obtain all the synonym DNA sequences that encode them. Ad hoc Perl scripts enable users to determine all synonym DNA sequences. After this step, another Perl script searches for restriction enzyme sites on all synonym DNA sequences. This in silico analysis is also performed using the ampicillin resistance gene (ampR) found on pUC18/19 plasmids. Users design oligonucleotides inside synonym regions to disrupt wildtype and ampR genes by PCR. After obtaining and purifying complementary DNA fragments, restriction enzyme digestion is accomplished. Chimera assembly is achieved by ligating appropriate complementary DNA fragments. pUC18/19 vectors are selected for CAPRRESI because they offer technical advantages, such as small size (2,686 base pairs), high copy number, advantageous sequencing reaction features, and commercial availability. The usage of restriction enzymes for chimera assembly eliminates the need for DNA polymerases yielding blunt-ended products. CAPRRESI is a fast and low-cost method for fusing protein-coding genes.

Transport synthetic acceleration for long-characteristics assembly-level transport problems

DOE Office of Scientific and Technical Information (OSTI.GOV)

Zika, M.R.; Adams, M.L.

2000-02-01

The authors apply the transport synthetic acceleration (TSA) scheme to the long-characteristics spatial discretization for the two-dimensional assembly-level transport problem. This synthetic method employs a simplified transport operator as its low-order approximation. Thus, in the acceleration step, the authors take advantage of features of the long-characteristics discretization that make it particularly well suited to assembly-level transport problems. The main contribution is to address difficulties unique to the long-characteristics discretization and produce a computationally efficient acceleration scheme. The combination of the long-characteristics discretization, opposing reflecting boundary conditions (which are present in assembly-level transport problems), and TSA presents several challenges. The authorsmore » devise methods for overcoming each of them in a computationally efficient way. Since the boundary angular data exist on different grids in the high- and low-order problems, they define restriction and prolongation operations specific to the method of long characteristics to map between the two grids. They implement the conjugate gradient (CG) method in the presence of opposing reflection boundary conditions to solve the TSA low-order equations. The CG iteration may be applied only to symmetric positive definite (SPD) matrices; they prove that the long-characteristics discretization yields an SPD matrix. They present results of the acceleration scheme on a simple test problem, a typical pressurized water reactor assembly, and a typical boiling water reactor assembly.« less

Interfacial Self-Assembly of Polyelectrolyte-Capped Gold Nanoparticles

DOE Office of Scientific and Technical Information (OSTI.GOV)

Zhang, Honghu; Nayak, Srikanth; Wang, Wenjie

Here, we report on pH- and salt-responsive assembly of nanoparticles capped with polyelectrolytes at vapor–liquid interfaces. Two types of alkylthiol-terminated poly(acrylic acid) (PAAs, varying in length) are synthesized and used to functionalize gold nanoparticles (AuNPs) to mimic similar assembly effects of single-stranded DNA-capped AuNPs using synthetic polyelectrolytes. Using surface-sensitive X-ray scattering techniques, including grazing incidence small-angle X-ray scattering (GISAXS) and X-ray reflectivity (XRR), we demonstrate that PAA-AuNPs spontaneously migrate to the vapor–liquid interfaces and form Gibbs monolayers by decreasing the pH of the suspension. The Gibbs monoalyers show chainlike structures of monoparticle thickness. The pH-induced self-assembly is attributed to themore » protonation of carboxyl groups and to hydrogen bonding between the neighboring PAA-AuNPs. In addition, we show that adding MgCl 2 to PAA-AuNP suspensions also induces adsorption at the interface and that the high affinity between magnesium ions and carboxyl groups leads to two- and three-dimensional clusters that yield partial surface coverage and poorer ordering of NPs at the interface. We also examine the assembly of PAA-AuNPs in the presence of a positively charged Langmuir monolayer that promotes the attraction of the negatively charged capped NPs by electrostatic forces. Our results show that synthetic polyelectrolyte-functionalized nanoparticles exhibit interfacial self-assembly behavior similar to that of DNA-functionalized nanoparticles, providing a pathway for nanoparticle assembly in general.« less

Interfacial Self-Assembly of Polyelectrolyte-Capped Gold Nanoparticles

DOE PAGES

Zhang, Honghu; Nayak, Srikanth; Wang, Wenjie; ...

2017-10-06

Here, we report on pH- and salt-responsive assembly of nanoparticles capped with polyelectrolytes at vapor–liquid interfaces. Two types of alkylthiol-terminated poly(acrylic acid) (PAAs, varying in length) are synthesized and used to functionalize gold nanoparticles (AuNPs) to mimic similar assembly effects of single-stranded DNA-capped AuNPs using synthetic polyelectrolytes. Using surface-sensitive X-ray scattering techniques, including grazing incidence small-angle X-ray scattering (GISAXS) and X-ray reflectivity (XRR), we demonstrate that PAA-AuNPs spontaneously migrate to the vapor–liquid interfaces and form Gibbs monolayers by decreasing the pH of the suspension. The Gibbs monoalyers show chainlike structures of monoparticle thickness. The pH-induced self-assembly is attributed to themore » protonation of carboxyl groups and to hydrogen bonding between the neighboring PAA-AuNPs. In addition, we show that adding MgCl 2 to PAA-AuNP suspensions also induces adsorption at the interface and that the high affinity between magnesium ions and carboxyl groups leads to two- and three-dimensional clusters that yield partial surface coverage and poorer ordering of NPs at the interface. We also examine the assembly of PAA-AuNPs in the presence of a positively charged Langmuir monolayer that promotes the attraction of the negatively charged capped NPs by electrostatic forces. Our results show that synthetic polyelectrolyte-functionalized nanoparticles exhibit interfacial self-assembly behavior similar to that of DNA-functionalized nanoparticles, providing a pathway for nanoparticle assembly in general.« less

Highly scalable, closed-loop synthesis of drug-loaded, layer-by-layer nanoparticles.

PubMed

Correa, Santiago; Choi, Ki Young; Dreaden, Erik C; Renggli, Kasper; Shi, Aria; Gu, Li; Shopsowitz, Kevin E; Quadir, Mohiuddin A; Ben-Akiva, Elana; Hammond, Paula T

2016-02-16

Layer-by-layer (LbL) self-assembly is a versatile technique from which multicomponent and stimuli-responsive nanoscale drug carriers can be constructed. Despite the benefits of LbL assembly, the conventional synthetic approach for fabricating LbL nanoparticles requires numerous purification steps that limit scale, yield, efficiency, and potential for clinical translation. In this report, we describe a generalizable method for increasing throughput with LbL assembly by using highly scalable, closed-loop diafiltration to manage intermediate purification steps. This method facilitates highly controlled fabrication of diverse nanoscale LbL formulations smaller than 150 nm composed from solid-polymer, mesoporous silica, and liposomal vesicles. The technique allows for the deposition of a broad range of polyelectrolytes that included native polysaccharides, linear polypeptides, and synthetic polymers. We also explore the cytotoxicity, shelf life and long-term storage of LbL nanoparticles produced using this approach. We find that LbL coated systems can be reliably and rapidly produced: specifically, LbL-modified liposomes could be lyophilized, stored at room temperature, and reconstituted without compromising drug encapsulation or particle stability, thereby facilitating large scale applications. Overall, this report describes an accessible approach that significantly improves the throughput of nanoscale LbL drug-carriers that show low toxicity and are amenable to clinically relevant storage conditions.

RNA encapsidation by SV40-derived nanoparticles follows a rapid two-state mechanism

PubMed Central

Kler, Stanislav; Asor, Roi; Li, Chenglei; Ginsburg, Avi; Harries, Daniel; Oppenheim, Ariella; Zlotnick, Adam; Raviv, Uri

2012-01-01

Remarkably, uniform virus-like particles self-assemble in a process that appears to follow a rapid kinetic mechanism. The mechanisms by which spherical viruses assemble from hundreds of capsid proteins around nucleic acid, however, are yet unresolved. Using Time-Resolved Small-Angle X-ray Scattering (TR-SAXS) we have been able to directly visualize SV40 VP1 pentamers encapsidating short RNA molecules (500 mers). This assembly process yields T = 1 icosahedral particles comprised of 12 pentamers and one RNA molecule. The reaction is nearly 1/3 complete within 35 milliseconds, following a two–state kinetic process with no detectable intermediates. Theoretical analysis of kinetics, using a master equation, shows that the assembly process nucleates at the RNA and continues by a cascade of elongation reactions in which one VP1 pentamer is added at a time, with a rate of approximately 109 M−1 s−1. The reaction is highly robust and faster than the predicted diffusion limit. The emerging molecular mechanism, which appears to be general to viruses that assemble around nucleic acids, implicates long-ranged electrostatic interactions. The model proposes that the growing nucleo-protein complex acts as an electrostatic antenna that attracts other capsid subunits for the encapsidation process. PMID:22329660

Nanoparticles of adaptive supramolecular networks self-assembled from nucleotides and lanthanide ions.

PubMed

Nishiyabu, Ryuhei; Hashimoto, Nozomi; Cho, Ten; Watanabe, Kazuto; Yasunaga, Takefumi; Endo, Ayataka; Kaneko, Kenji; Niidome, Takuro; Murata, Masaharu; Adachi, Chihaya; Katayama, Yoshiki; Hashizume, Makoto; Kimizuka, Nobuo

2009-02-18

Amorphous nanoparticles of supramolecular coordination polymer networks are spontaneously self-assembled from nucleotides and lanthanide ions in water. They show intrinsic functions such as energy transfer from nucleobase to lanthanide ions and excellent performance as contrast enhancing agents for magnetic resonance imaging (MRI). Furthermore, adaptive inclusion properties are observed in the self-assembly process: functional materials such as fluorescent dyes, metal nanoparticles, and proteins are facilely encapsulated. Dyes in these nanoparticles fluoresce in high quantum yields with a single exponential decay, indicating that guest molecules are monomerically wrapped in the network. Gold nanoparticles and ferritin were also wrapped by the supramolecular shells. In addition, these nucleotide/lanthanide nanoparticles also serve as scaffolds for immobilizing enzymes. The adaptive nature of present supramolecular nanoparticles provides a versatile platform that can be utilized in a variety of applications ranging from material to biomedical sciences. As examples, biocompatibility and liver-directing characteristics in in vivo tissue localization experiments are demonstrated.

Proteinase K-catalyzed synthesis of linear and star oligo(L-phenylalanine) conjugates.

PubMed

Ageitos, Jose M; Baker, Peter J; Sugahara, Michihiro; Numata, Keiji

2013-10-14

Chemoenzymatic synthesis of peptides is a green and clean chemical reaction that offers high yields without using organic synthesis and serves as an alternative to traditional peptide synthesis methods. This report describes the chemoenzymatic synthesis of oligo(L-phenylalanine) mediated by proteinase K from Tritirachium album, which is one of the most widely used proteases in molecular biological studies. The synthesized linear oligo-phenylalanine showed a unique self-assembly in aqueous solutions. To further functionalize linear oligo(L-phenylalanine) as a low-molecular-weight gelator, it was cosynthesized with tris(2-aminoethyl)amine to obtain star-oligo(L-phenylalanine), which was bioconjugated to demonstrate its self-assembly into fluorescent fibers. The self-assembled fibers of star-oligo(L-phenylalanine) formed fibrous networks with various branching ratios, which depended on the molecular weights and molecular aspect ratios of star-oligo(L-phenylalanine). This is the first study to demonstrate that proteinase K is a suitable enzyme for chemoenzymatic cosynthesis of oligopeptides and star-shaped heteropeptides.

[Microfabricated X-ray Optics Technology Development for the Constellation X-Mission

NASA Technical Reports Server (NTRS)

Schattenburg, Mark L.

2005-01-01

MIT has previously developed advanced methods for the application of silicon microstructures (so-called microcombs) in the precision assembly of foil x-ray optics in support of the Constellation-X Spectroscopy X-ray Telescope (SXT) technology development at the NASA Goddard Space Flight Center (GSFC). During the first year of the above Cooperative Agreement, MIT has developed a new, mature, potentially high- yield process for the manufacturing of microcombs that can be applied to a range of substrates independent of thickness. MIT also developed techniques to extract microcomb accuracy from an assembly truss metrology test stand and to extend the dynamic range of its Shack-Hartmann foil metrology tool. The placement repeatability of foil optics with microcombs in the assembly truss has been improved by a factor of two to approximately 0.15 micron. This was achieved by electric contact determination in favor of determining contact through force measurements. Development work on a stress-free thin foil holder was also supported by this agreement and successfully continued under a different grant.

Single-molecule sequencing and optical mapping yields an improved genome of woodland strawberry (Fragaria vesca) with chromosome-scale contiguity.

PubMed

Edger, Patrick P; VanBuren, Robert; Colle, Marivi; Poorten, Thomas J; Wai, Ching Man; Niederhuth, Chad E; Alger, Elizabeth I; Ou, Shujun; Acharya, Charlotte B; Wang, Jie; Callow, Pete; McKain, Michael R; Shi, Jinghua; Collier, Chad; Xiong, Zhiyong; Mower, Jeffrey P; Slovin, Janet P; Hytönen, Timo; Jiang, Ning; Childs, Kevin L; Knapp, Steven J

2018-02-01

Although draft genomes are available for most agronomically important plant species, the majority are incomplete, highly fragmented, and often riddled with assembly and scaffolding errors. These assembly issues hinder advances in tool development for functional genomics and systems biology. Here we utilized a robust, cost-effective approach to produce high-quality reference genomes. We report a near-complete genome of diploid woodland strawberry (Fragaria vesca) using single-molecule real-time sequencing from Pacific Biosciences (PacBio). This assembly has a contig N50 length of ∼7.9 million base pairs (Mb), representing a ∼300-fold improvement of the previous version. The vast majority (>99.8%) of the assembly was anchored to 7 pseudomolecules using 2 sets of optical maps from Bionano Genomics. We obtained ∼24.96 Mb of sequence not present in the previous version of the F. vesca genome and produced an improved annotation that includes 1496 new genes. Comparative syntenic analyses uncovered numerous, large-scale scaffolding errors present in each chromosome in the previously published version of the F. vesca genome. Our results highlight the need to improve existing short-read based reference genomes. Furthermore, we demonstrate how genome quality impacts commonly used analyses for addressing both fundamental and applied biological questions. © The Authors 2017. Published by Oxford University Press.

Cultivating Discontinuity: Pentecostal Pedagogies of Yielding and Control

ERIC Educational Resources Information Center

Brahinsky, Josh

2013-01-01

Exploring missionary study at an Assemblies of God Bible college through ethnography and training manuals demonstrates systematic pedagogies that cultivate sensory capabilities encouraging yielding, opening to rupture, and constraint. Ritual theory and the Anthropology of Christianity shift analytic scales to include "cultivation," a…

Assembly of Layered Monetite-Chitosan Nanocomposite and Its Transition to Organized Hydroxyapatite.

PubMed

Ruan, Qichao; Liberman, David; Zhang, Yuzheng; Ren, Dongni; Zhang, Yunpeng; Nutt, Steven; Moradian-Oldak, Janet

2016-06-13

Bioinspired synthesis of hierarchically structured calcium phosphate (CaP) material is a highly promising strategy for developing improved bone substitute materials. However, synthesis of CaP materials with outstanding mechanical properties still remains an ongoing challenge. Inspired by the formation of lamellar structure in nacre, we designed an organic matrix composed of chitosan and cis-butenediolic acid (maleic acid, MAc) that could assemble into a layered complex and further guide the mineralization of monetite crystals, resulting in the formation of organized and parallel arrays of monetite platelets with a brick-and-mortar structure. Using the layered monetite-chitosan composite as a precursor, we were able to synthesize hydroxyapatite (HAp) with multiscale hierarchically ordered structure via a topotactic phase transformation process. On the nanoscale, needlelike HAp crystallites assembled into organized bundles that aligned to form highly oriented plates on the microscale. On the large-scale level, these plates with different crystal orientations were stacked together to form a layered structure. The organized structures and composite feature yielded CaP materials with improved mechanical properties close to those of bone. Our study introduces a biomimetic approach that may be practical for the design of advanced, mechanically robust materials for biomedical applications.

Tunable Multiscale Nanoparticle Ordering by Polymer Crystallization

PubMed Central

2017-01-01

While ∼75% of commercially utilized polymers are semicrystalline, the generally low mechanical modulus of these materials, especially for those possessing a glass transition temperature below room temperature, restricts their use for structural applications. Our focus in this paper is to address this deficiency through the controlled, multiscale assembly of nanoparticles (NPs), in particular by leveraging the kinetics of polymer crystallization. This process yields a multiscale NP structure that is templated by the lamellar semicrystalline polymer morphology and spans NPs engulfed by the growing crystals, NPs ordered into layers in the interlamellar zone [spacing of (10–100 nm)], and NPs assembled into fractal objects at the interfibrillar scale, (1–10 μm). The relative fraction of NPs in this hierarchy is readily manipulated by the crystallization speed. Adding NPs usually increases the Young’s modulus of the polymer, but the effects of multiscale ordering are nearly an order of magnitude larger than those for a state where the NPs are not ordered, i.e., randomly dispersed in the matrix. Since the material’s fracture toughness remains practically unaffected in this process, this assembly strategy allows us to create high modulus materials that retain the attractive high toughness and low density of polymers. PMID:28776017

Construction of a controllable β-carotene biosynthetic pathway by decentralized assembly strategy in Saccharomyces cerevisiae.

PubMed

Xie, Wenping; Liu, Min; Lv, Xiaomei; Lu, Wenqiang; Gu, Jiali; Yu, Hongwei

2014-01-01

Saccharomyces cerevisiae is an important platform organism for the synthesis of a great number of natural products. However, the assembly of controllable and genetically stable heterogeneous biosynthetic pathways in S. cerevisiae still remains a significant challenge. Here, we present a strategy for reconstructing controllable multi-gene pathways by employing the GAL regulatory system. A set of marker recyclable integrative plasmids (pMRI) was designed for decentralized assembly of pathways. As proof-of-principle, a controllable β-carotene biosynthesis pathway (∼16 kb) was reconstructed and optimized by repeatedly using GAL10-GAL1 bidirectional promoters with high efficiency (80-100%). By controling the switch time of the pathway, production of 11 mg/g DCW of total carotenoids (72.57 mg/L) and 7.41 mg/g DCW of β-carotene was achieved in shake-flask culture. In addition, the engineered yeast strain exhibited high genetic stability after 20 generations of subculture. The results demonstrated a controllable and genetically stable biosynthetic pathway capable of increasing the yield of target products. Furthermore, the strategy presented in this study could be extended to construct other pathways in S. cerevisisae. © 2013 Wiley Periodicals, Inc.

A Multi-Platform Draft de novo Genome Assembly and Comparative Analysis for the Scarlet Macaw (Ara macao)

PubMed Central

Seabury, Christopher M.; Dowd, Scot E.; Seabury, Paul M.; Raudsepp, Terje; Brightsmith, Donald J.; Liboriussen, Poul; Halley, Yvette; Fisher, Colleen A.; Owens, Elaine; Viswanathan, Ganesh; Tizard, Ian R.

2013-01-01

Data deposition to NCBI Genomes This Whole Genome Shotgun project has been deposited at DDBJ/EMBL/GenBank under the accession AMXX00000000 (SMACv1.0, unscaffolded genome assembly). The version described in this paper is the first version (AMXX01000000). The scaffolded assembly (SMACv1.1) has been deposited at DDBJ/EMBL/GenBank under the accession AOUJ00000000, and is also the first version (AOUJ01000000). Strong biological interest in traits such as the acquisition and utilization of speech, cognitive abilities, and longevity catalyzed the utilization of two next-generation sequencing platforms to provide the first-draft de novo genome assembly for the large, new world parrot Ara macao (Scarlet Macaw). Despite the challenges associated with genome assembly for an outbred avian species, including 951,507 high-quality putative single nucleotide polymorphisms, the final genome assembly (>1.035 Gb) includes more than 997 Mb of unambiguous sequence data (excluding N’s). Cytogenetic analyses including ZooFISH revealed complex rearrangements associated with two scarlet macaw macrochromosomes (AMA6, AMA7), which supports the hypothesis that translocations, fusions, and intragenomic rearrangements are key factors associated with karyotype evolution among parrots. In silico annotation of the scarlet macaw genome provided robust evidence for 14,405 nuclear gene annotation models, their predicted transcripts and proteins, and a complete mitochondrial genome. Comparative analyses involving the scarlet macaw, chicken, and zebra finch genomes revealed high levels of nucleotide-based conservation as well as evidence for overall genome stability among the three highly divergent species. Application of a new whole-genome analysis of divergence involving all three species yielded prioritized candidate genes and noncoding regions for parrot traits of interest (i.e., speech, intelligence, longevity) which were independently supported by the results of previous human GWAS studies. We also observed evidence for genes and noncoding loci that displayed extreme conservation across the three avian lineages, thereby reflecting their likely biological and developmental importance among birds. PMID:23667475

RADseq dataset with 90% missing data fully resolves recent radiation of Petalidium (Acanthaceae) in the ultra-arid deserts of Namibia.

PubMed

Tripp, Erin A; Tsai, Yi-Hsin Erica; Zhuang, Yongbin; Dexter, Kyle G

2017-10-01

Deserts, even those at tropical latitudes, often have strikingly low levels of plant diversity, particularly within genera. One remarkable exception to this pattern is the genus Petalidium (Acanthaceae), in which 37 of 40 named species occupy one of the driest environments on Earth, the Namib Desert of Namibia and neighboring Angola. To contribute to understanding this enigmatic diversity, we generated RADseq data for 47 accessions of Petalidium representing 22 species. We explored the impacts of 18 different combinations of assembly parameters in de novo assembly of the data across nine levels of missing data plus a best practice assembly using a reference Acanthaceae genome for a total of 171 sequence datasets assembled. RADseq data assembled at several thresholds of missing data, including 90% missing data, yielded phylogenetic hypotheses of Petalidium that were confidently and nearly fully resolved, which is notable given that divergence time analyses suggest a crown age for African species of 3.6-1.4 Ma. De novo assembly of our data yielded the most strongly supported and well-resolved topologies; in contrast, reference-based assembly performed poorly, perhaps due in part to moderate phylogenetic divergence between the reference genome, Ruellia speciosa , and the ingroup. Overall, we found that Petalidium , despite the harshness of the environment in which species occur, shows a net diversification rate (0.8-2.1 species per my) on par with those of diverse genera in tropical, Mediterranean, and alpine environments.

Development of environmentally conscious cleaning process for leadless chip carrier assemblies. Final report

DOE Office of Scientific and Technical Information (OSTI.GOV)

Adams, B.E.

1995-04-01

A cross-functional team of process, product, quality, material, and design lab engineers was assembled to develop an environmentally friendly cleaning process for leadless chip carrier assemblies (LCCAs). Using flush and filter testing, Auger surface analysis, GC-Mass spectrophotometry, production yield results, and electrical testing results over an extended testing period, the team developed an aqueous cleaning process for LCCAs. The aqueous process replaced the Freon vapor degreasing/ultrasonic rinse process.

Stimuli-responsive cellulose-based nematogels

NASA Astrophysics Data System (ADS)

Liu, Qingkun; Smalyukh, Ivan

Physical properties of composite materials can be pre-engineered by controlling their structure and composition at the mesoscale. Yet, approaches for achieving this are limited and rarely scalable. We introduce a new breed of self-assembled nematogels formed by an orientationally ordered network of thin cellulose nanofibers infiltrated with a thermotropic nematic fluid. The interplay of orientational ordering within the nematic network and that of the small-molecule liquid crystal around it yields a composite with highly tunable optical properties. By means of combining experimental characterization and analytical modeling, we demonstrate sub-milisecond electric switching of transparency and also facile response of the composite to temperature changes and light illumination. Finally, we discuss a host of potential technological uses of these self-assembled nematogel composites, ranging from smart and privacy windows to novel flexible display modes.

Self-assembled vertically aligned Au nanorod arrays for surface-enhanced Raman scattering (SERS) detection of Cannabinol

NASA Astrophysics Data System (ADS)

Milliken, Sarah; Fraser, Jeff; Poirier, Shawn; Hulse, John; Tay, Li-Lin

2018-05-01

Self-assembled multi-layered vertically aligned gold nanorod (AuNR) arrays have been fabricated by a simple preparation process that requires a balance between the particle concentration and the ionic strength of the solvent. An experimentally determined critical AuNR concentration of 2.0 nM and 50 mM NaCl produces well-ordered vertically aligned hexagonally close-packed AuNR arrays. We demonstrate surface treatment via UV Ozone cleaning of such samples to allow introduction of analyte molecules (benzenethiol and cannabinol) for effective surface enhanced Raman scattering detection. This is the first demonstration of the SERS analysis of cannabinol. This approach demonstrates a cost-effective, high-yield and simple fabrication route to SERS sensors with application in the screening for the cannabinoids.

Complete mitochondrial genome of the versicoloured emerald hummingbird Amazilia versicolor, a polymorphic species.

PubMed

Prosdocimi, Francisco; Souto, Helena Magarinos; Ruschi, Piero Angeli; Furtado, Carolina; Jennings, W Bryan

2016-09-01

The genome of the versicoloured emerald hummingbird (Amazilia versicolor) was partially sequenced in one-sixth of an Illumina HiSeq lane. The mitochondrial genome was assembled using MIRA and MITObim software, yielding a circular molecule of 16,861 bp in length and deposited in GenBank under the accession number KF624601. The mitogenome contained 13 protein-coding genes, 22 transfer tRNAs, 2 ribosomal RNAs and 1 non-coding control region. The molecule was assembled using 21,927 sequencing reads of 100 bp each, resulting in ∼130 × coverage of uniformly distributed reads along the genome. This is the forth mitochondrial genome described for this highly diverse family of birds and may benefit further phylogenetic, phylogeographic, population genetic and species delimitation studies of hummingbirds.

Liquid crystalline cellulose-based nematogels

DOE PAGES

Liu, Qingkun; Smalyukh, Ivan I.

2017-08-18

Physical properties of composite materials can be pre-engineered by controlling their structure and composition at the mesoscale. However, approaches to achieving this are limited and rarely scalable. We introduce a new breed of self-assembled nematogels formed by an orientationally ordered network of thin cellulose nanofibers infiltrated with a thermotropic nematic fluid. The interplay between orientational ordering within the nematic network and that of the small-molecule liquid crystal around it yields a composite with highly tunable optical properties. By means of combining experimental characterization and modeling, we demonstrate submillisecond electric switching of transparency and facile responses of the composite to temperaturemore » changes. Finally, we discuss a host of potential technological uses of these self-assembled nematogel composites, ranging from smart and privacy windows to novel flexible displays.« less

Nano-Al{sub 2}O{sub 3} multilayer film deposition on cotton fabrics by layer-by-layer deposition method

DOE Office of Scientific and Technical Information (OSTI.GOV)

Ugur, Sule S., E-mail: sule@mmf.sdu.edu.tr; Sariisik, Merih; Aktas, A. Hakan

Highlights: {yields} Cationic charges were created on the cotton fibre surfaces with 2,3-epoxypropyltrimethylammonium chloride. {yields} Al{sub 2}O{sub 3} nanoparticles were deposited on the cotton fabrics by layer-by-layer deposition. {yields} The fabrics deposited with the Al{sub 2}O{sub 3} nanoparticles exhibit better UV-protection and significant flame retardancy properties. {yields} The mechanical properties were improved after surface film deposition. -- Abstract: Al{sub 2}O{sub 3} nanoparticles were used for fabrication of multilayer nanocomposite film deposition on cationic cotton fabrics by electrostatic self-assembly to improve the mechanical, UV-protection and flame retardancy properties of cotton fabrics. Cotton fabric surface was modified with a chemical reaction tomore » build-up cationic charge known as cationization. Attenuated Total Reflectance Fourier Transform Infrared Spectroscopy, X-ray Photoelectron Spectroscopy and Scanning Electron Microscopy were used to verify the presence of deposited nanolayers. Air permeability, whiteness value, tensile strength, UV-transmittance and Limited Oxygen Index properties of cotton fabrics were analyzed before and after the treatment of Al{sub 2}O{sub 3} nanoparticles by electrostatic self-assemblies. It was proved that the flame retardancy, tensile strength and UV-transmittance of cotton fabrics can be improved by Al{sub 2}O{sub 3} nanoparticle additive through electrostatic self-assembly process.« less

Optimization of Aircraft Seat Cushion Fire Blocking Layers.

DTIC Science & Technology

1983-03-01

function of cost and weight, and the costs of labor involved in assembling a ccmposite seat cushion. The same classes of high char yield polymers that are...SEAT LATER DESIGN REPORT NRBBNBsg$$$$$$NN$$R$$$$$ SEAT DESIGN NUMBER: 009 LAYER NAME CODE NO. S MANUFACTURER 5 COST FACTORS . LABOR ...72621, 9096.. 7SS43. 73757. 77147. DELTA COSTS 0. 8340. 2922. 1136. 4327. ACOSOS in Iho..aS Of dollars. COST SUIRNY REPORT Re ....... VONR3 MORFA

Producibility of Vertically Integrated Photodiode (VIP)tm scanning focal plane arrays

NASA Astrophysics Data System (ADS)

Turner, Arthur M.; Teherani, Towfik; Ehmke, John C.; Pettitt, Cindy; Conlon, Peggy; Beck, Jeffrey D.; McCormack, Kent; Colombo, Luigi; Lahutsky, Tom; Murphy, Terry; Williams, Robert L.

1994-07-01

Vertically integrated photodiode, VIPTM, technology is now being used to produce second generation infrared focal plane arrays with high yields and performance. The VIPTM process employs planar, ion implanted, n on p diodes in HgCdTe which is epoxy hybridized directly to the read out integrated circuits on 100 mm Si wafers. The process parameters that are critical for high performance and yield include: HgCdTe dislocation density and thickness, backside passivation, frontside passivation, and junction formation. Producibility of infrared focal plane arrays (IRFPAs) is also significantly enhanced by read out integrated circuits (ROICs) which have the ability to deselect defective pixels. Cold probe screening before lab dewar assembly reduces costs and improves cycle times. The 240 X 1 and 240 X 2 scanning array formats are used to demonstrate the effect of process optimization, deselect, and cold probe screening on yield and cycle time. The versatility of the VIPTM technology and its extension to large area arrays is demonstrated using 240/288 X 4 and 480 X 5 TDI formats. Finally, the high performance of VIPTM IRFPAs is demonstrated by comparing data from a 480 X 5 to the SADA-II specification.

"Chemical transformers" from nanoparticle ensembles operated with logic.

PubMed

Motornov, Mikhail; Zhou, Jian; Pita, Marcos; Gopishetty, Venkateshwarlu; Tokarev, Ihor; Katz, Evgeny; Minko, Sergiy

2008-09-01

The pH-responsive nanoparticles were coupled with information-processing enzyme-based systems to yield "smart" signal-responsive hybrid systems with built-in Boolean logic. The enzyme systems performed AND/OR logic operations, transducing biochemical input signals into reversible structural changes (signal-directed self-assembly) of the nanoparticle assemblies, thus resulting in the processing and amplification of the biochemical signals. The hybrid system mimics biological systems in effective processing of complex biochemical information, resulting in reversible changes of the self-assembled structures of the nanoparticles. The bioinspired approach to the nanostructured morphing materials could be used in future self-assembled molecular robotic systems.

Tunable Gas Sensing Gels by Cooperative Assembly

PubMed Central

Hussain, Abid; Semeano, Ana T. S.; Palma, Susana I. C. J.; Pina, Ana S.; Almeida, José; Medrado, Bárbara F.; Pádua, Ana C. C. S.; Carvalho, Ana L.; Dionísio, Madalena; Li, Rosamaria W. C.; Gamboa, Hugo; Ulijn, Rein V.; Gruber, Jonas; Roque, Ana C. A.

2017-01-01

The cooperative assembly of biopolymers and small molecules can yield functional materials with precisely tunable properties. Here, the fabrication, characterization, and use of multicomponent hybrid gels as selective gas sensors are reported. The gels are composed of liquid crystal droplets self-assembled in the presence of ionic liquids, which further coassemble with biopolymers to form stable matrices. Each individual component can be varied and acts cooperatively to tune gels’ structure and function. The unique molecular environment in hybrid gels is explored for supramolecular recognition of volatile compounds. Gels with distinct compositions are used as optical and electrical gas sensors, yielding a combinatorial response conceptually mimicking olfactory biological systems, and tested to distinguish volatile organic compounds and to quantify ethanol in automotive fuel. The gel response is rapid, reversible, and reproducible. These robust, versatile, modular, pliant electro-optical soft materials possess new possibilities in sensing triggered by chemical and physical stimuli. PMID:28747856

Method of forming and assembly of parts

DOEpatents

Ripley, Edward B.

2010-12-28

A method of assembling two or more parts together that may be metal, ceramic, metal and ceramic parts, or parts that have different CTE. Individual parts are formed and sintered from particles that leave a network of interconnecting porosity in each sintered part. The separate parts are assembled together and then a fill material is infiltrated into the assembled, sintered parts using a method such as capillary action, gravity, and/or pressure. The assembly is then cured to yield a bonded and fully or near-fully dense part that has the desired physical and mechanical properties for the part's intended purpose. Structural strength may be added to the parts by the inclusion of fibrous materials.

RNA extraction from self-assembling peptide hydrogels to allow qPCR analysis of encapsulated cells.

PubMed

Burgess, Kyle A; Workman, Victoria L; Elsawy, Mohamed A; Miller, Aline F; Oceandy, Delvac; Saiani, Alberto

2018-01-01

Self-assembling peptide hydrogels offer a novel 3-dimensional platform for many applications in cell culture and tissue engineering but are not compatible with current methods of RNA isolation; owing to interactions between RNA and the biomaterial. This study investigates the use of two techniques based on two different basic extraction principles: solution-based extraction and direct solid-state binding of RNA respectively, to extract RNA from cells encapsulated in four β-sheet forming self-assembling peptide hydrogels with varying net positive charge. RNA-peptide fibril interactions, rather than RNA-peptide molecular complexing, were found to interfere with the extraction process resulting in low yields. A column-based approach relying on RNA-specific binding was shown to be more suited to extracting RNA with higher purity from these peptide hydrogels owing to its reliance on strong specific RNA binding interactions which compete directly with RNA-peptide fibril interactions. In order to reduce the amount of fibrils present and improve RNA yields a broad spectrum enzyme solution-pronase-was used to partially digest the hydrogels before RNA extraction. This pre-treatment was shown to significantly increase the yield of RNA extracted, allowing downstream RT-qPCR to be performed.

Experiences in flip chip production of radiation detectors

NASA Astrophysics Data System (ADS)

Savolainen-Pulli, Satu; Salonen, Jaakko; Salmi, Jorma; Vähänen, Sami

2006-09-01

Modern imaging devices often require heterogeneous integration of different materials and technologies. Because of yield considerations, material availability, and various technological limitations, an extremely fine pitch is necessary to realize high-resolution images. Thus, there is a need for a hybridization technology that is able to join together readout amplifiers and pixel detectors at a very fine pitch. This paper describes radiation detector flip chip production at VTT. Our flip chip technology utilizes 25-μm diameter tin-lead solder bumps at a 50-μm pitch and is based on flux-free bonding. When preprocessed wafers are used, as is the case here, the total yield is defined only partly by the flip chip process. Wafer preprocessing done by a third-party silicon foundry and the flip chip process create different process defects. Wafer-level yield maps (based on probing) provided by the customer are used to select good readout chips for assembly. Wafer probing is often done outside of a real clean room environment, resulting in particle contamination and/or scratches on the wafers. Factors affecting the total yield of flip chip bonded detectors are discussed, and some yield numbers of the process are given. Ways to improve yield are considered, and finally guidelines for process planning and device design with respect to yield optimization are given.

An improved design of spiral tube assembly for separation of proteins by high-speed counter-current chromatography.

PubMed

Dasarathy, Dhweeja; Ito, Yoichiro

2015-10-30

A new spiral tube assembly was designed to improve the column capacity and partition efficiency for protein separation. This spiral tube assembly has greater column capacity than the original tubing because of an increase in radial grooves from 4 to 12 to accommodate more spiral layers and 12 narrow spots instead of 4 in each circular loop to interrupt the laminar flow that causes sample band broadening. Standard PTFE tubing (1.6mm ID) and the modified flat-twisted tubing were used as the separation column. The performances of both assemblies were compared for separating three stable test proteins including cytochrome c, myoglobin, and lysozyme using a two phase aqueous-aqueous solvent system composed of polyethylene glycol 1000 (12.5% w/w) and dibasic potassium phosphate (12.5% w/w). All samples were run at 1, 2, 3, and 5mL/min at both 800rpm and 1000rpm. The separation of these three protein samples produced high stationary phase retentions at 1, 2, and 3mL/min, yet separated efficiently at 5mL/min in 40min. After comparing the separation efficiency in terms of the peak resolutions, theoretical plate numbers, and separation times, it was determined that the flat-twisted tubing was more effective in separating these protein samples. In order to validate the efficacy of this novel assembly, a mixture of five protein samples (cytochrome c, myoglobin, ovalbumin, lysozyme, and hemoglobin) were separated, under the optimal conditions established with these three protein samples, at 1mL/min with a revolution speed of 1000rpm. There were high stationary phase retentions of around 60%, with effective separations, demonstrating the efficiency of the flat-twisted spiral tube assembly. The separation time of 6h was a limitation but can potentially be shortened by improving the strength of the column that will permit an increase in revolution speed and flow rate. This novel spiral separation column will allow rapid and efficient separation of mixtures with high yield of the constituent components. Published by Elsevier B.V.

Alignment of Gold Nanoparticle-Decorated DNA Origami Nanotubes: Substrate Prepatterning versus Molecular Combing.

PubMed

Teschome, Bezu; Facsko, Stefan; Gothelf, Kurt V; Keller, Adrian

2015-11-24

DNA origami has become an established technique for designing well-defined nanostructures with any desired shape and for the controlled arrangement of functional nanostructures with few nanometer resolution. These unique features make DNA origami nanostructures promising candidates for use as scaffolds in nanoelectronics and nanophotonics device fabrication. Consequently, a number of studies have shown the precise organization of metallic nanoparticles on various DNA origami shapes. In this work, we fabricated large arrays of aligned DNA origami decorated with a high density of gold nanoparticles (AuNPs). To this end, we first demonstrate the high-yield assembly of high-density AuNP arrangements on DNA origami adsorbed to Si surfaces with few unbound background nanoparticles by carefully controlling the concentrations of MgCl2 and AuNPs in the hybridization buffer and the hybridization time. Then, we evaluate two methods, i.e., hybridization to prealigned DNA origami and molecular combing in a receding meniscus, with respect to their potential to yield large arrays of aligned AuNP-decorated DNA origami nanotubes. Because of the comparatively low MgCl2 concentration required for the efficient immobilization of the AuNPs, the prealigned DNA origami become mobile and displaced from their original positions, thereby decreasing the alignment yield. This increased mobility, on the other hand, makes the adsorbed origami susceptible to molecular combing, and a total alignment yield of 86% is obtained in this way.

A general quantitative pH sensor developed with dicyandiamide N-doped high quantum yield graphene quantum dots.

PubMed

Wu, Zhu Lian; Gao, Ming Xuan; Wang, Ting Ting; Wan, Xiao Yan; Zheng, Lin Ling; Huang, Cheng Zhi

2014-04-07

A general quantitative pH sensor for environmental and intracellular applications was developed by the facile hydrothermal preparation of dicyandiamide (DCD) N-doped high quantum yield (QY) graphene quantum dots (GQDs) using citric acid (CA) as the carbon source. The obtained N-doped GQDs have excellent photoluminesence (PL) properties with a relatively high QY of 36.5%, suggesting that N-doped chemistry could promote the QY of carbon nanomaterials. The possible mechanism for the formation of the GQDs involves the CA self-assembling into a nanosheet structure through intermolecular H-bonding at the initial stage of the reaction, and then the pure graphene core with many function groups formed through the dehydration between the carboxyl and hydroxyl of the intermolecules under hydrothermal conditions. These N-doped GQDs have low toxicity, and are photostable and pH-sensitive between 1.81 to 8.96, giving a general pH sensor with a wide range of applications from real water to intracellular contents.

Star-like supramolecular polymers fabricated by a Keplerate cluster with cationic terminated polymers and their self-assembly into vesicles.

PubMed

Zhang, Qian; He, Lipeng; Wang, Hui; Zhang, Cheng; Liu, Weisheng; Bu, Weifeng

2012-07-18

The electrostatic combination of a Keplerate cluster, [Mo(132)O(372)(CH(3)COO)(30)(H(2)O)(72)](42-) with cationic terminated poly(styrene) yields polyoxometalate-based supramolecular star polymers, which can further self-assemble into vesicular aggregates in CHCl(3)-MeOH mixed solvent.

FUEL ASSEMBLY SHAKER TEST SIMULATION

DOE Office of Scientific and Technical Information (OSTI.GOV)

Klymyshyn, Nicholas A.; Sanborn, Scott E.; Adkins, Harold E.

This report describes the modeling of a PWR fuel assembly under dynamic shock loading in support of the Sandia National Laboratories (SNL) shaker test campaign. The focus of the test campaign is on evaluating the response of used fuel to shock and vibration loads that a can occur during highway transport. Modeling began in 2012 using an LS-DYNA fuel assembly model that was first created for modeling impact scenarios. SNL’s proposed test scenario was simulated through analysis and the calculated results helped guide the instrumentation and other aspects of the testing. During FY 2013, the fuel assembly model was refinedmore » to better represent the test surrogate. Analysis of the proposed loads suggested the frequency band needed to be lowered to attempt to excite the lower natural frequencies of the fuel assembly. Despite SNL’s expansion of lower frequency components in their five shock realizations, pretest predictions suggested a very mild dynamic response to the test loading. After testing was completed, one specific shock case was modeled, using recorded accelerometer data to excite the model. Direct comparison of predicted strain in the cladding was made to the recorded strain gauge data. The magnitude of both sets of strain (calculated and recorded) are very low, compared to the expected yield strength of the Zircaloy-4 material. The model was accurate enough to predict that no yielding of the cladding was expected, but its precision at predicting micro strains is questionable. The SNL test data offers some opportunity for validation of the finite element model, but the specific loading conditions of the testing only excite the fuel assembly to respond in a limited manner. For example, the test accelerations were not strong enough to substantially drive the fuel assembly out of contact with the basket. Under this test scenario, the fuel assembly model does a reasonable job of approximating actual fuel assembly response, a claim that can be verified through direct comparison of model results to recorded test results. This does not offer validation for the fuel assembly model in all conceivable cases, such as high kinetic energy shock cases where the fuel assembly might lift off the basket floor to strike to basket ceiling. This type of nonlinear behavior was not witnessed in testing, so the model does not have test data to be validated against.a basis for validation in cases that substantially alter the fuel assembly response range. This leads to a gap in knowledge that is identified through this modeling study. The SNL shaker testing loaded a surrogate fuel assembly with a certain set of artificially-generated time histories. One thing all the shock cases had in common was an elimination of low frequency components, which reduces the rigid body dynamic response of the system. It is not known if the SNL test cases effectively bound all highway transportation scenarios, or if significantly greater rigid body motion than was tested is credible. This knowledge gap could be filled through modeling the vehicle dynamics of a used fuel conveyance, or by collecting acceleration time history data from an actual conveyance under highway conditions.« less

Structural Investigation of Cesium Lead Halide Perovskites for High-Efficiency Quantum Dot Light-Emitting Diodes.

PubMed

Le, Quyet Van; Kim, Jong Beom; Kim, Soo Young; Lee, Byeongdu; Lee, Dong Ryeol

2017-09-07

We have investigated the effect of reaction temperature of hot-injection method on the structural properties of CsPbX 3 (X: Br, I, Cl) perovskite nanocrystals (NCs) using small- and wide-angle X-ray scattering. It is confirmed that the size of the NCs decreased as the reaction temperature decreased, resulting in stronger quantum confinement. The cubic-phase perovskite NCs formed despite the fact that the reaction temperatures increased from 140 to 180 °C; however, monodispersive NC cubes that are required for densely packing self-assembly film were formed only at lower temperatures. From the X-ray scattering measurements, the spin-coated film from more monodispersive perovskite nanocubes synthesized at lower temperatures resulted in more preferred orientation. This dense-packing perovskite film with preferred orientation yielded efficient light-emitting diode (LED) performance. Thus the dense-packing structure of NC assemblies formed after spin-coating should be considered for high-efficient LEDs based on perovskite quantum dots in addition to quantum confinement effect of the quantum dots.

Mucin gel assembly is controlled by a collective action of non-mucin proteins, disulfide bridges, Ca2+-mediated links, and hydrogen bonding.

PubMed

Meldrum, Oliver W; Yakubov, Gleb E; Bonilla, Mauricio R; Deshmukh, Omkar; McGuckin, Michael A; Gidley, Michael J

2018-04-11

Mucus is characterized by multiple levels of assembly at different length scales which result in a unique set of rheological (flow) and mechanical properties. These physical properties determine its biological function as a highly selective barrier for transport of water and nutrients, while blocking penetration of pathogens and foreign particles. Altered integrity of the mucus layer in the small intestine has been associated with a number of gastrointestinal tract pathologies such as Crohn's disease and cystic fibrosis. In this work, we uncover an intricate hierarchy of intestinal mucin (Muc2) assembly and show how complex rheological properties emerge from synergistic interactions between mucin glycoproteins, non-mucin proteins, and Ca 2+ . Using a novel method of mucus purification, we demonstrate the mechanism of assembly of Muc2 oligomers into viscoelastic microscale domains formed via hydrogen bonding and Ca 2+ -mediated links, which require the joint presence of Ca 2+ ions and non-mucin proteins. These microscale domains aggregate to form a heterogeneous yield stress gel-like fluid, the macroscopic rheological properties of which are virtually identical to that of native intestinal mucus. Through proteomic analysis, we short-list potential protein candidates implicated in mucin assembly, thus paving the way for identifying the molecules responsible for the physiologically critical biophysical properties of mucus.

Luminescent Carbon Dot Mimics Assembled on DNA

PubMed Central

Chan, Ke Min; Xu, Wang; Kwon, Hyukin; Kietrys, Anna M.; Kool, Eric T.

2018-01-01

Nanometer-sized fragments of carbon in the form of multilayer graphene (“carbon dots”) have been under highly active study for applications in imaging. While offering advantages of low toxicity and photostability, such nanomaterials are inhomogeneous and have limited wavelengths of emission. Here we address these issues by assembling luminescent aromatic C16–C38 hydrocarbons together on a DNA scaffold in homogeneous, soluble molecular compounds. Monomer deoxyribosides of five different aromatic hydrocarbons were synthesized and assembled into a library of 1296 different tetramer compounds on PEG-polystyrene beads. These were screened for photostability and a range of emission colors using 365 nm excitation, observing visible light (>400 nm) emission. We identified a set of six oligomers (DNA-carbon assemblies, DNA-CAs) with exceptional photostability that emit from 400 to 680 nm in water, with Stokes shifts of up to 110 nm, quantum yields ranging from 0.01 to 0.29, and fluorescence lifetimes from 3 to 42 ns. In addition, several of these DNA-CAs exhibited white emission in aqueous solution. The molecules were used in multispectral cell imaging experiments and were taken up into cells passively. The results expand the range of emission properties that can be achieved in water with all-hydrocarbon chromophores and establish the use of the DNA scaffold to arrange carbon layers in homogeneous, rapidly synthesized assemblies. PMID:28841010

Evidence that viral RNAs have evolved for efficient, two-stage packaging.

PubMed

Borodavka, Alexander; Tuma, Roman; Stockley, Peter G

2012-09-25

Genome packaging is an essential step in virus replication and a potential drug target. Single-stranded RNA viruses have been thought to encapsidate their genomes by gradual co-assembly with capsid subunits. In contrast, using a single molecule fluorescence assay to monitor RNA conformation and virus assembly in real time, with two viruses from differing structural families, we have discovered that packaging is a two-stage process. Initially, the genomic RNAs undergo rapid and dramatic (approximately 20-30%) collapse of their solution conformations upon addition of cognate coat proteins. The collapse occurs with a substoichiometric ratio of coat protein subunits and is followed by a gradual increase in particle size, consistent with the recruitment of additional subunits to complete a growing capsid. Equivalently sized nonviral RNAs, including high copy potential in vivo competitor mRNAs, do not collapse. They do support particle assembly, however, but yield many aberrant structures in contrast to viral RNAs that make only capsids of the correct size. The collapse is specific to viral RNA fragments, implying that it depends on a series of specific RNA-protein interactions. For bacteriophage MS2, we have shown that collapse is driven by subsequent protein-protein interactions, consistent with the RNA-protein contacts occurring in defined spatial locations. Conformational collapse appears to be a distinct feature of viral RNA that has evolved to facilitate assembly. Aspects of this process mimic those seen in ribosome assembly.

DOE Office of Scientific and Technical Information (OSTI.GOV)

Lyn, Rodney K.; Department of Chemistry, University of Ottawa, Ottawa; Kennedy, David C.

Research highlights: {yields} Hepatitis C virus uses lipid droplets (LD) onto which HCV core proteins bind. {yields} HCV core proteins on LDs facilitate viral particle assembly. {yields} We used a novel combination of CARS, two-photon fluorescence, and DIC microscopies. {yields} Particle tracking experiments show that core slowly affects LD localization. {yields} Particle tracking measured the change in speed and directionality of LD movement. -- Abstract: The hepatitis C virus (HCV) is a global health problem, with limited treatment options and no vaccine available. HCV uses components of the host cell to proliferate, including lipid droplets (LD) onto which HCV coremore » proteins bind and facilitate viral particle assembly. We have measured the dynamics of HCV core protein-mediated changes in LDs and rates of LD movement on microtubules using a combination of coherent anti-Stokes Raman scattering (CARS), two-photon fluorescence (TPF), and differential interference contrast (DIC) microscopies. Results show that the HCV core protein induces rapid increases in LD size. Particle tracking experiments show that HCV core protein slowly affects LD localization by controlling the directionality of LD movement on microtubules. These dynamic processes ultimately aid HCV in propagating and the molecules and interactions involved represent novel targets for potential therapeutic intervention.« less

The Inglorious Death of Jumbo

DOE Office of Scientific and Technical Information (OSTI.GOV)

Meade, Roger Allen

In the summer of 1944, J. Robert Oppenheimer and Los Alamos faced a crisis. An isotopic impurity in Plutonium rendered the metal unusable in a gun-assembled atomic bomb (i.e., Little Boy). Making this situation worse was a shortage of Uranium. The combination of these two problems threatened the entire wartime project. The answer to this dilemma, in part, was to develop a novel assembly method for Plutonium using the supersonic shock waves created by several tons of high explosives to compress a ball of Plutonium into a supercritical state. Since this method, implosion, was not much more than a theoreticalmore » construct, the Trinity test was devised to proof test the process. Given the speculative nature of implosion, Trinity was a gamble of sorts. If the test failed (i.e., little or no nuclear yield), the blast of the high explosives would scatter the scarce and expensive Plutonium over the surrounding desert. Since the probability of failure remained high into the early summer of 1945, some method of containing a failed nuclear explosion was needed. Jumbo was the answer.« less

Monochromatic multicomponent fluorescence sedimentation velocity for the study of high-affinity protein interactions

PubMed Central

Zhao, Huaying; Fu, Yan; Glasser, Carla; Andrade Alba, Eric J; Mayer, Mark L; Patterson, George; Schuck, Peter

2016-01-01

The dynamic assembly of multi-protein complexes underlies fundamental processes in cell biology. A mechanistic understanding of assemblies requires accurate measurement of their stoichiometry, affinity and cooperativity, and frequently consideration of multiple co-existing complexes. Sedimentation velocity analytical ultracentrifugation equipped with fluorescence detection (FDS-SV) allows the characterization of protein complexes free in solution with high size resolution, at concentrations in the nanomolar and picomolar range. Here, we extend the capabilities of FDS-SV with a single excitation wavelength from single-component to multi-component detection using photoswitchable fluorescent proteins (psFPs). We exploit their characteristic quantum yield of photo-switching to imprint spatio-temporal modulations onto the sedimentation signal that reveal different psFP-tagged protein components in the mixture. This novel approach facilitates studies of heterogeneous multi-protein complexes at orders of magnitude lower concentrations and for higher-affinity systems than previously possible. Using this technique we studied high-affinity interactions between the amino-terminal domains of GluA2 and GluA3 AMPA receptors. DOI: http://dx.doi.org/10.7554/eLife.17812.001 PMID:27436096

Method of forming and assembly of metal and ceramic parts

DOEpatents

Ripley, Edward B

2014-04-22

A method of forming and assembling at least two parts together that may be metal, ceramic, or a combination of metal and ceramic parts. Such parts may have different CTE. Individual parts that are formed and sintered from particles leave a network of interconnecting porosity in each sintered part. The separate parts are assembled together and then a fill material is infiltrated into the assembled parts using a method such as capillary action, gravity, and/or pressure. The assembly is then cured to yield a bonded and fully or near-fully dense part that has the desired physical and mechanical properties for the part's intended purpose. Structural strength may be added to the parts by the inclusion of fibrous materials.

Method of forming and assembly of metal parts and ceramic parts

DOEpatents

Ripley, Edward B [Knoxville, TN

2011-11-22

A method of forming and assembling at least two parts together that may be metal, ceramic, or a combination of metal and ceramic parts. Such parts may have different CTE. Individual parts that are formed and sintered from particles leave a network of interconnecting porosity in each sintered part. The separate parts are assembled together and then a fill material is infiltrated into the assembled parts using a method such as capillary action, gravity, and/or pressure. The assembly is then cured to yield a bonded and fully or near-fully dense part that has the desired physical and mechanical properties for the part's intended purpose. Structural strength may be added to the parts by the inclusion of fibrous materials.

1D vs. 2D shape selectivity in the crystallization-driven self-assembly of polylactide block copolymers.

PubMed

Inam, Maria; Cambridge, Graeme; Pitto-Barry, Anaïs; Laker, Zachary P L; Wilson, Neil R; Mathers, Robert T; Dove, Andrew P; O'Reilly, Rachel K

2017-06-01

2D materials such as graphene, LAPONITE® clays or molybdenum disulfide nanosheets are of extremely high interest to the materials community as a result of their high surface area and controllable surface properties. While several methods to access 2D inorganic materials are known, the investigation of 2D organic nanomaterials is less well developed on account of the lack of ready synthetic accessibility. Crystallization-driven self-assembly (CDSA) has become a powerful method to access a wide range of complex but precisely-defined nanostructures. The preparation of 2D structures, however, particularly those aimed towards biomedical applications, is limited, with few offering biocompatible and biodegradable characteristics as well as control over self-assembly in two dimensions. Herein, in contrast to conventional self-assembly rules, we show that the solubility of polylactide (PLLA)-based amphiphiles in alcohols results in unprecedented shape selectivity based on unimer solubility. We use log  P oct analysis to drive solvent selection for the formation of large uniform 2D diamond-shaped platelets, up to several microns in size, using long, soluble coronal blocks. By contrast, less soluble PLLA-containing block copolymers yield cylindrical micelles and mixed morphologies. The methods developed in this work provide a simple and consistently reproducible protocol for the preparation of well-defined 2D organic nanomaterials, whose size and morphology are expected to facilitate potential applications in drug delivery, tissue engineering and in nanocomposites.

Lanthanide-based coordination polymers assembled by a flexible multidentate linker: design, structure, photophysical properties, and dynamic solid-state behavior.

PubMed

Marchal, Claire; Filinchuk, Yaroslav; Chen, Xiao-Yan; Imbert, Daniel; Mazzanti, Marinella

2009-01-01

Four picolinate building blocks were implemented into the multidentate linker N,N',N'-tetrakis[(6-carboxypyridin-2-yl)methyl]butylenediamine (H(4)tpabn) with a linear flexible spacer to promote the assembly of lanthanide-based 1D coordination polymers. The role of the linker in directing the geometry of the final assembly is evidenced by the different results obtained in the presence of Htpabn(3-) and tpabn(4-) ions. The tpabn(4-) ion leads to the desired 1D polymer {[Nd(tpabn)]H(3)O x 6 H(2)O}(infinity) (12). The Htpabn(3-) ion leads to the assembly of Tb(III) and Er(III) ions into 1D zigzag chains of the general formula {[M(Htpabn)] x xH(2)O}(infinity) (M = Tb, x = 14 (1); M = Tb, x = 8 (11); M = Er, x = 14 (2); M = Er, x = 5.5 (4)), a 2D network is formed by the Eu(III) ion (i.e., {[Eu(Htpabn)] x 10 H(2)O}(infinity) (7)), and both supramolecular isomers (1D and 2D) are obtained by the Tb(III) ion. The high flexibility of the polymeric chains results in a dynamic behavior with a solvent-induced reversible structural transition. The Tb(III)- and Eu(III)-containing polymers display high-luminescence quantum yields (38 and 18%, respectively). A sizeable near-IR luminescence emission is observed for the Er(III)- and Nd(III)-containing polymers when lattice water molecules are removed.

An end-to-end workflow for engineering of biological networks from high-level specifications.

PubMed

Beal, Jacob; Weiss, Ron; Densmore, Douglas; Adler, Aaron; Appleton, Evan; Babb, Jonathan; Bhatia, Swapnil; Davidsohn, Noah; Haddock, Traci; Loyall, Joseph; Schantz, Richard; Vasilev, Viktor; Yaman, Fusun

2012-08-17

We present a workflow for the design and production of biological networks from high-level program specifications. The workflow is based on a sequence of intermediate models that incrementally translate high-level specifications into DNA samples that implement them. We identify algorithms for translating between adjacent models and implement them as a set of software tools, organized into a four-stage toolchain: Specification, Compilation, Part Assignment, and Assembly. The specification stage begins with a Boolean logic computation specified in the Proto programming language. The compilation stage uses a library of network motifs and cellular platforms, also specified in Proto, to transform the program into an optimized Abstract Genetic Regulatory Network (AGRN) that implements the programmed behavior. The part assignment stage assigns DNA parts to the AGRN, drawing the parts from a database for the target cellular platform, to create a DNA sequence implementing the AGRN. Finally, the assembly stage computes an optimized assembly plan to create the DNA sequence from available part samples, yielding a protocol for producing a sample of engineered plasmids with robotics assistance. Our workflow is the first to automate the production of biological networks from a high-level program specification. Furthermore, the workflow's modular design allows the same program to be realized on different cellular platforms simply by swapping workflow configurations. We validated our workflow by specifying a small-molecule sensor-reporter program and verifying the resulting plasmids in both HEK 293 mammalian cells and in E. coli bacterial cells.

Nanoparticle–Film Plasmon Ruler Interrogated with Transmission Visible Spectroscopy

PubMed Central

2015-01-01

The widespread use of plasmonic nanorulers (PNRs) in sensing platforms has been plagued by technical challenges associated with the development of methods to fabricate precisely controlled nanostructures with high yield and characterize them with high throughput. We have previously shown that creating PNRs in a nanoparticle–film (NP–film) format enables the fabrication of an extremely large population of uniform PNRs with 100% yield using a self-assembly approach, which facilitates high-throughput PNR characterization using ensemble spectroscopic measurements and eliminates the need for expensive microscopy systems required by many other PNR platforms. We expand upon this prior work herein, showing that the NP–film PNR can be made compatible with aqueous sensing studies by adapting it for use in a transmission localized surface plasmon resonance spectroscopy format, where the coupled NP–film resonance responsible for the PNR signal is directly probed using an extinction measurement from a standard spectrophotometer. We designed slide holders that fit inside standard spectrophotometer cuvettes and position NP–film samples so that the coupled NP–film resonance can be detected in a collinear optical configuration. Once the NP–film PNR samples are cuvette-compatible, it is straightforward to calibrate the PNR in aqueous solution and use it to characterize dynamic, angstrom-scale distance changes resulting from pH-induced swelling of polyelectrolyte (PE) spacer layers as thin as 1 PE layer and also of a self-assembled monolayer of an amine-terminated alkanethiol. This development is an important step toward making PNR sensors more user-friendly and encouraging their widespread use in various sensing schemes. PMID:25541618

Mapping Nanoscale Hotspots with Single-Molecule Emitters Assembled into Plasmonic Nanocavities Using DNA Origami.

PubMed

Chikkaraddy, Rohit; Turek, V A; Kongsuwan, Nuttawut; Benz, Felix; Carnegie, Cloudy; van de Goor, Tim; de Nijs, Bart; Demetriadou, Angela; Hess, Ortwin; Keyser, Ulrich F; Baumberg, Jeremy J

2018-01-10

Fabricating nanocavities in which optically active single quantum emitters are precisely positioned is crucial for building nanophotonic devices. Here we show that self-assembly based on robust DNA-origami constructs can precisely position single molecules laterally within sub-5 nm gaps between plasmonic substrates that support intense optical confinement. By placing single-molecules at the center of a nanocavity, we show modification of the plasmon cavity resonance before and after bleaching the chromophore and obtain enhancements of ≥4 × 10 3 with high quantum yield (≥50%). By varying the lateral position of the molecule in the gap, we directly map the spatial profile of the local density of optical states with a resolution of ±1.5 nm. Our approach introduces a straightforward noninvasive way to measure and quantify confined optical modes on the nanoscale.

Carbene based photochemical molecular assemblies for solar driven hydrogen generation.

PubMed

Peuntinger, Katrin; Pilz, T David; Staehle, Robert; Schaub, Markus; Kaufhold, Simon; Petermann, Lydia; Wunderlin, Markus; Görls, Helmar; Heinemann, Frank W; Li, Jing; Drewello, Thomas; Vos, Johannes G; Guldi, Dirk M; Rau, Sven

2014-09-28

Novel photocatalysts based on ruthenium complexes with NHC (N-heterocyclic carbene)-type bridging ligands have been prepared and structurally and photophysically characterised. The identity of the NHC-unit of the bridging ligand was established unambiguously by means of X-ray structural analysis of a heterodinuclear ruthenium-silver complex. The photophysical data indicate ultrafast intersystem crossing into an emissive and a non-emissive triplet excited state after excitation of the ruthenium centre. Exceptionally high luminescence quantum yields of up to 39% and long lifetimes of up to 2 μs are some of the triplet excited state characteristics. Preliminary studies into the visible light driven photocatalytic hydrogen formation show no induction phase and constant turnover frequencies that are independent on the concentration of the photocatalyst. In conclusion this supports the notion of a stable assembly under photocatalytic conditions.

Self-assembled vertically aligned Au nanorod arrays for surface-enhanced Raman scattering (SERS) detection of Cannabinol.

PubMed

Milliken, Sarah; Fraser, Jeff; Poirier, Shawn; Hulse, John; Tay, Li-Lin

2018-05-05

Self-assembled multi-layered vertically aligned gold nanorod (AuNR) arrays have been fabricated by a simple preparation process that requires a balance between the particle concentration and the ionic strength of the solvent. An experimentally determined critical AuNR concentration of 2.0nM and 50mM NaCl produces well-ordered vertically aligned hexagonally close-packed AuNR arrays. We demonstrate surface treatment via UV Ozone cleaning of such samples to allow introduction of analyte molecules (benzenethiol and cannabinol) for effective surface enhanced Raman scattering detection. This is the first demonstration of the SERS analysis of cannabinol. This approach demonstrates a cost-effective, high-yield and simple fabrication route to SERS sensors with application in the screening for the cannabinoids. Copyright © 2018. Published by Elsevier B.V.

Tuneable light-emitting carbon-dot/polymer flexible films prepared through one-pot synthesis

NASA Astrophysics Data System (ADS)

Bhunia, Susanta Kumar; Nandi, Sukhendu; Shikler, Rafi; Jelinek, Raz

2016-02-01

Development of efficient, inexpensive, and environmentally-friendly light emitters, particularly devices that produce white light, have drawn intense interest due to diverse applications in the lighting industry, photonics, solar energy, and others. We present a simple strategy for the fabrication of flexible transparent films exhibiting tuneable light emission through one-pot synthesis of polymer matrixes with embedded carbon dots assembled in situ. Importantly, different luminescence colours were produced simply by preparing C-dot/polymer films using carbon precursors that yielded C-dots exhibiting distinct fluorescence emission profiles. Furthermore, mixtures of C-dot precursors could be also employed for fabricating films exhibiting different colours. In particular, we successfully produced films emitting white light with attractive properties (i.e. ``warm'' white light with a high colour rendering index) - a highly sought after goal in optical technologies.Development of efficient, inexpensive, and environmentally-friendly light emitters, particularly devices that produce white light, have drawn intense interest due to diverse applications in the lighting industry, photonics, solar energy, and others. We present a simple strategy for the fabrication of flexible transparent films exhibiting tuneable light emission through one-pot synthesis of polymer matrixes with embedded carbon dots assembled in situ. Importantly, different luminescence colours were produced simply by preparing C-dot/polymer films using carbon precursors that yielded C-dots exhibiting distinct fluorescence emission profiles. Furthermore, mixtures of C-dot precursors could be also employed for fabricating films exhibiting different colours. In particular, we successfully produced films emitting white light with attractive properties (i.e. ``warm'' white light with a high colour rendering index) - a highly sought after goal in optical technologies. Electronic supplementary information (ESI) available. See DOI: 10.1039/c5nr08400h

Use of a draft genome of coffee (Coffea arabica) to identify SNPs associated with caffeine content.

PubMed

Tran, Hue T M; Ramaraj, Thiruvarangan; Furtado, Agnelo; Lee, Leonard Slade; Henry, Robert J

2018-03-07

Arabica coffee (Coffea arabica) has a small gene pool limiting genetic improvement. Selection for caffeine content within this gene pool would be assisted by identification of the genes controlling this important trait. Sequencing of DNA bulks from 18 genotypes with extreme high- or low-caffeine content from a population of 232 genotypes was used to identify linked polymorphisms. To obtain a reference genome, a whole genome assembly of arabica coffee (variety K7) was achieved by sequencing using short read (Illumina) and long-read (PacBio) technology. Assembly was performed using a range of assembly tools resulting in 76 409 scaffolds with a scaffold N50 of 54 544 bp and a total scaffold length of 1448 Mb. Validation of the genome assembly using different tools showed high completeness of the genome. More than 99% of transcriptome sequences mapped to the C. arabica draft genome, and 89% of BUSCOs were present. The assembled genome annotated using AUGUSTUS yielded 99 829 gene models. Using the draft arabica genome as reference in mapping and variant calling allowed the detection of 1444 nonsynonymous single nucleotide polymorphisms (SNPs) associated with caffeine content. Based on Kyoto Encyclopaedia of Genes and Genomes pathway-based analysis, 65 caffeine-associated SNPs were discovered, among which 11 SNPs were associated with genes encoding enzymes involved in the conversion of substrates, which participate in the caffeine biosynthesis pathways. This analysis demonstrated the complex genetic control of this key trait in coffee. © 2018 The Authors. Plant Biotechnology Journal published by Society for Experimental Biology and The Association of Applied Biologists and John Wiley & Sons Ltd.

The AMS-02 RICH detector: Performance during ground-based data taking at CERN

NASA Astrophysics Data System (ADS)

Pereira, R.; AMS RICH Collaboration

2011-05-01

The Alpha Magnetic Spectrometer (AMS), whose final version AMS-02 is to be installed on the International Space Station (ISS) in 2011, is a detector designed to measure charged cosmic ray spectra with energies up to the TeV region and with high energy photon detection capability up to a few hundred GeV, using state-of-the art particle identification techniques. Among several detector subsystems, AMS includes a proximity focusing RICH detector enabling precise measurements of particle electric charge (charge identification up to the iron region) and velocity ( Δβ/β˜10-3 for Z=1, Δβ/β˜10-4 for Z=10-20). The optimization of the RICH reconstruction efficiency imposed a dual radiator configuration with 16 NaF tiles ( n=1.33) in the centre and 92 aerogel tiles ( n=1.050) in the outer region, a pixelized detection matrix with 680 Hamamatsu R7600-M16 photomultipliers (each with 4×4 pixels) and a highly reflective conical mirror to increase photon collection. After its assembly at CIEMAT in Madrid, the RICH was taken to CERN in January 2008 and integrated into the full AMS-02 detector. AMS-02 underwent a pre-assembly in 2008 without magnet followed by a second detector assembly with a superconducting magnet in 2009 and the final assembly with a permanent magnet in mid-2010. Cosmic events were acquired in the context of the 2008 pre-assembly and in 2009, and two beam tests from CERN SPS took place in 2010. Results obtained with data from ground-based tests on the RICH performance are presented. A comparison with the aerogel light yield obtained on previous beam tests with a prototype detector is also discussed.

Highly efficient strategy for the heterologous expression and purification of soluble Cowpea chlorotic mottle virus capsid protein and in vitro pH-dependent assembly of virus-like particles.

PubMed

Díaz-Valle, Armando; García-Salcedo, Yardena M; Chávez-Calvillo, Gabriela; Silva-Rosales, Laura; Carrillo-Tripp, Mauricio

2015-12-01

Obtaining pure and soluble viral capsid proteins (CPs) has been a major challenge in the fields of science and technology in recent decades. In many cases, the CPs can self-assemble in the absence of a viral genome, resulting in non-infectious, empty virus-like particles (VLPs) which can be safely handled. The use of VLPs has found great potential in biotechnology and health purposes. In addition, VLPs are a good model system to study protein-protein interactions at the molecular level. In this work, an optimized strategy for the heterologous expression of the Cowpea chlorotic mottle virus (CCMV) CP based in Escherichia coli is described. The method is efficient, inexpensive and it consistently produces higher yields and greater purity levels than those reported so far. Additionally, one of the main advantages of this method is the prevention of the formation of inclusion bodies, thus allowing to directly obtain high amounts of the CP in a soluble and functionally active state with the capacity to readily form VLPs in vitro. The CCMV CP self-assembly pH dependence was also investigated, providing guidelines to easily modulate the process. Copyright © 2015 Elsevier B.V. All rights reserved.

Tunable elastin-like polypeptide hollow sphere as a high payload and controlled delivery gene depot.

PubMed

Dash, Biraja C; Mahor, Sunil; Carroll, Oliver; Mathew, Asha; Wang, Wenxin; Woodhouse, Kimberly A; Pandit, Abhay

2011-06-30

Self-assembly driven processes can be utilized to produce a variety of nanostructures useful for various in vitro and in vivo applications. Characteristics such as size, stability, biocompatibility, high therapeutic loading and controlled delivery of these nanostructures are particularly crucial in relation to in vivo applications. In this study, we report the fabrication of tunable monodispersed elastin-like polypeptide (ELP) hollow spheres of 100, 300, 500 and 1000 nm by exploiting the self-assembly property and net positive charge of ELP. The microbial transglutaminase (mTGase) cross-linking provided robustness and stability to the hollow spheres while maintaining surface functional groups for further modifications. The resulting hollow spheres showed a higher loading efficiency of plasmid DNA (pDNA) by using polyplex (~70 μg pDNA/mg of hollow sphere) than that of self-assembled ELP particles and demonstrated controlled release triggered by protease and elastase. Moreover, polyplex-loaded hollow spheres showed better cell viability than polyplex alone and yielded higher luciferase expression by providing protection against endosomal degradation. Overall, the monodispersed, tunable hollow spheres with a capability of post-functionalization can provide an exciting new opportunity for use in a range of therapeutic and diagnostic applications. Copyright © 2011 Elsevier B.V. All rights reserved.

Self-assembled monolayers of n-alkanethiols suppress hydrogen evolution and increase the efficiency of rechargeable iron battery electrodes.

PubMed

Malkhandi, Souradip; Yang, Bo; Manohar, Aswin K; Prakash, G K Surya; Narayanan, S R

2013-01-09

Iron-based rechargeable batteries, because of their low cost, eco-friendliness, and durability, are extremely attractive for large-scale energy storage. A principal challenge in the deployment of these batteries is their relatively low electrical efficiency. The low efficiency is due to parasitic hydrogen evolution that occurs on the iron electrode during charging and idle stand. In this study, we demonstrate for the first time that linear alkanethiols are very effective in suppressing hydrogen evolution on alkaline iron battery electrodes. The alkanethiols form self-assembled monolayers on the iron electrodes. The degree of suppression of hydrogen evolution by the alkanethiols was found to be greater than 90%, and the effectiveness of the alkanethiol increased with the chain length. Through steady-state potentiostatic polarization studies and impedance measurements on high-purity iron disk electrodes, we show that the self-assembly of alkanethiols suppressed the parasitic reaction by reducing the interfacial area available for the electrochemical reaction. We have modeled the effect of chain length of the alkanethiol on the surface coverage, charge-transfer resistance, and double-layer capacitance of the interface using a simple model that also yields a value for the interchain interaction energy. We have verified the improvement in charging efficiency resulting from the use of the alkanethiols in practical rechargeable iron battery electrodes. The results of battery tests indicate that alkanethiols yield among the highest faradaic efficiencies reported for the rechargeable iron electrodes, enabling the prospect of a large-scale energy storage solution based on low-cost iron-based rechargeable batteries.

Concentration-dependent photophysical switching in mixed self-assembled monolayers of pentacene and perylenediimide on gold nanoclusters.

PubMed

Kato, Daiki; Sakai, Hayato; Araki, Yasuyuki; Wada, Takehiko; Tkachenko, Nikolai V; Hasobe, Taku

2018-03-28

Photophysical control and switching on organic-inorganic hybrid interfaces are of great interest in diverse fundamental and applicative research areas. 6,13-Bis(triisopropylsilylethynyl)pentacene (TP) is well-known to exhibit efficient singlet fission (SF) for generation of high-yield triplet excited states in aggregated forms, whereas perylenediimide (PDI) ensembles show the characteristic excimer formation. Additionally, a combination of pentacene (electron donor: D) and PDI (electron acceptor: A) is expected to undergo an efficient photoinduced electron transfer (PET), and absorption of two chromophores combined covers the entire visible region. Therefore, the concentration-dependent mixed self-assembled monolayers (SAMs) composed of two chromophores enable us to control and switch the photophysical processes on a surface. In this work, a series of mixed SAMs composed of TP and PDI units on gold nanoclusters (GNCs) were newly synthesized by changing the relative molecular concentration ratios. Structural control of mixed SAMs on a gold surface based on the concentration ratios was successfully achieved. Time-resolved femtosecond and nanosecond transient absorption measurements clearly demonstrate photophysical control and switching of the above competitive reactions such as SF, electron transfer (ET) and excimer formation. The maximum quantum yields of triplet states (ΦT = ∼170%) and electron transfer (ΦET = ∼95%) were quantitatively evaluated by changing the concentration ratios. The rate constants of SF and excimer processes are largely dependent on the concentration ratios, whereas the rate constants of ET processes approximately remain constant. These findings are also discussed based on the statistical framework of the assembly of chromophores on the gold surface.

Integrating genome assemblies with MAIA

PubMed Central

Nijkamp, Jurgen; Winterbach, Wynand; van den Broek, Marcel; Daran, Jean-Marc; Reinders, Marcel; de Ridder, Dick

2010-01-01

Motivation: De novo assembly of a eukaryotic genome with next-generation sequencing data is still a challenging task. Over the past few years several assemblers have been developed, often suitable for one specific type of sequencing data. The number of known genomes is expanding rapidly, therefore it becomes possible to use multiple reference genomes for assembly projects. We introduce an assembly integrator that makes use of all available data, i.e. multiple de novo assemblies and mappings against multiple related genomes, by optimizing a weighted combination of criteria. Results: The developed algorithm was applied on the de novo sequencing of the Saccharomyces cerevisiae CEN.PK 113-7D strain. Using Solexa and 454 read data, two de novo and three comparative assemblies were constructed and subsequently integrated, yielding 29 contigs, covering more than 12 Mbp; a drastic improvement compared with the single assemblies. Availability: MAIA is available as a Matlab package and can be downloaded from http://bioinformatics.tudelft.nl Contact: j.f.nijkamp@tudelft.nl PMID:20823304

Programming Enzyme-Initiated Autonomous DNAzyme Nanodevices in Living Cells.

PubMed

Chen, Feng; Bai, Min; Cao, Ke; Zhao, Yue; Cao, Xiaowen; Wei, Jing; Wu, Na; Li, Jiang; Wang, Lihua; Fan, Chunhai; Zhao, Yongxi

2017-12-26

Molecular nanodevices are computational assemblers that switch defined states upon external stimulation. However, interfacing artificial nanodevices with natural molecular machineries in living cells remains a great challenge. Here, we delineate a generic method for programming assembly of enzyme-initiated DNAzyme nanodevices (DzNanos). Two programs including split assembly of two partzymes and toehold exchange displacement assembly of one intact DNAzyme initiated by telomerase are computed. The intact one obtains higher assembly yield and catalytic performance ascribed to proper conformation folding and active misplaced assembly. By employing MnO 2 nanosheets as both DNA carriers and source of Mn 2+ as DNAzyme cofactor, we find that this DzNano is well assembled via a series of conformational states in living cells and operates autonomously with sustained cleavage activity. Other enzymes can also induce corresponding DzNano assembly with defined programming modules. These DzNanos not only can monitor enzyme catalysis in situ but also will enable the implementation of cellular stages, behaviors, and pathways for basic science, diagnostic, and therapeutic applications as genetic circuits.

Surface-structured bacterial cellulose with guided assembly-based biolithography (GAB).

PubMed

Bottan, Simone; Robotti, Francesco; Jayathissa, Prageeth; Hegglin, Alicia; Bahamonde, Nicolas; Heredia-Guerrero, José A; Bayer, Ilker S; Scarpellini, Alice; Merker, Hannes; Lindenblatt, Nicole; Poulikakos, Dimos; Ferrari, Aldo

2015-01-27

A powerful replica molding methodology to transfer on-demand functional topographies to the surface of bacterial cellulose nanofiber textures is presented. With this method, termed guided assembly-based biolithography (GAB), a surface-structured polydimethylsiloxane (PDMS) mold is introduced at the gas-liquid interface of an Acetobacter xylinum culture. Upon bacterial fermentation, the generated bacterial cellulose nanofibers are assembled in a three-dimensional network reproducing the geometric shape imposed by the mold. Additionally, GAB yields directional alignment of individual nanofibers and memory of the transferred geometrical features upon dehydration and rehydration of the substrates. Scanning electron and atomic force microscopy are used to establish the good fidelity of this facile and affordable method. Interaction of surface-structured bacterial cellulose substrates with human fibroblasts and keratinocytes illustrates the efficient control of cellular activities which are fundamental in skin wound healing and tissue regeneration. The deployment of surface-structured bacterial cellulose substrates in model animals as skin wound dressing or body implant further proves the high durability and low inflammatory response to the material over a period of 21 days, demonstrating beneficial effects of surface structure on skin regeneration.

On the predictability of the orientation of protein domains joined by a spanning alpha-helical linker.

PubMed

Lai, Yen-Ting; Jiang, Lin; Chen, Wuyang; Yeates, Todd O

2015-11-01

Connecting proteins together in prescribed geometric arrangements is an important element in new areas of biomolecular design. In this study, we characterize the degree of three-dimensional orientational control that can be achieved when two protein domains that have alpha-helical termini are joined using an alpha-helical linker. A fusion between naturally oligomeric protein domains was designed in this fashion with the intent of creating a self-assembling 12-subunit tetrahedral protein cage. While the designed fusion protein failed to assemble into a tetrahedral cage in high yield, a series of crystal structures showed that the two fused components were indeed bridged by an intact alpha helix, although the fusion protein was distorted from the intended ideal configuration by bending of the helix, ranging from 7 to 35°. That range of deviation in orientation creates challenges for designing large, perfectly symmetric protein assemblies, although it should offer useful outcomes for other less geometrically demanding applications in synthetic biology. © The Author 2015. Published by Oxford University Press. All rights reserved. For Permissions, please e-mail: journals.permissions@oup.com.

Patterning nanofibrils through the templated growth of multiple modified amyloid peptides

PubMed Central

Sakai, Hiroki; Watanabe, Ken; Kudoh, Fuki; Kamada, Rui; Chuman, Yoshiro; Sakaguchi, Kazuyasu

2016-01-01

There has been considerable interest in the patterning of functionalized nanowires because of the potential applications of these materials to the construction of nanodevices. A variety of biomolecular building blocks containing amyloid peptides have been used to functionalize nanowires. However, the patterning of self-assembled nanowires can be challenging because of the difficulties associated with controlling the self-assembly of these functionalized building blocks. Herein, we present a versatile approach for the patterning of nanowires based on the combination of templated fibril growth with a versatile functionalization method using our structure-controllable amyloid peptides (SCAPs). Using this approach, we have succeeded in the formation of multi-type nanowires with tandem domain structures in high yields. Given that the mixing-SCAP method can lead to the formation of tandem fibrils, it is noteworthy that our method allowed us to control the initiation of fibril formation from the gold nanoparticles, which were attached to a short fibril as initiation points. This approach could be used to prepare a wide variety of fibril patterns, and therefore holds great potential for the development of novel self-assembled nanodevices. PMID:27559011

Fabrication of Polyhedral Particles from Spherical Colloids and Their Self-Assembly into Rotator Phases**

PubMed Central

Vutukuri, Hanumantha Rao; Imhof, Arnout; van Blaaderen, Alfons

2014-01-01

Particle shape is a critical parameter that plays an important role in self-assembly, for example, in designing targeted complex structures with desired properties. Over the last decades, an unprecedented range of monodisperse nanoparticle systems with control over the shape of the particles have become available. In contrast, the choice of micrometer-sized colloidal building blocks of particles with flat facets, that is, particles with polygonal shapes, is significantly more limited. This can be attributed to the fact that in contrast to nanoparticles, the larger colloids are significantly harder to synthesize as single crystals. It is now shown that a very simple building block, such as a micrometer-sized polymeric spherical colloidal particle, is already enough to fabricate particles with regularly placed flat facets, including completely polygonal shapes with sharp edges. As an illustration that the yields are high enough for further self-assembly studies, the formation of three-dimensional rotator phases of fluorescently labelled, micrometer-sized, and charged rhombic dodecahedron particles was demonstrated. This method for fabricating polyhedral particles opens a new avenue for designing new materials. PMID:25366869

Scalable and cleavable polysaccharide nanocarriers for the delivery of chemotherapy drugs.

PubMed

Wang, Hao; Dai, Tingting; Li, Shengli; Zhou, Shuyan; Yuan, Xiaojing; You, Jiayi; Wang, Chenglong; Mukwaya, Vincent; Zhou, Guangdong; Liu, Guojun; Wei, Xiaohui; Dou, Hongjing

2018-05-01

While polysaccharide-based nanocarriers have been recognized for their crucial roles in tumor theranostics, the industrial-scale production of nanotherapeutics still remains a significant challenge. Most current approaches adopt a postpolymerization self-assembly strategy that follows a separate synthetic step and thus suffers from subgram scale yields and a limited range of application. In this study, we demonstrate the kilogram-scale formation of polysaccharide-polyacrylate nanocarriers at concentrations of up to 5 wt% through a one-pot approach - starting from various acrylate monomers and polysaccharides - that combines aspects of hydrophobicity-induced self-assembly with the free radical graft copolymerization of acrylate monomers from polysaccharide backbones into a single process that is thus denoted as a graft copolymerization induced self-assembly. We also demonstrate that this novel approach is applicable to a broad range of polysaccharides and acrylates. Notably, by choosing a crosslinker that bears a disulfide group and two vinyl capping groups to structurally lock the nanocarriers, the products are rendered cleavable in the reducing environments encountered at tumor sites and thus provide ideal candidates for the construction of anticancer nanotherapeutic systems. In vitro and in vivo studies demonstrated that the use of this nanocarrier for the delivery of doxorubicin hydrochloride (DOX) significantly decreased the side effects of DOX and improved the bio-safety of the chemotherapy accordingly. While polysaccharide-based nanocarriers have been recognized for their crucial roles in tumor theranostics, the industrial-scale production of these nanotherapeutics still remains a significant challenge. Most current approaches adopt a post-polymerization self-assembly strategy which that follows a separate synthetic step, and thus suffers from sub-gram scale yields and a limited range of application. In this study, the hydrophobic effect was combined with free radical polymerization to facilitate the graft copolymerization-induced self-assembly (GISA) of acrylate monomers with various hydrophobicities to construct cleavable polysaccharide-polyacrylate nanocarriers at a high efficiency with excellent potential for industrial-scale production. We envision that these nanocarriers will contribute to the development of tumor nanotheranostics that combine the biological functionalities of polysaccharides with the unmatched application-specific flexibility of nanocarriers. Copyright © 2018 Acta Materialia Inc. Published by Elsevier Ltd. All rights reserved.

De novo transcriptome of Ischnura elegans provides insights into sensory biology, colour and vision genes.

PubMed

Chauhan, Pallavi; Hansson, Bengt; Kraaijeveld, Ken; de Knijff, Peter; Svensson, Erik I; Wellenreuther, Maren

2014-09-22

There is growing interest in odonates (damselflies and dragonflies) as model organisms in ecology and evolutionary biology but the development of genomic resources has been slow. So far only one draft genome (Ladona fulva) and one transcriptome assembly (Enallagma hageni) have been published. Odonates have some of the most advanced visual systems among insects and several species are colour polymorphic, and genomic and transcriptomic data would allow studying the genomic architecture of these interesting traits and make detailed comparative studies between related species possible. Here, we present a comprehensive de novo transcriptome assembly for the blue-tailed damselfly Ischnura elegans (Odonata: Coenagrionidae) built from short-read RNA-seq data. The transcriptome analysis in this paper provides a first step towards identifying genes and pathways underlying the visual and colour systems in this insect group. Illumina RNA sequencing performed on tissues from the head, thorax and abdomen generated 428,744,100 paired-ends reads amounting to 110 Gb of sequence data, which was assembled de novo with Trinity. A transcriptome was produced after filtering and quality checking yielding a final set of 60,232 high quality transcripts for analysis. CEGMA software identified 247 out of 248 ultra-conserved core proteins as 'complete' in the transcriptome assembly, yielding a completeness of 99.6%. BLASTX and InterProScan annotated 55% of the assembled transcripts and showed that the three tissue types differed both qualitatively and quantitatively in I. elegans. Differential expression identified 8,625 transcripts to be differentially expressed in head, thorax and abdomen. Targeted analyses of vision and colour functional pathways identified the presence of four different opsin types and three pigmentation pathways. We also identified transcripts involved in temperature sensitivity, thermoregulation and olfaction. All these traits and their associated transcripts are of considerable ecological and evolutionary interest for this and other insect orders. Our work presents a comprehensive transcriptome resource for the ancient insect order Odonata and provides insight into their biology and physiology. The transcriptomic resource can provide a foundation for future investigations into this diverse group, including the evolution of colour, vision, olfaction and thermal adaptation.

Layer-by-layer self-assembled multilayer films composed of graphene/polyaniline bilayers: high-energy electrode materials for supercapacitors.

PubMed

Sarker, Ashis K; Hong, Jong-Dal

2012-08-28

Multilayer assemblies of uniform ultrathin film electrodes with good electrical conductivity and very large surface areas were prepared for use as electrochemical capacitors. A layer-by-layer self-assembly approach was employed in an effort to improve the processability of highly conducting polyaniline (PANi) and chemically modified graphene. The electrochemical properties of the multilayer film (MF-) electrodes, including the sheet resistance, volumetric capacitance, and charge/discharge ratio, were determined by the morphological modification and the method used to reduce the graphene oxide (GO) to reduced graphene oxide (RGO) in the multilayer films. The PANi and GO concentrations could be modulated to control the morphology of the GO monolayer film in the multilayer assemblies. Optical ellipsometry was used to determine the thickness of the GO film in a single layer (1.32 nm), which agreed well with the literature value (~1.3 nm). Hydroiodic acid (HI), hydrazine, or pyrolysis were tested for the reduction of GO to RGO. HI was found to be the most efficient technique for reducing the GO to RGO in the multilayer assemblies while minimizing damage to the virgin state of the acid-doped PANi. Ultimately, the MF-electrode, which could be optimized by fine-tuning the nanostructure and selecting a suitable reduction method, exhibited an excellent volumetric capacitance, good cycling stability, and a rapid charge/discharge rate, which are required for supercapacitors. A MF-electrode composed of 15 PANi/RGO bilayers yielded a volumetric capacitance of 584 F/cm(3) at a current density of 3.0 A/cm(3). Although this value decreased exponentially as the current density increased, approaching a value of 170 F/cm(3) at 100 A/cm(3), this volumetric capacitance is one of the best yet reported for the other carbon-based materials. The intriguing features of the MF-electrodes composed of PANi/RGO multilayer films offer a new microdimensional design for high energy storage devices for use in small portable electronic devices.

Photonics and plasmonics go viral: self-assembly of hierarchical metamaterials

DOE PAGES

Wen, Amy M.; Podgornik, Rudolf; Strangi, Giuseppe; ...

2015-03-05

Sizing and shaping of mesoscale architectures with nanoscale features is a key opportunity to produce the next generation of higher-performing products and at the same time unveil completely new phenomena. This review article discusses recent advances in the design of novel photonic and plasmonic structures using a biology-inspired design. The proteinaceous capsids from viruses have long been discovered as platform technologies enabling unique applications in nanotechnology, materials, bioengineering, and medicine. In the context of materials applications, the highly organized structures formed by viral capsid proteins provide a 3D scaffold for the precise placement of plasmon and gain materials. Based onmore » their highly symmetrical structures, virus-based nanoparticles have a high propensity to self-assemble into higher-order crystalline structures, yielding hierarchical hybrid materials. Recent advances in the field have led to the development of virus-based light harvesting systems, plasmonic structures for application in high-performance metamaterials, binary nanoparticle lattices, and liquid crystalline arrays for sensing or display technologies. In conclusion, there is still much that could be explored in this area, and we foresee that this is only the beginning of great technological advances in virus-based materials for plasmonics and photonics applications.« less

Genomics of high molecular weight plasmids isolated from an on-farm biopurification system.

PubMed

Martini, María C; Wibberg, Daniel; Lozano, Mauricio; Torres Tejerizo, Gonzalo; Albicoro, Francisco J; Jaenicke, Sebastian; van Elsas, Jan Dirk; Petroni, Alejandro; Garcillán-Barcia, M Pilar; de la Cruz, Fernando; Schlüter, Andreas; Pühler, Alfred; Pistorio, Mariano; Lagares, Antonio; Del Papa, María F

2016-06-20

The use of biopurification systems (BPS) constitutes an efficient strategy to eliminate pesticides from polluted wastewaters from farm activities. BPS environments contain a high microbial density and diversity facilitating the exchange of information among bacteria, mediated by mobile genetic elements (MGEs), which play a key role in bacterial adaptation and evolution in such environments. Here we sequenced and characterized high-molecular-weight plasmids from a bacterial collection of an on-farm BPS. The high-throughput-sequencing of the plasmid pool yielded a total of several Mb sequence information. Assembly of the sequence data resulted in six complete replicons. Using in silico analyses we identified plasmid replication genes whose encoding proteins represent 13 different Pfam families, as well as proteins involved in plasmid conjugation, indicating a large diversity of plasmid replicons and suggesting the occurrence of horizontal gene transfer (HGT) events within the habitat analyzed. In addition, genes conferring resistance to 10 classes of antimicrobial compounds and those encoding enzymes potentially involved in pesticide and aromatic hydrocarbon degradation were found. Global analysis of the plasmid pool suggest that the analyzed BPS represents a key environment for further studies addressing the dissemination of MGEs carrying catabolic genes and pathway assembly regarding degradation capabilities.

Heteroleptic Copper(I)-Based Complexes for Photocatalysis: Combinatorial Assembly, Discovery, and Optimization.

PubMed

Minozzi, Clémentine; Caron, Antoine; Grenier-Petel, Jean-Christophe; Santandrea, Jeffrey; Collins, Shawn K

2018-05-04

A library of 50 copper-based complexes derived from bisphosphines and diamines was prepared and evaluated in three mechanistically distinct photocatalytic reactions. In all cases, a copper-based catalyst was identified to afford high yields, where new heteroleptic complexes derived from the bisphosphine BINAP displayed high efficiency across all reaction types. Importantly, the evaluation of the library of copper complexes revealed that even when photophysical data is available, it is not always possible to predict which catalyst structure will be efficient or inefficient in a given process, emphasizing the advantages for catalyst structures with high modularity and structural variability. © 2018 Wiley-VCH Verlag GmbH & Co. KGaA, Weinheim.

Diamond X-ray Photodiode for White and Monochromatic SR beams

PubMed Central

Keister, Jeffrey W.; Smedley, John; Muller, Erik M.; Bohon, Jen; Héroux, Annie

2011-01-01

High purity, single crystal CVD diamond plates are screened for quality and instrumented into a sensor assembly for quantitative characterization of flux and position sensitivity. Initial investigations have yielded encouraging results and have led to further development. Several limiting complications are observed and discussed, as well as mitigations thereof. For example, diamond quality requirements for x-ray diodes include low nitrogen impurity and crystallographic defectivity. Thin electrode windows and electronic readout performance are ultimately also critical to device performance. Promising features observed so far from prototype devices include calculable responsivity, flux linearity, position sensitivity and timing performance. Recent results from testing in high flux and high speed applications are described. PMID:21822344

Gate- and Light-Tunable pn Heterojunction Microwire Arrays Fabricated via Evaporative Assembly.

PubMed

Park, Jae Hoon; Kim, Jong Su; Choi, Young Jin; Lee, Wi Hyoung; Lee, Dong Yun; Cho, Jeong Ho

2017-02-01

One-dimensional (1D) nano/microwires have attracted considerable attention as versatile building blocks for use in diverse electronic, optoelectronic, and magnetic device applications. The large-area assembly of nano/microwires at desired positions presents a significant challenge for developing high-density electronic devices. Here, we demonstrated the fabrication of cross-stacked pn heterojunction diode arrays by integrating well-aligned inorganic and organic microwires fabricated via evaporative assembly. We utilized solution-processed n-type inorganic indium-gallium-zinc-oxide (IGZO) microwires and p-type organic 6,13-bis(triisopropylsilylethynyl)pentacene (TIPS-PEN) microwires. The formation of organic TIPS-PEN semiconductor microwire and their electrical properties were optimized by controlling both the amounts of added insulating polymer and the widths of the microwires. The resulting cross-stacked IGZO/TIPS-PEN microwire pn heterojunction devices exhibited rectifying behavior with a forward-to-reverse bias current ratio exceeding 10 2 . The ultrathin nature of the underlying n-type IGZO microwires yielded gate tunability in the charge transport behaviors, ranging from insulating to rectifying. The rectifying behaviors of the heterojunction devices could be modulated by controlling the optical power of the irradiated light. The fabrication of semiconducting microwires through evaporative assembly provides a facile and reliable approach to patterning or positioning 1D microwires for the fabrication of future flexible large-area electronics.

Self-assembly of a supramolecular hexagram and a supramolecular pentagram

NASA Astrophysics Data System (ADS)

Jiang, Zhilong; Li, Yiming; Wang, Ming; Song, Bo; Wang, Kun; Sun, Mingyu; Liu, Die; Li, Xiaohong; Yuan, Jie; Chen, Mingzhao; Guo, Yuan; Yang, Xiaoyu; Zhang, Tong; Moorefield, Charles N.; Newkome, George R.; Xu, Bingqian; Li, Xiaopeng; Wang, Pingshan

2017-05-01

Five- and six-pointed star structures occur frequently in nature as flowers, snow-flakes, leaves and so on. These star-shaped patterns are also frequently used in both functional and artistic man-made architectures. Here following a stepwise synthesis and self-assembly approach, pentagonal and hexagonal metallosupramolecules possessing star-shaped motifs were prepared based on the careful design of metallo-organic ligands (MOLs). In the MOL design and preparation, robust ruthenium-terpyridyl complexes were employed to construct brominated metallo-organic intermediates, followed by a Suzuki coupling reaction to achieve the required ensemble. Ligand LA (VRu2+X, V=bisterpyridine, X=tetraterpyridine, Ru=Ruthenium) was initially used for the self-assembly of an anticipated hexagram upon reaction with Cd2+ or Fe2+ however, unexpected pentagonal structures were formed, that is, [Cd5LA5]30+ and [Fe5LA5]30+. In our redesign, LB [V(Ru2+X)2] was synthesized and treated with 60° V-shaped bisterpyridine (V) and Cd2+ to create hexagonal hexagram [Cd12V3LB3]36+ along with traces of the triangle [Cd3V3]6+. Finally, a pure supramolecular hexagram [Fe12V3LB3]36+ was successfully isolated in a high yield using Fe2+ with a higher assembly temperature.

Self-assembly of a supramolecular hexagram and a supramolecular pentagram

PubMed Central

Jiang, Zhilong; Li, Yiming; Wang, Ming; Song, Bo; Wang, Kun; Sun, Mingyu; Liu, Die; Li, Xiaohong; Yuan, Jie; Chen, Mingzhao; Guo, Yuan; Yang, Xiaoyu; Zhang, Tong; Moorefield, Charles N.; Newkome, George R.; Xu, Bingqian; Li, Xiaopeng; Wang, Pingshan

2017-01-01

Five- and six-pointed star structures occur frequently in nature as flowers, snow-flakes, leaves and so on. These star-shaped patterns are also frequently used in both functional and artistic man-made architectures. Here following a stepwise synthesis and self-assembly approach, pentagonal and hexagonal metallosupramolecules possessing star-shaped motifs were prepared based on the careful design of metallo-organic ligands (MOLs). In the MOL design and preparation, robust ruthenium–terpyridyl complexes were employed to construct brominated metallo-organic intermediates, followed by a Suzuki coupling reaction to achieve the required ensemble. Ligand LA (VRu2+X, V=bisterpyridine, X=tetraterpyridine, Ru=Ruthenium) was initially used for the self-assembly of an anticipated hexagram upon reaction with Cd2+ or Fe2+; however, unexpected pentagonal structures were formed, that is, [Cd5LA5]30+ and [Fe5LA5]30+. In our redesign, LB [V(Ru2+X)2] was synthesized and treated with 60° V-shaped bisterpyridine (V) and Cd2+ to create hexagonal hexagram [Cd12V3LB3]36+ along with traces of the triangle [Cd3V3]6+. Finally, a pure supramolecular hexagram [Fe12V3LB3]36+ was successfully isolated in a high yield using Fe2+ with a higher assembly temperature. PMID:28524876

Castable Amorphous Metal Mirrors and Mirror Assemblies

NASA Technical Reports Server (NTRS)

Hofmann, Douglas C.; Davis, Gregory L.; Agnes, Gregory S.; Shapiro, Andrew A.

2013-01-01

A revolutionary way to produce a mirror and mirror assembly is to cast the entire part at once from a metal alloy that combines all of the desired features into the final part: optical smoothness, curvature, flexures, tabs, isogrids, low CTE, and toughness. In this work, it has been demonstrated that castable mirrors are possible using bulk metallic glasses (BMGs, also called amorphous metals) and BMG matrix composites (BMGMCs). These novel alloys have all of the desired mechanical and thermal properties to fabricate an entire mirror assembly without machining, bonding, brazing, welding, or epoxy. BMGs are multi-component metal alloys that have been cooled in such a manner as to avoid crystallization leading to an amorphous (non-crystalline) microstructure. This lack of crystal structure and the fact that these alloys are glasses, leads to a wide assortment of mechanical and thermal properties that are unlike those observed in crystalline metals. Among these are high yield strength, carbide-like hardness, low melting temperatures (making them castable like aluminum), a thermoplastic processing region (for improving smoothness), low stiffness, high strength-to-weight ratios, relatively low CTE, density similar to titanium alloys, high elasticity and ultra-smooth cast parts (as low as 0.2-nm surface roughness has been demonstrated in cast BMGs). BMGMCs are composite alloys that consist of a BMG matrix with crystalline dendrites embedded throughout. BMGMCs are used to overcome the typically brittle failure observed in monolithic BMGs by adding a soft phase that arrests the formation of cracks in the BMG matrix. In some cases, BMGMCs offer superior castability, toughness, and fatigue resistance, if not as good a surface finish as BMGs. This work has demonstrated that BMGs and BMGMCs can be cast into prototype mirrors and mirror assemblies without difficulty.

H-Bonding Assisted Self-Assembly of Anionic and Neutral Ligand on Metal: A Comprehensive Strategy To Mimic Ditopic Ligands in Olefin Polymerization.

PubMed

Mote, Nilesh R; Patel, Ketan; Shinde, Dinesh R; Gaikwad, Shahaji R; Koshti, Vijay S; Gonnade, Rajesh G; Chikkali, Samir H

2017-10-16

Self-assembly of two neutral ligands on a metal to mimic bidentate ligand coordination has been frequently encountered in the recent past, but self-assembly of an anionic ligand on a metal template alongside a neutral ligand remains an elusive target. Such a self-assembly is hampered by additional complexity, wherein a highly negatively charged anion can form intermolecular hydrogen bonding with the supramolecular motif, leaving no scope for self-assembly with neutral ligand. Presented here is the self-association of anionic ligand 3-ureidobenzoic acid (2a) and neutral ligand 1-(3-(diphenylphosphanyl)phenyl)urea (1a) on a metal template to yield metal complex [{COOC 6 H 4 NH(CO)NH 2 }{Ph 2 PC 6 H 4 NH(CO)NH 2 }PdMeDMSO] (4a). The identity of 4a was established by NMR and mass spectroscopy. Along the same lines, 3-(3-phenylureido)benzoic acid (2b) and 1-(3-(diphenylphosphanyl)phenyl)-3-phenylurea (1b) self-assemble on a metal template to produce palladium complex [{COOC 6 H 4 NH(CO)NHPh}{Ph 2 PC 6 H 4 NH(CO)NHPh}PdMePy] (5c). The existence of 5c was confirmed by Job plot, 1-2D NMR spectroscopy, deuterium labeling, IR spectroscopy, UV-vis spectroscopy, model complex synthesis, and DFT calculations. These solution and gas phase investigations authenticated the presence of intramolecular hydrogen bonding between hydrogen's of 1b and carbonyl oxygen of 2b. The generality of the supramolecular approach has been validated by preparing six complexes from four monodentate ligands, and their synthetic utility was demonstrated in ethylene polymerization. Complex 4a was found to be the most active, leading to the production of highly branched polyethylene with a molecular weight of 55700 g/mol and melting temperature of 112 °C.

Transcriptome Assembly, Gene Annotation and Tissue Gene Expression Atlas of the Rainbow Trout

PubMed Central

Salem, Mohamed; Paneru, Bam; Al-Tobasei, Rafet; Abdouni, Fatima; Thorgaard, Gary H.; Rexroad, Caird E.; Yao, Jianbo

2015-01-01

Efforts to obtain a comprehensive genome sequence for rainbow trout are ongoing and will be complemented by transcriptome information that will enhance genome assembly and annotation. Previously, transcriptome reference sequences were reported using data from different sources. Although the previous work added a great wealth of sequences, a complete and well-annotated transcriptome is still needed. In addition, gene expression in different tissues was not completely addressed in the previous studies. In this study, non-normalized cDNA libraries were sequenced from 13 different tissues of a single doubled haploid rainbow trout from the same source used for the rainbow trout genome sequence. A total of ~1.167 billion paired-end reads were de novo assembled using the Trinity RNA-Seq assembler yielding 474,524 contigs > 500 base-pairs. Of them, 287,593 had homologies to the NCBI non-redundant protein database. The longest contig of each cluster was selected as a reference, yielding 44,990 representative contigs. A total of 4,146 contigs (9.2%), including 710 full-length sequences, did not match any mRNA sequences in the current rainbow trout genome reference. Mapping reads to the reference genome identified an additional 11,843 transcripts not annotated in the genome. A digital gene expression atlas revealed 7,678 housekeeping and 4,021 tissue-specific genes. Expression of about 16,000–32,000 genes (35–71% of the identified genes) accounted for basic and specialized functions of each tissue. White muscle and stomach had the least complex transcriptomes, with high percentages of their total mRNA contributed by a small number of genes. Brain, testis and intestine, in contrast, had complex transcriptomes, with a large numbers of genes involved in their expression patterns. This study provides comprehensive de novo transcriptome information that is suitable for functional and comparative genomics studies in rainbow trout, including annotation of the genome. PMID:25793877

Cs4PbBr6/CsPbBr3 Perovskite Composites with Near-Unity Luminescence Quantum Yield: Large-Scale Synthesis, Luminescence and Formation Mechanism, and White Light-Emitting Diode Application.

PubMed

Chen, Ya-Meng; Zhou, Yang; Zhao, Qing; Zhang, Jun-Ying; Ma, Ju-Ping; Xuan, Tong-Tong; Guo, Shao-Qiang; Yong, Zi-Jun; Wang, Jing; Kuroiwa, Yoshihiro; Moriyoshi, Chikako; Sun, Hong-Tao

2018-05-09

All-inorganic perovskites have emerged as a new class of phosphor materials owing to their outstanding optical properties. Zero-dimensional inorganic perovskites, in particular the Cs 4 PbBr 6 -related systems, are inspiring intensive research owing to the high photoluminescence quantum yield (PLQY) and good stability. However, synthesizing such perovskites with high PLQYs through an environment-friendly, cost-effective, scalable, and high-yield approach remains challenging, and their luminescence mechanisms has been elusive. Here, we report a simple, scalable, room-temperature self-assembly strategy for the synthesis of Cs 4 PbBr 6 /CsPbBr 3 perovskite composites with near-unity PLQY (95%), high product yield (71%), and good stability using low-cost, low-toxicity chemicals as precursors. A broad range of experimental and theoretical characterizations suggest that the high-efficiency PL originates from CsPbBr 3 nanocrystals well passivated by the zero-dimensional Cs 4 PbBr 6 matrix that forms based on a dissolution-crystallization process. These findings underscore the importance in accurately identifying the phase purity of zero-dimensional perovskites by synchrotron X-ray technique to gain deep insights into the structure-property relationship. Additionally, we demonstrate that green-emitting Cs 4 PbBr 6 /CsPbBr 3 , combined with red-emitting K 2 SiF 6 :Mn 4+ , can be used for the construction of WLEDs. Our work may pave the way for the use of such composite perovskites as highly luminescent emitters in various applications such as lighting, displays, and other optoelectronic and photonic devices.

Influence of ionic strength and surfactant concentration on electrostatic surfacial assembly of cetyltrimethylammonium bromide-capped gold nanorods on fully immersed glass.

PubMed

Ferhan, Abdul Rahim; Guo, Longhua; Kim, Dong-Hwan

2010-07-20

The effect of ionic strength as well as surfactant concentration on the surface assembly of cetyltrimethylammonium bromide (CTAB)-capped gold nanorods (GNRs) has been studied. Glass substrates were modified to yield a net negative charge through electrostatic coating of polystyrenesulfonate (PSS) over a self-assembled monolayer (SAM) of positively charged aminopropyltriethoxysilane (APTS). The substrates were then fully immersed in GNR solutions at different CTAB concentrations and ionic strengths. Under slightly excess CTAB concentrations, it was observed that the density of GNRs immobilized on a substrate was predictably tunable through the adjustment of NaCl concentration over a wide range. Motivated by the experimental observation, we hypothesize that electrostatic shielding of charges around the GNRs affects the density of GNR immobilization. This model ultimately explains that at moderate to high CTAB concentrations a second electrostatic shielding effect contributed by excess CTAB molecules occurs, resulting in a parabolic trend of nanorod surface density when ionic strength is continually increased. In contrast, at a low CTAB concentration, the effect of ionic strength becomes much less significant due to insufficient CTAB molecules to provide for the second electrostatic shielding effect. The tunability of electrostatic-based surface assembly of GNRs enables the attainment of a dense surface assembly of nanorods without significant removal of CTAB or any other substituted stabilizing agent, both of which could compromise the stability and morphology of GNRs in solution. An additional study performed to investigate the robustness of such electrostatic-based surface assembly also proved its reliability to be used as biosensing platforms.

Key aromatic/hydrophobic amino acids controlling a cross-amyloid peptide interaction versus amyloid self-assembly.

PubMed

Bakou, Maria; Hille, Kathleen; Kracklauer, Michael; Spanopoulou, Anna; Frost, Christina V; Malideli, Eleni; Yan, Li-Mei; Caporale, Andrea; Zacharias, Martin; Kapurniotu, Aphrodite

2017-09-01

The interaction of the intrinsically disordered polypeptide islet amyloid polypeptide (IAPP), which is associated with type 2 diabetes (T2D), with the Alzheimer's disease amyloid-β (Aβ) peptide modulates their self-assembly into amyloid fibrils and may link the pathogeneses of these two cell-degenerative diseases. However, the molecular determinants of this interaction remain elusive. Using a systematic alanine scan approach, fluorescence spectroscopy, and other biophysical methods, including heterocomplex pulldown assays, far-UV CD spectroscopy, the thioflavin T binding assay, transmission EM, and molecular dynamics simulations, here we identified single aromatic/hydrophobic residues within the amyloid core IAPP region as hot spots or key residues of its cross-interaction with Aβ40(42) peptide. Importantly, we also find that none of these residues in isolation plays a key role in IAPP self-assembly, whereas simultaneous substitution of four aromatic/hydrophobic residues with Ala dramatically impairs both IAPP self-assembly and hetero-assembly with Aβ40(42). Furthermore, our experiments yielded several novel IAPP analogs, whose sequences are highly similar to that of IAPP but have distinct amyloid self- or cross-interaction potentials. The identified similarities and major differences controlling IAPP cross-peptide interaction with Aβ40(42) versus its amyloid self-assembly offer a molecular basis for understanding the underlying mechanisms. We propose that these insights will aid in designing intervention strategies and novel IAPP analogs for the management of type 2 diabetes, Alzheimer's disease, or other diseases related to IAPP dysfunction or cross-amyloid interactions. © 2017 by The American Society for Biochemistry and Molecular Biology, Inc.

A high quantum yield molecule-protein complex fluorophore for near-infrared II imaging

PubMed Central

Antaris, Alexander L.; Chen, Hao; Diao, Shuo; Ma, Zhuoran; Zhang, Zhe; Zhu, Shoujun; Wang, Joy; Lozano, Alexander X.; Fan, Quli; Chew, Leila; Zhu, Mark; Cheng, Kai; Hong, Xuechuan; Dai, Hongjie; Cheng, Zhen

2017-01-01

Fluorescence imaging in the second near-infrared window (NIR-II) allows visualization of deep anatomical features with an unprecedented degree of clarity. NIR-II fluorophores draw from a broad spectrum of materials spanning semiconducting nanomaterials to organic molecular dyes, yet unfortunately all water-soluble organic molecules with >1,000 nm emission suffer from low quantum yields that have limited temporal resolution and penetration depth. Here, we report tailoring the supramolecular assemblies of protein complexes with a sulfonated NIR-II organic dye (CH-4T) to produce a brilliant 110-fold increase in fluorescence, resulting in the highest quantum yield molecular fluorophore thus far. The bright molecular complex allowed for the fastest video-rate imaging in the second NIR window with ∼50-fold reduced exposure times at a fast 50 frames-per-second (FPS) capable of resolving mouse cardiac cycles. In addition, we demonstrate that the NIR-II molecular complexes are superior to clinically approved ICG for lymph node imaging deep within the mouse body. PMID:28524850

A high quantum yield molecule-protein complex fluorophore for near-infrared II imaging

DOE Office of Scientific and Technical Information (OSTI.GOV)

Antaris, Alexander L.; Chen, Hao; Diao, Shuo

Fluorescence imaging in the second near-infrared window (NIR-II) allows visualization of deep anatomical features with an unprecedented degree of clarity. NIR-II fluorophores draw from a broad spectrum of materials spanning semiconducting nanomaterials to organic molecular dyes, yet unfortunately all water-soluble organic molecules with 41,000 nm emission suffer from low quantum yields that have limited temporal resolution and penetration depth. We report tailoring the supramolecular assemblies of protein complexes with a sulfonated NIR-II organic dye (CH-4T) to produce a brilliant 110-fold increase in fluorescence, resulting in the highest quantum yield molecular fluorophore thus far. The bright molecular complex allowed for themore » fastest video-rate imaging in the second NIR window with B50-fold reduced exposure times at a fast 50 frames-per-second (FPS) capable of resolving mouse cardiac cycles. Additionally, we demonstrate that the NIR-II molecular complexes are superior to clinically approved ICG for lymph node imaging deep within the mouse body.« less

A high quantum yield molecule-protein complex fluorophore for near-infrared II imaging

DOE PAGES

Antaris, Alexander L.; Chen, Hao; Diao, Shuo; ...

2017-05-19

Fluorescence imaging in the second near-infrared window (NIR-II) allows visualization of deep anatomical features with an unprecedented degree of clarity. NIR-II fluorophores draw from a broad spectrum of materials spanning semiconducting nanomaterials to organic molecular dyes, yet unfortunately all water-soluble organic molecules with 41,000 nm emission suffer from low quantum yields that have limited temporal resolution and penetration depth. We report tailoring the supramolecular assemblies of protein complexes with a sulfonated NIR-II organic dye (CH-4T) to produce a brilliant 110-fold increase in fluorescence, resulting in the highest quantum yield molecular fluorophore thus far. The bright molecular complex allowed for themore » fastest video-rate imaging in the second NIR window with B50-fold reduced exposure times at a fast 50 frames-per-second (FPS) capable of resolving mouse cardiac cycles. Additionally, we demonstrate that the NIR-II molecular complexes are superior to clinically approved ICG for lymph node imaging deep within the mouse body.« less

Purification and characterization of sheep brain cold-stable microtubules.

PubMed Central

Pirollet, F; Job, D; Fischer, E H; Margolis, R L

1983-01-01

The isolation of cold-stable microtubules in high yields, described previously only from rodents, was extended to the brain of higher animals. Under optimal conditions, yields of 30 mg of cold-stable microtubles per 100 g of sheep brain could be obtained routinely. Material purified by two polymerization cycles displayed the same stability to cold temperature or to millimolar concentrations of calcium and the same lability to calmodulin and to ATP as did the purified material obtained from the rat [Job, D., Rauch, C.T., Fischer, E.H. & Margolis, R.L. (1982) Biochemistry 21, 509]. Furthermore, DE-52 chromatography of this material yielded a fraction that restored cold stability when added to cold-labile microtubules. Known to bind to calmodulin and to enhance microtubule assembly, tau proteins had no cold-stabilizing activity. Protein profiles of the cold-stabilizing fraction from sheep and rat brain were similar to one another but showed no protein bands corresponding to the tau proteins. Images PMID:6572919

Oxidative peptide /and amide/ formation from Schiff base complexes

NASA Technical Reports Server (NTRS)

Strehler, B. L.; Li, M. P.; Martin, K.; Fliss, H.; Schmid, P.

1982-01-01

One hypothesis of the origin of pre-modern forms of life is that the original replicating molecules were specific polypeptides which acted as templates for the assembly of poly-Schiff bases complementary to the template, and that these polymers were then oxidized to peptide linkages, probably by photo-produced oxidants. A double cycle of such anti-parallel complementary replication would yield the original peptide polymer. If this model were valid, the Schiff base between an N-acyl alpha mino aldehyde and an amino acid should yield a dipeptide in aqueous solution in the presence of an appropriate oxidant. In the present study it is shown that the substituted dipeptide, N-acetyl-tyrosyl-tyrosine, is produced in high yield in aqueous solution at pH 9 through the action of H2O2 on the Schiff-base complex between N-acetyl-tyrosinal and tyrosine and that a great variety of N-acyl amino acids are formed from amino acids and aliphatic aldehydes under similar conditions.

Supramolecule-to-supramolecule transformations of coordination-driven self-assembled polygons.

PubMed

Zhao, Liang; Northrop, Brian H; Stang, Peter J

2008-09-10

Two types of supramolecular transformations, wherein a self-assembled Pt(II)-pyridyl metal-organic polygon is controllably converted into an alternative polygon, have been achieved through the reaction between cobalt carbonyl and the acetylene moiety of a dipyridyl donor ligand. A [6 + 6] hexagon is transformed into two [3 + 3] hexagons, and a triangle-square mixture is converted into [2 + 2] rhomboids. 1H and 31P NMR spectra are used to track the transformation process and evaluate the yield of new self-assembled polygons. Such transformed species are identified by electrospray ionization (ESI) mass spectrometry. This new kind of supramolecule-to-supramolecule transformations provides a viable means for constructing, and then converting, new self-assembled polygons.

Low-cost optical interconnect module for parallel optical data links

NASA Astrophysics Data System (ADS)

Noddings, Chad; Hirsch, Tom J.; Olla, M.; Spooner, C.; Yu, Jason J.

1995-04-01

We have designed, fabricated, and tested a prototype parallel ten-channel unidirectional optical data link. When scaled to production, we project that this technology will satisfy the following market penetration requirements: (1) up to 70 meters transmission distance, (2) at least 1 gigabyte/second data rate, and (3) 0.35 to 0.50 MByte/second volume selling price. These goals can be achieved by means of the assembly innovations described in this paper: a novel alignment method that is integrated with low-cost, few chip module packaging techniques, yielding high coupling and reducing the component count. Furthermore, high coupling efficiency increases projected reliability reducing the driver's power requirements.

Broadband Fluorescence Enhancement with Self-Assembled Silver Nanoparticle Optical Antennas.

PubMed

Vietz, Carolin; Kaminska, Izabela; Sanz Paz, Maria; Tinnefeld, Philip; Acuna, Guillermo P

2017-05-23

Plasmonic structures are known to affect the fluorescence properties of dyes placed in close proximity. This effect has been exploited in combination with single-molecule techniques for several applications in the field of biosensing. Among these plasmonic structures, top-down zero-mode waveguides stand out due to their broadband capabilities. In contrast, optical antennas based on gold nanostructures exhibit fluorescence enhancement on a narrow fraction of the visible spectrum typically restricted to the red to near-infrared region. In this contribution, we exploit the DNA origami technique to self-assemble optical antennas based on large (80 nm) silver nanoparticles. We have studied the performance of these antennas with far- and near-field simulations and characterized them experimentally with single-molecule fluorescence measurements. We demonstrate that silver-based optical antennas can yield a fluorescence enhancement of more than 2 orders of magnitude throughout the visible spectral range for high intrinsic quantum yield dyes. Additionally, a comparison between the performance of gold and silver-based antennas is included. The results indicate that silver-based antennas strongly outperform their gold counterparts in the blue and green ranges and exhibit marginal differences in the red range. These characteristics render silver-based optical antennas ready for applications involving several fluorescently labeled species across the visible spectrum.

Dual-fission chamber and neutron beam characterization for fission product yield measurements using monoenergetic neutrons

NASA Astrophysics Data System (ADS)

Bhatia, C.; Fallin, B.; Gooden, M. E.; Howell, C. R.; Kelley, J. H.; Tornow, W.; Arnold, C. W.; Bond, E. M.; Bredeweg, T. A.; Fowler, M. M.; Moody, W. A.; Rundberg, R. S.; Rusev, G.; Vieira, D. J.; Wilhelmy, J. B.; Becker, J. A.; Macri, R.; Ryan, C.; Sheets, S. A.; Stoyer, M. A.; Tonchev, A. P.

2014-09-01

A program has been initiated to measure the energy dependence of selected high-yield fission products used in the analysis of nuclear test data. We present out initial work of neutron activation using a dual-fission chamber with quasi-monoenergetic neutrons and gamma-counting method. Quasi-monoenergetic neutrons of energies from 0.5 to 15 MeV using the TUNL 10 MV FM tandem to provide high-precision and self-consistent measurements of fission product yields (FPY). The final FPY results will be coupled with theoretical analysis to provide a more fundamental understanding of the fission process. To accomplish this goal, we have developed and tested a set of dual-fission ionization chambers to provide an accurate determination of the number of fissions occurring in a thick target located in the middle plane of the chamber assembly. Details of the fission chamber and its performance are presented along with neutron beam production and characterization. Also presented are studies on the background issues associated with room-return and off-energy neutron production. We show that the off-energy neutron contribution can be significant, but correctable, while room-return neutron background levels contribute less than <1% to the fission signal.

Identification and reproducibility of diagnostic DNA markers for tuber starch and yield optimization in a novel association mapping population of potato (Solanum tuberosum L.).

PubMed

Schönhals, E M; Ortega, F; Barandalla, L; Aragones, A; Ruiz de Galarreta, J I; Liao, J-C; Sanetomo, R; Walkemeier, B; Tacke, E; Ritter, E; Gebhardt, C

2016-04-01

SNPs in candidate genes Pain - 1, InvCD141 (invertases), SSIV (starch synthase), StCDF1 (transcription factor), LapN (leucine aminopeptidase), and cytoplasm type are associated with potato tuber yield, starch content and/or starch yield. Tuber yield (TY), starch content (TSC), and starch yield (TSY) are complex characters of high importance for the potato crop in general and for industrial starch production in particular. DNA markers associated with superior alleles of genes that control the natural variation of TY, TSC, and TSY could increase precision and speed of breeding new cultivars optimized for potato starch production. Diagnostic DNA markers are identified by association mapping in populations of tetraploid potato varieties and advanced breeding clones. A novel association mapping population of 282 genotypes including varieties, breeding clones and Andean landraces was assembled and field evaluated in Northern Spain for TY, TSC, TSY, tuber number (TN) and tuber weight (TW). The landraces had lower mean values of TY, TW, TN, and TSY. The population was genotyped for 183 microsatellite alleles, 221 single nucleotide polymorphisms (SNPs) in fourteen candidate genes and eight known diagnostic markers for TSC and TSY. Association test statistics including kinship and population structure reproduced five known marker-trait associations of candidate genes and discovered new ones, particularly for tuber yield and starch yield. The inclusion of landraces increased the number of detected marker-trait associations. Integration of the present association mapping results with previous QTL linkage mapping studies for TY, TSC, TSY, TW, TN, and tuberization revealed some hot spots of QTL for these traits in the potato genome. The genomic positions of markers linked or associated with QTL for complex tuber traits suggest high multiplicity and genome wide distribution of the underlying genes.

A self-assembly aptasensor based on thick-shell quantum dots for sensing of ochratoxin A

NASA Astrophysics Data System (ADS)

Chu, Xianfeng; Dou, Xiaowen; Liang, Ruizheng; Li, Menghua; Kong, Weijun; Yang, Xihui; Luo, Jiaoyang; Yang, Meihua; Zhao, Ming

2016-02-01

A novel self-assembling aptasensor was fabricated by precisely attaching three phosphorothioate-modified capture aptamers onto a single thick-shell quantum dot in a controllable manner for monitoring of ochratoxin A (OTA), a poisonous contaminant widespread in foodstuffs. Herein, CdSe/CdS QDs coated in ten layer CdS shells were synthesized using a continual precursor injection method. Analysis of the prepared CdSe/CdS QDs showed a zinc-blende structure, high photoluminescence quantum yields (>80%), and a photoemission peak with a narrow full-width at half-maximum (about 29 nm), all qualities that render them as a superior choice for optical applications. By adjusting the number of phosphorothioate bases in the anchor domain, the tunable-valency aptasensor was able to self-assemble. In the sensing strategy, the thick-shell quantum dot was provided as an acceptor while OTA itself was used as a donor. In the presence of OTA, the capture aptamers drive the aptasensor function into a measurable signal through a fluorescence resonance energy transfer (FRET) system. The newly developed aptasensor had a detection limit as low as 0.5 ng mL-1, with a linear concentration in the range of 1 to 30 ng mL-1, and therefore meets the requirements for rapid, effective, and anti-interference sensors for real-world applications. Moreover, the high quality thick-shell QDs provide an ideal alternative for highly sensitive imaging and intensive illumination in the fields of biotechnology and bioengineering.A novel self-assembling aptasensor was fabricated by precisely attaching three phosphorothioate-modified capture aptamers onto a single thick-shell quantum dot in a controllable manner for monitoring of ochratoxin A (OTA), a poisonous contaminant widespread in foodstuffs. Herein, CdSe/CdS QDs coated in ten layer CdS shells were synthesized using a continual precursor injection method. Analysis of the prepared CdSe/CdS QDs showed a zinc-blende structure, high photoluminescence quantum yields (>80%), and a photoemission peak with a narrow full-width at half-maximum (about 29 nm), all qualities that render them as a superior choice for optical applications. By adjusting the number of phosphorothioate bases in the anchor domain, the tunable-valency aptasensor was able to self-assemble. In the sensing strategy, the thick-shell quantum dot was provided as an acceptor while OTA itself was used as a donor. In the presence of OTA, the capture aptamers drive the aptasensor function into a measurable signal through a fluorescence resonance energy transfer (FRET) system. The newly developed aptasensor had a detection limit as low as 0.5 ng mL-1, with a linear concentration in the range of 1 to 30 ng mL-1, and therefore meets the requirements for rapid, effective, and anti-interference sensors for real-world applications. Moreover, the high quality thick-shell QDs provide an ideal alternative for highly sensitive imaging and intensive illumination in the fields of biotechnology and bioengineering. Electronic supplementary information (ESI) available: Table S1. See DOI: 10.1039/c5nr08284f

Growth and yield of white spruce plantations in the Lake States (a literature review).

Treesearch

H. Michael Rauscher

1984-01-01

This summary of the white spruce literature covers the structure, site relations, population dynamics, and cultural practices applicable to established plantations in the Lake States. The objective of this paper is to assemble and organize all information relevant to the silviculture, growth, and yield of white spruce plantations in the Lake States .

Increasing cancer detection yield of breast MRI using a new CAD scheme of mammograms

NASA Astrophysics Data System (ADS)

Tan, Maxine; Aghaei, Faranak; Hollingsworth, Alan B.; Stough, Rebecca G.; Liu, Hong; Zheng, Bin

2016-03-01

Although breast MRI is the most sensitive imaging modality to detect early breast cancer, its cancer detection yield in breast cancer screening is quite low (< 3 to 4% even for the small group of high-risk women) to date. The purpose of this preliminary study is to test the potential of developing and applying a new computer-aided detection (CAD) scheme of digital mammograms to identify women at high risk of harboring mammography-occult breast cancers, which can be detected by breast MRI. For this purpose, we retrospectively assembled a dataset involving 30 women who had both mammography and breast MRI screening examinations. All mammograms were interpreted as negative, while 5 cancers were detected using breast MRI. We developed a CAD scheme of mammograms, which include a new quantitative mammographic image feature analysis based risk model, to stratify women into two groups with high and low risk of harboring mammography-occult cancer. Among 30 women, 9 were classified into the high risk group by CAD scheme, which included all 5 women who had cancer detected by breast MRI. All 21 low risk women remained negative on the breast MRI examinations. The cancer detection yield of breast MRI applying to this dataset substantially increased from 16.7% (5/30) to 55.6% (5/9), while eliminating 84% (21/25) unnecessary breast MRI screenings. The study demonstrated the potential of applying a new CAD scheme to significantly increase cancer detection yield of breast MRI, while simultaneously reducing the number of negative MRIs in breast cancer screening.

DOE Office of Scientific and Technical Information (OSTI.GOV)

Wang, Wei; Liu, Yang; Zu, Xiangyang

Highlights: {yields} Successfully selected specific PreS1-interacting peptides by using phage displayed library. {yields} Alignment of the positive phage clones revealed a consensus PreS1 binding motif. {yields} A highly enriched peptide named P7 had a strong binding ability for PreS1. {yields} P7 could block PreS1 attachment. -- Abstract: The PreS1 protein is present on the outermost part of the hepatitis B virus (HBV) surface and has been shown to have a pivotal function in viral infectivity and assembly. The development of reagents with high affinity and specificity for PreS1 is of great significance for early diagnosis and treatment of HBV infection.more » A phage display library of dodecapeptide was screened for interactions with purified PreS1 protein. Alignment of the positive phage clones revealed a putative consensus PreS1 binding motif of HX{sub n}HX{sub m}HP/R. Moreover, a peptide named P7 (KHMHWHPPALNT) was highly enriched and occurred with a surprisingly high frequency of 72%. A thermodynamic study revealed that P7 has a higher binding affinity to PreS1 than the other peptides. Furthermore, P7 was able to abrogate the binding of HBV virions to the PreS1 antibody, suggesting that P7 covers key functional sites on the native PreS1 protein. This newly isolated peptide may, therefore, be a new therapeutic candidate for the treatment of HBV. The consensus motif could be modified to deliver imaging, diagnostic, and therapeutic agents to tissues affected by HBV.« less

SAP-like domain in nucleolar spindle associated protein mediates mitotic chromosome loading as well as interphase chromatin interaction

DOE Office of Scientific and Technical Information (OSTI.GOV)

Verbakel, Werner, E-mail: werner.verbakel@chem.kuleuven.be; Carmeliet, Geert, E-mail: geert.carmeliet@med.kuleuven.be; Engelborghs, Yves, E-mail: yves.engelborghs@fys.kuleuven.be

2011-08-12

Highlights: {yields} The SAP-like domain in NuSAP is a functional DNA-binding domain with preference for dsDNA. {yields} This SAP-like domain is essential for chromosome loading during early mitosis. {yields} NuSAP is highly dynamic on mitotic chromatin, as evident from photobleaching experiments. {yields} The SAP-like domain also mediates NuSAP-chromatin interaction in interphase nucleoplasm. -- Abstract: Nucleolar spindle associated protein (NuSAP) is a microtubule-stabilizing protein that localizes to chromosome arms and chromosome-proximal microtubules during mitosis and to the nucleus, with enrichment in the nucleoli, during interphase. The critical function of NuSAP is underscored by the finding that its depletion in HeLa cellsmore » results in various mitotic defects. Moreover, NuSAP is found overexpressed in multiple cancers and its expression levels often correlate with the aggressiveness of cancer. Due to its localization on chromosome arms and combination of microtubule-stabilizing and DNA-binding properties, NuSAP takes a special place within the extensive group of spindle assembly factors. In this study, we identify a SAP-like domain that shows DNA binding in vitro with a preference for dsDNA. Deletion of the SAP-like domain abolishes chromosome arm binding of NuSAP during mitosis, but is not sufficient to abrogate its chromosome-proximal localization after anaphase onset. Fluorescence recovery after photobleaching experiments revealed the highly dynamic nature of this NuSAP-chromatin interaction during mitosis. In interphase cells, NuSAP also interacts with chromatin through its SAP-like domain, as evident from its enrichment on dense chromatin regions and intranuclear mobility, measured by fluorescence correlation spectroscopy. The obtained results are in agreement with a model where NuSAP dynamically stabilizes newly formed microtubules on mitotic chromosomes to enhance chromosome positioning without immobilizing these microtubules. Interphase NuSAP-chromatin interaction suggests additional functions for NuSAP, as recently identified for other nuclear spindle assembly factors with a role in gene expression or DNA damage response.« less

Fluid driven reciprocating apparatus

DOEpatents

Whitehead, J.C.

1997-04-01

An apparatus is described comprising a pair of fluid driven pump assemblies in a back-to-back configuration to yield a bi-directional pump. Each of the pump assemblies includes a piston or diaphragm which divides a chamber therein to define a power section and a pumping section. An intake-exhaust valve is connected to each of the power sections of the pump chambers, and function to direct fluid, such as compressed air, into the power section and exhaust fluid therefrom. At least one of the pistons or diaphragms is connected by a rod assembly which is constructed to define a signal valve, whereby the intake-exhaust valve of one pump assembly is controlled by the position or location of the piston or diaphragm in the other pump assembly through the operation of the rod assembly signal valve. Each of the pumping sections of the pump assemblies are provided with intake and exhaust valves to enable filling of the pumping section with fluid and discharging fluid therefrom when a desired pressure has been reached. 13 figs.

Fluid driven recipricating apparatus

DOEpatents

Whitehead, John C.

1997-01-01

An apparatus comprising a pair of fluid driven pump assemblies in a back-to-back configuration to yield a bi-directional pump. Each of the pump assemblies includes a piston or diaphragm which divides a chamber therein to define a power section and a pumping section. An intake-exhaust valve is connected to each of the power sections of the pump chambers, and function to direct fluid, such as compressed air, into the power section and exhaust fluid therefrom. At least one of the pistons or diaphragms is connected by a rod assembly which is constructed to define a signal valve, whereby the intake-exhaust valve of one pump assembly is controlled by the position or location of the piston or diaphragm in the other pump assembly through the operation of the rod assembly signal valve. Each of the pumping sections of the pump assemblies are provided with intake and exhaust valves to enable filling of the pumping section with fluid and discharging fluid therefrom when a desired pressure has been reached.

Synthesis, characterization, molecular docking and biological studies of self assembled transition metal dithiocarbamates of substituted pyrrole-2-carboxaldehyde.

PubMed

Nami, Shahab A A; Ullah, Irfan; Alam, Mahboob; Lee, Dong-Ung; Sarikavakli, Nursabah

2016-07-01

A series of self assembled 3d transition metal dithiocarbamate, M(pdtc) [where M=Mn(II), Fe(II), Co(II), Ni(II) and Cu(II)] have been synthesized and spectroscopically characterized. The bidentate dithiocarbamate ligand Na2pdtc (Disodium-1,4-phenyldiaminobis (pyrrole-1-sulfino)dithioate) was prepared by insertion reaction of carbondisulfide with Schiff base, N,N'-bis-(1H-pyrrol-2-ylmethylene)-benzene-1,4-diamine (L1) in basic medium. The simple substitution reaction between the metal halide and Na2pdtc yielded the title complexes in moderate yields. However, the in situ procedure gives high yield with the formation of single product as evident by TLC. Elemental analysis, IR, (1)H and (13)C NMR spectra, UV-vis., magnetic susceptibility and conductance measurements were done to characterize the complexes, M(pdtc). All the evidences suggest that the complexes have tetrahedral geometry excepting Cu(II) which is found to be square planar. A symmetrical bidentate coordination of the dithiocarbamato moiety has been observed in all the complexes. The conductivity data show that the complexes are non-electrolyte in nature. The anti-oxidant activity of the ligand, Na2pdtc and its transition metal complexes, M(pdtc) have been carried out using DPPH and Cu(pdtc) was found to be most effective. The anti-microbial activity of the Na2pdtc and M(pdtc) complexes have been carried out and on this basis the molecular docking study of the most effective complex, Cu(pdtc) has also been reported. Copyright © 2016 Elsevier B.V. All rights reserved.

Mapping Nanoscale Hotspots with Single-Molecule Emitters Assembled into Plasmonic Nanocavities Using DNA Origami

PubMed Central

2017-01-01

Fabricating nanocavities in which optically active single quantum emitters are precisely positioned is crucial for building nanophotonic devices. Here we show that self-assembly based on robust DNA-origami constructs can precisely position single molecules laterally within sub-5 nm gaps between plasmonic substrates that support intense optical confinement. By placing single-molecules at the center of a nanocavity, we show modification of the plasmon cavity resonance before and after bleaching the chromophore and obtain enhancements of ≥4 × 103 with high quantum yield (≥50%). By varying the lateral position of the molecule in the gap, we directly map the spatial profile of the local density of optical states with a resolution of ±1.5 nm. Our approach introduces a straightforward noninvasive way to measure and quantify confined optical modes on the nanoscale. PMID:29166033

A transfer matrix approach to vibration localization in mistuned blade assemblies

NASA Technical Reports Server (NTRS)

Ottarson, Gisli; Pierre, Chritophe

1993-01-01

A study of mode localization in mistuned bladed disks is performed using transfer matrices. The transfer matrix approach yields the free response of a general, mono-coupled, perfectly cyclic assembly in closed form. A mistuned structure is represented by random transfer matrices, and the expansion of these matrices in terms of the small mistuning parameter leads to the definition of a measure of sensitivity to mistuning. An approximation of the localization factor, the spatially averaged rate of exponential attenuation per blade-disk sector, is obtained through perturbation techniques in the limits of high and low sensitivity. The methodology is applied to a common model of a bladed disk and the results verified by Monte Carlo simulations. The easily calculated sensitivity measure may prove to be a valuable design tool due to its system-independent quantification of mistuning effects such as mode localization.

Mapping Nanoscale Hotspots with Single-Molecule Emitters Assembled into Plasmonic Nanocavities Using DNA Origami

NASA Astrophysics Data System (ADS)

Chikkaraddy, Rohit; Turek, V. A.; Kongsuwan, Nuttawut; Benz, Felix; Carnegie, Cloudy; van de Goor, Tim; de Nijs, Bart; Demetriadou, Angela; Hess, Ortwin; Keyser, Ulrich F.; Baumberg, Jeremy J.

2018-01-01

Fabricating nanocavities in which optically-active single quantum emitters are precisely positioned, is crucial for building nanophotonic devices. Here we show that self-assembly based on robust DNA-origami constructs can precisely position single molecules laterally within sub-5nm gaps between plasmonic substrates that support intense optical confinement. By placing single-molecules at the center of a nanocavity, we show modification of the plasmon cavity resonance before and after bleaching the chromophore, and obtain enhancements of $\\geq4\\times10^3$ with high quantum yield ($\\geq50$%). By varying the lateral position of the molecule in the gap, we directly map the spatial profile of the local density of optical states with a resolution of $\\pm1.5$ nm. Our approach introduces a straightforward non-invasive way to measure and quantify confined optical modes on the nanoscale.

Self-Assembly of Helical Ribbons

NASA Astrophysics Data System (ADS)

Zastavker, Yevgeniya V.; Asherie, Neer; Lomakin, Aleksey; Pande, Jayanti; Donovan, Joanne M.; Schnur, Joel M.; Benedek, George B.

1999-07-01

The self-assembly of helical ribbons is examined in a variety of multicomponent enantiomerically pure systems that contain a bile salt or a nonionic detergent, a phosphatidylcholine or a fatty acid, and a steroid analog of cholesterol. In almost all systems, two different pitch types of helical ribbons are observed: high pitch, with a pitch angle of 54± 2 degrees, and low pitch, with a pitch angle of 11± 2 degrees. Although the majority of these helices are right-handed, a small proportion of left-handed helices is observed. Additionally, a third type of helical ribbon, with a pitch angle in the range 30-47 degrees, is occasionally found. These experimental findings suggest that the helical ribbons are crystalline rather than liquid crystal in nature and also suggest that molecular chirality may not be the determining factor in helix formation. The large yields of helices produced will permit a systematic investigation of their individual kinetic evolution and their elastic moduli.

V2O5 encapsulated MWCNTs in 2D surface architecture: Complete solid-state bendable highly stabilized energy efficient supercapacitor device

NASA Astrophysics Data System (ADS)

Pandit, Bidhan; Dubal, Deepak P.; Gómez-Romero, Pedro; Kale, Bharat B.; Sankapal, Babasaheb R.

2017-03-01

A simple and scalable approach has been reported for V2O5 encapsulation over interconnected multi-walled carbon nanotubes (MWCNTs) network using chemical bath deposition method. Chemically synthesized V2O5/MWCNTs electrode exhibited excellent charge-discharge capability with extraordinary cycling retention of 93% over 4000 cycles in liquid-electrolyte. Electrochemical investigations have been performed to evaluate the origin of capacitive behavior from dual contribution of surface-controlled and diffusion-controlled charge components. Furthermore, a complete flexible solid-state, flexible symmetric supercapacitor (FSS-SSC) device was assembled with V2O5/MWCNTs electrodes which yield remarkable values of specific power and energy densities along with enhanced cyclic stability over liquid configuration. As a practical demonstration, the constructed device was used to lit the ‘VNIT’ acronym assembled using 21 LED’s.

Driven evolution of a constitutional dynamic library of molecular helices toward the selective generation of [2 x 2] gridlike arrays under the pressure of metal ion coordination.

PubMed

Giuseppone, Nicolas; Schmitt, Jean-Louis; Lehn, Jean-Marie

2006-12-27

Constitutional dynamics, self-assembly, and helical-folding control are brought together in the efficient Sc(OTf)3/microwave-catalyzed transimination of helical oligohydrazone strands, yielding highly diverse dynamic libraries of interconverting constituents through assembly, dissociation, and exchange of components. The transimination-type mechanism of the ScIII-promoted exchange, as well as its regioselectivity, occurring only at the extremities of the helical strands, allow one to perform directional terminal polymerization/depolymerization processes when starting with dissymmetric strands. A particular library is subsequently brought to express quantitatively [2 x 2] gridlike metallosupramolecular arrays in the presence of ZnII ions by component recombination generating the correct ligand from the dynamic set of interconverting strands. This behavior represents a process of driven evolution of a constitutional dynamic chemical system under the pressure (coordination interaction) of an external effector (metal ions).

Draft genome of the gayal, Bos frontalis

PubMed Central

Wang, Ming-Shan; Zeng, Yan; Wang, Xiao; Nie, Wen-Hui; Wang, Jin-Huan; Su, Wei-Ting; Xiong, Zi-Jun; Wang, Sheng; Qu, Kai-Xing; Yan, Shou-Qing; Yang, Min-Min; Wang, Wen; Dong, Yang; Zhang, Ya-Ping

2017-01-01

Abstract Gayal (Bos frontalis), also known as mithan or mithun, is a large endangered semi-domesticated bovine that has a limited geographical distribution in the hill-forests of China, Northeast India, Bangladesh, Myanmar, and Bhutan. Many questions about the gayal such as its origin, population history, and genetic basis of local adaptation remain largely unresolved. De novo sequencing and assembly of the whole gayal genome provides an opportunity to address these issues. We report a high-depth sequencing, de novo assembly, and annotation of a female Chinese gayal genome. Based on the Illumina genomic sequencing platform, we have generated 350.38 Gb of raw data from 16 different insert-size libraries. A total of 276.86 Gb of clean data is retained after quality control. The assembled genome is about 2.85 Gb with scaffold and contig N50 sizes of 2.74 Mb and 14.41 kb, respectively. Repetitive elements account for 48.13% of the genome. Gene annotation has yielded 26 667 protein-coding genes, of which 97.18% have been functionally annotated. BUSCO assessment shows that our assembly captures 93% (3183 of 4104) of the core eukaryotic genes and 83.1% of vertebrate universal single-copy orthologs. We provide the first comprehensive de novo genome of the gayal. This genetic resource is integral for investigating the origin of the gayal and performing comparative genomic studies to improve understanding of the speciation and divergence of bovine species. The assembled genome could be used as reference in future population genetic studies of gayal. PMID:29048483

Hierarchically structured lithium titanate for ultrafast charging in long-life high capacity batteries

NASA Astrophysics Data System (ADS)

Odziomek, Mateusz; Chaput, Frédéric; Rutkowska, Anna; Świerczek, Konrad; Olszewska, Danuta; Sitarz, Maciej; Lerouge, Frédéric; Parola, Stephane

2017-05-01

High-performance Li-ion batteries require materials with well-designed and controlled structures on nanometre and micrometre scales. Electrochemical properties can be enhanced by reducing crystallite size and by manipulating structure and morphology. Here we show a method for preparing hierarchically structured Li4Ti5O12 yielding nano- and microstructure well-suited for use in lithium-ion batteries. Scalable glycothermal synthesis yields well-crystallized primary 4-8 nm nanoparticles, assembled into porous secondary particles. X-ray photoelectron spectroscopy reveals presence of Ti+4 only; combined with chemical analysis showing lithium deficiency, this suggests oxygen non-stoichiometry. Electron microscopy confirms hierarchical morphology of the obtained material. Extended cycling tests in half cells demonstrates capacity of 170 mAh g-1 and no sign of capacity fading after 1,000 cycles at 50C rate (charging completed in 72 s). The particular combination of nanostructure, microstructure and non-stoichiometry for the prepared lithium titanate is believed to underlie the observed electrochemical performance of material.

High Current Hollow Cathode Plasma Plume Measurements

NASA Technical Reports Server (NTRS)

Thomas, Robert E.; Kamhawi, Hani; Williams, George J., Jr.

2014-01-01

Plasma plume measurements are reported for a hollow cathode assembly (HCA) operated at discharge currents of 50, 70, and 100 A at xenon flow rates between 19 - 46 standard cubic centimeter per minute. The HCA was centrally mounted in the NASA-300MS Hall Thruster and was operated in the "spot" and "plume" modes with additional data taken with an applied magnetic field. Langmuir probes, retarding potential analyzers, and optical emission spectroscopy were employed to measure plasma properties near the orifice of the HCA and to assess the charge state of the near-field plasma. Electron temperatures (2-6 electron volt) and plasma potentials are consistent with probe-measured values in previous investigations. Operation with an applied-field yields higher discharge voltages, increased Xe III production, and increased signals from the 833.5 nm C I line. While operating in plume mode and with an applied field, ion energy distribution measurements yield ions with energies significantly exceeding the applied discharge voltage. These findings are correlated with high-frequency oscillations associated with each mode.

Outbred genome sequencing and CRISPR/Cas9 gene editing in butterflies

PubMed Central

Li, Xueyan; Fan, Dingding; Zhang, Wei; Liu, Guichun; Zhang, Lu; Zhao, Li; Fang, Xiaodong; Chen, Lei; Dong, Yang; Chen, Yuan; Ding, Yun; Zhao, Ruoping; Feng, Mingji; Zhu, Yabing; Feng, Yue; Jiang, Xuanting; Zhu, Deying; Xiang, Hui; Feng, Xikan; Li, Shuaicheng; Wang, Jun; Zhang, Guojie; Kronforst, Marcus R.; Wang, Wen

2015-01-01

Butterflies are exceptionally diverse but their potential as an experimental system has been limited by the difficulty of deciphering heterozygous genomes and a lack of genetic manipulation technology. Here we use a hybrid assembly approach to construct high-quality reference genomes for Papilio xuthus (contig and scaffold N50: 492 kb, 3.4 Mb) and Papilio machaon (contig and scaffold N50: 81 kb, 1.15 Mb), highly heterozygous species that differ in host plant affiliations, and adult and larval colour patterns. Integrating comparative genomics and analyses of gene expression yields multiple insights into butterfly evolution, including potential roles of specific genes in recent diversification. To functionally test gene function, we develop an efficient (up to 92.5%) CRISPR/Cas9 gene editing method that yields obvious phenotypes with three genes, Abdominal-B, ebony and frizzled. Our results provide valuable genomic and technological resources for butterflies and unlock their potential as a genetic model system. PMID:26354079

A Clonal Selection Algorithm for Minimizing Distance Travel and Back Tracking of Automatic Guided Vehicles in Flexible Manufacturing System

NASA Astrophysics Data System (ADS)

Chawla, Viveak Kumar; Chanda, Arindam Kumar; Angra, Surjit

2018-03-01

The flexible manufacturing system (FMS) constitute of several programmable production work centers, material handling systems (MHSs), assembly stations and automatic storage and retrieval systems. In FMS, the automatic guided vehicles (AGVs) play a vital role in material handling operations and enhance the performance of the FMS in its overall operations. To achieve low makespan and high throughput yield in the FMS operations, it is highly imperative to integrate the production work centers schedules with the AGVs schedules. The Production schedule for work centers is generated by application of the Giffler and Thompson algorithm under four kind of priority hybrid dispatching rules. Then the clonal selection algorithm (CSA) is applied for the simultaneous scheduling to reduce backtracking as well as distance travel of AGVs within the FMS facility. The proposed procedure is computationally tested on the benchmark FMS configuration from the literature and findings from the investigations clearly indicates that the CSA yields best results in comparison of other applied methods from the literature.

High Current Hollow Cathode Plasma Plume Measurements

NASA Technical Reports Server (NTRS)

Thomas, Robert E.; Kamhawi, Hani; Williams, George J., Jr.

2013-01-01

Plasma plume measurements are reported for a hollow cathode assembly (HCA) oper-ated at discharge currents of 50, 70, and 100 A at xenon ow rates between 19 - 46 sccm.The HCA was centrally mounted in the annulus of the NASA-300MS Hall Thruster andwas operated in the spot and plume modes with additional data taken with an appliedmagnetic eld. Langmuir probes, retarding potential analyzers, and optical emission spec-troscopy were employed to measure plasma properties near the orice of the HCA and toassess the charge state of the near-eld plasma. Electron temperatures (2-6 eV) and plasmapotentials are consistent with probe-measured values in previous investigations. Operationwith an applied-eld yields higher discharge voltages, increased Xe III production, andincreased signals from the 833.5 nm C I line. While operating in plume mode and with anapplied eld, ion energy distribution measurements yield ions with energies signicantlyexceeding the applied discharge voltage. These ndings are correlated with high-frequencyoscillations associated with each mode.

Intelligent Fasteners

NASA Technical Reports Server (NTRS)

1997-01-01

Under a Small Business Innovation Research contract from Marshall Space Flight Center, Ultrafast, Inc. developed the world's first, high-temperature resistant, "intelligent" fastener. NASA needed a critical-fastening appraisal and validation of spacecraft segments that are coupled together in space. The intelligent-bolt technology deletes the self-defeating procedure of having to untighten the fastener, and thus upset the joint, during inspection and maintenance. The Ultrafast solution yielded an innovation that is likely to revolutionize manufacturing assembly, particularly the automobile industry. Other areas of application range from aircraft, computers and fork-lifts to offshore platforms, buildings, and bridges.

Genome sequence of M6, a diploid inbred clone of the high-glycoalkaloid-producing tuber-bearing potato species Solanum chacoense, reveals residual heterozygosity.

PubMed

Leisner, Courtney P; Hamilton, John P; Crisovan, Emily; Manrique-Carpintero, Norma C; Marand, Alexandre P; Newton, Linsey; Pham, Gina M; Jiang, Jiming; Douches, David S; Jansky, Shelley H; Buell, C Robin

2018-05-01

Cultivated potato (Solanum tuberosum L.) is a highly heterozygous autotetraploid that presents challenges in genome analyses and breeding. Wild potato species serve as a resource for the introgression of important agronomic traits into cultivated potato. One key species is Solanum chacoense and the diploid, inbred clone M6, which is self-compatible and has desirable tuber market quality and disease resistance traits. Sequencing and assembly of the genome of the M6 clone of S. chacoense generated an assembly of 825 767 562 bp in 8260 scaffolds with an N50 scaffold size of 713 602 bp. Pseudomolecule construction anchored 508 Mb of the genome assembly into 12 chromosomes. Genome annotation yielded 49 124 high-confidence gene models representing 37 740 genes. Comparative analyses of the M6 genome with six other Solanaceae species revealed a core set of 158 367 Solanaceae genes and 1897 genes unique to three potato species. Analysis of single nucleotide polymorphisms across the M6 genome revealed enhanced residual heterozygosity on chromosomes 4, 8 and 9 relative to the other chromosomes. Access to the M6 genome provides a resource for identification of key genes for important agronomic traits and aids in genome-enabled development of inbred diploid potatoes with the potential to accelerate potato breeding. © 2018 The Authors The Plant Journal © 2018 John Wiley & Sons Ltd.

The SPIDER fission fragment spectrometer for fission product yield measurements

DOE PAGES

Meierbachtol, K.; Tovesson, F.; Shields, D.; ...

2015-04-01

We developed the SPectrometer for Ion DEtermination in fission Research (SPIDER) for measuring mass yield distributions of fission products from spontaneous and neutron-induced fission. The 2E–2v method of measuring the kinetic energy (E) and velocity (v) of both outgoing fission products has been utilized, with the goal of measuring the mass of the fission products with an average resolution of 1 atomic mass unit (amu). Moreover, the SPIDER instrument, consisting of detector components for time-of-flight, trajectory, and energy measurements, has been assembled and tested using 229Th and 252Cf radioactive decay sources. For commissioning, the fully assembled system measured fission productsmore » from spontaneous fission of 252Cf. Individual measurement resolutions were met for time-of-flight (250 ps FWHM), spacial resolution (2 mm FHWM), and energy (92 keV FWHM for 8.376 MeV). Finally, these mass yield results measured from 252Cf spontaneous fission products are reported from an E–v measurement.« less

All-fiber wavelength swept ring laser based on Fabry-Perot filter for optical frequency domain imaging

PubMed Central

Jun, Changsu; Villiger, Martin; Oh, Wang-Yuhl; Bouma, Brett E.

2014-01-01

Innovations in laser engineering have yielded several novel configurations for high repetition rate, broad sweep range, and long coherence length wavelength swept lasers. Although these lasers have enabled high performance frequency-domain optical coherence tomography, they are typically complicated and costly and many require access to proprietary materials or devices. Here, we demonstrate a simplified ring resonator configuration that is straightforward to construct from readily available materials at a low total cost. It was enabled by an insight regarding the significance of isolation against bidirectional operation and by configuring the sweep range of the intracavity filter to exceed its free spectral range. The design can easily be optimized to meet a range of operating specifications while yielding robust and stable performance. As an example, we demonstrate 240 kHz operation with 125 nm sweep range and >70 mW of average output power and demonstrate high quality frequency domain OCT imaging. The complete component list and directions for assembly of the laser are posted on-line at www.octresearch.org. PMID:25401614

Acousto-fluidic system assisting in-liquid self-assembly of microcomponents

NASA Astrophysics Data System (ADS)

Goldowsky, J.; Mastrangeli, M.; Jacot-Descombes, L.; Gullo, M. R.; Mermoud, G.; Brugger, J.; Martinoli, A.; Nelson, B. J.; Knapp, Helmut F.

2013-12-01

In this paper, we present the theoretical background, design, fabrication and characterization of a micromachined chamber assisting the fluidic self-assembly of micro-electro-mechanical systems in a bulk liquid. Exploiting bubble-induced acoustic microstreaming, several structurally-robust driving modes are excited inside the chamber. The modes promote the controlled aggregation and disaggregation of microcomponents relying on strong and reproducible fluid mixing effects achieved even at low Reynolds numbers. The functionality of the microfluidic chamber is demonstrated through the fast and repeatable geometrical pairing and subsequent unpairing of polymeric microcylinders. Relying only on drag and radiation forces and on the natural hydrophobicity of SU-8 in aqueous solutions, assembly yields of approximately 50% are achieved in no longer than ten seconds of agitation. The system can stochastically control the assembly process and significantly reduce the time-to-assembly of building blocks.

Little Boy replication: justification and construction

DOE Office of Scientific and Technical Information (OSTI.GOV)

Malenfant, R.E.

A reconstruction of the Little Boy weapon allowed experiments to evaluate yield, leakage measurements for comparison with calculations, and phenomenological measurements to evaluate various in-situ dosimeters. The reconstructed weapon was operated at sustained delayed critical at the Los Alamos Critical Assembly Facility. The present experiments provide a wealth of information to benchmark calculations and demonstrate that the 1965 measurements on the Ichiban assembly (a spherical mockup of Little Boy) were in error.

The Design of a Molecular Assembly Line Based on Biological Molecules

DTIC Science & Technology

2003-06-01

and will demonstrate how one can construct a purely synthetic analogue of a polyketide synthase . 15. SUBJECT TERMS 16. SECURITY CLASSIFICATION OF...scaffold in programmed assembly and molecular electronics. It is based on the principles of the biological molecules polyketide synthase and kinesin, and in...stereoselective centers) with any reasonable yield, not including the R&D and process development time. Figure 1.6 shows how a polyketide synthase

Charge Separation Mechanisms in Ordered Films of Self-Assembled Donor–Acceptor Dyad Ribbons

DOE Office of Scientific and Technical Information (OSTI.GOV)

Logsdon, Jenna L.; Hartnett, Patrick E.; Nelson, Jordan N.

2017-04-21

Orthogonal attachment of polar and nonpolar side-chains to a zinc porphyrin-perylenediimide dyad (ZnP-PDI, 1a) is shown to result in self-assembly of ordered supramolecular ribbons in which the ZnP and PDI molecules form segregated π-stacked columns. Following photoexcitation of the ordered ribbons, ZnP+•-PDI–• radical ion pairs form in <200 fs and subsequently produce a 30 ± 3% yield of free charge carriers that live for about 100 μs. Elongating the side chains on ZnP and PDI in 1b enhances the order of the films, but does not result in an increase in free charge carrier yield. In addition, this yield ismore » independent of temperature, free energy of reaction, and the ZnP-PDI distance in the covalent dyad. These results suggest that the free charge carrier yield in this system is not limited by a bound charge transfer (CT) state or promoted by a vibronically hot CT state. Instead, it is likely that π-stacking of the segregated donors and acceptors within the ribbons results in delocalization of the charges following photoexcitation, allowing them to overcome Coulombic attraction and generate free charge carriers.« less

Supramolecule-to-Supramolecule Transformations of Coordination-Driven Self-Assembled Polygons

PubMed Central

Zhao, Liang; Northrop, Brian H.; Stang, Peter J.

2009-01-01

Two types of supramolecular transformations, wherein a self-assembled Pt(II)-pyridyl metal-organic polygon is controllably converted into an alternative polygon, have been achieved through the reaction between cobalt carbonyl and the acetylene moiety of a dipyridyl donor ligand. A [6+6] hexagon is transformed into two [3+3] hexagons and a triangle-square mixture is converted into [2+2] rhomboids. 1H and 31P NMR spectra are used to track the transformation process and evaluate the yield of new self-assembled polygons. Such transformed species are identified by electrospray ionization (ESI) mass spectrometry. This new kind of supramolecule-to-supramolecule transformations provides a viable means for constructing, and then converting, new self-assembled polygons. PMID:18702485

Spin morphologies and heat dissipation in spherical assemblies of magnetic nanoparticles

NASA Astrophysics Data System (ADS)

Anand, Manish; Carrey, Julian; Banerjee, Varsha

2016-09-01

Aggregates of magnetic nanoparticles (MNPs) exhibit unusual properties due to the interplay of small system size and long-range dipole-dipole interactions. Using the micromagnetic simulation software oommf, we study the spin morphologies and heat dissipation in micron-size spherical assemblies of MNPs. In particular, we examine the sensitivity of these properties to the dipolar strength, manipulated by the interparticle separation. As oommf is not designed for such a study, we have incorporated a novel scaling protocol for this purpose. We believe that it is essential for all studies where volume fractions are varied. Our main results are as follows: (i) Dense assemblies exhibit strong dipolar effects which yield local magnetic order in the core but not on the surface, where moments are randomly oriented. (ii) The probability distribution of ground-state energy exhibits a long high-energy tail for surface spins in contrast to small tails for the core spins. Consequently, there is a wide variation in the energy of surface spins but not the core spins. (iii) There is strong correlation between ground-state energy and heating properties on application of an oscillating magnetic field h (t ) =hocos2 π f t : the particles in the core heat uniformly, while those on the surface exhibit a wide range from cold to intensely hot. (iv) Specific choices of ho and f yield characteristic spatial heat distributions, e.g., hot surface and cold core, or vice versa. (iv) For all values of ho and f that we consider, heating was maximum at a specific volume fraction. These results are especially relevant in the context of contemporary applications such as hyperthermia and chemotherapy, and also for novel materials such as smart polymer beads and superspin glasses.

Gelation-driven component selection in the generation of constitutional dynamic hydrogels based on guanine-quartet formation

PubMed Central

Sreenivasachary, Nampally; Lehn, Jean-Marie

2005-01-01

The guanosine hydrazide 1 yields a stable supramolecular hydrogel based on the formation of a guanine quartet (G-quartet) in presence of metal cations. The effect of various parameters (concentration, nature of metal ion, and temperature) on the properties of this gel has been studied. Proton NMR spectroscopy is shown to allow a molecular characterization of the gelation process. Hydrazide 1 and its assemblies can be reversibly decorated by acylhydrazone formation with various aldehydes, resulting in formation of highly viscous dynamic hydrogels. When a mixture of aldehydes is used, the dynamic system selects the aldehyde that leads to the most stable gel. Mixing hydrazides 1, 9 and aldehydes 6, 8 in 1:1:1:1 ratio generated a constitutional dynamic library containing the four acylhydrazone derivatives A, B, C, and D. The library constitution displayed preferential formation of the acylhydrazone B that yields the strongest gel. Thus, gelation redirects the acylhydrazone distribution in the dynamic library as guanosine hydrazide 1 scavenges preferentially aldehyde 8, under the pressure of gelation because of the collective interactions in the assemblies of G-quartets B, despite the strong preference of the competing hydrazide 9 for 8. Gel formation and component selection are thermoreversible. The process amounts to gelation-driven self-organization with component selection and amplification in constitutional dynamic hydrogels based on G-quartet formation and reversible covalent connections. The observed self-organization and component selection occur by means of a multilevel self-assembly involving three dynamic processes, two of supramolecular and one of reversible covalent nature. They extend constitutional dynamic chemistry to phase-organization and phase-transition events. PMID:15840720

Gelation-driven component selection in the generation of constitutional dynamic hydrogels based on guanine-quartet formation.

PubMed

Sreenivasachary, Nampally; Lehn, Jean-Marie

2005-04-26

The guanosine hydrazide 1 yields a stable supramolecular hydrogel based on the formation of a guanine quartet (G-quartet) in presence of metal cations. The effect of various parameters (concentration, nature of metal ion, and temperature) on the properties of this gel has been studied. Proton NMR spectroscopy is shown to allow a molecular characterization of the gelation process. Hydrazide 1 and its assemblies can be reversibly decorated by acylhydrazone formation with various aldehydes, resulting in formation of highly viscous dynamic hydrogels. When a mixture of aldehydes is used, the dynamic system selects the aldehyde that leads to the most stable gel. Mixing hydrazides 1, 9 and aldehydes 6, 8 in 1:1:1:1 ratio generated a constitutional dynamic library containing the four acylhydrazone derivatives A, B, C, and D. The library constitution displayed preferential formation of the acylhydrazone B that yields the strongest gel. Thus, gelation redirects the acylhydrazone distribution in the dynamic library as guanosine hydrazide 1 scavenges preferentially aldehyde 8, under the pressure of gelation because of the collective interactions in the assemblies of G-quartets B, despite the strong preference of the competing hydrazide 9 for 8. Gel formation and component selection are thermoreversible. The process amounts to gelation-driven self-organization with component selection and amplification in constitutional dynamic hydrogels based on G-quartet formation and reversible covalent connections. The observed self-organization and component selection occur by means of a multilevel self-assembly involving three dynamic processes, two of supramolecular and one of reversible covalent nature. They extend constitutional dynamic chemistry to phase-organization and phase-transition events.

Application of synthetic biology for production of chemicals in yeast Saccharomyces cerevisiae.

PubMed

Li, Mingji; Borodina, Irina

2015-02-01

Synthetic biology and metabolic engineering enable generation of novel cell factories that efficiently convert renewable feedstocks into biofuels, bulk, and fine chemicals, thus creating the basis for biosustainable economy independent on fossil resources. While over a hundred proof-of-concept chemicals have been made in yeast, only a very small fraction of those has reached commercial-scale production so far. The limiting factor is the high research cost associated with the development of a robust cell factory that can produce the desired chemical at high titer, rate, and yield. Synthetic biology has the potential to bring down this cost by improving our ability to predictably engineer biological systems. This review highlights synthetic biology applications for design, assembly, and optimization of non-native biochemical pathways in baker's yeast Saccharomyces cerevisiae We describe computational tools for the prediction of biochemical pathways, molecular biology methods for assembly of DNA parts into pathways, and for introducing the pathways into the host, and finally approaches for optimizing performance of the introduced pathways. © FEMS 2015. All rights reserved. For permissions, please e-mail: journals.permission@oup.com.

Bioorthogonal layer-by-layer encapsulation of pancreatic islets via hyperbranched polymers

PubMed Central

Gattás-Asfura, Kerim M.; Stabler, Cherie L.

2013-01-01

The encapsulation of viable tissues via layer-by-layer polymer assembly provides a versatile platform for cell surface engineering, with nanoscale control over capsule properties. Herein, we report the development of a hyperbranched polymer-based, ultrathin capsule architecture expressing bioorthogonal functionality and tailored physiochemical properties. Random carbodiimide-based condensation of 3,5-dicarboxyphenyl glycineamide on alginate yielded a highly branched polysaccharide with multiple, spatially restricted, and readily functionalizable terminal carboxylate moieties. Poly(ethylene glycol) (PEG) was utilized to link azido end groups to the structured alginate. Together with phosphine functionalized poly(amido amine) (PAMAM) dendrimer, nanoscale layer-by-layer coatings, covalently stabilized via Staudinger ligation, were assembled onto solid surfaces and pancreatic islets. The effects of electrostatic and/or bioorthogonal covalent interlayer interactions on the resulting coating efficiency and stability, as well as pancreatic islet viability and function, were studied. These hyperbranched polymers provide a flexible platform for the formation of covalently stabilized ultrathin coatings on viable cells and tissues. In addition, the hyperbranched nature of the polymers presents a highly functionalized surface capable of bioorthogonal conjugation of additional bioactive or labeling motifs. PMID:24063764

Moleculo Long-Read Sequencing Facilitates Assembly and Genomic Binning from Complex Soil Metagenomes

DOE Office of Scientific and Technical Information (OSTI.GOV)

White, Richard Allen; Bottos, Eric M.; Roy Chowdhury, Taniya

ABSTRACT Soil metagenomics has been touted as the “grand challenge” for metagenomics, as the high microbial diversity and spatial heterogeneity of soils make them unamenable to current assembly platforms. Here, we aimed to improve soil metagenomic sequence assembly by applying the Moleculo synthetic long-read sequencing technology. In total, we obtained 267 Gbp of raw sequence data from a native prairie soil; these data included 109.7 Gbp of short-read data (~100 bp) from the Joint Genome Institute (JGI), an additional 87.7 Gbp of rapid-mode read data (~250 bp), plus 69.6 Gbp (>1.5 kbp) from Moleculo sequencing. The Moleculo data alone yielded over 5,600more » reads of >10 kbp in length, and over 95% of the unassembled reads mapped to contigs of >1.5 kbp. Hybrid assembly of all data resulted in more than 10,000 contigs over 10 kbp in length. We mapped three replicate metatranscriptomes derived from the same parent soil to the Moleculo subassembly and found that 95% of the predicted genes, based on their assignments to Enzyme Commission (EC) numbers, were expressed. The Moleculo subassembly also enabled binning of >100 microbial genome bins. We obtained via direct binning the first complete genome, that of “CandidatusPseudomonas sp. strain JKJ-1” from a native soil metagenome. By mapping metatranscriptome sequence reads back to the bins, we found that several bins corresponding to low-relative-abundanceAcidobacteriawere highly transcriptionally active, whereas bins corresponding to high-relative-abundanceVerrucomicrobiawere not. These results demonstrate that Moleculo sequencing provides a significant advance for resolving complex soil microbial communities. IMPORTANCESoil microorganisms carry out key processes for life on our planet, including cycling of carbon and other nutrients and supporting growth of plants. However, there is poor molecular-level understanding of their functional roles in ecosystem stability and responses to environmental perturbations. This knowledge gap is largely due to the difficulty in culturing the majority of soil microbes. Thus, use of culture-independent approaches, such as metagenomics, promises the direct assessment of the functional potential of soil microbiomes. Soil is, however, a challenge for metagenomic assembly due to its high microbial diversity and variable evenness, resulting in low coverage and uneven sampling of microbial genomes. Despite increasingly large soil metagenome data volumes (>200 Gbp), the majority of the data do not assemble. Here, we used the cutting-edge approach of synthetic long-read sequencing technology (Moleculo) to assemble soil metagenome sequence data into long contigs and used the assemblies for binning of genomes. Author Video: Anauthor video summaryof this article is available.« less

Moleculo Long-Read Sequencing Facilitates Assembly and Genomic Binning from Complex Soil Metagenomes

PubMed Central

White, Richard Allen; Bottos, Eric M.; Roy Chowdhury, Taniya; Zucker, Jeremy D.; Brislawn, Colin J.; Nicora, Carrie D.; Fansler, Sarah J.; Glaesemann, Kurt R.; Glass, Kevin

2016-01-01

ABSTRACT Soil metagenomics has been touted as the “grand challenge” for metagenomics, as the high microbial diversity and spatial heterogeneity of soils make them unamenable to current assembly platforms. Here, we aimed to improve soil metagenomic sequence assembly by applying the Moleculo synthetic long-read sequencing technology. In total, we obtained 267 Gbp of raw sequence data from a native prairie soil; these data included 109.7 Gbp of short-read data (~100 bp) from the Joint Genome Institute (JGI), an additional 87.7 Gbp of rapid-mode read data (~250 bp), plus 69.6 Gbp (>1.5 kbp) from Moleculo sequencing. The Moleculo data alone yielded over 5,600 reads of >10 kbp in length, and over 95% of the unassembled reads mapped to contigs of >1.5 kbp. Hybrid assembly of all data resulted in more than 10,000 contigs over 10 kbp in length. We mapped three replicate metatranscriptomes derived from the same parent soil to the Moleculo subassembly and found that 95% of the predicted genes, based on their assignments to Enzyme Commission (EC) numbers, were expressed. The Moleculo subassembly also enabled binning of >100 microbial genome bins. We obtained via direct binning the first complete genome, that of “Candidatus Pseudomonas sp. strain JKJ-1” from a native soil metagenome. By mapping metatranscriptome sequence reads back to the bins, we found that several bins corresponding to low-relative-abundance Acidobacteria were highly transcriptionally active, whereas bins corresponding to high-relative-abundance Verrucomicrobia were not. These results demonstrate that Moleculo sequencing provides a significant advance for resolving complex soil microbial communities. IMPORTANCE Soil microorganisms carry out key processes for life on our planet, including cycling of carbon and other nutrients and supporting growth of plants. However, there is poor molecular-level understanding of their functional roles in ecosystem stability and responses to environmental perturbations. This knowledge gap is largely due to the difficulty in culturing the majority of soil microbes. Thus, use of culture-independent approaches, such as metagenomics, promises the direct assessment of the functional potential of soil microbiomes. Soil is, however, a challenge for metagenomic assembly due to its high microbial diversity and variable evenness, resulting in low coverage and uneven sampling of microbial genomes. Despite increasingly large soil metagenome data volumes (>200 Gbp), the majority of the data do not assemble. Here, we used the cutting-edge approach of synthetic long-read sequencing technology (Moleculo) to assemble soil metagenome sequence data into long contigs and used the assemblies for binning of genomes. Author Video: An author video summary of this article is available. PMID:27822530

Exciplex fluorescence emission from simple organic intramolecular constructs in non-polar and highly polar media as model systems for DNA-assembled exciplex detectors.

PubMed

Bichenkova, Elena V; Sardarian, Ali R; Wilton, Amanda N; Bonnet, Pascal; Bryce, Richard A; Douglas, Kenneth T

2006-01-21

Organic intramolecular exciplexes, N-(4-dimethylaminobenzyl)-N-(1-pyrenemethyl)amine (1) and N'-4-dimethylaminonaphthyl-N-(1-pyrenemethyl)amine (2), were used as model systems to reveal major factors affecting their exciplex fluorescence, and thus lay the basis for developing emissive target-assembled exciplexes for DNA-mounted systems in solution. These models with an aromatic pyrenyl hydrocarbon moiety as an electron acceptor appropriately connected to an aromatic dimethylamino electron donor component (N,N-dimethylaminophenyl or N,N-dimethylaminonaphthyl) showed strong intramolecular exciplex emission in both non-polar and highly polar solvents. The effect of dielectric constant on the maximum wavelength for exciplex emission was studied, and emission was observed for 1 and 2 over the full range of solvent from non-polar hydrocarbons up to N-methylformamide with a dielectric constant of 182. Quantum yields were determined for these intramolecular exciplexes in a range of solvents relative to that for Hoechst 33,258. Conformational analysis of 1 was performed both computationally and via qualitative 2D NMR using (1)H-NOESY experiments. The results obtained indicated the contribution of pre-folded conformation(s) to the ground state of 1 conducive to exciplex emission. This research provides the initial background for design of self-assembled, DNA-mounted exciplexes and underpins further development of exciplex-based hybridisation bioassays.

Atomistic and Coarse-Grained Modeling of the Adsorption of Graphene Nanoflakes at the Oil-Water Interface.

PubMed

Ardham, Vikram Reddy; Leroy, Frédéric

2018-03-01

The high interfacial tension between two immiscible liquids can provide the necessary driving force for the self-assembly of nanoparticles at the interface. Particularly, the interface between water and oily liquids (hydrocarbon chains) has been exploited to prepare networks of highly interconnected graphene sheets of only a few layers thickness, which are well suited for industrial applications. Studying such complex systems through particle-based simulations could greatly enhance the understanding of the various driving forces in action and could possibly give more control over the self-assembly process. However, the interaction potentials used in particle-based simulations are typically derived by reproducing bulk properties and are therefore not suitable for describing systems dominated by interfaces. To address this issue, we introduce a methodology to derive solid-liquid interaction potentials that yield an accurate representation of the balance between interfacial interactions at atomistic and coarse-grained resolutions. Our approach is validated through its ability to lead to the adsorption of graphene nanoflakes at the interface between water and n-hexane. The development of accurate coarse-grained potentials that our approach enables will allow us to perform large-scale simulations to study the assembly of graphene nanoparticles at the interface between immiscible liquids. Our methodology is illustrated through a simulation of many graphene nanoflakes adsorbing at the interface.

Production of porcine parvovirus empty capsids with high immunogenic activity.

PubMed

Martínez, C; Dalsgaard, K; López de Turiso, J A; Cortés, E; Vela, C; Casal, J I

1992-01-01

The VP2 gene of porcine parvovirus was cloned in the baculovirus system and expressed in insect cells. The resulting product was present in high yield. It self-assembled into particles which were structurally and antigenically indistinguishable from regular PPV capsids. A high degree of purity of the recombinant capsids was obtained by ammonium sulphate precipitation of cell lysates. These virus-like particles were used as antigen in the immunization of two pigs. The pigs elicited an immune response which, when assayed by standard serological techniques, was identical to that of a commercial vaccine. The amount of recombinant antigen needed in a vaccine dose was only 3 micrograms in a primary dose and 1.5 micrograms in the booster.

Template mediated protein self-assembly as a valuable tool in regenerative therapy.

PubMed

Kundu, B; Eltohamy, M; Yadavalli, V K; Reis, R L; Kim, H W

2018-04-11

The assembly of natural proteinaceous biopolymers into macro-scale architectures is of great importance in synthetic biology, soft-material science and regenerative therapy. The self-assembly of protein tends to be limited due to anisotropic interactions among protein molecules, poor solubility and stability. Here, we introduce a unique platform to self-immobilize diverse proteins (fibrous and globular, positively and negatively charged, low and high molecular weight) using silicon surfaces with pendant -NH 2 groups via a facile one step diffusion limited aggregation (DLA) method. All the experimental proteins (type I collagen, bovine serum albumin and cytochrome C) self-assemble into seaweed-like branched dendritic architectures via classical DLA in the absence of any electrolytes. The notable differences in branching architectures are due to dissimilarities in protein colloidal sub-units, which is typical for each protein type, along with the heterogeneous distribution of surface -NH 2 groups. Fractal analysis of assembled structures is used to explain the underlying route of fractal deposition; which concludes how proteins with different functionality can yield similar assembly. Further, the nano-micro-structured surfaces can be used to provide functional topographical cues to study cellular responses, as demonstrated using rat bone marrow stem cells. The results indicate that the immobilization of proteins via DLA does not affect functionality, instead serving as topographical cues to guide cell morphology. This indicates a promising design strategy at the tissue-material interface and is anticipated to guide future surface modifications. A cost-effective standard templating strategy is therefore proposed for fundamental and applied particle aggregation studies, which can be used at multiple length scales for biomaterial design and surface reformation.

Draft genome of the lined seahorse, Hippocampus erectus.

PubMed

Lin, Qiang; Qiu, Ying; Gu, Ruobo; Xu, Meng; Li, Jia; Bian, Chao; Zhang, Huixian; Qin, Geng; Zhang, Yanhong; Luo, Wei; Chen, Jieming; You, Xinxin; Fan, Mingjun; Sun, Min; Xu, Pao; Venkatesh, Byrappa; Xu, Junming; Fu, Hongtuo; Shi, Qiong

2017-06-01

The lined seahorse, Hippocampus erectus , is an Atlantic species and mainly inhabits shallow sea beds or coral reefs. It has become very popular in China for its wide use in traditional Chinese medicine. In order to improve the aquaculture yield of this valuable fish species, we are trying to develop genomic resources for assistant selection in genetic breeding. Here, we provide whole genome sequencing, assembly, and gene annotation of the lined seahorse, which can enrich genome resource and further application for its molecular breeding. A total of 174.6 Gb (Gigabase) raw DNA sequences were generated by the Illumina Hiseq2500 platform. The final assembly of the lined seahorse genome is around 458 Mb, representing 94% of the estimated genome size (489 Mb by k-mer analysis). The contig N50 and scaffold N50 reached 14.57 kb and 1.97 Mb, respectively. Quality of the assembled genome was assessed by BUSCO with prediction of 85% of the known vertebrate genes and evaluated using the de novo assembled RNA-seq transcripts to prove a high mapping ratio (more than 99% transcripts could be mapped to the assembly). Using homology-based, de novo and transcriptome-based prediction methods, we predicted 20 788 protein-coding genes in the generated assembly, which is less than our previously reported gene number (23 458) of the tiger tail seahorse ( H. comes ). We report a draft genome of the lined seahorse. These generated genomic data are going to enrich genome resource of this economically important fish, and also provide insights into the genetic mechanisms of its iconic morphology and male pregnancy behavior. © The Authors 2017. Published by Oxford University Press.

Draft genome of the lined seahorse, Hippocampus erectus

PubMed Central

Lin, Qiang; Qiu, Ying; Gu, Ruobo; Xu, Meng; Li, Jia; Bian, Chao; Zhang, Huixian; Qin, Geng; Zhang, Yanhong; Luo, Wei; Chen, Jieming; You, Xinxin; Fan, Mingjun; Sun, Min; Xu, Pao; Venkatesh, Byrappa

2017-01-01

Abstract Background: The lined seahorse, Hippocampus erectus, is an Atlantic species and mainly inhabits shallow sea beds or coral reefs. It has become very popular in China for its wide use in traditional Chinese medicine. In order to improve the aquaculture yield of this valuable fish species, we are trying to develop genomic resources for assistant selection in genetic breeding. Here, we provide whole genome sequencing, assembly, and gene annotation of the lined seahorse, which can enrich genome resource and further application for its molecular breeding. Findings: A total of 174.6 Gb (Gigabase) raw DNA sequences were generated by the Illumina Hiseq2500 platform. The final assembly of the lined seahorse genome is around 458 Mb, representing 94% of the estimated genome size (489 Mb by k-mer analysis). The contig N50 and scaffold N50 reached 14.57 kb and 1.97 Mb, respectively. Quality of the assembled genome was assessed by BUSCO with prediction of 85% of the known vertebrate genes and evaluated using the de novo assembled RNA-seq transcripts to prove a high mapping ratio (more than 99% transcripts could be mapped to the assembly). Using homology-based, de novo and transcriptome-based prediction methods, we predicted 20 788 protein-coding genes in the generated assembly, which is less than our previously reported gene number (23 458) of the tiger tail seahorse (H. comes). Conclusion: We report a draft genome of the lined seahorse. These generated genomic data are going to enrich genome resource of this economically important fish, and also provide insights into the genetic mechanisms of its iconic morphology and male pregnancy behavior. PMID:28444302

Study of low energy neutron beam formation based on GEANT4 simulations

NASA Astrophysics Data System (ADS)

Avagyan, R.; Avetisyan, R.; Ivanyan, V.; Kerobyan, I.

2017-07-01

The possibility of obtaining thermal/epithermal energy neutron beams using external protons from cyclotron C18/18 is studied based on GEANT4 simulations. This study will be the basis of the Beam Shaped Assembly (BSA) development for future Boron Neutron Capture Therapy (BNCT). Proton induced reactions on 9Be target are considered as a neutron source, and dependence of neutron yield on target thickness is investigated. The problem of reducing the ratio of gamma to neutron yields by inserting a lead sheet after the beryllium target is studied as well. By GEANT4 modeling the optimal thicknesses of 9Be target and lead absorber are determined and the design characteristics of beam shaping assembly, including the materials and thicknesses of reflector and moderator are considered.

Assembly and analysis of fragmentation data for liquid propellant vessels

NASA Technical Reports Server (NTRS)

Baker, W. E.; Parr, V. B.; Bessey, R. L.; Cox, P. A.

1974-01-01

Fragmentation data was assembled and analyzed for exploding liquid propellant vessels. These data were to be retrieved from reports of tests and accidents, including measurements or estimates of blast yield, etc. A significant amount of data was retrieved from a series of tests conducted for measurement of blast and fireball effects of liquid propellant explosions (Project PYRO), a few well-documented accident reports, and a series of tests to determine auto-ignition properties of mixing liquid propellants. The data were reduced and fitted to various statistical functions. Comparisons were made with methods of prediction for blast yield, initial fragment velocities, and fragment range. Reasonably good correlation was achieved. Methods presented in the report allow prediction of fragment patterns, given type and quantity of propellant, type of accident, and time of propellant mixing.

Redesigning Channel-Forming Peptides: Amino Acid Substitutions that Enhance Rates of Supramolecular Self-Assembly and Raise Ion Transport Activity

PubMed Central

Shank, Lalida P.; Broughman, James R.; Takeguchi, Wade; Cook, Gabriel; Robbins, Ashley S.; Hahn, Lindsey; Radke, Gary; Iwamoto, Takeo; Schultz, Bruce D.; Tomich, John M.

2006-01-01

Three series of 22-residue peptides derived from the transmembrane M2 segment of the glycine receptor α1-subunit (M2GlyR) have been designed, synthesized, and tested to determine the plasticity of a channel-forming sequence and to define whether channel pores with enhanced conductive properties could be created. Sixteen sequences were examined for aqueous solubility, solution-association tendency, secondary structure, and half-maximal concentration for supramolecular assembly, channel activity, and ion transport properties across epithelial monolayers. All peptides interact strongly with membranes: associating with, inserting across, and assembling to form homooligomeric bundles when in micromolar concentrations. Single and double amino acid replacements involving arginine and/or aromatic amino acids within the final five C-terminal residues of the peptide cause dramatic effects on the concentration dependence, yielding a range of K1/2 values from 36 ± 5 to 390 ± 220 μM for transport activity. New water/lipid interfacial boundaries were established for the transmembrane segment using charged or aromatic amino acids, thus limiting the peptides' ability to move perpendicularly to the plane of the bilayer. Formation of discrete water/lipid interfacial boundaries appears to be necessary for efficient supramolecular assembly and high anion transport activity. A peptide sequence is identified that may show efficacy in channel replacement therapy for channelopathies such as cystic fibrosis. PMID:16387776

Manufacturing and testing VLPC hybrids

NASA Astrophysics Data System (ADS)

Adkins, L. R.; Ingram, C. M.; Anderson, E. J.

1998-11-01

To insure that the manufacture of VLPC devices is a reliable, cost-effective technology, hybrid assembly procedures and testing methods suitable for large scale production have been developed. This technology has been developed under a contract from Fermilab as part of the D-Zero upgrade program. Each assembled hybrid consists of a VLPC chip mounted on an AlN substrate. The VLPC chip is provided with bonding pads (one connected to each pixel) which are wire bonded to gold traces on the substrate. The VLPC/AlN hybrids are mated in a vacuum sealer using solder preforms and a specially designed carbon boat. After mating, the VLPC pads are bonded to the substrate with an automatic wire bonder. Using this equipment we have achieved a thickness tolerance of ±0.0007 inches and a production rate of 100 parts per hour. After assembly the VLPCs are tested for optical response at an operating temperature of 7K. The parts are tested in a custom designed continuous-flow dewar with a capacity 15 hybrids, and one Lake Shore DT470-SD-11 calibrated temperature sensor mounted to an AlN substrate. Our facility includes five of these dewars with an ultimate test capacity of 75 parts per day. During the course of the Dzero program we have assembled more than 4,000 VLPC hybrids and have tested more than 2,500 with a high yield.

Self-assembly of hexahistidine-tagged tobacco etch virus capsid protein into microfilaments that induce IgG2-specific response against a soluble porcine reproductive and respiratory syndrome virus chimeric protein.

PubMed

Manuel-Cabrera, Carlos Alberto; Vallejo-Cardona, Alba Adriana; Padilla-Camberos, Eduardo; Hernández-Gutiérrez, Rodolfo; Herrera-Rodríguez, Sara Elisa; Gutiérrez-Ortega, Abel

2016-11-29

Assembly of recombinant capsid proteins into virus-like particles (VLPs) still represents an interesting challenge in virus-based nanotechnologies. The structure of VLPs has gained importance for the development and design of new adjuvants and antigen carriers. The potential of Tobacco etch virus capsid protein (TEV CP) as adjuvant has not been evaluated to date. Two constructs for TEV CP expression in Escherichia coli were generated: a wild-type version (TEV-CP) and a C-terminal hexahistidine (His)-tagged version (His-TEV-CP). Although both versions were expressed in the soluble fraction of E. coli lysates, only His-TEV-CP self-assembled into micrometric flexuous filamentous VLPs. In addition, the His-tag enabled high yields and facilitated purification of TEV VLPs. These TEV VLPs elicited broader IgG2-specific antibody response against a novel porcine reproductive and respiratory syndrome virus (PRRSV) protein when compared to the potent IgG1 response induced by the protein alone. His-TEV CP was purified by immobilized metal affinity chromatography and assembled into VLPs, some of them reaching 2-μm length. TEV VLPs administered along with PRRSV chimeric protein changed the IgG2/IgG1 ratio against the chimeric protein, suggesting that TEV CP can modulate the immune response against a soluble antigen.

Lipid dip-pen nanolithography on self-assembled monolayers

NASA Astrophysics Data System (ADS)

Gavutis, Martynas; Navikas, Vytautas; Rakickas, Tomas; Vaitekonis, Šarūnas; Valiokas, Ramūnas

2016-02-01

Dip-pen nanolithography (DPN) with lipids as an ink enables functional micro/nanopatterning on different substrates at high process speeds. However, only a few studies have addressed the influence of the physicochemical properties of the surface on the structure and phase behavior of DPN-printed lipid assemblies. Therefore, by combining the scanning probe and optical imaging techniques in this work we have analyzed lipid microdomain formation on the self-assembled monolayers (SAMs) on gold as well-defined model surfaces that displayed hydrophilic (protein-repellent) or hydrophobic (protein-adhesive) characteristics. We have found that on the tri(ethylene glycol)-terminated SAM the lipid ink transfer was fast (~10-1 μm3 s-1), quasi-linear and it yielded unstable, sparsely packed lipid microspots. Contrary to this, on the methyl-terminated SAM the lipid transfer was ~20 times slower, nonlinear, and the obtained stable dots of ~1 μm in diameter consisted of lipid multilayers. Our comparative analysis indicated that the measured lipid transfer was consistent with the previously reported so-called polymer transfer model (Felts et al 2012, Nanotechnology 23 215301). Further on, by employing the observed distinct contrast in the DPN ink behavior we constructed confined lipid microdomains on pre-patterned SAMs, in which the lipids assembled either into monolayer or multilamellar phases. Such microdomains can be further utilized for lipid membrane mimetics in microarray and lab-on-a-chip device formats.

Self-assembly of single "square" quantum rings in gold-free GaAs nanowires.

PubMed

Zha, Guowei; Shang, Xiangjun; Su, Dan; Yu, Ying; Wei, Bin; Wang, Li; Li, Mifeng; Wang, Lijuan; Xu, Jianxing; Ni, Haiqiao; Ji, Yuan; Sun, Baoquan; Niu, Zhichuan

2014-03-21

Single nanostructures embedded within nanowires (NWs) represent one of the most promising technologies for applications in quantum photonics. However, fabrication imperfections and etching-induced defects are inevitable for top-down fabrications, whereas self-assembly bottom-up approaches cannot avoid the difficulties of its stochastic nature and are limited to restricted heterogeneous material systems. Here we demonstrate the versatile self-assembly of single "square" quantum rings (QR) on the sidewalls of gold-free GaAs NWs for the first time. By tuning the deposition temperature, As overpressure and amount of gallium-droplets, we were able to control the density and morphology of the structure, yielding novel single quantum dots, QR, coupled QRs, and nano-antidots. A proposed model based on a strain-driven, transport-dependent nucleation of gallium droplets at high temperature accounts for the formation mechanism of these structures. We achieved a single-QR-in-NW structure, of which the optical properties were analyzed using micro-photoluminescence at 10 K and a spatially resolved cathodoluminescence technique at 77 K. The spectra show sharp discrete peaks; of these peaks, the narrowest linewidth (separation) was 578 μeV (1-3 meV), reflecting the quantized nature of the ring-type electronic states.

Physically unclonable cryptographic primitives using self-assembled carbon nanotubes.

PubMed

Hu, Zhaoying; Comeras, Jose Miguel M Lobez; Park, Hongsik; Tang, Jianshi; Afzali, Ali; Tulevski, George S; Hannon, James B; Liehr, Michael; Han, Shu-Jen

2016-06-01

Information security underpins many aspects of modern society. However, silicon chips are vulnerable to hazards such as counterfeiting, tampering and information leakage through side-channel attacks (for example, by measuring power consumption, timing or electromagnetic radiation). Single-walled carbon nanotubes are a potential replacement for silicon as the channel material of transistors due to their superb electrical properties and intrinsic ultrathin body, but problems such as limited semiconducting purity and non-ideal assembly still need to be addressed before they can deliver high-performance electronics. Here, we show that by using these inherent imperfections, an unclonable electronic random structure can be constructed at low cost from carbon nanotubes. The nanotubes are self-assembled into patterned HfO2 trenches using ion-exchange chemistry, and the width of the trench is optimized to maximize the randomness of the nanotube placement. With this approach, two-dimensional (2D) random bit arrays are created that can offer ternary-bit architecture by determining the connection yield and switching type of the nanotube devices. As a result, our cryptographic keys provide a significantly higher level of security than conventional binary-bit architecture with the same key size.

Physically unclonable cryptographic primitives using self-assembled carbon nanotubes

NASA Astrophysics Data System (ADS)

Hu, Zhaoying; Comeras, Jose Miguel M. Lobez; Park, Hongsik; Tang, Jianshi; Afzali, Ali; Tulevski, George S.; Hannon, James B.; Liehr, Michael; Han, Shu-Jen

2016-06-01

Information security underpins many aspects of modern society. However, silicon chips are vulnerable to hazards such as counterfeiting, tampering and information leakage through side-channel attacks (for example, by measuring power consumption, timing or electromagnetic radiation). Single-walled carbon nanotubes are a potential replacement for silicon as the channel material of transistors due to their superb electrical properties and intrinsic ultrathin body, but problems such as limited semiconducting purity and non-ideal assembly still need to be addressed before they can deliver high-performance electronics. Here, we show that by using these inherent imperfections, an unclonable electronic random structure can be constructed at low cost from carbon nanotubes. The nanotubes are self-assembled into patterned HfO2 trenches using ion-exchange chemistry, and the width of the trench is optimized to maximize the randomness of the nanotube placement. With this approach, two-dimensional (2D) random bit arrays are created that can offer ternary-bit architecture by determining the connection yield and switching type of the nanotube devices. As a result, our cryptographic keys provide a significantly higher level of security than conventional binary-bit architecture with the same key size.

Evaluation of ENDF/B-IV and Hansen--Roach /sup 233/U cross sections for use in criticality calculations

DOE Office of Scientific and Technical Information (OSTI.GOV)

McNeany, S.R.; Jenkins, J.D.

Eleven /sup 233/U solution critical assemblies spanning an H//sup 233/U ratio range of 40 to 2000 and an unreflected metal /sup 233/U assembly were calculated with ENDF/B-IV and Hansen--Roach cross sections. Results from these calculations are compared with the experimental results and with each other. An increasing disagreement is observed between calculations with ENDF/B and Hansen--Roach data with decreasing H//sup 233/U ratio, indicative of large differences in their intermediate-energy cross sections. The Hansen--Roach cross sections appeared to give reasonably good agreement with experiments over the whole range, whereas the ENDF/B calculations yielded high values for k/sub eff/ on assemblies ofmore » low moderation. It is concluded that serious problems exist in the ENDF/B-IV representation of the /sup 233/U cross sections in the intermediate energy range and that further evaluation of this nuclide is warranted. In addition, it is recommended that an experimental program be undertaken to obtain /sup 233/U criticality data at low H//sup 233/U ratios for verification of generalized criticality safety guidelines. 3 figures, 15 tables.« less

Sprayable, Paintable Layer-by-Layer Polyaniline Nanofiber/Graphene Electrodes for Electrochemical Energy Storage

NASA Astrophysics Data System (ADS)

Kwon, Se Ra; Jeon, Ju-Won; Lutkenhus, Jodie

2015-03-01

Sprayable batteries are growing in interest for applications in structural energy storage and power or flexible power. Spray-assisted layer-by-layer (LbL) assembly, in which complementary species are alternately sprayed onto a surface, is particularly amenable toward this application. Here, we report on the fabrication of composite films containing polyaniline nanofibers (PANI NF) and graphene oxide (GO) sheets fabricated via spray-assisted LbL assembly. The resulting films are electrochemical reduced to yield PANI NF/electrochemically reduced graphene (ERGO) electrodes for use as a cathode in non-aqueous energy storage systems. Through the spray-assisted LbL process, the hybrid electrodes could be fabricated 74 times faster than competing dip-assisted LbL assembly. The resulting electrodes are highly porous (0.72 void fraction), and are comprised of 67 wt% PANI NF and 33 wt% ERGO. The sprayed electrodes showed better rate capability, higher specific power, as well as more stable cycle life than dip-assisted LbL electrodes. It is shown here that the spray-assisted LbL approach is well-suited towards the fabrication of paintable electrodes containing polyaniline nanofibers and electrochemically reduced graphene oxide sheets.

Bipartite design of a self-fibrillating protein copolymer with nanopatterned peptide display capabilities.

PubMed

Bruning, Marc; Kreplak, Laurent; Leopoldseder, Sonja; Müller, Shirley A; Ringler, Philippe; Duchesne, Laurence; Fernig, David G; Engel, Andreas; Ucurum-Fotiadis, Zöhre; Mayans, Olga

2010-11-10

The development of biomatrices for technological and biomedical applications employs self-assembled scaffolds built from short peptidic motifs. However, biopolymers composed of protein domains would offer more varied molecular frames to introduce finer and more complex functionalities in bioreactive scaffolds using bottom-up approaches. Yet, the rules governing the three-dimensional organization of protein architectures in nature are complex and poorly understood. As a result, the synthetic fabrication of ordered protein association into polymers poses major challenges to bioengineering. We have now fabricated a self-assembling protein nanofiber with predictable morphologies and amenable to bottom-up customization, where features supporting function and assembly are spatially segregated. The design was inspired by the cross-linking of titin filaments by telethonin in the muscle sarcomere. The resulting fiber is a two-protein system that has nanopatterned peptide display capabilities as shown by the recruitment of functionalized gold nanoparticles at regular intervals of ∼ 5 nm, yielding a semiregular linear array over micrometers. This polymer promises the uncomplicated display of biologically active motifs to selectively bind and organize matter in the fine nanoscale. Further, its conceptual design has high potential for controlled plurifunctionalization.

Little Boy replication: justification and construction

DOE Office of Scientific and Technical Information (OSTI.GOV)

Malenfant, R.E.

A reconstruction of the Little Boy weapon allowed experiments to evaluate yield, leakage measurements for comparison with calculations, and phenomenological measurements to evaluate various in-situ dosimeters. The reconstructed weapon was operated at sustained delayed critical at the Los Alamos Critical Assembly Facility. The present experiments provide a wealth of information to benchmark calculations and demonstrate that the 1965 measurements on the Ichiban assembly (a spherical mockup of Little Boy) were in error. 5 references, 2 figures.

Self-assembly of nucleic acids, silk and hybrid materials thereof.

PubMed

Humenik, Martin; Scheibel, Thomas

2014-12-17

Top-down approaches based on etching techniques have almost reached their limits in terms of dimension. Therefore, novel assembly strategies and types of nanomaterials are required to allow technological advances. Self-assembly processes independent of external energy sources and unlimited in dimensional scaling have become a very promising approach. Here,we highlight recent developments in self-assembled DNA-polymer, silk-polymer and silk-DNA hybrids as promising materials with biotic and abiotic moieties for constructing complex hierarchical materials in ‘bottom-up’ approaches. DNA block copolymers assemble into nanostructures typically exposing a DNA corona which allows functionalization, labeling and higher levels of organization due to its specific addressable recognition properties. In contrast, self-assembly of natural silk proteins as well as their recombinant variants yields mechanically stable β-sheet rich nanostructures. The combination of silk with abiotic polymers gains hybrid materials with new functionalities. Together, the precision of DNA hybridization and robustness of silk fibrillar structures combine in novel conjugates enable processing of higher-order structures with nanoscale architecture and programmable functions.

Self-assembly of nucleic acids, silk and hybrid materials thereof

NASA Astrophysics Data System (ADS)

Humenik, Martin; Scheibel, Thomas

2014-12-01

Top-down approaches based on etching techniques have almost reached their limits in terms of dimension. Therefore, novel assembly strategies and types of nanomaterials are required to allow technological advances. Self-assembly processes independent of external energy sources and unlimited in dimensional scaling have become a very promising approach. Here, we highlight recent developments in self-assembled DNA-polymer, silk-polymer and silk-DNA hybrids as promising materials with biotic and abiotic moieties for constructing complex hierarchical materials in ‘bottom-up’ approaches. DNA block copolymers assemble into nanostructures typically exposing a DNA corona which allows functionalization, labeling and higher levels of organization due to its specific addressable recognition properties. In contrast, self-assembly of natural silk proteins as well as their recombinant variants yields mechanically stable β-sheet rich nanostructures. The combination of silk with abiotic polymers gains hybrid materials with new functionalities. Together, the precision of DNA hybridization and robustness of silk fibrillar structures combine in novel conjugates enable processing of higher-order structures with nanoscale architecture and programmable functions.

Stepwise Assembly and Characterization of DNA Linked Two-Color Quantum Dot Clusters.

PubMed

Coopersmith, Kaitlin; Han, Hyunjoo; Maye, Mathew M

2015-07-14

The DNA-mediated self-assembly of multicolor quantum dot (QD) clusters via a stepwise approach is described. The CdSe/ZnS QDs were synthesized and functionalized with an amphiphilic copolymer, followed by ssDNA conjugation. At each functionalization step, the QDs were purified via gradient ultracentrifugation, which was found to remove excess polymer and QD aggregates, allowing for improved conjugation yields and assembly reactivity. The QDs were then assembled and disassembled in a stepwise manner at a ssDNA functionalized magnetic colloid, which provided a convenient way to remove unreacted QDs and ssDNA impurities. After assembly/disassembly, the clusters' optical characteristics were studied by fluorescence spectroscopy and the assembly morphology and stoichiometry was imaged via electron microscopy. The results indicate that a significant amount of QD-to-QD energy transfer occurred in the clusters, which was studied as a function of increasing acceptor-to-donor ratios, resulting in increased QD acceptor emission intensities compared to controls.

Molecular Design of Performance Proteins With Repetitive Sequences

NASA Astrophysics Data System (ADS)

Vendrely, Charlotte; Ackerschott, Christian; Römer, Lin; Scheibel, Thomas

Most performance proteins responsible for the mechanical stability of cells and organisms reveal highly repetitive sequences. Mimicking such performance proteins is of high interest for the design of nanostructured biomaterials. In this article, flagelliform silk is exemplary introduced to describe a general principle for designing genes of repetitive performance proteins for recombinant expression in Escherichia coli . In the first step, repeating amino acid sequence motifs are reversely transcripted into DNA cassettes, which can in a second step be seamlessly ligated, yielding a designed gene. Recombinant expression thereof leads to proteins mimicking the natural ones. The recombinant proteins can be assembled into nanostructured materials in a controlled manner, allowing their use in several applications.

High-yield production of canine parvovirus virus-like particles in a baculovirus expression system.

PubMed

Jin, Hongli; Xia, Xiaohong; Liu, Bing; Fu, Yu; Chen, Xianping; Wang, Huihui; Xia, Zhenqiang

2016-03-01

An optimized VP2 gene from the current prevalent CPV strain (new CPV-2a) in China was expressed in a baculovirus expression system. It was found that the VP2 proteins assembled into virus-like particles (VLPs) with antigenic properties similar to those of natural CPV and with an especially high hemagglutination (HA) titer (1:2(20)). Dogs intramuscularly or orally immunized with VLPs produced antibodies against CPV with >1:80 hemagglutination inhibition (HI) units for at least 3 months. The CPV VLPs could be considered for use as a vaccine against CPV or as a platform for research on chimeric VLP vaccines against other diseases.

Amphiphilic complexes of Ho(iii), Dy(iii), Tb(iii) and Eu(iii) for optical and high field magnetic resonance imaging.

PubMed

Harris, Michael; Henoumont, Céline; Peeters, Wannes; Toyouchi, Shuichi; Vander Elst, Luce; Parac-Vogt, Tatjana N

2018-05-29

Lanthanides, holmium(iii), dysprosium(iii), and terbium(iii), were coordinated to an amphiphilic DOTA bis-coumarin derivative and then further assembled with an amphiphilic europium(iii) DTPA bis-coumarin derivative into mono-disperse micelles. The self-assembled micelles were characterized and assessed for their potential as bimodal contrast agents for high field magnetic resonance and optical imaging applications. All micelles showed a high transverse relaxation (r2) of 46, 34, and 30 s-1 mM-1 at 500 MHz and 37 °C for Dy(iii), Ho(iii) and Tb(iii), respectively, which is a result of the high magnetic moment of these lanthanides and the long rotational correlation time of the micelles. The quantum yield in aqueous solution ranged from 1.8% for Tb/Eu to 1.4% for Dy/Eu and 1.0% for the Ho/Eu micelles. Multi-photon excited emission spectroscopy has shown that due to the two-photon absorption of the coumarin chromophore the characteristic Eu(iii) emission could be observed upon excitation at 800 nm, demonstrating the usefulness of the system for in vivo fluorescence imaging applications. To the best of our knowledge, this is the first example reporting the potential of a holmium(iii) chelate as a negative MRI contrast agent.

Detection of Intermediates And Kinetic Control During Assembly of Bacteriophage P22 Procapsid

DOE Office of Scientific and Technical Information (OSTI.GOV)

Tuma, R.; Tsuruta, H.; French, K.H.

2009-05-26

Bacteriophage P22 serves as a model for the assembly and maturation of other icosahedral double-stranded DNA viruses. P22 coat and scaffolding proteins assemble in vitro into an icosahedral procapsid, which then expands during DNA packaging (maturation). Efficient in vitro assembly makes this system suitable for design and production of monodisperse spherical nanoparticles (diameter {approx} 50 nm). In this work, we explore the possibility of controlling the outcome of assembly by scaffolding protein engineering. The scaffolding protein exists in monomer-dimer-tetramer equilibrium. We address the role of monomers and dimers in assembly by using three different scaffolding proteins with altered monomer-dimer equilibriummore » (weak dimer, covalent dimer, monomer). The progress and outcome of assembly was monitored by time-resolved X-ray scattering, which allowed us to distinguish between closed shells and incomplete assembly intermediates. Binding of scaffolding monomer activates the coat protein for assembly. Excess dimeric scaffolding protein resulted in rapid nucleation and kinetic trapping yielding incomplete shells. Addition of monomeric wild-type scaffold with excess coat protein completed these metastable shells. Thus, the monomeric scaffolding protein plays an essential role in the elongation phase by activating the coat and effectively lowering its critical concentration for assembly.« less

Control and automation of multilayered integrated microfluidic device fabrication.

PubMed

Kipper, Sarit; Frolov, Ludmila; Guy, Ortal; Pellach, Michal; Glick, Yair; Malichi, Asaf; Knisbacher, Binyamin A; Barbiro-Michaely, Efrat; Avrahami, Dorit; Yavets-Chen, Yehuda; Levanon, Erez Y; Gerber, Doron

2017-01-31

Integrated microfluidics is a sophisticated three-dimensional (multi layer) solution for high complexity serial or parallel processes. Fabrication of integrated microfluidic devices requires soft lithography and the stacking of thin-patterned PDMS layers. Precise layer alignment and bonding is crucial. There are no previously reported standards for alignment of the layers, which is mostly performed using uncontrolled processes with very low alignment success. As a result, integrated microfluidics is mostly used in academia rather than in the many potential industrial applications. We have designed and manufactured a semiautomatic Microfluidic Device Assembly System (μDAS) for full device production. μDAS comprises an electrooptic mechanical system consisting of four main parts: optical system, smart media holder (for PDMS), a micropositioning xyzθ system and a macropositioning XY mechanism. The use of the μDAS yielded valuable information regarding PDMS as the material for device fabrication, revealed previously unidentified errors, and enabled optimization of a robust fabrication process. In addition, we have demonstrated the utilization of the μDAS technology for fabrication of a complex 3 layered device with over 12 000 micromechanical valves and an array of 64 × 64 DNA spots on a glass substrate with high yield and high accuracy. We increased fabrication yield from 25% to about 85% with an average layer alignment error of just ∼4 μm. It also increased our protein expression yields from 80% to over 90%, allowing us to investigate more proteins per experiment. The μDAS has great potential to become a valuable tool for both advancing integrated microfluidics in academia and producing and applying microfluidic devices in the industry.

Electrorheological suspensions of laponite in oil: rheometry studies.

PubMed

Parmar, K P S; Méheust, Y; Schjelderupsen, Børge; Fossum, J O

2008-03-04

We have studied the effect of an external direct current (DC) electric field ( approximately 1 kV/mm) on the rheological properties of colloidal suspensions consisting of aggregates of laponite particles in a silicone oil. Microscopy observations show that, under application of an electric field greater than a triggering electric field Ec approximately 0.6 kV/mm, laponite aggregates assemble into chain- and/or columnlike structures in the oil. Without an applied electric field, the steady-state shear behavior of such suspensions is Newtonian-like. Under application of an electric field larger than Ec, it changes dramatically as a result of the changes in the microstructure: a significant yield stress is measured, and under continuous shear the fluid is shear-thinning. The rheological properties, in particular the dynamic and static shear stress, were studied as a function of particle volume fraction for various strengths (including null) of the applied electric field. The flow curves at constant shear rate can be scaled with respect to both the particle fraction and electric field strength onto a master curve. This scaling is consistent with simple scaling arguments. The shape of the master curve accounts for the system's complexity; it approaches a standard power-law model at high Mason numbers. Both dynamic and static yield stresses are observed to depend on the particle fraction Phi and electric field E as PhibetaEalpha, with alpha approximately 1.85 and beta approximately 1 and 1.70 for the dynamic and static yield stresses, respectively. The yield stress was also determined as the critical stress at which there occurs a bifurcation in the rheological behavior of suspensions that are submitted to a constant shear stress; a scaling law with alpha approximately 1.84 and beta approximately 1.70 was obtained. The effectiveness of the latter technique confirms that such electrorheological (ER) fluids can be studied in the framework of thixotropic fluids. The method is very reproducible; we suggest that it could be used routinely for studying ER fluids. The measured overall yield stress behavior of the suspensions may be explained in terms of standard conduction models for electrorheological systems. Interesting prospects include using such systems for guided self-assembly of clay nanoparticles.

Structural assembly demonstration experiment, phase 1

NASA Astrophysics Data System (ADS)

Akin, David L.; Bowden, Mary L.; Miller, Rene H.

1983-03-01

The goal of this phase of the structural assembly and demonstration experiment (SADE) program was to begin to define a shuttle flight experiment that would yield data to compare on-orbit assembly operations of large space structures with neutral buoyancy simulations. In addition, the experiment would be an early demonstration of structural hardware and human capabilities in extravehicular activity (EVA). The objectives of the MIT study, as listed in the statement of work, were: to provide support in establishing a baseline neutral buoyancy testing data base, to develop a correlation technique between neutral buoyancy test results and on-orbit operations, and to prepare the SADE experiment plan (MSFC-PLAN-913).

Building superlattices from individual nanoparticles via template-confined DNA-mediated assembly

NASA Astrophysics Data System (ADS)

Lin, Qing-Yuan; Mason, Jarad A.; Li, Zhongyang; Zhou, Wenjie; O’Brien, Matthew N.; Brown, Keith A.; Jones, Matthew R.; Butun, Serkan; Lee, Byeongdu; Dravid, Vinayak P.; Aydin, Koray; Mirkin, Chad A.

2018-02-01

DNA programmable assembly has been combined with top-down lithography to construct superlattices of discrete, reconfigurable nanoparticle architectures on a gold surface over large areas. Specifically, the assembly of individual colloidal plasmonic nanoparticles with different shapes and sizes is controlled by oligonucleotides containing “locked” nucleic acids and confined environments provided by polymer pores to yield oriented architectures that feature tunable arrangements and independently controllable distances at both nanometer- and micrometer-length scales. These structures, which would be difficult to construct by other common assembly methods, provide a platform to systematically study and control light-matter interactions in nanoparticle-based optical materials. The generality and potential of this approach are explored by identifying a broadband absorber with a solvent polarity response that allows dynamic tuning of visible light absorption.

Water droplets as template for next-generation self-assembled poly-(etheretherketone) with cardo membranes.

PubMed

Gugliuzza, Annarosa; Aceto, Marianna Carmela; Macedonio, Francesca; Drioli, Enrico

2008-08-28

Next generation PEEK-WC membranes have been fabricated by using an innovative self-assembly technique. Patterned architectures have been achieved via a solvent-reduced and water-assisted process, resulting in honeycomb packed geometry. The membranes exhibit monodisperse pores with size and shape comparable to those left by templating water droplets. Influencing factors for the formation of self-assembled poly-(etheretherketone) with Cardo [PEEK-WC] membranes have been evaluated, identifying the critical parameters for nucleation, growth, and propagation of the droplet-mobile arrays through the overall films. Structure-transport relationships have been discussed according to the results achieved from the implementation of membrane distillation processes, yielding indication about the suitability of self-assembled PEEK-WC films to work as interfaces in contactor operations.

A novel form of β-strand assembly observed in Aβ33-42 adsorbed onto graphene

NASA Astrophysics Data System (ADS)

Wang, Xiaofeng; Weber, Jeffrey K.; Liu, Lei; Dong, Mingdong; Zhou, Ruhong; Li, Jingyuan

2015-09-01

Peptide assembly plays a seminal role in the fabrication of structural and functional architectures in cells. Characteristically, peptide assemblies are often dominated by β-sheet structures, wherein component molecules are connected by backbone hydrogen bonds in a parallel or an antiparallel fashion. While β-rich peptide scaffolds are implicated in an array of neurodegenerative diseases, the mechanisms by which toxic peptides assemble and mediate neuropathic effects are still poorly understood. In this work, we employ molecular dynamics simulations to study the adsorption and assembly of the fragment Aβ33-42 (taken from the Aβ-42 peptide widely associated with Alzheimer's disease) on a graphene surface. We observe that such Aβ33-42 fragments, which are largely hydrophobic in character, readily adsorb onto the graphitic surface and coalesce into a well-structured, β-strand-like assembly. Strikingly, the structure of such complex is quite unique: hydrophobic side-chains extend over the graphene surface and interact with adjacent peptides, yielding a well-defined mosaic of hydrophobic interaction patches. This ordered structure is markedly depleted of backbone hydrogen bonds. Hence, our simulation results reveal a distinct type of β-strand assembly, maintained by hydrophobic side-chain interactions. Our finding suggests the backbone hydrogen bond is no longer crucial to the peptide assembly. Further studies concerning whether such β-strand assembly can be realized in other peptide systems and in biologically-relevant contexts are certainly warranted.Peptide assembly plays a seminal role in the fabrication of structural and functional architectures in cells. Characteristically, peptide assemblies are often dominated by β-sheet structures, wherein component molecules are connected by backbone hydrogen bonds in a parallel or an antiparallel fashion. While β-rich peptide scaffolds are implicated in an array of neurodegenerative diseases, the mechanisms by which toxic peptides assemble and mediate neuropathic effects are still poorly understood. In this work, we employ molecular dynamics simulations to study the adsorption and assembly of the fragment Aβ33-42 (taken from the Aβ-42 peptide widely associated with Alzheimer's disease) on a graphene surface. We observe that such Aβ33-42 fragments, which are largely hydrophobic in character, readily adsorb onto the graphitic surface and coalesce into a well-structured, β-strand-like assembly. Strikingly, the structure of such complex is quite unique: hydrophobic side-chains extend over the graphene surface and interact with adjacent peptides, yielding a well-defined mosaic of hydrophobic interaction patches. This ordered structure is markedly depleted of backbone hydrogen bonds. Hence, our simulation results reveal a distinct type of β-strand assembly, maintained by hydrophobic side-chain interactions. Our finding suggests the backbone hydrogen bond is no longer crucial to the peptide assembly. Further studies concerning whether such β-strand assembly can be realized in other peptide systems and in biologically-relevant contexts are certainly warranted. Electronic supplementary information (ESI) available. See DOI: 10.1039/c5nr00555h

Unc-45 Mutations in Caenorhabditis elegans Implicate a CRO1/She4p-like Domain in Myosin Assembly

PubMed Central

Barral, José M.; Bauer, Christopher C.; Ortiz, Irving; Epstein, Henry F.

1998-01-01

The Caenorhabditis elegans unc-45 locus has been proposed to encode a protein machine for myosin assembly. The UNC-45 protein is predicted to contain an NH2-terminal domain with three tetratricopeptide repeat motifs, a unique central region, and a COOH-terminal domain homologous to CRO1 and She4p. CRO1 and She4p are fungal proteins required for the segregation of other molecules in budding, endocytosis, and septation. Three mutations that lead to temperature-sensitive (ts) alleles have been localized to conserved residues within the CRO1/She4p-like domain, and two lethal alleles were found to result from stop codon mutations in the central region that would prevent translation of the COOH-terminal domain. Electron microscopy shows that thick filament accumulation in vivo is decreased by ∼50% in the CB286 ts mutant grown at the restrictive temperature. The thick filaments that assemble have abnormal structure. Immunofluorescence and immunoelectron microscopy show that myosins A and B are scrambled, in contrast to their assembly into distinct regions at the permissive temperature and in wild type. This abnormal structure correlates with the high degree of instability of the filaments in vitro as reflected by their extremely low yields and shortened lengths upon isolation. These results implicate the UNC-45 CRO1/She4p-like region in the assembly of myosin isoforms in C. elegans and suggest a possible common mechanism for the function of this UCS (UNC-45/CRO1/She4p) protein family. PMID:9832550

An efficient optical-electrochemical dual probe for highly sensitive recognition of dopamine based on terbium complex functionalized reduced graphene oxide

NASA Astrophysics Data System (ADS)

Zhou, Zhan; Wang, Qianming

2014-04-01

A novel organic-inorganic hybrid sensor based on diethylenetriaminepentaacetic acid (DTPA) modified reduced graphene oxide (RGO-DTPA) chelated with terbium ions allows detection of dopamine (DA) through an emission enhancement effect. Its luminescence, peaking at 545 nm, has been improved by a factor of 25 in the presence of DA (detection limit = 80 nM). In addition, this covalently bonded terbium complex functionalized reduced graphene oxide (RGO-DTPA-Tb) can be successfully assembled on a glassy carbon electrode. The assay performed through differential pulse voltammetry (DPV) yielded obvious peak separation between DA and excessive amounts of the interfering ascorbic acid (AA).A novel organic-inorganic hybrid sensor based on diethylenetriaminepentaacetic acid (DTPA) modified reduced graphene oxide (RGO-DTPA) chelated with terbium ions allows detection of dopamine (DA) through an emission enhancement effect. Its luminescence, peaking at 545 nm, has been improved by a factor of 25 in the presence of DA (detection limit = 80 nM). In addition, this covalently bonded terbium complex functionalized reduced graphene oxide (RGO-DTPA-Tb) can be successfully assembled on a glassy carbon electrode. The assay performed through differential pulse voltammetry (DPV) yielded obvious peak separation between DA and excessive amounts of the interfering ascorbic acid (AA). Electronic supplementary information (ESI) available. See DOI: 10.1039/c3nr06156f

Cataphoretic assembly of cationic dyes and deposition of carbon nanotube and graphene films.

PubMed

Su, Y; Zhitomirsky, I

2013-06-01

Cathodic electrophoretic deposition (EPD) method has been developed for the fabrication of thin films from aqueous solutions of crystal violet (CV) dyes. The films contained rod-like particles with a long axis oriented perpendicular to the substrate surface. The proposed deposition mechanism involved cataphoresis of cationic CV(+) species, base generation in the cathodic reactions, and charge neutralization at the electrode surface. The assembly of rod-like particles was governed by π-π interactions of polyaromatic CV molecules. The deposition kinetics was studied by quartz crystal microbalance. CV dyes allowed efficient dispersion of multiwalled carbon nanotubes (MWCNTs) and graphene in water at relatively low CV concentrations. The feasibility of cathodic EPD of MWCNT and graphene from aqueous suspensions, containing CV, has been demonstrated. The deposition yield was investigated at different CV concentrations and deposition voltages. The relatively high deposition yield of MWCNT and graphene indicated that CV is an efficient dispersing, charging, and film forming agent for EPD. Electron microscopy data showed that at low CV concentrations in MWCNT or graphene suspensions and low deposition voltages, the films contained mainly MWCNT or graphene. The increase in the CV concentration and/or deposition voltage resulted in enhanced co-deposition of CV. The EPD method developed in this investigation paves the way for the fabrication of advanced nanocomposites by cathodic electrodeposition. Copyright © 2013 Elsevier Inc. All rights reserved.

Influences of urea–glycerol mixtures as mixed mesopore-controlling agents on tailoring physicochemical properties and photocatalytic H{sub 2} production activity of sol–gel-derived mesoporous-assembled TiO{sub 2} nanocrystals

DOE Office of Scientific and Technical Information (OSTI.GOV)

Sreethawong, Thammanoon, E-mail: sreethawongt@imre.a-star.edu.sg; Ngamsinlapasathian, Supachai, E-mail: wonone@hotmail.com; Yoshikawa, Susumu

2013-01-15

Graphical abstract: Display Omitted Highlights: ► Mesoporous-assembled TiO{sub 2} nanocrystals were synthesized by modified sol–gel process. ► Urea–glycerol mixtures were applied as mixed mesopore-controlling agents. ► Urea and glycerol contents affected physicochemical properties of synthesized TiO{sub 2}. ► Photocatalytic H{sub 2} production activity also depended on urea and glycerol contents. ► 75 mol% urea and 25 mol% glycerol yielded the most photocatalytically active TiO{sub 2}. -- Abstract: In this work, the mesoporous-assembled TiO{sub 2} nanocrystal photocatalysts were successfully synthesized by a sol–gel process with the aid of urea–glycerol mixtures used as mixed mesopore-controlling agents. The photocatalytic activity of the synthesizedmore » mesoporous-assembled TiO{sub 2} nanocrystal photocatalysts was investigated for hydrogen production from the water splitting reaction using methanol as a hole scavenger under UV light irradiation. The synthesized TiO{sub 2} nanocrystal photocatalysts were systematically characterized by TG–DTA, N{sub 2} adsorption–desorption, SEM, high resolution TEM, and XRD analyses. The characterization results showed that the well-controlled contents of urea and glycerol in a urea–glycerol mixture at 75 mol% urea and 25 mol% glycerol resulted in not only the most highly porous network (i.e. the highest specific surface area and total pore volume, and the smallest mean mesopore diameter), but also the smallest crystallite size of the synthesized TiO{sub 2} nanocrystal photocatalyst. The photocatalytic reaction results, hence, revealed a much superior photocatalytic hydrogen production activity of the mesoporous-assembled TiO{sub 2} nanocrystal synthesized with 75 mol% urea and 25 mol% glycerol to the other synthesized TiO{sub 2} nanocrystals, also being much higher than those of the commercially available P-25 TiO{sub 2} and ST-01 TiO{sub 2} powders.« less

An Assessment of the Detection of Highly Enriched Uranium and its Use in an Improvised Nuclear Device using the Monte Carlo Computer Code MCNP-5

NASA Astrophysics Data System (ADS)

Cochran, Thomas

2007-04-01

In 2002 and again in 2003, an investigative journalist unit at ABC News transported a 6.8 kilogram metallic slug of depleted uranium (DU) via shipping container from Istanbul, Turkey to Brooklyn, NY and from Jakarta, Indonesia to Long Beach, CA. Targeted inspection of these shipping containers by Department of Homeland Security (DHS) personnel, included the use of gamma-ray imaging, portal monitors and hand-held radiation detectors, did not uncover the hidden DU. Monte Carlo analysis of the gamma-ray intensity and spectrum of a DU slug and one consisting of highly-enriched uranium (HEU) showed that DU was a proper surrogate for testing the ability of DHS to detect the illicit transport of HEU. Our analysis using MCNP-5 illustrated the ease of fully shielding an HEU sample to avoid detection. The assembly of an Improvised Nuclear Device (IND) -- a crude atomic bomb -- from sub-critical pieces of HEU metal was then examined via Monte Carlo criticality calculations. Nuclear explosive yields of such an IND as a function of the speed of assembly of the sub-critical HEU components were derived. A comparison was made between the more rapid assembly of sub-critical pieces of HEU in the ``Little Boy'' (Hiroshima) weapon's gun barrel and gravity assembly (i.e., dropping one sub-critical piece of HEU on another from a specified height). Based on the difficulty of detection of HEU and the straightforward construction of an IND utilizing HEU, current U.S. government policy must be modified to more urgently prioritize elimination of and securing the global inventories of HEU.

An exactly solvable model of hierarchical self-assembly

NASA Astrophysics Data System (ADS)

Dudowicz, Jacek; Douglas, Jack F.; Freed, Karl F.

2009-06-01

Many living and nonliving structures in the natural world form by hierarchical organization, but physical theories that describe this type of organization are scarce. To address this problem, a model of equilibrium self-assembly is formulated in which dynamically associating species organize into hierarchical structures that preserve their shape at each stage of assembly. In particular, we consider symmetric m-gons that associate at their vertices into Sierpinski gasket structures involving the hierarchical association of triangles, squares, hexagons, etc., at their corner vertices, thereby leading to fractal structures after many generations of assembly. This rather idealized model of hierarchical assembly yields an infinite sequence of self-assembly transitions as the morphology progressively organizes to higher levels of the hierarchy, and these structures coexists at dynamic equilibrium, as found in real hierarchically self-assembling systems such as amyloid fiber forming proteins. Moreover, the transition sharpness progressively grows with increasing m, corresponding to larger and larger loops in the assembled structures. Calculations are provided for several basic thermodynamic properties (including the order parameters for assembly for each stage of the hierarchy, average mass of clusters, specific heat, transition sharpness, etc.) that are required for characterizing the interaction parameters governing this type of self-assembly and for elucidating other basic qualitative aspects of these systems. Our idealized model of hierarchical assembly gives many insights into this ubiquitous type of self-organization process.

An electrochemical rebalance cell for Redox systems

NASA Technical Reports Server (NTRS)

Acevedo, J. C.; Stalnaker, D. K.

1983-01-01

An electrochemical rebalance cell for maintaining electrochemical balance, at the system level, of the acidified aqueous iron chloride and chromium chloride reactant solutions in the redox energy storage system was constructed and evaluated. The electrochemical reaction for the cathode is Fe(+3) + e(-) yields Fe(+2), and that for the anode is 1/2H2 yields H(+) + e(-). The iron (carbon felt) electrode and the hydrogen (platinized carbon) electrode are separated by an anion exchange membrane. The performance of the rebalance cell is discussed as well as the assembly of a single rebalance cell and multicell stacks. Various cell configurations were tested and the results are presented and discussed. The rebalance cell was also used to demonstrate its ability, as a preparative tool, for making high purity solutions of soluble reduced metal ionic species. Preparations of titanium, copper, vanadium and chromium ions in acidified solutions were evaluated.

The heterogeneous integration of single-walled carbon nanotubes onto complementary metal oxide semiconductor circuitry for sensing applications.

PubMed

Chen, Chia-Ling; Agarwal, Vinay; Sonkusale, Sameer; Dokmeci, Mehmet R

2009-06-03

A simple methodology for integrating single-walled carbon nanotubes (SWNTs) onto complementary metal oxide semiconductor (CMOS) circuitry is presented. The SWNTs were incorporated onto the CMOS chip as the feedback resistor of a two-stage Miller compensated operational amplifier utilizing dielectrophoretic assembly. The measured electrical properties from the integrated SWNTs yield ohmic behavior with a two-terminal resistance of approximately 37.5 kOmega and the measured small signal ac gain (-2) from the inverting amplifier confirmed successful integration of carbon nanotubes onto the CMOS circuitry. Furthermore, the temperature response of the SWNTs integrated onto CMOS circuitry has been measured and had a thermal coefficient of resistance (TCR) of -0.4% degrees C(-1). This methodology, demonstrated for the integration of SWNTs onto CMOS technology, is versatile, high yield and paves the way for the realization of novel miniature carbon-nanotube-based sensor systems.

RNA-Seq Analysis Using De Novo Transcriptome Assembly as a Reference for the Salmon Louse Caligus rogercresseyi

PubMed Central

Gallardo-Escárate, Cristian; Valenzuela-Muñoz, Valentina; Nuñez-Acuña, Gustavo

2014-01-01

Despite the economic and environmental impacts that sea lice infestations have on salmon farming worldwide, genomic data generated by high-throughput transcriptome sequencing for different developmental stages, sexes, and strains of sea lice is still limited or unknown. In this study, RNA-seq analysis was performed using de novo transcriptome assembly as a reference for evidenced transcriptional changes from six developmental stages of the salmon louse Caligus rogercresseyi. EST-datasets were generated from the nauplius I, nauplius II, copepodid and chalimus stages and from female and male adults using MiSeq Illumina sequencing. A total of 151,788,682 transcripts were yielded, which were assembled into 83,444 high quality contigs and subsequently annotated into roughly 24,000 genes based on known proteins. To identify differential transcription patterns among salmon louse stages, cluster analyses were performed using normalized gene expression values. Herein, four clusters were differentially expressed between nauplius I–II and copepodid stages (604 transcripts), five clusters between copepodid and chalimus stages (2,426 transcripts), and six clusters between female and male adults (2,478 transcripts). Gene ontology analysis revealed that the nauplius I–II, copepodid and chalimus stages are mainly annotated to aminoacid transfer/repair/breakdown, metabolism, molting cycle, and nervous system development. Additionally, genes showing differential transcription in female and male adults were highly related to cytoskeletal and contractile elements, reproduction, cell development, morphogenesis, and transcription-translation processes. The data presented in this study provides the most comprehensive transcriptome resource available for C. rogercresseyi, which should be used for future genomic studies linked to host-parasite interactions. PMID:24691066

RNA-Seq analysis using de novo transcriptome assembly as a reference for the salmon louse Caligus rogercresseyi.

PubMed

Gallardo-Escárate, Cristian; Valenzuela-Muñoz, Valentina; Nuñez-Acuña, Gustavo

2014-01-01

Despite the economic and environmental impacts that sea lice infestations have on salmon farming worldwide, genomic data generated by high-throughput transcriptome sequencing for different developmental stages, sexes, and strains of sea lice is still limited or unknown. In this study, RNA-seq analysis was performed using de novo transcriptome assembly as a reference for evidenced transcriptional changes from six developmental stages of the salmon louse Caligus rogercresseyi. EST-datasets were generated from the nauplius I, nauplius II, copepodid and chalimus stages and from female and male adults using MiSeq Illumina sequencing. A total of 151,788,682 transcripts were yielded, which were assembled into 83,444 high quality contigs and subsequently annotated into roughly 24,000 genes based on known proteins. To identify differential transcription patterns among salmon louse stages, cluster analyses were performed using normalized gene expression values. Herein, four clusters were differentially expressed between nauplius I-II and copepodid stages (604 transcripts), five clusters between copepodid and chalimus stages (2,426 transcripts), and six clusters between female and male adults (2,478 transcripts). Gene ontology analysis revealed that the nauplius I-II, copepodid and chalimus stages are mainly annotated to aminoacid transfer/repair/breakdown, metabolism, molting cycle, and nervous system development. Additionally, genes showing differential transcription in female and male adults were highly related to cytoskeletal and contractile elements, reproduction, cell development, morphogenesis, and transcription-translation processes. The data presented in this study provides the most comprehensive transcriptome resource available for C. rogercresseyi, which should be used for future genomic studies linked to host-parasite interactions.

Stresses in Solder Joints of Electronic Packages

DTIC Science & Technology

1991-12-31

soldering process. The device is soldered to the circuit board at a temperature of +185zc and this tempature is assumed to propagate only to the lead wire...tri-material assembly, showing the notation used hereafter, is shown in Figure 7. The Suhir model is applicable to assemblies with continuous...therefore the radii of curvature of layers are all equal. Using equilibrium equation (7) and moment-curvature equation (9) yields ()D D Xp (x) D T() -m 3 x

A Monte Carlo studies of the entrance foil material in a target assembly for FDG production

DOE Office of Scientific and Technical Information (OSTI.GOV)

Merouani, A.; El Khayati, N.; EL Ghayour, A.

2015-07-01

In this work, a Monte Carlo simulation was performed for different entrance foil Materials in the target assembly for [{sup 18}F] FDG production, to investigate the neutron generations in the entrance foil. However, the objective is to study a materials that has the more or less similar mechanical properties as the Havar{sup R} foil with less generation of secondary particles and without affecting, the yield of FDG production. (authors)

DNA Assembly with De Bruijn Graphs Using an FPGA Platform.

PubMed

Poirier, Carl; Gosselin, Benoit; Fortier, Paul

2018-01-01

This paper presents an FPGA implementation of a DNA assembly algorithm, called Ray, initially developed to run on parallel CPUs. The OpenCL language is used and the focus is placed on modifying and optimizing the original algorithm to better suit the new parallelization tool and the radically different hardware architecture. The results show that the execution time is roughly one fourth that of the CPU and factoring energy consumption yields a tenfold savings.

Spin Forming of Aluminum Metal Matrix Composites

NASA Technical Reports Server (NTRS)

Lee, Jonathan A.; Munafo, Paul M. (Technical Monitor)

2001-01-01

An exploratory effort between NASA-Marshall Space Flight Center (MSFC) and SpinCraft, Inc., to experimentally spin form cylinders and concentric parts from small and thin sheets of aluminum Metal Matrix Composites (MMC), successfully yielded good microstructure data and forming parameters. MSFC and SpinCraft will collaborate on the recent technical findings and develop strategy to implement this technology for NASA's advanced propulsion and airframe applications such as pressure bulkheads, combustion liner assemblies, propellant tank domes, and nose cone assemblies.

Self-Assembled α-Fe2O3 mesocrystals/graphene nanohybrid for enhanced electrochemical capacitors.

PubMed

Yang, Shuhua; Song, Xuefeng; Zhang, Peng; Sun, Jing; Gao, Lian

2014-06-12

Self-assembled α-Fe2O3 mesocrystals/graphene nanohybrids have been successfully synthesized and have a unique mesocrystal porous structure, a large specific surface area, and high conductivity. Mesocrystal structures have recently attracted unparalleled attention owing to their promising application in energy storage as electrochemical capacitors. However, mesocrystal/graphene nanohybrids and their growth mechanism have not been clearly investigated. Here we show a facile fabrication of short rod-like α-Fe2O3 mesocrystals/graphene nanohybrids by self-assembly of FeOOH nanorods as the primary building blocks on graphene under hydrothermal conditions, accompanied and promoted by concomitant phase transition from FeOOH to α-Fe2O3. A systematic study of the formation mechanism is also presented. The galvanostatic charge/discharge curve shows a superior specific capacitance of the as-prepared α-Fe2O3 mesocrystals/graphene nanohybrid (based on total mass of active materials), which is 306.9 F g(-1) at 3 A g(-1) in the aqueous electrolyte under voltage ranges of up to 1 V. The nanohybrid with unique sufficient porous structure and high electrical conductivity allows for effective ion and charge transport in the whole electrode. Even at a high discharge current density of 10 A g(-1), the enhanced ion and charge transport still yields a higher capacitance (98.2 F g(-1)), exhibiting enhanced rate capability. The α-Fe2O3 mesocrystal/graphene nanohybrid electrode also demonstrates excellent cyclic performance, which is superior to previously reported graphene-based hematite electrode, suggesting it is highly stable as an electrochemical capacitor. © 2014 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Reducing Bolt Preload Variation with Angle-of-Twist Bolt Loading

NASA Technical Reports Server (NTRS)

Thompson, Bryce; Nayate, Pramod; Smith, Doug; McCool, Alex (Technical Monitor)

2001-01-01

Critical high-pressure sealing joints on the Space Shuttle reusable solid rocket motor require precise control of bolt preload to ensure proper joint function. As the reusable solid rocket motor experiences rapid internal pressurization, correct bolt preloads maintain the sealing capability and structural integrity of the hardware. The angle-of-twist process provides the right combination of preload accuracy, reliability, process control, and assembly-friendly design. It improves significantly over previous methods. The sophisticated angle-of-twist process controls have yielded answers to all discrepancies encountered while the simplicity of the root process has assured joint preload reliability.

The Evolution of Spiral Disks

NASA Astrophysics Data System (ADS)

Bershady, Matthew A.; Andersen, David R.

We report on aspects of an observational study to probe the mass assembly of large galaxy disks. In this contribution we focus on a new survey of integral-field Hα velocity-maps of nearby, face on disks. Preliminary results yield disk asymmetry amplitudes consistent with estimates based on the scatter in the local Tully-Fisher relation. We also show how the high quality of integral-field echelle spectroscopy enables determinations of kinematic inclinations to i ~20 °. This holds the promise that nearly-face-on galaxies can be included in the Tully-Fisher relation. Finally, we discuss the prospects for measuring dynamical asymmetries of distant galaxies.

Nanopore DNA Sequencing and Genome Assembly on the International Space Station.

PubMed

Castro-Wallace, Sarah L; Chiu, Charles Y; John, Kristen K; Stahl, Sarah E; Rubins, Kathleen H; McIntyre, Alexa B R; Dworkin, Jason P; Lupisella, Mark L; Smith, David J; Botkin, Douglas J; Stephenson, Timothy A; Juul, Sissel; Turner, Daniel J; Izquierdo, Fernando; Federman, Scot; Stryke, Doug; Somasekar, Sneha; Alexander, Noah; Yu, Guixia; Mason, Christopher E; Burton, Aaron S

2017-12-21

We evaluated the performance of the MinION DNA sequencer in-flight on the International Space Station (ISS), and benchmarked its performance off-Earth against the MinION, Illumina MiSeq, and PacBio RS II sequencing platforms in terrestrial laboratories. Samples contained equimolar mixtures of genomic DNA from lambda bacteriophage, Escherichia coli (strain K12, MG1655) and Mus musculus (female BALB/c mouse). Nine sequencing runs were performed aboard the ISS over a 6-month period, yielding a total of 276,882 reads with no apparent decrease in performance over time. From sequence data collected aboard the ISS, we constructed directed assemblies of the ~4.6 Mb E. coli genome, ~48.5 kb lambda genome, and a representative M. musculus sequence (the ~16.3 kb mitochondrial genome), at 100%, 100%, and 96.7% consensus pairwise identity, respectively; de novo assembly of the E. coli genome from raw reads yielded a single contig comprising 99.9% of the genome at 98.6% consensus pairwise identity. Simulated real-time analyses of in-flight sequence data using an automated bioinformatic pipeline and laptop-based genomic assembly demonstrated the feasibility of sequencing analysis and microbial identification aboard the ISS. These findings illustrate the potential for sequencing applications including disease diagnosis, environmental monitoring, and elucidating the molecular basis for how organisms respond to spaceflight.

Self-assembly of Metallamacrocycles Employing a New Benzil-based Organometallic Bisplatinum(II) Acceptor.

PubMed

Roy, Bijan; Shanmugaraju, Sankarasekaran; Saha, Rupak; Mukherjee, Partha Sarathi

2015-01-01

A benzil-based semi-rigid dinuclear-organometallic acceptor 4,4'-bis[trans-Pt(PEt(3))(2)(NO(3))(ethynyl)]benzil (bisPt-NO(3)) containing a Pt-ethynyl functionality was synthesized in good yield and characterized by multinuclear NMR ((1)H, (31)P, and (13)C), electrospray ionization mass spectrometry (ESI-MS), and single-crystal X-ray diffraction analysis of the iodide analogue bisPt-I. The stoichiometric (1:1) combination of the acceptor bisPt-NO(3) separately with four different ditopic donors (L(1)-L(4); L(1) = 9-ethyl-3,6-di(1H-imidazol-1-yl)-9H-carbazole, L(2) = 1,4-bis((1H-imidazol-1-yl)methyl)benzene, L(3) = 1,3-bis((1H-imidazol-1-yl)methyl)benzene and L(4) = 9,10-bis((1H-imidazol-1-yl) methyl)anthracene) yielded four [2 + 2] self-assembled metallacycles M(1)-M(4) in quantitative yields, respectively. All these newly synthesized assemblies were characterized by various spectroscopic techniques (NMR, IR, ESI-MS) and their sizes/shapes were predicted through geometry optimization employing the PM6 semi-empirical method. The benzil moiety was introduced in the backbone of the acceptor bisPt-NO(3) due to the interesting structural feature of long carbonyl C-C bond (∼1.54 Å), which enabled us to probe the role of conformational flexibility on size and shapes of the resulting coordination ensembles.

Intermediate filament mechanics in vitro and in the cell: from coiled coils to filaments, fibers and networks.

PubMed

Köster, Sarah; Weitz, David A; Goldman, Robert D; Aebi, Ueli; Herrmann, Harald

2015-02-01

Intermediate filament proteins form filaments, fibers and networks both in the cytoplasm and the nucleus of metazoan cells. Their general structural building plan accommodates highly varying amino acid sequences to yield extended dimeric α-helical coiled coils of highly conserved design. These 'rod' particles are the basic building blocks of intrinsically flexible, filamentous structures that are able to resist high mechanical stresses, that is, bending and stretching to a considerable degree, both in vitro and in the cell. Biophysical and computer modeling studies are beginning to unfold detailed structural and mechanical insights into these major supramolecular assemblies of cell architecture, not only in the 'test tube' but also in the cellular and tissue context. Copyright © 2015 Elsevier Ltd. All rights reserved.

High-power density piezoelectric energy harvesting using radially strained ultrathin trigonal tellurium nanowire assembly.

PubMed

Lee, Tae Il; Lee, Sangmin; Lee, Eungkyu; Sohn, Sungwoo; Lee, Yean; Lee, Sujeong; Moon, Geondae; Kim, Dohyang; Kim, Youn Sang; Myoung, Jae Min; Wang, Zhong Lin

2013-06-04

A high-yield solution-processed ultrathin (<10 nm) trigonal tellurium (t-Te) nanowire (NW) is introduced as a new class of piezoelectric nanomaterial with a six-fold higher piezoelectric constant compared to conventional ZnO NWs for a high-volume power-density nanogenerator (NG). While determining the energy-harvesting principle in a NG consisting of t-Te NW, it is theoretically and experimentally found that t-Te NW is piezoelectrically activated only by creating strain in its radial direction, along which it has an asymmetric crystal structure. Based upon this mechanism, a NG with a monolayer consisting of well-aligned t-Te NWs and a power density of 9 mW/cm(3) is fabricated. Copyright © 2013 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

High-performance supercapacitors based on poly(ionic liquid)-modified graphene electrodes.

PubMed

Kim, Tae Young; Lee, Hyun Wook; Stoller, Meryl; Dreyer, Daniel R; Bielawski, Christopher W; Ruoff, Rodney S; Suh, Kwang S

2011-01-25

We report a high-performance supercapacitor incorporating a poly(ionic liquid)-modified reduced graphene oxide (PIL:RG-O) electrode and an ionic liquid (IL) electrolyte (specifically, 1-ethyl-3-methylimidazolium bis(trifluoromethylsulfonyl)amide or EMIM-NTf(2)). PIL:RG-O provides enhanced compatibility with the IL electrolyte, thereby increasing the effective electrode surface area accessible to electrolyte ions. The supercapacitor assembled with PIL:RG-O electrode and EMIM-NTf(2) electrolyte showed a stable electrochemical response up to 3.5 V operating voltage and was capable of yielding a maximum energy density of 6.5 W·h/kg with a power density of 2.4 kW/kg. These results demonstrate the potential of the PIL:RG-O material as an electrode in high-performance supercapacitors.

Formation of active inclusion bodies induced by hydrophobic self-assembling peptide GFIL8.

PubMed

Wang, Xu; Zhou, Bihong; Hu, Weike; Zhao, Qing; Lin, Zhanglin

2015-06-16

In the last few decades, several groups have observed that proteins expressed as inclusion bodies (IBs) in bacteria could still be biologically active when terminally fused to an appropriate aggregation-prone partner such as pyruvate oxidase from Paenibacillus polymyxa (PoxB). More recently, we have demonstrated that three amphipathic self-assembling peptides, an alpha helical peptide 18A, a beta-strand peptide ELK16, and a surfactant-like peptide L6KD, have properties that induce target proteins into active IBs. We have developed an efficient protein expression and purification approach for these active IBs by introducing a self-cleavable intein molecule. In this study, the self-assembling peptide GFIL8 (GFILGFIL) with only hydrophobic residues was analyzed, and this peptide effectively induced the formation of cytoplasmic IBs in Escherichia coli when terminally attached to lipase A and amadoriase II. The protein aggregates in cells were confirmed by transmission electron microscopy analysis and retained ~50% of their specific activities relative to the native counterparts. We constructed an expression and separation coupled tag (ESCT) by incorporating an intein molecule, the Mxe GyrA intein. Soluble target proteins were successfully released from active IBs upon cleavage of the intein between the GFIL8 tag and the target protein, which was mediated by dithiothreitol. A variant of GFIL8, GFIL16 (GFILGFILGFILGFIL), improved the ESCT scheme by efficiently eliminating interference from the soluble intein-GFIL8 molecule. The yields of target proteins at the laboratory scale were 3.0-7.5 μg/mg wet cell pellet, which is comparable to the yields from similar ESCT constructs using 18A, ELK16, or the elastin-like peptide tag scheme. The all-hydrophobic self-assembling peptide GFIL8 induced the formation of active IBs in E. coli when terminally attached to target proteins. GFIL8 and its variant GFIL16 can act as a "pull-down" tag to produce purified soluble proteins with reasonable quantity and purity from active aggregates. Owing to the structural simplicity, strong hydrophobicity, and high aggregating efficiency, these peptides can be further explored for enzyme production and immobilization.

Successful Recovery of Nuclear Protein-Coding Genes from Small Insects in Museums Using Illumina Sequencing.

PubMed

Kanda, Kojun; Pflug, James M; Sproul, John S; Dasenko, Mark A; Maddison, David R

2015-01-01

In this paper we explore high-throughput Illumina sequencing of nuclear protein-coding, ribosomal, and mitochondrial genes in small, dried insects stored in natural history collections. We sequenced one tenebrionid beetle and 12 carabid beetles ranging in size from 3.7 to 9.7 mm in length that have been stored in various museums for 4 to 84 years. Although we chose a number of old, small specimens for which we expected low sequence recovery, we successfully recovered at least some low-copy nuclear protein-coding genes from all specimens. For example, in one 56-year-old beetle, 4.4 mm in length, our de novo assembly recovered about 63% of approximately 41,900 nucleotides in a target suite of 67 nuclear protein-coding gene fragments, and 70% using a reference-based assembly. Even in the least successfully sequenced carabid specimen, reference-based assembly yielded fragments that were at least 50% of the target length for 34 of 67 nuclear protein-coding gene fragments. Exploration of alternative references for reference-based assembly revealed few signs of bias created by the reference. For all specimens we recovered almost complete copies of ribosomal and mitochondrial genes. We verified the general accuracy of the sequences through comparisons with sequences obtained from PCR and Sanger sequencing, including of conspecific, fresh specimens, and through phylogenetic analysis that tested the placement of sequences in predicted regions. A few possible inaccuracies in the sequences were detected, but these rarely affected the phylogenetic placement of the samples. Although our sample sizes are low, an exploratory regression study suggests that the dominant factor in predicting success at recovering nuclear protein-coding genes is a high number of Illumina reads, with success at PCR of COI and killing by immersion in ethanol being secondary factors; in analyses of only high-read samples, the primary significant explanatory variable was body length, with small beetles being more successfully sequenced.

Successful Recovery of Nuclear Protein-Coding Genes from Small Insects in Museums Using Illumina Sequencing

PubMed Central

Dasenko, Mark A.

2015-01-01

In this paper we explore high-throughput Illumina sequencing of nuclear protein-coding, ribosomal, and mitochondrial genes in small, dried insects stored in natural history collections. We sequenced one tenebrionid beetle and 12 carabid beetles ranging in size from 3.7 to 9.7 mm in length that have been stored in various museums for 4 to 84 years. Although we chose a number of old, small specimens for which we expected low sequence recovery, we successfully recovered at least some low-copy nuclear protein-coding genes from all specimens. For example, in one 56-year-old beetle, 4.4 mm in length, our de novo assembly recovered about 63% of approximately 41,900 nucleotides in a target suite of 67 nuclear protein-coding gene fragments, and 70% using a reference-based assembly. Even in the least successfully sequenced carabid specimen, reference-based assembly yielded fragments that were at least 50% of the target length for 34 of 67 nuclear protein-coding gene fragments. Exploration of alternative references for reference-based assembly revealed few signs of bias created by the reference. For all specimens we recovered almost complete copies of ribosomal and mitochondrial genes. We verified the general accuracy of the sequences through comparisons with sequences obtained from PCR and Sanger sequencing, including of conspecific, fresh specimens, and through phylogenetic analysis that tested the placement of sequences in predicted regions. A few possible inaccuracies in the sequences were detected, but these rarely affected the phylogenetic placement of the samples. Although our sample sizes are low, an exploratory regression study suggests that the dominant factor in predicting success at recovering nuclear protein-coding genes is a high number of Illumina reads, with success at PCR of COI and killing by immersion in ethanol being secondary factors; in analyses of only high-read samples, the primary significant explanatory variable was body length, with small beetles being more successfully sequenced. PMID:26716693

High-yield fermentation and a novel heat-precipitation purification method for hydrophobin HGFI from Grifola frondosa in Pichia pastoris.

PubMed

Song, Dongmin; Gao, Zhendong; Zhao, Liqiang; Wang, Xiangxiang; Xu, Haijin; Bai, Yanling; Zhang, Xiuming; Linder, Markus B; Feng, Hui; Qiao, Mingqiang

2016-12-01

Hydrophobins are proteins produced by filamentous fungi with high natural-surfactant activities and that can self-assemble in interfaces of air-water or solid-water to form amphiphilic membranes. Here, we reported a high-yield fermentation method for hydrophobin HGFI from Grifola frondosa in Pichia pastoris, attaining production of 300 mg/L by keeping the dissolved oxygen level at 15%-25% by turning the methanol-feeding speed. We also developed a novel HGFI-purification method enabling large-scare purification of HGFI, with >90% recovery. Additionally, we observed that hydrophobin HGFI in fermentation broth precipitated at pH < 7.0 and temperatures >90 °C. We also identified the structure and properties of proteins purified by this method through atomic force microscopy, circular dichroism, X-ray photoelectron spectroscopy, and water-contact angle measurement, which is similar to protein purification by ultrafiltration without heating treatment that enables our method to maintain native HGFI structure and properties. Furthermore, the purification method presented here can be applied to large-scale purification of other type I hydrophobins. Copyright © 2016. Published by Elsevier Inc.

Unlocking the genetic diversity of Creole wheats.

PubMed

Vikram, Prashant; Franco, Jorge; Burgueño-Ferreira, Juan; Li, Huihui; Sehgal, Deepmala; Saint Pierre, Carolina; Ortiz, Cynthia; Sneller, Clay; Tattaris, Maria; Guzman, Carlos; Sansaloni, Carolina Paola; Ellis, Mark; Fuentes-Davila, Guillermo; Reynolds, Matthew; Sonders, Kai; Singh, Pawan; Payne, Thomas; Wenzl, Peter; Sharma, Achla; Bains, Navtej Singh; Singh, Gyanendra Pratap; Crossa, José; Singh, Sukhwinder

2016-03-15

Climate change and slow yield gains pose a major threat to global wheat production. Underutilized genetic resources including landraces and wild relatives are key elements for developing high-yielding and climate-resilient wheat varieties. Landraces introduced into Mexico from Europe, also known as Creole wheats, are adapted to a wide range of climatic regimes and represent a unique genetic resource. Eight thousand four hundred and sixteen wheat landraces representing all dimensions of Mexico were characterized through genotyping-by-sequencing technology. Results revealed sub-groups adapted to specific environments of Mexico. Broadly, accessions from north and south of Mexico showed considerable genetic differentiation. However, a large percentage of landrace accessions were genetically very close, although belonged to different regions most likely due to the recent (nearly five centuries before) introduction of wheat in Mexico. Some of the groups adapted to extreme environments and accumulated high number of rare alleles. Core reference sets were assembled simultaneously using multiple variables, capturing 89% of the rare alleles present in the complete set. Genetic information about Mexican wheat landraces and core reference set can be effectively utilized in next generation wheat varietal improvement.

Non-native three-dimensional block copolymer morphologies

DOE PAGES

Rahman, Atikur; Majewski, Pawel W.; Doerk, Gregory; ...

2016-12-22

Self-assembly is a powerful paradigm, wherein molecules spontaneously form ordered phases exhibiting well-defined nanoscale periodicity and shapes. However, the inherent energy-minimization aspect of self-assembly yields a very limited set of morphologies, such as lamellae or hexagonally packed cylinders. Here, we show how soft self-assembling materials—block copolymer thin films—can be manipulated to form a diverse library of previously unreported morphologies. In this iterative assembly process, each polymer layer acts as both a structural component of the final morphology and a template for directing the order of subsequent layers. Specifically, block copolymer films are immobilized on surfaces, and template successive layers throughmore » subtle surface topography. As a result, this strategy generates an enormous variety of three-dimensional morphologies that are absent in the native block copolymer phase diagram.« less

Process for preparing an assembly of an article and a polyimide which resists dimensional change, delamination and debonding when exposed to changes in temperature

NASA Technical Reports Server (NTRS)

Stoakley, Diane M. (Inventor); St.clair, Anne K. (Inventor)

1994-01-01

An assembly of an article and a polyimide composition is prepared. The assembly resists dimensional change, delamination, or debonding when exposed to changes in temperature. An article is provided. A polyamic acid solution which yields a polyimide having a low coefficient of thermal expansion (CTE) was prepared. Equimolar quantities of an aromatic diamine and an aromatic dianhydride were reacted in a solvent medium to form a polyamic acid solution. A metal ion-containing additive was added to the solution. Examples of this additive are: TbCl3, DyCl3, ErCl3, TmCl3, Al(C5H7O2)3, and Er2S3. The polyamic acid solution was imidized and is combined with the article to form the assembly.

Electrical Programming of Soft Matter: Using Temporally Varying Electrical Inputs To Spatially Control Self Assembly.

PubMed

Yan, Kun; Liu, Yi; Zhang, Jitao; Correa, Santiago O; Shang, Wu; Tsai, Cheng-Chieh; Bentley, William E; Shen, Jana; Scarcelli, Giuliano; Raub, Christopher B; Shi, Xiao-Wen; Payne, Gregory F

2018-02-12

The growing importance of hydrogels in translational medicine has stimulated the development of top-down fabrication methods, yet often these methods lack the capabilities to generate the complex matrix architectures observed in biology. Here we show that temporally varying electrical signals can cue a self-assembling polysaccharide to controllably form a hydrogel with complex internal patterns. Evidence from theory and experiment indicate that internal structure emerges through a subtle interplay between the electrical current that triggers self-assembly and the electrical potential (or electric field) that recruits and appears to orient the polysaccharide chains at the growing gel front. These studies demonstrate that short sequences (minutes) of low-power (∼1 V) electrical inputs can provide the program to guide self-assembly that yields hydrogels with stable, complex, and spatially varying structure and properties.

Non-native three-dimensional block copolymer morphologies

DOE Office of Scientific and Technical Information (OSTI.GOV)

Rahman, Atikur; Majewski, Pawel W.; Doerk, Gregory

Self-assembly is a powerful paradigm, wherein molecules spontaneously form ordered phases exhibiting well-defined nanoscale periodicity and shapes. However, the inherent energy-minimization aspect of self-assembly yields a very limited set of morphologies, such as lamellae or hexagonally packed cylinders. Here, we show how soft self-assembling materials—block copolymer thin films—can be manipulated to form a diverse library of previously unreported morphologies. In this iterative assembly process, each polymer layer acts as both a structural component of the final morphology and a template for directing the order of subsequent layers. Specifically, block copolymer films are immobilized on surfaces, and template successive layers throughmore » subtle surface topography. As a result, this strategy generates an enormous variety of three-dimensional morphologies that are absent in the native block copolymer phase diagram.« less

Measurement of the 235U Induced Fission Gamma-ray Spectrum as an Active Non-destructive Assay of Fresh Nucleear Fuel

DOE Office of Scientific and Technical Information (OSTI.GOV)

Sarnoski, Sarah E.; Fast, James E.; Fulsom, Bryan G.

2017-07-17

Non-destructive assay is a powerful tool the International Atomic Energy Agency (IAEA) employs to verify adherence to safeguards agreements. Current IAEA veri- cation techniques for fresh nuclear fuel include passive gamma-ray spectroscopy to determine fuel enrichment. This technique suers from self-shielding and lakes the percision to detect diversion of central fuel rods. The aim of this research is to develop a new, more capable non-destructive analysis technique using active neutron interroga- tion of fuel assemblies and determining the yields of short-lived ssion products from high-resolution gamma-ray spectroscopy using high-purity germanium (HPGe). This paper reports results from irradiation of a onemore » meter tall mock fresh fuel assembly with low enriched uranium (LEU) or depleted uranium (DU) rods using a down-scattered deuterium-tritium (D-T) neutron source. Both prompt and delayed gamma-ray spec- tra were collected as time-stamped list-mode data in a coax detector and without list mode data in a planar strip detector. No dierentiating signatures were observed in the prompt spectra in either detector; however, both detectors observed several short-lived ssion product signatures in LEU and not DU fuel, indicating that this technique has potential for determination of enrichment of fresh fuel assemblies. There were eight unique ssion products observed in the LEU spectra with the coax detector spectra, and three ssion products were observed in the LEU spectra with the strip detector.« less

ScanIndel: a hybrid framework for indel detection via gapped alignment, split reads and de novo assembly.

PubMed

Yang, Rendong; Nelson, Andrew C; Henzler, Christine; Thyagarajan, Bharat; Silverstein, Kevin A T

2015-12-07

Comprehensive identification of insertions/deletions (indels) across the full size spectrum from second generation sequencing is challenging due to the relatively short read length inherent in the technology. Different indel calling methods exist but are limited in detection to specific sizes with varying accuracy and resolution. We present ScanIndel, an integrated framework for detecting indels with multiple heuristics including gapped alignment, split reads and de novo assembly. Using simulation data, we demonstrate ScanIndel's superior sensitivity and specificity relative to several state-of-the-art indel callers across various coverage levels and indel sizes. ScanIndel yields higher predictive accuracy with lower computational cost compared with existing tools for both targeted resequencing data from tumor specimens and high coverage whole-genome sequencing data from the human NIST standard NA12878. Thus, we anticipate ScanIndel will improve indel analysis in both clinical and research settings. ScanIndel is implemented in Python, and is freely available for academic use at https://github.com/cauyrd/ScanIndel.

Design, Optimization and Evaluation of Integrally Stiffened Al 7050 Panel with Curved Stiffeners

NASA Technical Reports Server (NTRS)

Slemp, Wesley C. H.; Bird, R. Keith; Kapania, Rakesh K.; Havens, David; Norris, Ashley; Olliffe, Robert

2011-01-01

A curvilinear stiffened panel was designed, manufactured, and tested in the Combined Load Test Fixture at NASA Langley Research Center. The panel was optimized for minimum mass subjected to constraints on buckling load, yielding, and crippling or local stiffener failure using a new analysis tool named EBF3PanelOpt. The panel was designed for a combined compression-shear loading configuration that is a realistic load case for a typical aircraft wing panel. The panel was loaded beyond buckling and strains and out-of-plane displacements were measured. The experimental data were compared with the strains and out-of-plane deflections from a high fidelity nonlinear finite element analysis and linear elastic finite element analysis of the panel/test-fixture assembly. The numerical results indicated that the panel buckled at the linearly elastic buckling eigenvalue predicted for the panel/test-fixture assembly. The experimental strains prior to buckling compared well with both the linear and nonlinear finite element model.

Complex supramolecular interfacial tessellation through convergent multi-step reaction of a dissymmetric simple organic precursor

NASA Astrophysics Data System (ADS)

Zhang, Yi-Qi; Paszkiewicz, Mateusz; Du, Ping; Zhang, Liding; Lin, Tao; Chen, Zhi; Klyatskaya, Svetlana; Ruben, Mario; Seitsonen, Ari P.; Barth, Johannes V.; Klappenberger, Florian

2018-03-01

Interfacial supramolecular self-assembly represents a powerful tool for constructing regular and quasicrystalline materials. In particular, complex two-dimensional molecular tessellations, such as semi-regular Archimedean tilings with regular polygons, promise unique properties related to their nontrivial structures. However, their formation is challenging, because current methods are largely limited to the direct assembly of precursors, that is, where structure formation relies on molecular interactions without using chemical transformations. Here, we have chosen ethynyl-iodophenanthrene (which features dissymmetry in both geometry and reactivity) as a single starting precursor to generate the rare semi-regular (3.4.6.4) Archimedean tiling with long-range order on an atomically flat substrate through a multi-step reaction. Intriguingly, the individual chemical transformations converge to form a symmetric alkynyl-Ag-alkynyl complex as the new tecton in high yields. Using a combination of microscopy and X-ray spectroscopy tools, as well as computational modelling, we show that in situ generated catalytic Ag complexes mediate the tecton conversion.

Delamination measurement of a laminates composite panel due to hole punching based on the focus variation technique

NASA Astrophysics Data System (ADS)

Abdullah, A. B.; Zain, M. S. M.; Abdullah, M. S.; Samad, Z.

2017-07-01

Structural materials, such as composite panels, must be assembled, and such panels are typically constructed via the insertion of a fastener through a drilled hole. The main problem encountered in drilling is delamination, which affects assembly strength. The cost of drilling is also high because of the severe wear on drill bits. The main goal of this research is to develop a new punching method as an alternative to drilling during hole preparation. In this study, the main objective is to investigate the effect of different puncher profiles on the quality of holes punched into carbon fiber reinforcement polymer (CFRP) composite panels. Six types of puncher profiles were fabricated with minimum die clearance (1%), and two quality aspects, namely, incomplete shearing and delamination factor, were measured. The conical puncher incurred the least defects in terms of delamination and yielded an acceptable amount of incomplete shearing in comparison with the other punchers.

WHEAT GERM CELL-FREE TRANSLATION, PURIFICATION, AND ASSEMBLY OF A FUNCTIONAL HUMAN STEAROYL-COA DESATURASE COMPLEX

PubMed Central

Goren, Michael A.; Fox, Brian G.

2008-01-01

A wheat germ cell-free extract was used to perform in vitro translation of human stearoyl-CoA desaturase in the presence of unilamelar liposomes, and near complete transfer of the expressed integral membrane protein into the liposome was observed. Moreover, co-translation of the desaturase along with human cytochrome b5 led to transfer of both membrane proteins into the liposomes. A simple, single step purification via centrifugation in a density gradient yielded proteoliposomes with the desaturase in high purity as judged by capillary electrophoresis. After in vitro reconstitution of the non-heme iron and heme active sites, the function of the reconstituted enzyme complex was demonstrated by conversion of stearoyl-CoA to oleoyl-CoA. This simple translation approach obviates the use of detergents or other lipids to stabilize and isolate a catalytically active integral membrane enzyme. The applicability of cell-free translation to the assembly and purification of other integral membrane protein complexes is discussed. PMID:18765284

Wheat germ cell-free translation, purification, and assembly of a functional human stearoyl-CoA desaturase complex.

PubMed

Goren, Michael A; Fox, Brian G

2008-12-01

A wheat germ cell-free extract was used to perform in vitro translation of human stearoyl-CoA desaturase in the presence of unilamelar liposomes, and near complete transfer of the expressed integral membrane protein into the liposome was observed. Moreover, co-translation of the desaturase along with human cytochrome b(5) led to transfer of both membrane proteins into the liposomes. A simple, single step purification via centrifugation in a density gradient yielded proteoliposomes with the desaturase in high purity as judged by capillary electrophoresis. After in vitro reconstitution of the non-heme iron and heme active sites, the function of the reconstituted enzyme complex was demonstrated by conversion of stearoyl-CoA to oleoyl-CoA. This simple translation approach obviates the use of detergents or other lipids to stabilize and isolate a catalytically active integral membrane enzyme. The applicability of cell-free translation to the assembly and purification of other integral membrane protein complexes is discussed.

Synthesis of anatase TiO2 nanoparticles with beta-cyclodextrin as a supramolecular shell.

PubMed

Li, Landong; Sun, Xiaohong; Yang, Yali; Guan, Naijia; Zhang, Fuxiang

2006-11-20

We report a novel, green hydrothermal-synthesis route to well-dispersed anatase TiO2 nanoparticles with particle sizes of 9-16 nm in the presence of beta-CD (beta-cyclodextrin). During the synthesis process, the CD-containing synthesis mixture assembled in both longitudinal and latitudinal directions. Driven by the interaction between molecules, the beta-CDs assembled in the longitudinal direction to form long-chain compounds, whereas in the latitudinal direction, they tended to form regular aggregates through coordination with the Ti species from the hydrolysis of tetrabutyl titanate. In view of the effect of the coordination and the steric hindrance of beta-CDs as a supramolecular shell, homogeneous nuclei and slow growth of TiO2 crystals during the synthesis process was observed, which was responsible for the formation of uniform TiO2 nanoparticles. The low beta-CD dosage and the high product yield (>90%) demonstrated well the potential of this synthesis route in the large-scale industrial production of anatase nanoparticles.

Structure and organization of paramyxovirus particles.

PubMed

Cox, Robert M; Plemper, Richard K

2017-06-01

The paramyxovirus family comprises major human and animal pathogens such as measles virus (MeV), mumps virus (MuV), the parainfluenzaviruses, Newcastle disease virus (NDV), and the highly pathogenic zoonotic hendra (HeV) and nipah (NiV) viruses. Paramyxovirus particles are pleomorphic, with a lipid envelope, nonsegmented RNA genomes of negative polarity, and densely packed glycoproteins on the virion surface. A number of crystal structures of different paramyxovirus proteins and protein fragments were solved, but the available information concerning overall virion organization remains limited. However, recent studies have reported cryo-electron tomography-based reconstructions of Sendai virus (SeV), MeV, NDV, and human parainfluenza virus type 3 (HPIV3) particles and a surface assessment of NiV-derived virus-like particles (VLPs), which have yielded innovative hypotheses concerning paramyxovirus particle assembly, budding, and organization. Following a summary of the current insight into paramyxovirus virion morphology, this review will focus on discussing the implications of these particle reconstructions on the present models of paramyxovirus assembly and infection. Copyright © 2017 Elsevier B.V. All rights reserved.

Flower-Like Nanoparticles of Pt-BiIII Assembled on Agmatine Sulfate Modified Glassy Carbon Electrode and Their Electrocatalysis of H2O2

NASA Astrophysics Data System (ADS)

Xiao, Mingshu; Yan, Yuhua; Feng, Kai; Tian, Yanping; Miao, Yuqing

2015-04-01

A new electrochemical technique to detect hydrogen peroxide (H2O2) was developed. The Pt nanoparticles and BiIII were subsequently assembled on agmatine sulfate (AS) modified glassy carbon electrode (GCE) and the prepared GCE-AS-Pt-BiIII was characterized by scanning electron microscopy (SEM) with result showing that the flower-like nanostructure of Pt-BiIII was yielded. Compared with Pt nanoparticles, the flower-like nanostructure of Pt-BiIII greatly enhanced the electrocatalysis of GCE-AS-Pt-BiIII towards H2O2, which is ascribed to more Pt-OH obtained on GCE-AS-Pt-BiIII surface for the presence of BiIII. Based on its high electrocatalysis, GCE-AS-Pt-BiIII was used to determine the content of H2O2 in the sample of sheet bean curd with standard addition method. Meantime, its electrocatalytic activity also was studied.

Unexpected Rotamerism at the Origin of a Chessboard Supramolecular Assembly of Ruthenium Phthalocyanine.

PubMed

Mattioli, Giuseppe; Larciprete, Rosanna; Alippi, Paola; Bonapasta, Aldo Amore; Filippone, Francesco; Lacovig, Paolo; Lizzit, Silvano; Paoletti, Anna Maria; Pennesi, Giovanna; Ronci, Fabio; Zanotti, Gloria; Colonna, Stefano

2017-11-16

We have investigated the formation and the properties of ultrathin films of ruthenium phthalocyanine (RuPc) 2 vacuum deposited on graphite by scanning tunneling microscopy and synchrotron photoemission spectroscopy measurements, interpreted in close conjunction with ab initio simulations. Thanks to its unique dimeric structure connected by a direct Ru-Ru bond, (RuPc) 2 can be found in two stable rotameric forms separated by a low-energy barrier. Such isomerism leads to a peculiar organization of the molecules in flat, horizontal layers on the graphite surface, characterized by a chessboard-like alternation of the two rotamers. Moreover, the molecules are vertically connected to form π-stacked columnar pillars of akin rotamers, compatible with the high conductivity measured in (RuPc) 2 powders. Such features yield an unprecedented supramolecular assembly of phthalocyanine films, which could open interesting perspectives toward the realization of new architectures of organic electronic devices. © 2017 Wiley-VCH Verlag GmbH & Co. KGaA, Weinheim.

DOE Office of Scientific and Technical Information (OSTI.GOV)

Le, Quyet Van; Kim, Jong Beom; Kim, Soo Young

We have investigated the effect of reaction temperature of hot-injection method on the structural properties of CsPbX3 (X: Br, I, Cl) perovskite nanocrystals (NCs) using the small- and wide-angle X-ray scattering. It is confirmed that the size of the NCs decreased as the reaction temperature decreased, resulting stronger quantum confinement. The cubic-phase perovskite NCs were formed despite the reaction temperatures increased from 140 to 180 °C. However, monodispersive NC cubes which are required for densely packing self-assembly film were only formed at lower temperatures. From the X-ray scattering measurements, the spin-coated film from more monodispersive perovskite nanocubes synthesized at lowermore » temperatures resulted in more preferred orientation. This dense-packing perovskite film with preferred orientation yielded efficient light-emitting diode (LED) performance. Thus, the dense-packing structure of NC assemblies formed after spin-coating should be considered for high-efficient LEDs based on perovskite quantum dots in addition to quantum confinement effect of the quantum dots.« less

Automated eukaryotic gene structure annotation using EVidenceModeler and the Program to Assemble Spliced Alignments

PubMed Central

Haas, Brian J; Salzberg, Steven L; Zhu, Wei; Pertea, Mihaela; Allen, Jonathan E; Orvis, Joshua; White, Owen; Buell, C Robin; Wortman, Jennifer R

2008-01-01

EVidenceModeler (EVM) is presented as an automated eukaryotic gene structure annotation tool that reports eukaryotic gene structures as a weighted consensus of all available evidence. EVM, when combined with the Program to Assemble Spliced Alignments (PASA), yields a comprehensive, configurable annotation system that predicts protein-coding genes and alternatively spliced isoforms. Our experiments on both rice and human genome sequences demonstrate that EVM produces automated gene structure annotation approaching the quality of manual curation. PMID:18190707

Determination of relative krypton fission product yields from 14 MeV neutron induced fission of 238U at the National Ignition Facility

DOE PAGES

Edwards, E. R.; Cassata, W. S.; Velsko, C. A.; ...

2016-09-22

Precisely-known fission yield distributions are needed to determine a fissioning isotope and the incident neutron energy in nuclear security applications. 14 MeV neutrons from DT fusion at the National Ignition Facility (NIF) induce fission in depleted uranium (DU) contained in the target assembly hohlraum. The fission yields of Kr isotopes (85m, 87, 88, and 89) are measured relative to the cumulative yield of 88Kr and compared to previously tabulated values. Here, the results from this experiment and England and Rider are in agreement, except for the 85mKr/ 88Kr ratio, which may be the result of incorrect nuclear data.

Determination of relative krypton fission product yields from 14 MeV neutron induced fission of 238U at the National Ignition Facility.

PubMed

Edwards, E R; Cassata, W S; Velsko, C A; Yeamans, C B; Shaughnessy, D A

2016-11-01

Precisely-known fission yield distributions are needed to determine a fissioning isotope and the incident neutron energy in nuclear security applications. 14 MeV neutrons from DT fusion at the National Ignition Facility induce fission in depleted uranium contained in the target assembly hohlraum. The fission yields of Kr isotopes (85m, 87, 88, and 89) are measured relative to the cumulative yield of 88 Kr and compared to previously tabulated values. The results from this experiment and England and Rider are in agreement, except for the 85m Kr/ 88 Kr ratio, which may be the result of incorrect nuclear data.

Membrane-on-a-chip: microstructured silicon/silicon-dioxide chips for high-throughput screening of membrane transport and viral membrane fusion.

PubMed

Kusters, Ilja; van Oijen, Antoine M; Driessen, Arnold J M

2014-04-22

Screening of transport processes across biological membranes is hindered by the challenge to establish fragile supported lipid bilayers and the difficulty to determine at which side of the membrane reactants reside. Here, we present a method for the generation of suspended lipid bilayers with physiological relevant lipid compositions on microstructured Si/SiO2 chips that allow for high-throughput screening of both membrane transport and viral membrane fusion. Simultaneous observation of hundreds of single-membrane channels yields statistical information revealing population heterogeneities of the pore assembly and conductance of the bacterial toxin α-hemolysin (αHL). The influence of lipid composition and ionic strength on αHL pore formation was investigated at the single-channel level, resolving features of the pore-assembly pathway. Pore formation is inhibited by a specific antibody, demonstrating the applicability of the platform for drug screening of bacterial toxins and cell-penetrating agents. Furthermore, fusion of H3N2 influenza viruses with suspended lipid bilayers can be observed directly using a specialized chip architecture. The presented micropore arrays are compatible with fluorescence readout from below using an air objective, thus allowing high-throughput screening of membrane transport in multiwell formats in analogy to plate readers.

GaAs photovoltaics and optoelectronics using releasable multilayer epitaxial assemblies.

PubMed

Yoon, Jongseung; Jo, Sungjin; Chun, Ik Su; Jung, Inhwa; Kim, Hoon-Sik; Meitl, Matthew; Menard, Etienne; Li, Xiuling; Coleman, James J; Paik, Ungyu; Rogers, John A

2010-05-20

Compound semiconductors like gallium arsenide (GaAs) provide advantages over silicon for many applications, owing to their direct bandgaps and high electron mobilities. Examples range from efficient photovoltaic devices to radio-frequency electronics and most forms of optoelectronics. However, growing large, high quality wafers of these materials, and intimately integrating them on silicon or amorphous substrates (such as glass or plastic) is expensive, which restricts their use. Here we describe materials and fabrication concepts that address many of these challenges, through the use of films of GaAs or AlGaAs grown in thick, multilayer epitaxial assemblies, then separated from each other and distributed on foreign substrates by printing. This method yields large quantities of high quality semiconductor material capable of device integration in large area formats, in a manner that also allows the wafer to be reused for additional growths. We demonstrate some capabilities of this approach with three different applications: GaAs-based metal semiconductor field effect transistors and logic gates on plates of glass, near-infrared imaging devices on wafers of silicon, and photovoltaic modules on sheets of plastic. These results illustrate the implementation of compound semiconductors such as GaAs in applications whose cost structures, formats, area coverages or modes of use are incompatible with conventional growth or integration strategies.

Robust Low-Cost Cathode for Commercial Applications

NASA Technical Reports Server (NTRS)

Patterson, Michael J.

2007-01-01

Under funding from the NASA Commercial Technology Office, a cathode assembly was designed, developed, fabricated, and tested for use in plasma sources for ground-based materials processing applications. The cathode development activity relied on the large prior NASA investment and successful development of high-current, high-efficiency, long-life hollow cathodes for use on the International Space Station Plasma Contactor System. The hollow cathode was designed and fabricated based on known engineering criteria and manufacturing processes for compatibility with the requirements of the plasma source. The transfer of NASA GRC-developed hollow cathode technology for use as an electron emitter in the commercial plasma source is anticipated to yield a significant increase in process control, while eliminating the present issues of electron emitter lifetime and contamination.

Biological synthesis of triangular gold nanoprisms

NASA Astrophysics Data System (ADS)

Shankar, S. Shiv; Rai, Akhilesh; Ankamwar, Balaprasad; Singh, Amit; Ahmad, Absar; Sastry, Murali

2004-07-01

The optoelectronic and physicochemical properties of nanoscale matter are a strong function of particle size. Nanoparticle shape also contributes significantly to modulating their electronic properties. Several shapes ranging from rods to wires to plates to teardrop structures may be obtained by chemical methods; triangular nanoparticles have been synthesized by using a seeded growth process. Here, we report the discovery that the extract from the lemongrass plant, when reacted with aqueous chloroaurate ions, yields a high percentage of thin, flat, single-crystalline gold nanotriangles. The nanotriangles seem to grow by a process involving rapid reduction, assembly and room-temperature sintering of 'liquid-like' spherical gold nanoparticles. The anisotropy in nanoparticle shape results in large near-infrared absorption by the particles, and highly anisotropic electron transport in films of the nanotriangles.

Templated electrokinetic directed chemical assembly for the fabrication of close-packed plasmonic metamolecules

NASA Astrophysics Data System (ADS)

Thrift, W. J.; Darvishzadeh-Varcheie, M.; Capolino, F.; Ragan, R.

2017-08-01

Colloidal self-assembly combined with templated surfaces holds the promise of fabricating large area devices in a low cost facile manner. This directed assembly approach improves the complexity of assemblies that can be achieved with self-assembly while maintaining advantages of molecular scale control. In this work, electrokinetic driving forces, i.e., electrohydrodynamic flow, are paired with chemical crosslinking between colloidal particles to form close-packed plasmonic metamolecules. This method addresses challenges of obtaining uniformity in nanostructure geometry and nanometer scale gap spacings in structures. Electrohydrodynamic flows yield robust driving forces between the template and nanoparticles as well as between nanoparticles on the surface promoting the assembly of close-packed metamolecules. Here, electron beam lithography defined Au pillars are used as seed structures that generate electrohydrodynamic flows. Chemical crosslinking between Au surfaces enables molecular control over gap spacings between nanoparticles and Au pillars. An as-fabricated structure is analyzed via full wave electromagnetic simulations and shown to produce large magnetic field enhancements on the order of 3.5 at optical frequencies. This novel method for directed self-assembly demonstrates the synergy between colloidal driving forces and chemical crosslinking for the fabrication of plasmonic metamolecules with unique electromagnetic properties.

The Key Role of U28 in the Aqueous Self-Assembly of Uranyl Peroxide Nanocages.

PubMed

Falaise, Clément; Nyman, May

2016-10-04

For 11 years now, the structural diversity and aesthetic beauty of uranyl-peroxide capsules have fascinated researchers from the diverse fields of mineralogy, polyoxometalate chemistry, and nuclear fuel technologies. There is still much to be learned about the mechanisms of the self-assembly process, and the role of solution parameters including pH, alkali template, temperature, time, and others. Here we have exploited the high solubility of the UO2 (2+) /H2 O2 /LiOH aqueous system to address the effect of the hydroxide concentration. Important techniques of this study are single-crystal X-ray diffraction, small-angle X-ray scattering, and Raman spectroscopy. Three key phases dominate the solution speciation as a function of time and the LiOH/UO2 (2+) ratio: the uranyl-triperoxide monomer [UO2 (O2 )3 ](4-) and the two capsules [(UO2 )(O2 )(OH)]24 (24-) (U24 ) and [(UO2 )(O2 )1.5 ]28 (28-) (U28 ). When the LiOH/U ratio is around three, U28 forms rapidly and this cluster can be isolated in high yield and purity. This result was most surprising and challenges the hypothesis that alkali templating is the most important determinant in the cluster geometry. Moreover, analogous experiments with KOH, NH4 OH, and TEAOH (TEA=tetraethylammonium) also rapidly yield U28 , which suggests that U28 is the kinetically favored species. Complete mapping of the pH-time phase space reveals only a narrow window of the U28 dominance, which is why it was previously overlooked as an important kinetic species in this chemical system, as well as others with different counterions. © 2016 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

DOE Office of Scientific and Technical Information (OSTI.GOV)

Moosakhani, S.; Color and Polymer Research Center; Sabbagh Alvani, A.A., E-mail: sabbagh_alvani@aut.ac.ir

Highlights: • We have demonstrated AgI sensitized solar cell for the first time. • Obtained mesoporous titania powders possessed small crystallite size, high purity and surface area, and developed mesopores with a narrow pore size distribution. • Photovoltaic measurements revealed the electron injection from AgI to TiO{sub 2}. • The assembled AgI-QD solar cells yielded a power conversion efficiency of 0.64% under one sun illumination. • AgI may be a suitable candidate material for use as a non-toxic sensitizer in QDSSC. - Abstract: The present study reports the performance of a new photosensitizer -AgI quantum dots (QDs)- and mesoporous titaniamore » (TiO{sub 2}) nanocrystals synthesized by sol–gel (SG) method for solar cells. Furthermore, the effects of n-heptane on the textural properties of TiO{sub 2} nanocrystals were comprehensively investigated by X-ray diffraction (XRD), Fourier transform infrared spectroscopy (FTIR), scanning electron microscopy (SEM), N{sub 2} adsorption–desorption measurements, and UV–vis spectroscopy. TiO{sub 2} powders exhibited an anatase-type mesoporous structure with a high surface area of 89.7 m{sup 2}/g. Afterwards, the QDs were grown on mesoporous TiO{sub 2} surface to fabricate a TiO{sub 2}/AgI electrode by a successive ionic layer adsorption and reaction (SILAR) deposition route. Current–voltage characteristics and electrochemical impedance spectroscopy (EIS) data demonstrated that the injection of photoexcited electrons from AgI QDs into the TiO{sub 2} matrix produces photocurrents. The assembled AgI-QD solar cells yielded a power conversion efficiency of 0.64% and a short-circuit current of 2.13 mA/cm{sup 2} under one sun illumination.« less

Photoprotection vs. Photoinhibition of Photosystem II in Transplastomic Lettuce (Lactuca sativa) Dominantly Accumulating Astaxanthin.

PubMed

Fujii, Ritsuko; Yamano, Nami; Hashimoto, Hideki; Misawa, Norihiko; Ifuku, Kentaro

2016-07-01

Transplastomic (chloroplast genome-modified; CGM) lettuce that dominantly accumulates astaxanthin grows similarly to a non-transgenic control with almost no accumulation of naturally occurring photosynthetic carotenoids. In this study, we evaluated the activity and assembly of PSII in CGM lettuce. The maximum quantum yield of PSII in CGM lettuce was <0.6; however, the quantum yield of PSII was comparable with that in control leaves under higher light intensity. CGM lettuce showed a lower ability to induce non-photochemical quenching (NPQ) than the control under various light intensities. The fraction of slowly recovering NPQ in CGM lettuce, which is considered to be photoinhibitory quenching (qI), was less than half that of the control. In fact, 1 O 2 generation was lower in CGM than in control leaves under high light intensity. CGM lettuce contained less PSII, accumulated mostly as a monomer in thylakoid membranes. The PSII monomers purified from the CGM thylakoids bound echinenone and canthaxanthin in addition to β-carotene, suggesting that a shortage of β-carotene and/or the binding of carbonyl carotenoids would interfere with the photophysical function as well as normal assembly of PSII. In contrast, high accumulation of astaxanthin and other carbonyl carotenoids was found within the thylakoid membranes. This finding would be associated with the suppression of photo-oxidative stress in the thylakoid membranes. Our observation suggests the importance of a specific balance between photoprotection and photoinhibition that can support normal photosynthesis in CGM lettuce producing astaxanthin. © The Author 2015. Published by Oxford University Press on behalf of Japanese Society of Plant Physiologists. All rights reserved. For permissions, please email: journals.permissions@oup.com.

Detection of Missing Assemblies and Estimation of the Scattering Densities in a VSC-24 Dry Storage Cask with Cosmic-Ray-Muon-Based Computed Tomography

DOE Office of Scientific and Technical Information (OSTI.GOV)

Liu, Zhengzhi; Hayward, Jason; Liao, Can

We report that highly energetic, cosmic-ray muons can penetrate a dry storage cask and yield information about the material inside it by making use of the physics of multiple Coulomb scattering. Work by others has shown this information may be used for verification of dry storage cask contents after continuity of knowledge has been lost. In our modeling and simulation approach, we use ideal planar radiation detectors to record the trajectories and momentum of both incident and exiting cosmic ray muons; this choice allows us to demonstrate the fundamental limit of the technology for a particular measurement and reconstruction method.more » In a method analogous to computed tomography with the attenuation coefficient replaced by scattering density, we apply a filtered back projection algorithm in order to reconstruct the geometry in modeled scenarios for a VSC-24 concrete-walled cask. We also report on our attempt to estimate material-specific information. A scenario where one of the middle four spent nuclear fuel assemblies is missing—undetectable with a simple PoCA-based approach—is expected to be detectable with a CT-based approach. Moreover, a trickier scenario where one or more assemblies is replaced by a dummy assembly is put forward. Lastly, in this case, we expect that this dry storage cask should be found to be not as declared based on our simulation and reconstruction results.« less

Rab33B Controls Hepatitis B Virus Assembly by Regulating Core Membrane Association and Nucleocapsid Processing.

PubMed

Bartusch, Christina; Döring, Tatjana; Prange, Reinhild

2017-06-21

Many viruses take advantage of cellular trafficking machineries to assemble and release new infectious particles. Using RNA interference (RNAi), we demonstrate that the Golgi/autophagosome-associated Rab33B is required for hepatitis B virus (HBV) propagation in hepatoma cell lines. While Rab33B is dispensable for the secretion of HBV subviral envelope particles, its knockdown reduced the virus yield to 20% and inhibited nucleocapsid (NC) formation and/or NC trafficking. The overexpression of a GDP-restricted Rab33B mutant phenocopied the effect of deficit Rab33B, indicating that Rab33B-specific effector proteins may be involved. Moreover, we found that HBV replication enhanced Rab33B expression. By analyzing HBV infection cycle steps, we identified a hitherto unknown membrane targeting module in the highly basic C-terminal domain of the NC-forming core protein. Rab33B inactivation reduced core membrane association, suggesting that membrane platforms participate in HBV assembly reactions. Biochemical and immunofluorescence analyses provided further hints that the viral core, rather than the envelope, is the main target for Rab33B intervention. Rab33B-deficiency reduced core protein levels without affecting viral transcription and hampered core/NC sorting to envelope-positive, intracellular compartments. Together, these results indicate that Rab33B is an important player in intracellular HBV trafficking events, guiding core transport to NC assembly sites and/or NC transport to budding sites.

Computational Modeling of Tissue Self-Assembly

NASA Astrophysics Data System (ADS)

Neagu, Adrian; Kosztin, Ioan; Jakab, Karoly; Barz, Bogdan; Neagu, Monica; Jamison, Richard; Forgacs, Gabor

As a theoretical framework for understanding the self-assembly of living cells into tissues, Steinberg proposed the differential adhesion hypothesis (DAH) according to which a specific cell type possesses a specific adhesion apparatus that combined with cell motility leads to cell assemblies of various cell types in the lowest adhesive energy state. Experimental and theoretical efforts of four decades turned the DAH into a fundamental principle of developmental biology that has been validated both in vitro and in vivo. Based on computational models of cell sorting, we have developed a DAH-based lattice model for tissues in interaction with their environment and simulated biological self-assembly using the Monte Carlo method. The present brief review highlights results on specific morphogenetic processes with relevance to tissue engineering applications. Our own work is presented on the background of several decades of theoretical efforts aimed to model morphogenesis in living tissues. Simulations of systems involving about 105 cells have been performed on high-end personal computers with CPU times of the order of days. Studied processes include cell sorting, cell sheet formation, and the development of endothelialized tubes from rings made of spheroids of two randomly intermixed cell types, when the medium in the interior of the tube was different from the external one. We conclude by noting that computer simulations based on mathematical models of living tissues yield useful guidelines for laboratory work and can catalyze the emergence of innovative technologies in tissue engineering.

Detection of Missing Assemblies and Estimation of the Scattering Densities in a VSC-24 Dry Storage Cask with Cosmic-Ray-Muon-Based Computed Tomography

DOE PAGES

Liu, Zhengzhi; Hayward, Jason; Liao, Can; ...

2017-08-01

We report that highly energetic, cosmic-ray muons can penetrate a dry storage cask and yield information about the material inside it by making use of the physics of multiple Coulomb scattering. Work by others has shown this information may be used for verification of dry storage cask contents after continuity of knowledge has been lost. In our modeling and simulation approach, we use ideal planar radiation detectors to record the trajectories and momentum of both incident and exiting cosmic ray muons; this choice allows us to demonstrate the fundamental limit of the technology for a particular measurement and reconstruction method.more » In a method analogous to computed tomography with the attenuation coefficient replaced by scattering density, we apply a filtered back projection algorithm in order to reconstruct the geometry in modeled scenarios for a VSC-24 concrete-walled cask. We also report on our attempt to estimate material-specific information. A scenario where one of the middle four spent nuclear fuel assemblies is missing—undetectable with a simple PoCA-based approach—is expected to be detectable with a CT-based approach. Moreover, a trickier scenario where one or more assemblies is replaced by a dummy assembly is put forward. Lastly, in this case, we expect that this dry storage cask should be found to be not as declared based on our simulation and reconstruction results.« less

Quantized Self-Assembly of Discotic Rings in a Liquid Crystal Confined in Nanopores

NASA Astrophysics Data System (ADS)

Sentker, Kathrin; Zantop, Arne W.; Lippmann, Milena; Hofmann, Tommy; Seeck, Oliver H.; Kityk, Andriy V.; Yildirim, Arda; Schönhals, Andreas; Mazza, Marco G.; Huber, Patrick

2018-02-01

Disklike molecules with aromatic cores spontaneously stack up in linear columns with high, one-dimensional charge carrier mobilities along the columnar axes, making them prominent model systems for functional, self-organized matter. We show by high-resolution optical birefringence and synchrotron-based x-ray diffraction that confining a thermotropic discotic liquid crystal in cylindrical nanopores induces a quantized formation of annular layers consisting of concentric circular bent columns, unknown in the bulk state. Starting from the walls this ring self-assembly propagates layer by layer towards the pore center in the supercooled domain of the bulk isotropic-columnar transition and thus allows one to switch on and off reversibly single, nanosized rings through small temperature variations. By establishing a Gibbs free energy phase diagram we trace the phase transition quantization to the discreteness of the layers' excess bend deformation energies in comparison to the thermal energy, even for this near room-temperature system. Monte Carlo simulations yielding spatially resolved nematic order parameters, density maps, and bond-orientational order parameters corroborate the universality and robustness of the confinement-induced columnar ring formation as well as its quantized nature.

Luminescent properties and energy transfer of luminescent carbon dots assembled mesoporous Al(2)O(3): Eu(3) co-doped materials for temperature sensing.

PubMed

He, Youling; He, Jiangling; Zhang, Haoran; Liu, Yingliang; Lei, Bingfu

2017-06-15

Owning to the hydrogen-band interactions, blue-light-emitting luminescent carbon dots (CDs) synthesized by one-pot hydrothermal treatment were successfully assembled into Eu 3+ doped mesoporous aluminas (MAs). Interesting, dual-emissive CDs/MAs co-doped materials with higher quantum yield (QY), long-term stability, mesoporous structure, high thermal stability, and large surface areas were obtained. Furthermore, the obtained CDs/MAs co-doped materials possessed tunable color, and excellent temperature sensitivity due to the existing of energy transfer between CDs and Eu 3+ ion. The energy transfer efficiency (η) and energy transfer probability (P) for CDs/Eu 3+ co-doped materials possessed a monotonous tendency with the change of Eu 3+ content. More importantly, the dual-emissive colors can be regularly adjusted through regulating their excitation wavelength or relative mass ratio. In addition, the emission intensity of the CDs/MAs co-doped materials gradually decreased with increasing temperature showing the clear temperature dependence, this dual-emissive thermometer was with high sensitivity, owning a great fitted curve in the range from 100 to 360K under a single wavelength excitation. Copyright © 2017 Elsevier Inc. All rights reserved.

Overcrowding drives the unjamming transition of gap-free monolayers

NASA Astrophysics Data System (ADS)

Lan, Ganhui; Su, Tao

Collective cell motility plays central roles in various biological phenomena such as wound healing, cancer metastasis and embryogenesis. These are demonstrations of the unjamming transition in biology. However, contradictory to the typical density-driven jamming in particulate assemblies, cellular systems often get unjammed in highly packed, sometimes overcrowding environments. Here, we investigate monolayers' collective behaviors when cell number changes under the gap-free constraint. We report that overcrowding can unjam gap-free monolayers through increasing isotropic compression. We show that the transition boundary is determined by the isotropic compression and the cell-cell adhesion. Furthermore, we construct the free energy landscape for the T1 topological transition during monolayer rearrangement, and discover that the landscape evolves from single-barrier W shape to double-barrier M shape during the unjamming process. We also discover a distributed-to-disordered morphological transition of cells' geometry, coinciding with the unjamming transition. Our analyses reveal that the overcrowding and adhesion induced unjamming reflects the mechanical yielding of the highly deformable monolayer, suggesting an alternative mechanism that cells may robustly gain collective mobility through proliferation in confined environments, which differs from those caused by loosing up a packed particulate assembly. This work is supported by the GWU College Facilitating Funds.

Nanoporous Membranes with Chemically-Tailored Pore Walls from Triblock Terpolymer Templates

NASA Astrophysics Data System (ADS)

Mulvenna, Ryan; Weidman, Jacob; Pople, John; Boudouris, Bryan; Phillip, William

2014-03-01

Membranes generated from self-assembled block polymers have shown promise as highly permeable and selective filters; however, current syntheses of such materials lack diverse pore wall chemical functionality. Here, we report the facile synthesis of polyisoprene- b-polystyrene- b-poly(N , N -dimethylacrylamide) (PI-PS-PDMA) using a controlled reversible addition-fragmentation chain transfer (RAFT) polymerization mechanism to yield a macromolecule with an easily-tunable molecular weight and a narrow molecular weight distribution. The PI-PS-PDMA is then cast into an anisotropic membrane using the self-assembly and non-solvent induced phase separation process (SNIPS) protocol. These membranes can be used in size-selective separations for particles as small as 8 nm in diameter. Furthermore, the PDMA block can be converted to poly(acrylic acid) (PAA) readily in the solid state, and this PI-PS-PAA terpolymer membrane can separate particles as low as 2 nm in diameter while still retaining a relatively high flux. This is the smallest reported separation for a block polymer-based membrane to date. Additionally, the PAA-lined pores serve as a conversion platform to be tuned to any other pore chemistry, which allows the membrane to be of great utility in optimizing chemistry-specific separations.

Metal Ion-Induced Self-Assembly of a Multi-Responsive Block Copolypeptide into Well-Defined Nanocapsules.

PubMed

van Eldijk, Mark B; Schoonen, Lise; Cornelissen, Jeroen J L M; Nolte, Roeland J M; van Hest, Jan C M

2016-05-01

Protein cages are an interesting class of biomaterials with potential applications in bionanotechnology. Therefore, substantial effort is spent on the development of capsule-forming designer polypeptides with a tailor-made assembly profile. The expanded assembly profile of a triblock copolypeptide consisting of a metal ion chelating hexahistidine-tag, a stimulus-responsive elastin-like polypeptide block, and a pH-responsive morphology-controlling viral capsid protein is presented. The self-assembly of this multi-responsive protein-based block copolymer is triggered by the addition of divalent metal ions. This assembly process yields monodisperse nanocapsules with a 20 nm diameter composed of 60 polypeptides. The well-defined nanoparticles are the result of the emergent properties of all the blocks of the polypeptide. These results demonstrate the feasibility of hexahistidine-tags to function as supramolecular cross-linkers. Furthermore, their potential for the metal ion-mediated encapsulation of hexahistidine-tagged proteins is shown. © 2016 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Two-dimensional honeycomb network through sequence-controlled self-assembly of oligopeptides.

PubMed

Abb, Sabine; Harnau, Ludger; Gutzler, Rico; Rauschenbach, Stephan; Kern, Klaus

2016-01-12

The sequence of a peptide programs its self-assembly and hence the expression of specific properties through non-covalent interactions. A large variety of peptide nanostructures has been designed employing different aspects of these non-covalent interactions, such as dispersive interactions, hydrogen bonding or ionic interactions. Here we demonstrate the sequence-controlled fabrication of molecular nanostructures using peptides as bio-organic building blocks for two-dimensional (2D) self-assembly. Scanning tunnelling microscopy reveals changes from compact or linear assemblies (angiotensin I) to long-range ordered, chiral honeycomb networks (angiotensin II) as a result of removal of steric hindrance by sequence modification. Guided by our observations, molecular dynamic simulations yield atomistic models for the elucidation of interpeptide-binding motifs. This new approach to 2D self-assembly on surfaces grants insight at the atomic level that will enable the use of oligo- and polypeptides as large, multi-functional bio-organic building blocks, and opens a new route towards rationally designed, bio-inspired surfaces.

Cellular imaging by targeted assembly of hot-spot SERS and photoacoustic nanoprobes using split-fluorescent protein scaffolds.

PubMed

Köker, Tuğba; Tang, Nathalie; Tian, Chao; Zhang, Wei; Wang, Xueding; Martel, Richard; Pinaud, Fabien

2018-02-09

The in cellulo assembly of plasmonic nanomaterials into photo-responsive probes is of great interest for many bioimaging and nanophotonic applications but remains challenging with traditional nucleic acid scaffolds-based bottom-up methods. Here, we address this quandary using split-fluorescent protein (FP) fragments as molecular glue and switchable Raman reporters to assemble gold or silver plasmonic nanoparticles (NPs) into photonic clusters directly in live cells. When targeted to diffusing surface biomarkers in cancer cells, the NPs self-assemble into surface-enhanced Raman-scattering (SERS) nanoclusters having hot spots homogenously seeded by the reconstruction of full-length FPs. Within plasmonic hot spots, autocatalytic activation of the FP chromophore and near-field amplification of its Raman fingerprints enable selective and sensitive SERS imaging of targeted cells. This FP-driven assembly of metal colloids also yields enhanced photoacoustic signals, allowing the hybrid FP/NP nanoclusters to serve as contrast agents for multimodal SERS and photoacoustic microscopy with single-cell sensitivity.

Goose parvovirus structural proteins expressed by recombinant baculoviruses self-assemble into virus-like particles with strong immunogenicity in goose

DOE Office of Scientific and Technical Information (OSTI.GOV)

Ju, Huanyu; Wei, Na; Wang, Qian

Highlights: {yields} All three capsid proteins can be expressed in insect cells in baculovirus expression system. {yields} All three recombinant proteins were spontaneously self-assemble into virus-like particles whose size and appearance were similar to those of native purified GPV virions. {yields} The immunogenicity of GPV-VLPs was better than commercial inactivated vaccine and attenuated vaccine. -- Abstract: Goose parvovirus (GPV), a small non-enveloped ssDNA virus, can cause Derzsy's disease, and three capsid proteins of VP1, VP2, and VP3 are encoded by an overlapping nucleotide sequence. However, little is known on whether recombinant viral proteins (VPs) could spontaneously assemble into virus-like particlesmore » (VLPs) in insect cells and whether these VLPs could retain their immunoreactivity and immunogenicity in susceptible geese. To address these issues, genes for these GPV VPs were amplified by PCR, and the recombinant VPs proteins were expressed in insect cells using a baculovirus expression system for the characterization of their structures, immunoreactivity, and immunogenicity. The rVP1, rVP2, and rVP3 expressed in Sf9 cells were detected by anti-GPV sera, anti-VP3 sera, and anti-His antibodies, respectively. Electron microscopy revealed that these rVPs spontaneously assembled into VLPs in insect cells, similar to that of the purified wild-type GPV virions. In addition, vaccination with individual types of VLPs, particularly with the rVP2-VLPs, induced higher titers of antibodies and neutralized different strains of GPVs in primary goose and duck embryo fibroblast cells in vitro. These data indicated that these VLPs retained immunoreactivity and had strong immunogenicity in susceptible geese. Therefore, our findings may provide a framework for development of new vaccines for the prevention of Derzsy's disease and vehicles for the delivery of drugs.« less

DOE Office of Scientific and Technical Information (OSTI.GOV)

Meierbachtol, K.; Tovesson, F.; Shields, D.

We developed the SPectrometer for Ion DEtermination in fission Research (SPIDER) for measuring mass yield distributions of fission products from spontaneous and neutron-induced fission. The 2E–2v method of measuring the kinetic energy (E) and velocity (v) of both outgoing fission products has been utilized, with the goal of measuring the mass of the fission products with an average resolution of 1 atomic mass unit (amu). Moreover, the SPIDER instrument, consisting of detector components for time-of-flight, trajectory, and energy measurements, has been assembled and tested using 229Th and 252Cf radioactive decay sources. For commissioning, the fully assembled system measured fission productsmore » from spontaneous fission of 252Cf. Individual measurement resolutions were met for time-of-flight (250 ps FWHM), spacial resolution (2 mm FHWM), and energy (92 keV FWHM for 8.376 MeV). Finally, these mass yield results measured from 252Cf spontaneous fission products are reported from an E–v measurement.« less

More on the elongational viscosity of an oriented fiber assembly

NASA Technical Reports Server (NTRS)

Pipes, R. Byron, Jr.; Beaussart, A. J.; Okine, R. K.

1990-01-01

The effective elongational viscosity for an oriented fiber assembly of discontinuous fibers suspended in a viscous matrix fluid is developed for a fiber array with variable overlap length of both symmetric and asymmetric geometries. Further, the relation is developed for a power-law matrix fluid with finite yield stress. The developed relations for a Newtonian fluid reveal that the influence of overlap length upon elongational viscosity may be expressed as a polynomial of second order. The results for symmetric and asymmetric geometries are shown to be equivalent. Finally, for the power-law fluid the influence of fiber aspect ratio on elongational viscosity was shown to be of order m + 1, where m is greater than 0 and less than 1, as compared to 2 for the Newtonian fluid, while the effective yield stress was found to be proportional to the fiber aspect ratio and volume fraction.

"Stealth and Fully-Laden" Drug Carriers: Self-Assembled Nanogels Encapsulated with Epigallocatechin Gallate and siRNA for Drug-Resistant Breast Cancer Therapy.

PubMed

Ding, Jie; Liang, Tingxizi; Min, Qianhao; Jiang, Liping; Zhu, Jun-Jie

2018-03-28

For codelivery of therapeutic genes and chemical agents in combined therapy, the ideal drug delivery system entails high-capacity and low-body toxicity carriers, allowing adequate drug dose for tumor regions while yielding low residues in normal tissues. To augment the gene/drug load capacity and circumvent the potential toxicity brought by traditional inorganic and polymeric nanocarriers, a "stealth" carrier was herein designed in a simple self-assembly of (-)-epigallocatechin-3- O-gallate (EGCG) and small interfering RNA (siRNA) by recruiting protamine as a biodegradable medium for the treatment of drug-resistant triple-negative breast cancer. In the self-assembled nanogel, entrapped siRNA played a central role in sensitizing the tumor response to EGCG-involved chemotherapy, and the positively charged protamine served as the assembly skeleton to fully accommodate gene and drug molecules and minimize the factors causing side effects. As compared to stand-alone chemotherapy with EGCG, the multicomponent nanogel revealed a 15-fold increase in the cytotoxicity to drug-resistant MDA-MB-231 cell line. Moreover, equipped with hyaluronic acid and tumor-homing cell-penetrating peptide as the outmost targeting ligands, the siRNA- and EGCG-loaded nanogel demonstrates superior selectivity and tumor growth inhibition to free EGCG in xenograft MDA-MB-231 tumor-bearing mice. Meanwhile, thanks to the acknowledged biosafety of protamine, little toxicity was found to normal tissues and organs in the animal model. This gene/drug self-assembly caged in a biodegradable carrier opens up an effective and secure route for drug-resistant cancer therapy and provides a versatile approach for codelivery of other genes and drugs for different medical purposes.

The head-regeneration transcriptome of the planarian Schmidtea mediterranea.

PubMed

Sandmann, Thomas; Vogg, Matthias C; Owlarn, Suthira; Boutros, Michael; Bartscherer, Kerstin

2011-08-16

Planarian flatworms can regenerate their head, including a functional brain, within less than a week. Despite the enormous potential of these animals for medical research and regenerative medicine, the mechanisms of regeneration and the molecules involved remain largely unknown. To identify genes that are differentially expressed during early stages of planarian head regeneration, we generated a de novo transcriptome assembly from more than 300 million paired-end reads from planarian fragments regenerating the head at 16 different time points. The assembly yielded 26,018 putative transcripts, including very long transcripts spanning multiple genomic supercontigs, and thousands of isoforms. Using short-read data from two platforms, we analyzed dynamic gene regulation during the first three days of head regeneration. We identified at least five different temporal synexpression classes, including genes specifically induced within a few hours after injury. Furthermore, we characterized the role of a conserved Runx transcription factor, smed-runt-like1. RNA interference (RNAi) knockdown and immunofluorescence analysis of the regenerating visual system indicated that smed-runt-like1 encodes a transcriptional regulator of eye morphology and photoreceptor patterning. Transcriptome sequencing of short reads allowed for the simultaneous de novo assembly and differential expression analysis of transcripts, demonstrating highly dynamic regulation during head regeneration in planarians.

The head-regeneration transcriptome of the planarian Schmidtea mediterranea

PubMed Central

2011-01-01

Background Planarian flatworms can regenerate their head, including a functional brain, within less than a week. Despite the enormous potential of these animals for medical research and regenerative medicine, the mechanisms of regeneration and the molecules involved remain largely unknown. Results To identify genes that are differentially expressed during early stages of planarian head regeneration, we generated a de novo transcriptome assembly from more than 300 million paired-end reads from planarian fragments regenerating the head at 16 different time points. The assembly yielded 26,018 putative transcripts, including very long transcripts spanning multiple genomic supercontigs, and thousands of isoforms. Using short-read data from two platforms, we analyzed dynamic gene regulation during the first three days of head regeneration. We identified at least five different temporal synexpression classes, including genes specifically induced within a few hours after injury. Furthermore, we characterized the role of a conserved Runx transcription factor, smed-runt-like1. RNA interference (RNAi) knockdown and immunofluorescence analysis of the regenerating visual system indicated that smed-runt-like1 encodes a transcriptional regulator of eye morphology and photoreceptor patterning. Conclusions Transcriptome sequencing of short reads allowed for the simultaneous de novo assembly and differential expression analysis of transcripts, demonstrating highly dynamic regulation during head regeneration in planarians. PMID:21846378

Dynamic Response of an Optomechanical System to a Stationary Random Excitation in the Time Domain

DOE PAGES

Palmer, Jeremy A.; Paez, Thomas L.

2011-01-01

Modern electro-optical instruments are typically designed with assemblies of optomechanical members that support optics such that alignment is maintained in service environments that include random vibration loads. This paper presents a nonlinear numerical analysis that calculates statistics for the peak lateral response of optics in an optomechanical sub-assembly subject to random excitation of the housing. The work is unique in that the prior art does not address peak response probability distribution for stationary random vibration in the time domain for a common lens-retainer-housing system with Coulomb damping. Analytical results are validated by using displacement response data from random vibration testingmore » of representative prototype sub-assemblies. A comparison of predictions to experimental results yields reasonable agreement. The Type I Asymptotic form provides the cumulative distribution function for peak response probabilities. Probabilities are calculated for actual lens centration tolerances. The probability that peak response will not exceed the centration tolerance is greater than 80% for prototype configurations where the tolerance is high (on the order of 30 micrometers). Conversely, the probability is low for those where the tolerance is less than 20 micrometers. The analysis suggests a design paradigm based on the influence of lateral stiffness on the magnitude of the response.« less

De novo assembly of the transcriptome of Aegiceras corniculatum, a mangrove species in the Indo-West Pacific region.

PubMed

Fang, Lu; Yang, Yuchen; Guo, Wuxia; Li, Jianfang; Zhong, Cairong; Huang, Yelin; Zhou, Renchao; Shi, Suhua

2016-08-01

Aegiceras corniculatum (L.) Blanco is one of the most salt tolerant mangrove species and can thrive in 3% salinity at the seaward edge of mangrove forests. Here we sequenced the transcriptome of A. corniculatum used Illumina GA platform to develop its genomic resources for ecological and evolutionary studies. We obtained about 50 million high-quality paired-end reads with 75bp in length. Using the short read assembler Velvet, we yielded 49,437 contigs with the average length of 625bp. A total of 32,744 (66.23%) contigs showed significant similarity to the GenBank non-redundant (NR) protein database. 30,911 and 18,004 of these sequences were assigned to Gene Ontology and eukaryotic orthologous groups of proteins (KOG). A total of 4942 transcripts from our assemblies had significant similarity with KEGG Orthologs and were involved in 144 KEGG pathways, while 9899 unigenes had enzyme commission (EC) numbers. In addition, 9792 transcriptome-derived SSRs were identified from 7342 sequences. With our strict criteria, 4165 candidate SNPs were also identified from 2058 contigs. Some of these SNPs were further validated by Sanger sequencing. Genomic resources generated in this study should be valuable in ecological, evolutionary, and functional genomics studies for this mangrove species. Copyright © 2016 Elsevier B.V. All rights reserved.

DOE Office of Scientific and Technical Information (OSTI.GOV)

Cheng, J.P., E-mail: chengjp@zju.edu.cn; Chen, X.; Ma, R.

Flower-like Co{sub 3}O{sub 4} hierarchical microspheres composed of self-assembled porous nanoplates have been prepared by a two-step method without employing templates. The first step involves the synthesis of flower-like Co(OH){sub 2} microspheres by a solution route at low temperatures. The second step includes the calcination of the as-prepared Co(OH){sub 2} microspheres at 200 deg. C for 1 h, causing their decomposition to form porous Co{sub 3}O{sub 4} microspheres without destruction of their original morphology. The samples were characterized by scanning electron microscope, transmission electron microscope, X-ray diffractormeter and Fourier transform infrared spectroscope. Some experimental factors including solution temperature and surfactantmore » on the morphologies of the final products have been investigated. The magnetic properties of Co{sub 3}O{sub 4} microspheres were also investigated. - Graphical Abstract: Flower-like Co{sub 3}O{sub 4} microspheres are composed of self-assembled nanoplates and these nanoplates appear to be closely packed in the microspheres. These nanoplates consist of a large number of nanocrystallites less than 5 nm in size with a porous structure, in which the connection between nanocrystallites is random. Research Highlights: {yields} Flower-like Co{sub 3}O{sub 4} hierarchical microspheres composed of self-assembled porous nanoplates have been prepared by a two-step method without employing templates. {yields} Layered Co(OH){sub 2} microspheres were prepared with an appropriate approach under low temperatures for 1 h reaction. {yields} Calcination caused Co(OH){sub 2} decomposition to form porous Co{sub 3}O{sub 4} microspheres without destruction of their original morphology.« less

Infrared Thermal Testing Of Mechanical Assemblies At The Military Depot And Field Level: A Progress Report

NASA Astrophysics Data System (ADS)

Kaplan, Herbert

1988-01-01

Based on encouraging results on the Army's programs for infrared mass screening of printed circuit boards at the depot level, the US Army CECOM (Communication-Electronics Command) undertook a one-year investigation of the applicability of similar techniques to screening and diagnostics of mechanical assemblies. These included tanks, helicopters, transport vehicles and their major subassemblies (transmissions, engines, axles, etc.) at field and depot levels. Honeyhill Technical Company was tasked to classify candidate assemblies and perform preliminary measurements using Army-owned general-purpose thermal imaging equipment. The investigations yielded positive results, and it was decided to pursue a comprehensive measurements program using field-mobile equipment specifically procured for the program. This paper summarizes the results of the investigations, outlines the measurements techniques utilized, describes the classification and selection of candidate assemblies, and reports on progress toward the goals of the program.

Monoatomic and cluster beam effect on ToF-SIMS spectra of self-assembled monolayers on gold

NASA Astrophysics Data System (ADS)

Tuccitto, N.; Torrisi, V.; Delfanti, I.; Licciardello, A.

2008-12-01

Self-assembled monolayers represent well-defined systems that is a good model surface to study the effect of primary ion beams used in secondary ion mass spectrometry. The effect of polyatomic primary beams on both aliphatic and aromatic self-assembled monolayers has been studied. In particular, we analysed the variation of the relative secondary ion yield of both substrate metal-cluster (Au n-) in comparison with the molecular ions (M -) and clusters (M xAu y-) by using Bi +, Bi 3+, Bi 5+ beams. Moreover, the differences in the secondary ion generation efficiency are discussed. The main effect of the cluster beams is related to an increased formation of low-mass fragments and to the enhancement of the substrate related gold-clusters. The results show that, at variance of many other cases, the static SIMS of self-assembled monolayers does not benefit of the use of polyatomic primary ions.

Controlled evaporative self-assembly of confined microfluids: A route to complex ordered structures

NASA Astrophysics Data System (ADS)

Byun, Myunghwan

The evaporative self-assembly of nonvolatile solutes such as polymers, nanocrystals, and carbon nanotubes has been widely recognized as a non-lithographic means of producing a diverse range of intriguing complex structures. Due to the spatial variation of evaporative flux and possible convection, however, these non-equilibrium dissipative structures (e.g., fingering patterns and polygonal network structures) are often irregularly and stochastically organized. Yet for many applications in microelectronics, data storage devices, and biotechnology, it is highly desirable to achieve surface patterns having a well-controlled spatial arrangement. To date, only a few elegant studies have centered on precise control over the evaporation process to produce ordered structures. In a remarked comparison with conventional lithography techniques, surface patterning by controlled solvent evaporation is simple and cost-effective, offering a lithography- and external field-free means to organize nonvolatile materials into ordered microscopic structures over large surface areas. The ability to engineer an evaporative self-assembly process that yields a wide range of complex, self-organizing structures over large areas offers tremendous potential for applications in electronics, optoelectronics, and bio- or chemical sensors. We developed a facile, robust tool for evaporating polymer, nanoparticle, or DNA solutions in curve-on-flat geometries to create versatile, highly regular microstructures, including hierarchically structured polymer blend rings, conjugated polymer "snake-skins", block copolymer stripes, and punch-hole-like meshes, biomolecular microring arrays, etc. The mechanism of structure formation was elucidated both experimentally and theoretically. Our method further enhances current fabrication approaches to creating highly ordered structures in a simple and cost-effective manner, envisioning the potential to be tailored for use in photonics, optoelectronics, microfluidic devices, nanotechnology and biotechnology, etc.

Genetic evidence for the coordinated regulation of collagen fibrillogenesis in the cornea by decorin and biglycan.

PubMed

Zhang, Guiyun; Chen, Shoujun; Goldoni, Silvia; Calder, Bennett W; Simpson, Holly C; Owens, Rick T; McQuillan, David J; Young, Marian F; Iozzo, Renato V; Birk, David E

2009-03-27

Decorin and biglycan are class I small leucine-rich proteoglycans (SLRPs) involved in regulation of collagen fibril and matrix assembly. We hypothesize that tissue-specific matrix assembly, such as in the cornea, requires a coordinate regulation involving multiple SLRPs. To this end, we investigated the expression of decorin and biglycan in the cornea of mice deficient in either SLRP gene and in double-mutant mice. Decorin and biglycan exhibited overlapping spatial expression patterns throughout the corneal stroma with differential temporal expression. Whereas decorin was expressed at relatively high levels in all developmental stages, biglycan expression was high early, decreased during development, and was present at very low levels in the mature cornea. Ultrastructural analyses demonstrated comparable fibril structure in the decorin- and biglycan-null corneas compared with wild-type controls. We found a compensatory up-regulation of biglycan gene expression in the decorin-deficient mice, but not the reverse. Notably, the corneas of compound decorin/biglycan-null mice showed severe disruption in fibril structure and organization, especially affecting the posterior corneal regions, corroborating the idea that biglycan compensates for the loss of decorin. Fibrillogenesis assays using recombinant decorin and biglycan confirmed a functional compensation, with both having similar effects at high SLRP/collagen ratios. However, at low ratios decorin was a more efficient regulator. The use of proteoglycan or protein core yielded comparable results. These findings provide firm genetic evidence for an interaction of decorin and biglycan during corneal development and further suggest that decorin has a primary role in regulating fibril assembly, a function that can be fine-tuned by biglycan during early development.

Cocoa/Cotton Comparative Genomics

USDA-ARS?s Scientific Manuscript database

With genome sequence from two members of the Malvaceae family recently made available, we are exploring syntenic relationships, gene content, and evolutionary trajectories between the cacao and cotton genomes. An assembly of cacao (Theobroma cacao) using Illumina and 454 sequence technology yielded ...

Metamagnetism in hydrophobically induced carboxylate (phenylmalonate)-bridged copper(II) layers.

PubMed

Pasán, Jorge; Sanchiz, Joaquín; Ruiz-Pérez, Catalina; Campo, Javier; Lloret, Francesc; Julve, Miguel

2006-07-21

Self-assembly of copper(l) ions, phenylmalonate and pyrimidine yields the layered compound [Cu(pym)(Phmal)n (1) where intralayer ferro- and interlayer antiferromagnetic interactions occur with three-dimensional antiferromagnetic ordering at T(c) = 2.15 K.

The potential of the fresh-water fern Azolla in aquatic farming systems

NASA Astrophysics Data System (ADS)

Bijl, Peter K.; Werf, vd, Adrie; Schluepmann, Henriette; Reichart, Gert-Jan; Brouwer, Paul; Nierop, Klaas G. J.; Hellgardt, Klaus; Brinkhuis, Henk

2014-05-01

With aquatic farming systems a new avenue in agriculture is explored, in which the competition with conventional arable land is avoided. The aquatic, ubiquitous, floating fern Azolla is not yet widely explored as potential crop in such farming systems, despite its high potential because it grows in many natural systems under low-light intensities, has an enormous annual yield, and has special biomass qualities for applications in food, feed and specialty chemical industries. But, what makes Azolla particularly interesting as cost-effective crop is its capability to take up atmospheric nitrogen through symbiosis with nitrogen-fixing bacteria Anabaena azollae. This makes Azolla independent of nitrogen fertilization. In order to explore the potential of Azolla as a crop for a suite of applications, we have assembled a team of expertise: AZOFAST, consisting of agricultural engineers, plant physiologists, chemical engineers and organic chemists. Our growth experiments reveal high annual production yields with constant harvest. We are developing a germination and spore collecting/preservation protocol as a first step to domestication. Finally we have explored the biomass quality of different species of extant Azolla. We performed organic chemical analyses on lipid and tannin extracts, and quantified yields of specific compounds within these fractions. In our presentation we will present some of our results to show the potential of Azolla as a new, sustainable aquatic crop serving all kinds of industrial streams from protein feed to platform chemicals.

Recent advances in reconstructing microbial secondary metabolites biosynthesis in Aspergillus spp.

PubMed

He, Yi; Wang, Bin; Chen, Wanping; Cox, Russell J; He, Jingren; Chen, Fusheng

High throughput genome sequencing has revealed a multitude of potential secondary metabolites biosynthetic pathways that remain cryptic. Pathway reconstruction coupled with genetic engineering via heterologous expression enables discovery of novel compounds, elucidation of biosynthetic pathways, and optimization of product yields. Apart from Escherichia coli and yeast, fungi, especially Aspergillus spp., are well known and efficient heterologous hosts. This review summarizes recent advances in heterologous expression of microbial secondary metabolite biosynthesis in Aspergillus spp. We also discuss the technological challenges and successes in regard to heterologous host selection and DNA assembly behind the reconstruction of microbial secondary metabolite biosynthesis. Copyright © 2018 Elsevier Inc. All rights reserved.

Synthesis of silica-polymer core-shell nanoparticles by reversible addition-fragmentation chain transfer polymerization.

PubMed

Moraes, John; Ohno, Kohji; Maschmeyer, Thomas; Perrier, Sébastien

2013-10-14

Hybrid nanoparticles hold great promise for a range of applications such as drug-delivery vectors or colloidal crystal self-assemblies. The challenge of preparing highly monodisperse particles for these applications has recently been overcome by using living radical polymerization techniques. In particular, the use of reversible addition-fragmentation chain transfer (RAFT), initiated from silica surfaces, yields well-defined particles from a range of precursor monomers resulting in nanoparticles of tailored sizes that are accessible via the rational selection of polymerization conditions. Furthermore, using RAFT allows post-polymerization modification to afford multifunctional, monodisperse, nanostructures under mild and non-stringent reaction conditions.

Efficient perovskite light-emitting diodes featuring nanometre-sized crystallites

NASA Astrophysics Data System (ADS)

Xiao, Zhengguo; Kerner, Ross A.; Zhao, Lianfeng; Tran, Nhu L.; Lee, Kyung Min; Koh, Tae-Wook; Scholes, Gregory D.; Rand, Barry P.

2017-01-01

Organic-inorganic hybrid perovskite materials are emerging as highly attractive semiconductors for use in optoelectronics. In addition to their use in photovoltaics, perovskites are promising for realizing light-emitting diodes (LEDs) due to their high colour purity, low non-radiative recombination rates and tunable bandgap. Here, we report highly efficient perovskite LEDs enabled through the formation of self-assembled, nanometre-sized crystallites. Large-group ammonium halides added to the perovskite precursor solution act as a surfactant that dramatically constrains the growth of 3D perovskite grains during film forming, producing crystallites with dimensions as small as 10 nm and film roughness of less than 1 nm. Coating these nanometre-sized perovskite grains with longer-chain organic cations yields highly efficient emitters, resulting in LEDs that operate with external quantum efficiencies of 10.4% for the methylammonium lead iodide system and 9.3% for the methylammonium lead bromide system, with significantly improved shelf and operational stability.

QCM-D Investigation of Swelling Behavior of Layer-by-Layer Thin Films upon Exposure to Monovalent Ions.

PubMed

O'Neal, Joshua T; Dai, Ethan Y; Zhang, Yanpu; Clark, Kyle B; Wilcox, Kathryn G; George, Ian M; Ramasamy, Nandha E; Enriquez, Daisy; Batys, Piotr; Sammalkorpi, Maria; Lutkenhaus, Jodie L

2018-01-23

Polyelectrolyte multilayers and layer-by-layer assemblies are susceptible to structural changes in response to ionic environment. By altering the salt type and ionic strength, structural changes can be induced by disruption of intrinsically bound ion pairs within the multilayer network via electrostatic screening. Notably, high salt concentrations have been used for the purposes of salt-annealing and self-healing of LbL assemblies with KBr, in particular, yielding a remarkably rapid response. However, to date, the structural and swelling effects of various monovalent ion species on the behavior of LbL assemblies remain unclear, including a quantitative view of ion content in the LbL assembly and thickness changes over a wide concentration window. Here, we investigate the effects of various concentrations of KBr (0 to 1.6 M) on the swelling and de-swelling of LbL assemblies formed from poly(diallyldimethylammonium) polycation (PDADMA) and poly(styrene sulfonate) polyanion (PSS) in 0.5 M NaCl using quartz-crystal microbalance with dissipation (QCM-D) monitoring as compared to KCl, NaBr, and NaCl. The ion content after salt exchange is quantified using neutron activation analysis (NAA). Our results demonstrate that Br - ions have a much greater effect on the structure of as-prepared thin films than Cl - at ionic strengths above assembly conditions, which is possibly caused by the more chaotropic nature of Br - . It is also found that the anion in general dominates the swelling response as compared to the cation because of the excess PDADMA in the multilayer. Four response regimes are identified that delineate swelling due to electrostatic repulsion, slight contraction, swelling due to doping, and film destruction as ionic strength increases. This understanding is critical if such materials are to be used in applications requiring submersion in chemically dynamic environments such as sensors, coatings on biomedical implants, and filtration membranes.

Choice of Reference Sequence and Assembler for Alignment of Listeria monocytogenes Short-Read Sequence Data Greatly Influences Rates of Error in SNP Analyses

PubMed Central

Pightling, Arthur W.; Petronella, Nicholas; Pagotto, Franco

2014-01-01

The wide availability of whole-genome sequencing (WGS) and an abundance of open-source software have made detection of single-nucleotide polymorphisms (SNPs) in bacterial genomes an increasingly accessible and effective tool for comparative analyses. Thus, ensuring that real nucleotide differences between genomes (i.e., true SNPs) are detected at high rates and that the influences of errors (such as false positive SNPs, ambiguously called sites, and gaps) are mitigated is of utmost importance. The choices researchers make regarding the generation and analysis of WGS data can greatly influence the accuracy of short-read sequence alignments and, therefore, the efficacy of such experiments. We studied the effects of some of these choices, including: i) depth of sequencing coverage, ii) choice of reference-guided short-read sequence assembler, iii) choice of reference genome, and iv) whether to perform read-quality filtering and trimming, on our ability to detect true SNPs and on the frequencies of errors. We performed benchmarking experiments, during which we assembled simulated and real Listeria monocytogenes strain 08-5578 short-read sequence datasets of varying quality with four commonly used assemblers (BWA, MOSAIK, Novoalign, and SMALT), using reference genomes of varying genetic distances, and with or without read pre-processing (i.e., quality filtering and trimming). We found that assemblies of at least 50-fold coverage provided the most accurate results. In addition, MOSAIK yielded the fewest errors when reads were aligned to a nearly identical reference genome, while using SMALT to align reads against a reference sequence that is ∼0.82% distant from 08-5578 at the nucleotide level resulted in the detection of the greatest numbers of true SNPs and the fewest errors. Finally, we show that whether read pre-processing improves SNP detection depends upon the choice of reference sequence and assembler. In total, this study demonstrates that researchers should test a variety of conditions to achieve optimal results. PMID:25144537

Extracellular matrix components and culture regimen selectively regulate cartilage formation by self-assembling human mesenchymal stem cells in vitro and in vivo.

PubMed

Ng, Johnathan; Wei, Yiyong; Zhou, Bin; Burapachaisri, Aonnicha; Guo, Edward; Vunjak-Novakovic, Gordana

2016-12-09

Cartilage formation from self-assembling mesenchymal stem cells (MSCs) in vitro recapitulate important cellular events during mesenchymal condensation that precedes native cartilage development. The goal of this study was to investigate the effects of cartilaginous extracellular matrix (ECM) components and culture regimen on cartilage formation by self-assembling human MSCs in vitro and in vivo. Human bone marrow-derived MSCs (hMSCs) were seeded and compacted in 6.5-mm-diameter transwell inserts with coated (type I, type II collagen) or uncoated (vehicle) membranes, at different densities (0.5 × 10 6 , 1.0 × 10 6 , 1.5 × 10 6 per insert). Pellets were formed by aggregating hMSCs (0.25 × 10 6 ) in round-bottomed wells. All tissues were cultured for up to 6 weeks for in vitro analyses. Discs (cultured for 6, 8 or 10 weeks) and pellets (cultured for 10 weeks) were implanted subcutaneously in immunocompromised mice to evaluate the cartilage stability in vivo. Type I and type II collagen coatings enabled cartilage disc formation from self-assembling hMSCs. Without ECM coating, hMSCs formed dome-shaped tissues resembling the pellets. Type I collagen, expressed in the prechondrogenic mesenchyme, improved early chondrogenesis versus type II collagen. High seeding density improved cartilage tissue properties but resulted in a lower yield of disc formation. Discs and pellets exhibited compositional and organizational differences in vitro and in vivo. Prolonged chondrogenic induction of the discs in vitro expedited endochondral ossification in vivo. The outcomes of cartilage tissues formed from self-assembling MSCs in vitro and in vivo can be modulated by the control of culture parameters. These insights could motivate new directions for engineering cartilage and bone via a cartilage template from self-assembling MSCs.

The unique self-assembly/disassembly property of Archaeoglobus fulgidus ferritin and its implications on molecular release from the protein cage.

PubMed

Sana, Barindra; Johnson, Eric; Lim, Sierin

2015-12-01

In conventional in vitro encapsulation of molecular cargo, the multi-subunit ferritin protein cages are disassembled in extremely acidic pH and re-assembled in the presence of highly concentrated cargo materials, which results in poor yields due to the low-pH treatment. In contrast, Archaeoglobus fulgidus open-pore ferritin (AfFtn) and its closed-pore mutant (AfFtn-AA) are present as dimeric species in neutral buffers that self-assemble into cage-like structure upon addition of metal ions. To understand the iron-mediated self-assembly and ascorbate-mediated disassembly properties, we studied the iron binding and release profile of the AfFtn and AfFtn-AA, and the corresponding oligomerization of their subunits. Fe(2+) binding and conversion to Fe(3+) triggered the self-assembly of cage-like structures from dimeric species of AfFtn and AfFtn-AA subunits, while disassembly was induced by dissolving the iron core with reducing agents. The closed-pore AfFtn-AA has identical iron binding kinetics but lower iron release rates when compared to AfFtn. While the iron binding rate is proportional to Fe(2+) concentration, the iron release rate can be controlled by varying ascorbate concentrations. The AfFtn and AfFtn-AA cages formed by iron mineralization could be disassembled by dissolving the iron core. The open-pores of AfFtn contribute to enhanced reductive iron release while the small channels located at the 3-fold symmetry axis (3-fold channels) are used for iron uptake. The iron-mediated self-assembly/disassembly property of AfFtn offers a new set of molecular trigger for formation and dissociation of the protein cage, which can potentially regulate uptake and release of molecular cargo from protein cages. Copyright © 2015 Elsevier B.V. All rights reserved.

Freestanding and Reactive Thin Films Fabricated by Covalent Layer-by-Layer Assembly and Subsequent Lift-Off of Azlactone-Containing Polymer Multilayers

PubMed Central

Buck, Maren E.

2010-01-01

We report an approach to the fabrication of freestanding and amine-reactive thin films that is based on the reactive layer-by-layer assembly and subsequent lift-off of azlactone-containing polymer multilayers. We demonstrate that covalently crosslinked multilayers fabricated using the azlactone-functionalized polymer poly(2-vinyl-4,4-dimethylazlactone) (PVDMA) and a primary amine-containing polymer [poly(ethyleneimine) (PEI)] can be delaminated from planar glass and silicon surfaces by immersion in mildly acidic aqueous environments to yield flexible freestanding membranes. These freestanding membranes are robust and can withstand exposure to strong acid, strong base, or incubation in high ionic strength solutions that typically lead to the disruption and erosion of polymer multilayers assembled by reversible weak interactions (e.g., ‘polyelectrolyte multilayers’ assembled by electrostatic interactions or hydrogen bonding). We demonstrate further that these PEI/PVDMA assemblies contain residual reactive azlactone functionality that can be exploited to chemically modify the films (either directly after fabrication or after they have been lifted off of the substrates on which they were fabricated) using a variety of amine-functionalized small molecules. These freestanding membranes can also be transferred readily onto other objects (for example, onto the surfaces of planar substrates containing holes or pores) to fabricate suspended polymer membranes and other film-functionalized interfaces. In addition to planar, two-dimensional freestanding films, this approach can be used to fabricate and isolate three-dimensional freestanding membranes (e.g., curved films or tubes) by layer-by-layer assembly on, and subsequent lift-off from, the surfaces of topologically complex substrates (e.g., the curved ends of glass tubing, etc.). The results of this investigation, when combined, suggest the basis of methods for the fabrication of stable, chemically-reactive, and flexible polymer thin films and membranes of potential utility in a variety of fundamental and applied contexts. PMID:20857952

Role of Side Chains in β-Sheet Self-Assembly into Peptide Fibrils. IR and VCD Spectroscopic Studies of Glutamic Acid-Containing Peptides.

PubMed

Tobias, Fernando; Keiderling, Timothy A

2016-05-10

Poly(glutamic acid) at low pH self-assembles after incubation at higher temperature into fibrils composed of antiparallel sheets that are stacked in a β2-type structure whose amide carbonyls have bifurcated H-bonds involving the side chains from the next sheet. Oligomers of Glu can also form such structures, and isotope labeling has provided insight into their out-of-register antiparallel structure [ Biomacromolecules 2013 , 14 , 3880 - 3891 ]. In this paper we report IR and VCD spectra and transmission electron micrograph (TEM) images for a series of alternately sequenced oligomers, Lys-(Aaa-Glu)5-Lys-NH2, where Aaa was varied over a variety of polar, aliphatic, or aromatic residues. Their spectral and TEM data show that these oligopeptides self-assemble into different structures, both local and morphological, that are dependent on both the nature of the Aaa side chains and growth conditions employed. Such alternate peptides substituted with small or polar residues, Ala and Thr, do not yield fibrils; but with β-branched aliphatic residues, Val and Ile, that could potentially pack with Glu side chains, these oligopeptides do show evidence of β2-stacking. By contrast, for Leu, with longer side chains, only β1-stacking is seen while with even larger Phe side chains, either β-form can be detected separately, depending on preparation conditions. These structures are dependent on high temperature incubation after reducing the pH and in some cases after sonication of initial fibril forms and reincubation. Some of these fibrillar peptides, but not all, show enhanced VCD, which can offer evidence for formation of long, multistrand, often twisted structures. Substitution of Glu with residues having selected side chains yields a variety of morphologies, leading to both β1- and β2-structures, that overall suggests two different packing modes for the hydrophobic side chains depending on size and type.

Piezoelectric resonator assembly with thin molybdenum mounting clips

DOEpatents

Peters, R. Donald

1981-01-01

A resonator mounting assembly wherein the resonator blank is mounted agai an essentially planar surface presented by a plurality of peripherally disposed mounting clips and bonded to this surface to provide substantially all the mechanical support for the blank in a direction normal to the major faces of the resonator blank, while being flexible in the directions parallel to said major faces so as to minimize radial stresses on the resonator blank, particularly during thermal cycling of the resonator assembly. The clips are fabricated of a low thermal expansion material, such as molybdenum, which also has considerable yield strength after exposure to processing temperatures; the bonding of the clips to the edges of the resonator blank can be achieved by a polyimide containing electrically conductive particles.

WaferOptics® mass volume production and reliability

NASA Astrophysics Data System (ADS)

Wolterink, E.; Demeyer, K.

2010-05-01

The Anteryon WaferOptics® Technology platform contains imaging optics designs, materials, metrologies and combined with wafer level based Semicon & MEMS production methods. WaferOptics® first required complete new system engineering. This system closes the loop between application requirement specifications, Anteryon product specification, Monte Carlo Analysis, process windows, process controls and supply reject criteria. Regarding the Anteryon product Integrated Lens Stack (ILS), new design rules, test methods and control systems were assessed, implemented, validated and customer released for mass production. This includes novel reflowable materials, mastering process, replication, bonding, dicing, assembly, metrology, reliability programs and quality assurance systems. Many of Design of Experiments were performed to assess correlations between optical performance parameters and machine settings of all process steps. Lens metrologies such as FFL, BFL, and MTF were adapted for wafer level production and wafer mapping was introduced for yield management. Test methods for screening and validating suitable optical materials were designed. Critical failure modes such as delamination and popcorning were assessed and modeled with FEM. Anteryon successfully managed to integrate the different technologies starting from single prototypes to high yield mass volume production These parallel efforts resulted in a steep yield increase from 30% to over 90% in a 8 months period.

Improving the reactivity of phenylacetylene macrocycles toward topochemical polymerization by side chains modification

PubMed Central

Daigle, Maxime; Cantin, Katy

2014-01-01

Summary The synthesis and self-assembly of two new phenylacetylene macrocycle (PAM) organogelators were performed. Polar 2-hydroxyethoxy side chains were incorporated in the inner part of the macrocycles to modify the assembly mode in the gel state. With this modification, it was possible to increase the reactivity of the macrocycles in the xerogel state to form polydiacetylenes (PDAs), leading to a significant enhancement of the polymerization yields. The organogels and the PDAs were characterized using Raman spectroscopy, X-ray diffraction (XRD) and scanning electron microscopy (SEM). PMID:25161718

Ionically self-assembled monolayers (ISAMs)

NASA Astrophysics Data System (ADS)

Janik, John

2001-04-01

Ionically self-assembled monolayers (ISAMs), fabricated by alternate adsorption of cationic and anionic components, yield exceptionally homogeneous thin films with sub-nanometer control of the thickness and relative special location of the component materials. Using organic electrochromic materials such as polyaniline, we report studies of electrochromic responses in ISAM films. Reversible changes in the absorption spectrum are observed with the application of voltages on the order of 1.0 V. Measurements are made using both liquid electrolytes and in all-solid state devices incorporating solid polyelectrolytes such as poly(2-acylamido 2-methyl propane sulfonic acid) (PAMPS).

Modelling Polar Self Assembly

NASA Astrophysics Data System (ADS)

Olvera de La Cruz, Monica; Sayar, Mehmet; Solis, Francisco J.; Stupp, Samuel I.

2001-03-01

Recent experimental studies in our group have shown that self assembled thin films of noncentrosymmetric supramolecular objects composed of triblock rodcoil molecules exhibit finite polar order. These aggregates have both long range dipolar and short range Ising-like interactions. We study the ground state of a simple model with these competing interactions. We find that the competition between Ising-like and dipolar forces yield a periodic domain structure, which can be controlled by adjusting the force constants and film thickness. When the surface forces are included in the potential, the system exhibits a finite macroscopic polar order.

Imine-based [2]catenanes in water.

PubMed

Caprice, Kenji; Pupier, Marion; Kruve, Anneli; Schalley, Christoph A; Cougnon, Fabien B L

2018-02-07

We report the efficient condensation of imine-based macrocycles from dialdehyde A and aliphatic diamines B n in pure water. Within the libraries, we identified a family of homologous amphiphilic [2]catenanes, whose self-assembly is primarily driven by the hydrophobic effect. The length and odd-even character of the diamine alkyl linker dictate both the yield and the conformation of the [2]catenanes, whose particular thermodynamic stability further shifts the overall equilibrium in favour of imine condensation. These findings highlight the role played by solvophobic effects in the self-assembly of complex architectures.

Structural characterisation of medically relevant protein assemblies by integrating mass spectrometry with computational modelling.

PubMed

Politis, Argyris; Schmidt, Carla

2018-03-20

Structural mass spectrometry with its various techniques is a powerful tool for the structural elucidation of medically relevant protein assemblies. It delivers information on the composition, stoichiometries, interactions and topologies of these assemblies. Most importantly it can deal with heterogeneous mixtures and assemblies which makes it universal among the conventional structural techniques. In this review we summarise recent advances and challenges in structural mass spectrometric techniques. We describe how the combination of the different mass spectrometry-based methods with computational strategies enable structural models at molecular levels of resolution. These models hold significant potential for helping us in characterizing the function of protein assemblies related to human health and disease. In this review we summarise the techniques of structural mass spectrometry often applied when studying protein-ligand complexes. We exemplify these techniques through recent examples from literature that helped in the understanding of medically relevant protein assemblies. We further provide a detailed introduction into various computational approaches that can be integrated with these mass spectrometric techniques. Last but not least we discuss case studies that integrated mass spectrometry and computational modelling approaches and yielded models of medically important protein assembly states such as fibrils and amyloids. Copyright © 2017 The Author(s). Published by Elsevier B.V. All rights reserved.

Terminating DNA Tile Assembly with Nanostructured Caps.

PubMed

Agrawal, Deepak K; Jiang, Ruoyu; Reinhart, Seth; Mohammed, Abdul M; Jorgenson, Tyler D; Schulman, Rebecca

2017-10-24

Precise control over the nucleation, growth, and termination of self-assembly processes is a fundamental tool for controlling product yield and assembly dynamics. Mechanisms for altering these processes programmatically could allow the use of simple components to self-assemble complex final products or to design processes allowing for dynamic assembly or reconfiguration. Here we use DNA tile self-assembly to develop general design principles for building complexes that can bind to a growing biomolecular assembly and terminate its growth by systematically characterizing how different DNA origami nanostructures interact with the growing ends of DNA tile nanotubes. We find that nanostructures that present binding interfaces for all of the binding sites on a growing facet can bind selectively to growing ends and stop growth when these interfaces are presented on either a rigid or floppy scaffold. In contrast, nucleation of nanotubes requires the presentation of binding sites in an arrangement that matches the shape of the structure's facet. As a result, it is possible to build nanostructures that can terminate the growth of existing nanotubes but cannot nucleate a new structure. The resulting design principles for constructing structures that direct nucleation and termination of the growth of one-dimensional nanostructures can also serve as a starting point for programmatically directing two- and three-dimensional crystallization processes using nanostructure design.

High-power lightweight external-cavity quantum cascade lasers

NASA Astrophysics Data System (ADS)

Day, Timothy; Takeuchi, Eric B.; Weida, Miles; Arnone, David; Pushkarsky, Michael; Boyden, David; Caffey, David

2009-05-01

Commercially available quantum cascade gain media has been integrated with advanced coating and die attach technologies, mid-IR micro-optics and telecom-style assembly and packaging to yield cutting edge performance. When combined into Daylight's external-cavity quantum cascade laser (ECqcL) platform, multi-Watt output power has been obtained. Daylight will describe their most recent results obtained from this platform, including high cw power from compact hermetically sealed packages and narrow spectral linewidth devices. Fiber-coupling and direct amplitude modulation from such multi-Watt lasers will also be described. In addition, Daylight will present the most recent results from their compact, portable, battery-operated "thermal laser pointers" that are being used for illumination and aiming applications. When combined with thermal imaging technology, such devices provide significant benefits in contrast and identification.

Assembly of P3HT/CdSe nanowire networks in an insulating polymer host.

PubMed

Heo, Kyuyoung; Miesch, Caroline; Na, Jun-Hee; Emrick, Todd; Hayward, Ryan C

2018-06-27

Nanoparticles may act as compatibilizing agents for blending of immiscible polymers, leading to changes in blend morphology through a variety of mechanisms including interfacial adsorption, aggregation, and nucleation of polymer crystals. Herein, we report an approach to define highly structured donor/acceptor networks based on poly(3-hexylthiophene) (P3HT) and CdSe quantum dots (QDs) by demixing from an insulating polystyrene (PS) matrix. The incorporation of QDs led to laterally phase-separated co-continuous structures with sub-micrometer dimensions, and promoted crystallization of P3HT, yielding highly interconnected P3HT/QD hybrid nanowires embedded in the polymer matrix. These nanohybrid materials formed by controlling phase separation, interfacial activity, and crystallization within ternary donor/acceptor/insulator blends, offer attractive morphologies for potential use in optoelectronics.

Universal chemiluminescence flow-through device based on directed self-assembly of solid-state organic chromophores on layered double hydroxide matrix.

PubMed

Wang, Zhihua; Teng, Xu; Lu, Chao

2013-02-19

In this work, a universal chemiluminescence (CL) flow-through device suitable for various CL resonance energy transfer (CRET) systems has been successfully fabricated. Highly efficient CRET in solid-state photoactive organic molecules can be achieved by assembling them on the surface of layered double hydroxides (LDHs). We attribute these observations to the suppression of the intermolecular π-π stacking interactions among aromatic rings and the improvement of molecular orientation and planarity in the LDH matrix, enabling a remarkable increase in fluorescence lifetime and quantum yield of organic molecules. Under optimal conditions, using peroxynitrous acid-fluorescein dianion (FLUD) as a model CRET system, trace FLUD (10 μM) was assembled on the surface of LDHs. Peroxynitrous acid/nitrite could be assayed in the range of 1.0-500 μM, and the detection limit for peroxynitrous acid/nitrite (S/N = 3) was 0.6 μM. This CL flow-through device exhibited operational stability, high reproducibility, and long lifetime. While LDHs were immobilized in a flow-through device in the absence of FLUD, the detection limit for peroxynitrous acid/nitrite was 100 μM. On the other hand, FLUD at the same concentration can not enhance the CL intensity of peroxynitrous acid system. This fabricated CL flow-through column has been successfully applied to determine nitrite in sausage samples with recoveries of 98-102%. These satisfactory results demonstrated that our studies pave a novel way toward flow-through column-based CRET using solid-state organic molecules as acceptors for signal amplification.

Dissolution and degradation of Fmoc-diphenylalanine self-assembled gels results in necrosis at high concentrations in vitro.

PubMed

Truong, Warren Ty; Su, Yingying; Gloria, Danmar; Braet, Filip; Thordarson, Pall

2015-02-01

Herein we report an approach to assess in vitro cellular responses to the dissolution or degradation products from Fmoc-diphenylalanine (Fmoc-FF) self-assembled hydrogels. Three cell lines were used in these studies and two-way ANOVA was used to assess (i) the age of gel dissolution and degradation products and (ii) exposure time on cell fate and state, using viability assays in conjunction with time-lapse fluorescence and high-resolution scanning electron microscopy investigation. The studies show that leaching time but not the exposure time affects the overall cell viability. The cytotoxic effect was only observed once the gel is completely dissolved. Further analysis revealed that the principal mechanism of cell death is necrosis. In addition, the effect of chemotherapeutics (5-fluorouracil and paclitaxel) released from the Fmoc-FF gel (with addition before and after gelation) on colorectal cancer cells were investigated using this methodology, demonstrating enhanced activity of these drugs compared to bulk control. This enhanced activity, however, appears to be a combination of the apoptosis caused by the cancer drugs and necrosis caused by gel dissolution and degradation products. Given that in vivo studies by others on Fmoc-peptides that this material is not harmful to animals, our work highlights that conventional in vitro cellular assays may yield conflicting messages when used for the evaluation of cytotoxicity and drug release from self-assembled gels such as Fmoc-FF and that better in vitro models, (e.g. 3D cell culture systems) need to be developed to evaluate these materials for biomedical applications.

A DNA Crystal Designed to Contain Two Molecules per Asymmetric Unit

DOE Office of Scientific and Technical Information (OSTI.GOV)

T Wang; R Sha; J Birktoft

2011-12-31

We describe the self-assembly of a DNA crystal that contains two tensegrity triangle molecules per asymmetric unit. We have used X-ray crystallography to determine its crystal structure. In addition, we have demonstrated control over the colors of the crystals by attaching either Cy3 dye (pink) or Cy5 dye (blue-green) to the components of the crystal, yielding crystals of corresponding colors. Attaching the pair of dyes to the pair of molecules yields a purple crystal.

1,2,4,5-Benzenetetracarboxylic acid: a versatile hydrogen bonding template for controlling the regioselective topochemical synthesis of head-to-tail photodimers from stilbazole derivatives.

PubMed

Ortega, Gabriela; Hernández, Jesús; González, Teresa; Dorta, Romano; Briceño, Alexander

2018-05-16

The crystal engineering of hydrogen bonded organic assemblies based on 1,2,4,5-benzenetetracarboxylic acid (H4bta) and stilbazole derivatives (1-10) is exploited to provide regio-controlled [2 + 2] photocycloadditions in the solid state. Single crystal X-ray diffraction analyses have revealed that all the arrays are built-up from the self-assembly of the (H2bta)2- dianion with two stilbazolium cations via O-HO- and N+-HO- charge-assisted H-bonding synthons: (4-Hstilbazolium+)2(H2bta2-). The dianion displays an interesting diversity of H-bonding motifs. Such structural flexibility allowed us to obtain four structure-types defined by the preferential formation of intramolecular or intermolecular hydrogen bonds between carboxylate-carboxylic groups. In these ionic assemblies two predominant structural H-bonding patterns were observed. The first pattern is characterised by the formation of intramolecular H-bonds in the dianion, leading to discrete assemblies based on ternary arrays. The second hydrogen pattern consists of 2-D hydrogen networks built-up from the self-assembly of anions via intermolecular H-bonds that are linked to the cations. Two additional examples, in which the dianion is self-assembled in two types of ribbons, were also observed. Another supramolecular feature predominant in all these arrays is the stacking of the cations in a head-to-tail fashion, which is controlled via cation-π interactions. These arrays are photoactive in the solid state upon UV-irradiation leading to the regioselective synthesis of rctt-cyclobutane head-to-tail-isomers in high to quantitative yield. In this work, the template tolerance either to steric or electronic effects by changing the number or positions of the supramolecular interactions exerted by distinctive functional groups was also explored. In addition, assemblies bearing 2-chloro (7 and 8) and 3-chloro-4-stilbazole (1 and 9) crystallize in two different crystalline forms, leading to novel examples of supramolecular isomers with similar solid state reactivity.

Synthesis of Water-Soluble Amino Functionalized Multithiacalix[4]arene via Quaternization of Tertiary Amino Groups.

PubMed

Nosov, Roman; Padnya, Pavel; Shurpik, Dmitriy; Stoikov, Ivan

2018-05-08

A convenient approach to the synthesis of multithiacalix[4]arene derivatives containing amino groups and phthalimide fragments by the formation of quaternary ammonium salts is presented. As the initial macrocycle for the synthesis of multithiacalix[4]arenes, a differently substituted p-tert- butylthiacalix[4]arene containing bromoacetamide and three phthalimide fragments was used in a 1,3-alternate conformation. The macrocycle in cone conformation containing the tertiary amino groups was found to be a convenient core for the multithiacalix[4]arene systems. Interaction of the core multithiacalix[4]arene with monobromoacetamide derivatives of p-tert- butylthiacalix[4]arene resulted in formation in high yields of pentakisthiacalix[4]arene containing quaternary ammonium and phthalimide fragments. The removal of phthalimide groups led to the formation of amino multithiacalix[4]arene in a good yield. Based on dynamic light scattering, it was shown that the synthesized amino multithiacalix[4]arene, with pronounced hydrophobic and hydrophilic fragments, formed dendrimer-like nanoparticles in water via direct supramolecular self-assembly.

Draft genome of the leopard gecko, Eublepharis macularius.

PubMed

Xiong, Zijun; Li, Fang; Li, Qiye; Zhou, Long; Gamble, Tony; Zheng, Jiao; Kui, Ling; Li, Cai; Li, Shengbin; Yang, Huanming; Zhang, Guojie

2016-10-26

Geckos are among the most species-rich reptile groups and the sister clade to all other lizards and snakes. Geckos possess a suite of distinctive characteristics, including adhesive digits, nocturnal activity, hard, calcareous eggshells, and a lack of eyelids. However, one gecko clade, the Eublepharidae, appears to be the exception to most of these 'rules' and lacks adhesive toe pads, has eyelids, and lays eggs with soft, leathery eggshells. These differences make eublepharids an important component of any investigation into the underlying genomic innovations contributing to the distinctive phenotypes in 'typical' geckos. We report high-depth genome sequencing, assembly, and annotation for a male leopard gecko, Eublepharis macularius (Eublepharidae). Illumina sequence data were generated from seven insert libraries (ranging from 170 to 20 kb), representing a raw sequencing depth of 136X from 303 Gb of data, reduced to 84X and 187 Gb after filtering. The assembled genome of 2.02 Gb was close to the 2.23 Gb estimated by k-mer analysis. Scaffold and contig N50 sizes of 664 and 20 kb, respectively, were comparable to the previously published Gekko japonicus genome. Repetitive elements accounted for 42 % of the genome. Gene annotation yielded 24,755 protein-coding genes, of which 93 % were functionally annotated. CEGMA and BUSCO assessment showed that our assembly captured 91 % (225 of 248) of the core eukaryotic genes, and 76 % of vertebrate universal single-copy orthologs. Assembly of the leopard gecko genome provides a valuable resource for future comparative genomic studies of geckos and other squamate reptiles.

De novo assembly of highly polymorphic metagenomic data using in situ generated reference sequences and a novel BLAST-based assembly pipeline.

PubMed

Lin, You-Yu; Hsieh, Chia-Hung; Chen, Jiun-Hong; Lu, Xuemei; Kao, Jia-Horng; Chen, Pei-Jer; Chen, Ding-Shinn; Wang, Hurng-Yi

2017-04-26

The accuracy of metagenomic assembly is usually compromised by high levels of polymorphism due to divergent reads from the same genomic region recognized as different loci when sequenced and assembled together. A viral quasispecies is a group of abundant and diversified genetically related viruses found in a single carrier. Current mainstream assembly methods, such as Velvet and SOAPdenovo, were not originally intended for the assembly of such metagenomics data, and therefore demands for new methods to provide accurate and informative assembly results for metagenomic data. In this study, we present a hybrid method for assembling highly polymorphic data combining the partial de novo-reference assembly (PDR) strategy and the BLAST-based assembly pipeline (BBAP). The PDR strategy generates in situ reference sequences through de novo assembly of a randomly extracted partial data set which is subsequently used for the reference assembly for the full data set. BBAP employs a greedy algorithm to assemble polymorphic reads. We used 12 hepatitis B virus quasispecies NGS data sets from a previous study to assess and compare the performance of both PDR and BBAP. Analyses suggest the high polymorphism of a full metagenomic data set leads to fragmentized de novo assembly results, whereas the biased or limited representation of external reference sequences included fewer reads into the assembly with lower assembly accuracy and variation sensitivity. In comparison, the PDR generated in situ reference sequence incorporated more reads into the final PDR assembly of the full metagenomics data set along with greater accuracy and higher variation sensitivity. BBAP assembly results also suggest higher assembly efficiency and accuracy compared to other assembly methods. Additionally, BBAP assembly recovered HBV structural variants that were not observed amongst assembly results of other methods. Together, PDR/BBAP assembly results were significantly better than other compared methods. Both PDR and BBAP independently increased the assembly efficiency and accuracy of highly polymorphic data, and assembly performances were further improved when used together. BBAP also provides nucleotide frequency information. Together, PDR and BBAP provide powerful tools for metagenomic data studies.

Self-Assembly of Octopus Nanoparticles into Pre-Programmed Finite Clusters

NASA Astrophysics Data System (ADS)

Halverson, Jonathan; Tkachenko, Alexei

2012-02-01

The precise control of the spatial arrangement of nanoparticles (NP) is often required to take full advantage of their novel optical and electronic properties. NPs have been shown to self-assemble into crystalline structures using either patchy surface regions or complementary DNA strands to direct the assembly. Due to a lack of specificity of the interactions these methods lead to only a limited number of structures. An emerging approach is to bind ssDNA at specific sites on the particle surface making so-called octopus NPs. Using octopus NPs we investigate the inverse problem of the self-assembly of finite clusters. That is, for a given target cluster (e.g., arranging the NPs on the vertices of a dodecahedron) what are the minimum number of complementary DNA strands needed for the robust self-assembly of the cluster from an initially homogeneous NP solution? Based on the results of Brownian dynamics simulations we have compiled a set of design rules for various target clusters including cubes, pyramids, dodecahedrons and truncated icosahedrons. Our approach leads to control over the kinetic pathway and has demonstrated nearly perfect yield of the target.

Active turbulence in a gas of self-assembled spinners

PubMed Central

Kokot, Gašper; Das, Shibananda; Winkler, Roland G.; Aranson, Igor S.; Snezhko, Alexey

2017-01-01

Colloidal particles subject to an external periodic forcing exhibit complex collective behavior and self-assembled patterns. A dispersion of magnetic microparticles confined at the air–liquid interface and energized by a uniform uniaxial alternating magnetic field exhibits dynamic arrays of self-assembled spinners rotating in either direction. Here, we report on experimental and simulation studies of active turbulence and transport in a gas of self-assembled spinners. We show that the spinners, emerging as a result of spontaneous symmetry breaking of clock/counterclockwise rotation of self-assembled particle chains, generate vigorous vortical flows at the interface. An ensemble of spinners exhibits chaotic dynamics due to self-generated advection flows. The same-chirality spinners (clockwise or counterclockwise) show a tendency to aggregate and form dynamic clusters. Emergent self-induced interface currents promote active diffusion that could be tuned by the parameters of the external excitation field. Furthermore, the erratic motion of spinners at the interface generates chaotic fluid flow reminiscent of 2D turbulence. Our work provides insight into fundamental aspects of collective transport in active spinner materials and yields rules for particle manipulation at the microscale. PMID:29158382

Self-assembly of multi-stranded RNA motifs into lattices and tubular structures

PubMed Central

Stewart, Jaimie Marie; Subramanian, Hari K. K.

2017-01-01

Abstract Rational design of nucleic acid molecules yields self-assembling scaffolds with increasing complexity, size and functionality. It is an open question whether design methods tailored to build DNA nanostructures can be adapted to build RNA nanostructures with comparable features. Here we demonstrate the formation of RNA lattices and tubular assemblies from double crossover (DX) tiles, a canonical motif in DNA nanotechnology. Tubular structures can exceed 1 μm in length, suggesting that this DX motif can produce very robust lattices. Some of these tubes spontaneously form with left-handed chirality. We obtain assemblies by using two methods: a protocol where gel-extracted RNA strands are slowly annealed, and a one-pot transcription and anneal procedure. We identify the tile nick position as a structural requirement for lattice formation. Our results demonstrate that stable RNA structures can be obtained with design tools imported from DNA nanotechnology. These large assemblies could be potentially integrated with a variety of functional RNA motifs for drug or nanoparticle delivery, or for colocalization of cellular components. PMID:28204562

A supersaturating delivery system of silibinin exhibiting high payload achieved by amorphous nano-complexation with chitosan.

PubMed

Nguyen, Minh-Hiep; Yu, Hong; Dong, Bingxue; Hadinoto, Kunn

2016-06-30

The therapeutic potentials of silibinin - a phytochemical isolated from milk thistle plants - have not been fully realized due to its poor oral bioavailability caused by the low aqueous solubility. Existing solubility enhancement strategies of silibinin by nanonization were limited by their low payload. Herein we developed a supersaturating delivery system of silibinin exhibiting a high payload (≈76%) in the form of amorphous silibinin-chitosan nanoparticle complex (or silibinin nanoplex in short) prepared by self-assembly drug-polysaccharide complexation. The effects of (1) pH and (2) charge ratio of chitosan to silibinin on the nanoplex's physical characteristics (i.e. size, zeta potential, and payload) and preparation efficiency (i.e. silibinin utilization, overall yield) were investigated. The formation of nanoplex (≈240nm) was feasible only in a narrow pH range (5.1-5.8) and favored charge ratio below unity. At the optimal condition (pH 5.8 and charge ratio of 0.30), the nanoplex preparation exhibited 87% silibinin utilization rate and 63% yield signifying its high efficiency. The amorphous state and colloidal stabilities of the nanoplex during storage, and prolonged supersaturation generation (3h) at more than 10× of the saturation solubility were successfully demonstrated. Copyright © 2016 Elsevier B.V. All rights reserved.

Assessing pooled BAC and whole genome shotgun strategies for assembly of complex genomes.

PubMed

Haiminen, Niina; Feltus, F Alex; Parida, Laxmi

2011-04-15

We investigate if pooling BAC clones and sequencing the pools can provide for more accurate assembly of genome sequences than the "whole genome shotgun" (WGS) approach. Furthermore, we quantify this accuracy increase. We compare the pooled BAC and WGS approaches using in silico simulations. Standard measures of assembly quality focus on assembly size and fragmentation, which are desirable for large whole genome assemblies. We propose additional measures enabling easy and visual comparison of assembly quality, such as rearrangements and redundant sequence content, relative to the known target sequence. The best assembly quality scores were obtained using 454 coverage of 15× linear and 5× paired (3kb insert size) reads (15L-5P) on Arabidopsis. This regime gave similarly good results on four additional plant genomes of very different GC and repeat contents. BAC pooling improved assembly scores over WGS assembly, coverage and redundancy scores improving the most. BAC pooling works better than WGS, however, both require a physical map to order the scaffolds. Pool sizes up to 12Mbp work well, suggesting this pooling density to be effective in medium-scale re-sequencing applications such as targeted sequencing of QTL intervals for candidate gene discovery. Assuming the current Roche/454 Titanium sequencing limitations, a 12 Mbp region could be re-sequenced with a full plate of linear reads and a half plate of paired-end reads, yielding 15L-5P coverage after read pre-processing. Our simulation suggests that massively over-sequencing may not improve accuracy. Our scoring measures can be used generally to evaluate and compare results of simulated genome assemblies.

Optics assembly for high power laser tools

DOEpatents

Fraze, Jason D.; Faircloth, Brian O.; Zediker, Mark S.

2016-06-07

There is provided a high power laser rotational optical assembly for use with, or in high power laser tools for performing high power laser operations. In particular, the optical assembly finds applications in performing high power laser operations on, and in, remote and difficult to access locations. The optical assembly has rotational seals and bearing configurations to avoid contamination of the laser beam path and optics.

HRTEM and neutron diffraction study of Li{sub x}Mo{sub 5}O{sub 17}: From the ribbon (x=5) structure to the rock salt (x=12) structure

DOE Office of Scientific and Technical Information (OSTI.GOV)

Lebedev, O.I.; Caignaert, V.; Raveau, B.

2011-04-15

Structure determination of the fully intercalated phase Li{sub 12}Mo{sub 5}O{sub 17} and of the deintercalated oxide Li{sub 5}Mo{sub 5}O{sub 17} has been carried out by electron microscopy and neutron powder diffraction. The reversible topotactic transformation between the ordered rock salt structure of the former and the ribbon structure of the latter (closely related to that of Li{sub 4}Mo{sub 5}O{sub 17}) is explained on the following basis: both structures can be described as strips built up as an assembly of infinite ribbons of MoO{sub 6} octahedra that are five octahedra thick, and that differ by slight displacements of the octahedral ribbons.more » We show that the electrochemical behavior of the Li{sub x}Mo{sub 5}O{sub 17} system is based on two sorts of Li{sup +} sites; those that are located within the strips between the ribbons, and those that are located at the border of the strips. The high rate of Li intercalation in this oxide and its reversibility are discussed in terms of its peculiar structure. -- Graphical abstract: Structure determination of the fully intercalated phase Li{sub 12}Mo{sub 5}O{sub 17} and of the deintercalated oxide Li{sub 5}Mo{sub 5}O{sub 17} has been carried out by electron microscopy and neutron powder diffraction. The reversible topotactic transformation between the ordered rock salt structure of the former and the ribbon structure of the latter is explained on the following basis: both structures can be described as strips built up as an assembly of infinite ribbons of MoO{sub 6} octahedra that are five octahedra thick, and that differ by slight displacements of the octahedral ribbons. We show that the electrochemical behavior of the Li{sub x}Mo{sub 5}O{sub 17} system is based on two sorts of Li{sup +} sites; those that are located within the strips between the ribbons, and those that are located at the border of the strips. The high rate of Li intercalation in this oxide and its reversibility are discussed in terms of its peculiar structure. Research highlights: {yields} Electron microscopy and neutron powder diffraction structure determination {yields} We have explained the reversible topotactic transformation between an ordered rock salt structure and a ribbon structure {yields} We show that the electrochemical behavior of the Li{sub x}Mo{sub 5}O{sub 17} system is based on two sorts of Li{sup +} sites {yields} The high rate of Li intercalation in this oxide and its reversibility are discussed in terms of its peculiar structure.« less

Yield stress materials in soft condensed matter

NASA Astrophysics Data System (ADS)

Bonn, Daniel; Denn, Morton M.; Berthier, Ludovic; Divoux, Thibaut; Manneville, Sébastien

2017-07-01

A comprehensive review is presented of the physical behavior of yield stress materials in soft condensed matter, which encompasses a broad range of materials from colloidal assemblies and gels to emulsions and non-Brownian suspensions. All these disordered materials display a nonlinear flow behavior in response to external mechanical forces due to the existence of a finite force threshold for flow to occur: the yield stress. Both the physical origin and rheological consequences associated with this nonlinear behavior are discussed and an overview is given of experimental techniques available to measure the yield stress. Recent progress is discussed concerning a microscopic theoretical description of the flow dynamics of yield stress materials, emphasizing, in particular, the role played by relaxation time scales, the interplay between shear flow and aging behavior, the existence of inhomogeneous shear flows and shear bands, wall slip, and nonlocal effects in confined geometries.

Fe-porphyrin-based metal–organic framework films as high-surface concentration, heterogeneous catalysts for electrochemical reduction of CO 2

DOE PAGES

Hod, Idan; Sampson, Matthew D.; Deria, Pravas; ...

2015-09-18

Realization of heterogeneous electrochemical CO 2-to-fuel conversion via molecular catalysis under high-flux conditions requires the assembly of large quantities of reactant-accessible catalysts on conductive surfaces. As a proof of principle, we demonstrate that electrophoretic deposition of thin films of an appropriately chosen metal–organic framework (MOF) material is an effective method for immobilizing the needed quantity of catalyst. For electrocatalytic CO 2 reduction, we used a material that contains functionalized Fe-porphyrins as catalytically competent, redox-conductive linkers. The approach yields a high effective surface coverage of electrochemically addressable catalytic sites (~10 15 sites/cm 2). The chemical products of the reduction, obtained withmore » ~100% Faradaic efficiency, are mixtures of CO and H 2. The results validate the strategy of using MOF chemistry to obtain porous, electrode-immobilized, networks of molecular catalysts having competency for energy-relevant electrochemical reactions.« less

Real-time fuzzy inference based robot path planning

NASA Technical Reports Server (NTRS)

Pacini, Peter J.; Teichrow, Jon S.

1990-01-01

This project addresses the problem of adaptive trajectory generation for a robot arm. Conventional trajectory generation involves computing a path in real time to minimize a performance measure such as expended energy. This method can be computationally intensive, and it may yield poor results if the trajectory is weakly constrained. Typically some implicit constraints are known, but cannot be encoded analytically. The alternative approach used here is to formulate domain-specific knowledge, including implicit and ill-defined constraints, in terms of fuzzy rules. These rules utilize linguistic terms to relate input variables to output variables. Since the fuzzy rulebase is determined off-line, only high-level, computationally light processing is required in real time. Potential applications for adaptive trajectory generation include missile guidance and various sophisticated robot control tasks, such as automotive assembly, high speed electrical parts insertion, stepper alignment, and motion control for high speed parcel transfer systems.

Production of Japanese encephalitis virus-like particles in insect cells.

PubMed

Yamaji, Hideki; Konishi, Eiji

2013-01-01

Virus-like particles (VLPs) are composed of one or several recombinant viral surface proteins that spontaneously assemble into particulate structures without the incorporation of virus DNA or RNA. The baculovirus-insect cell system has been used extensively for the production of recombinant virus proteins including VLPs. While the baculovirus-insect cell system directs the transient expression of recombinant proteins in a batch culture, stably transformed insect cells allow constitutive production. In our recent study, a secretory form of Japanese encephalitis (JE) VLPs was successfully produced by Trichoplusia ni BTI-TN-5B1-4 (High Five) cells engineered to coexpress the JE virus (JEV) premembrane (prM) and envelope (E) proteins. A higher yield of E protein was attained with recombinant High Five cells than with the baculovirus-insect cell system. This study demonstrated that recombinant insect cells offer a promising approach to the high-level production of VLPs for use as vaccines and diagnostic antigens.

A facile synthesis of zinc oxide/multiwalled carbon nanotube nanocomposite lithium ion battery anodes by sol-gel method

NASA Astrophysics Data System (ADS)

Köse, Hilal; Karaal, Şeyma; Aydın, Ali Osman; Akbulut, Hatem

2015-11-01

Free standing zinc oxide (ZnO) and multiwalled carbon nanotube (MWCNT) nanocomposite materials are prepared by a sol gel technique giving a new high capacity anode material for lithium ion batteries. Free-standing ZnO/MWCNT nanocomposite anodes with two different chelating agent additives, triethanolamine (TEA) and glycerin (GLY), yield different electrochemical performances. Field emission gun scanning electron microscopy (FEG-SEM), energy dispersive X-ray spectrometer (EDS), high resolution transmission electron microscopy (HRTEM) and X-ray diffraction (XRD) analyses reveal the produced anode electrodes exhibit a unique structure of ZnO coating on the MWCNT surfaces. Li-ion cell assembly using a ZnO/MWCNT/GLY free-standing anode and Li metal cathode possesses the best discharge capacity, remaining as high as 460 mAh g-1 after 100 cycles. This core-shell structured anode can offer increased energy storage and performance over conventional anodes in Li-ion batteries.

Highly phosphorescent hollow fibers inner-coated with tungstate nanocrystals

NASA Astrophysics Data System (ADS)

Ng, Pui Fai; Bai, Gongxun; Si, Liping; Lee, Ka I.; Hao, Jianhua; Xin, John H.; Fei, Bin

2017-12-01

In order to develop luminescent microtubes from natural fibers, a facile biomimetic mineralization method was designed to introduce the CaWO4-based nanocrystals into kapok lumens. The structure, composition, and luminescence properties of resultant fibers were investigated with microscopes, x-ray diffraction, thermogravimetric analysis, and fluorescence spectrometry. The yield of tungstate crystals inside kapok was significantly promoted with a process at high temperature and pressure—the hydrothermal treatment. The tungstate crystals grown on the inner wall of kapok fibers showed the same crystal structure with those naked powders, but smaller in crystal size. The resultant fiber assemblies demonstrated reduced phosphorescence intensity in comparison to the naked tungstate powders. However, the fibers gave more stable luminescence than the naked powders in wet condition. This approach explored the possibility of decorating natural fibers with high load of nanocrystals, hinting potential applications in anti-counterfeit labels, security textiles, and even flexible and soft optical devices.

Shock waves in molecular solids: ultrafast vibrational spectroscopy of the first nanosecond

NASA Astrophysics Data System (ADS)

Franken, J.; Hambir, S. A.; Hare, D. E.; Dlott, D. D.

A novel technique which uses a microfabricated shock target array assembly is described, where the passage of a shock front through a thin (0.5μm) polycrystalline layer and the subsequent unloading process is monitored in real time with ultrafast coherent Raman spectroscopy. Using a high repetition rate laser shock generation technique, high resolution, coherent Raman spectra are obtained in shocked anthracene and in a high explosive material, NTO, with time resolution of 50 ps. Spectroscopic measurements are presented which yield the shock pressure (up to 5 GPa), the shock velocity ( 4 km/s), the shock front risetime (tr < 25 ps), and the temperature ( 400°C). A brief discussion is presented, how this new technique can be used to determine the Hugoniot, the equation of state, the entropy increase across the shock front, and monitor shock induced chemical reactions in real time.

Two-Dimensional Metal-Organic Layers as a Bright and Processable Phosphor for Fast White-Light Communication.

PubMed

Hu, Xuefu; Wang, Zi; Lin, Bangjiang; Zhang, Cankun; Cao, Lingyun; Wang, Tingting; Zhang, Jingzheng; Wang, Cheng; Lin, Wenbin

2017-06-22

A metal-organic layer (MOL) is a new type of 2D material that is derived from metal-organic frameworks (MOFs) by reducing one dimension to a single layer or a few layers. Tetraphenylethylene-based tetracarboxylate ligands (TCBPE), with aggregation-induced emission properties, were assembled into the first luminescent MOL by linking with Zr 6 O 4 (OH) 6 (H 2 O) 2 (HCO 2 ) 6 clusters. The emissive MOL can replace the lanthanide phosphors in white light emitting diodes (WLEDs) with remarkable processability, color rendering, and brightness. Importantly, the MOL-WLED exhibited a physical switching speed three times that of commercial WLEDs, which is crucial for visible-light communication (VLC), an alternative wireless communication technology to Wi-Fi and Bluetooth, by using room lighting to carry transmitted signals. The short fluorescence lifetime (2.6 ns) together with high quantum yield (50 %) of the MOL affords fast switching of the assembled WLEDs for efficient information encoding and transmission. © 2017 Wiley-VCH Verlag GmbH & Co. KGaA, Weinheim.

Assembly and enlargement of the primary cell wall in plants

NASA Technical Reports Server (NTRS)

Cosgrove, D. J.

1997-01-01

Growing plant cells are shaped by an extensible wall that is a complex amalgam of cellulose microfibrils bonded noncovalently to a matrix of hemicelluloses, pectins, and structural proteins. Cellulose is synthesized by complexes in the plasma membrane and is extruded as a self-assembling microfibril, whereas the matrix polymers are secreted by the Golgi apparatus and become integrated into the wall network by poorly understood mechanisms. The growing wall is under high tensile stress from cell turgor and is able to enlarge by a combination of stress relaxation and polymer creep. A pH-dependent mechanism of wall loosening, known as acid growth, is characteristic of growing walls and is mediated by a group of unusual wall proteins called expansins. Expansins appear to disrupt the noncovalent bonding of matrix hemicelluloses to the microfibril, thereby allowing the wall to yield to the mechanical forces generated by cell turgor. Other wall enzymes, such as (1-->4) beta-glucanases and pectinases, may make the wall more responsive to expansin-mediated wall creep whereas pectin methylesterases and peroxidases may alter the wall so as to make it resistant to expansin-mediated creep.

Assembly and enlargement of the primary cell wall in plants.

PubMed

Cosgrove, D J

1997-01-01

Growing plant cells are shaped by an extensible wall that is a complex amalgam of cellulose microfibrils bonded noncovalently to a matrix of hemicelluloses, pectins, and structural proteins. Cellulose is synthesized by complexes in the plasma membrane and is extruded as a self-assembling microfibril, whereas the matrix polymers are secreted by the Golgi apparatus and become integrated into the wall network by poorly understood mechanisms. The growing wall is under high tensile stress from cell turgor and is able to enlarge by a combination of stress relaxation and polymer creep. A pH-dependent mechanism of wall loosening, known as acid growth, is characteristic of growing walls and is mediated by a group of unusual wall proteins called expansins. Expansins appear to disrupt the noncovalent bonding of matrix hemicelluloses to the microfibril, thereby allowing the wall to yield to the mechanical forces generated by cell turgor. Other wall enzymes, such as (1-->4) beta-glucanases and pectinases, may make the wall more responsive to expansin-mediated wall creep whereas pectin methylesterases and peroxidases may alter the wall so as to make it resistant to expansin-mediated creep.

Galaxy and Mass Assembly (GAMA): small-scale anisotropic galaxy clustering and the pairwise velocity dispersion of galaxies

NASA Astrophysics Data System (ADS)

Loveday, J.; Christodoulou, L.; Norberg, P.; Peacock, J. A.; Baldry, I. K.; Bland-Hawthorn, J.; Brown, M. J. I.; Colless, M.; Driver, S. P.; Holwerda, B. W.; Hopkins, A. M.; Kafle, P. R.; Liske, J.; Lopez-Sanchez, A. R.; Taylor, E. N.

2018-03-01

The galaxy pairwise velocity dispersion (PVD) can provide important tests of non-standard gravity and galaxy formation models. We describe measurements of the PVD of galaxies in the Galaxy and Mass Assembly (GAMA) survey as a function of projected separation and galaxy luminosity. Due to the faint magnitude limit (r < 19.8) and highly complete spectroscopic sampling of the GAMA survey, we are able to reliably measure the PVD to smaller scales (r⊥ = 0.01 h - 1 Mpc) than previous work. The measured PVD at projected separations r⊥ ≲ 1 h - 1 Mpc increases near monotonically with increasing luminosity from σ12 ≈ 200 km s - 1 at Mr = -17 mag to σ12 ≈ 600 km s - 1 at Mr ≈ -22 mag. Analysis of the Gonzalez-Perez et al. (2014) GALFORM semi-analytic model yields no such trend of PVD with luminosity: the model overpredicts the PVD for faint galaxies. This is most likely a result of the model placing too many low-luminosity galaxies in massive haloes.

Metagenomic Signatures of Bacterial Adaptation to Life in the Phyllosphere of a Salt-Secreting Desert Tree.

PubMed

Finkel, Omri M; Delmont, Tom O; Post, Anton F; Belkin, Shimshon

2016-05-01

The leaves of Tamarix aphylla, a globally distributed, salt-secreting desert tree, are dotted with alkaline droplets of high salinity. To successfully inhabit these organic carbon-rich droplets, bacteria need to be adapted to multiple stress factors, including high salinity, high alkalinity, high UV radiation, and periodic desiccation. To identify genes that are important for survival in this harsh habitat, microbial community DNA was extracted from the leaf surfaces of 10 Tamarix aphylla trees along a 350-km longitudinal gradient. Shotgun metagenomic sequencing, contig assembly, and binning yielded 17 genome bins, six of which were >80% complete. These genomic bins, representing three phyla (Proteobacteria,Bacteroidetes, and Firmicutes), were closely related to halophilic and alkaliphilic taxa isolated from aquatic and soil environments. Comparison of these genomic bins to the genomes of their closest relatives revealed functional traits characteristic of bacterial populations inhabiting the Tamarix phyllosphere, independent of their taxonomic affiliation. These functions, most notably light-sensing genes, are postulated to represent important adaptations toward colonization of this habitat. Plant leaves are an extensive and diverse microbial habitat, forming the main interface between solar energy and the terrestrial biosphere. There are hundreds of thousands of plant species in the world, exhibiting a wide range of morphologies, leaf surface chemistries, and ecological ranges. In order to understand the core adaptations of microorganisms to this habitat, it is important to diversify the type of leaves that are studied. This study provides an analysis of the genomic content of the most abundant bacterial inhabitants of the globally distributed, salt-secreting desert tree Tamarix aphylla Draft genomes of these bacteria were assembled, using the culture-independent technique of assembly and binning of metagenomic data. Analysis of the genomes reveals traits that are important for survival in this habitat, most notably, light-sensing and light utilization genes. Copyright © 2016, American Society for Microbiology. All Rights Reserved.

Electron transport in gold colloidal nanoparticle-based strain gauges.

PubMed

Moreira, Helena; Grisolia, Jérémie; Sangeetha, Neralagatta M; Decorde, Nicolas; Farcau, Cosmin; Viallet, Benoit; Chen, Ke; Viau, Guillaume; Ressier, Laurence

2013-03-08

A systematic approach for understanding the electron transport mechanisms in resistive strain gauges based on assemblies of gold colloidal nanoparticles (NPs) protected by organic ligands is described. The strain gauges were fabricated from parallel micrometer wide wires made of 14 nm gold (Au) colloidal NPs on polyethylene terephthalate substrates, elaborated by convective self-assembly. Electron transport in such devices occurs by inter-particle electron tunneling through the tunnel barrier imposed by the organic ligands protecting the NPs. This tunnel barrier was varied by changing the nature of organic ligands coating the nanoparticles: citrate (CIT), phosphines (BSPP, TDSP) and thiols (MPA, MUDA). Electro-mechanical tests indicate that only the gold NPs protected by phosphine and thiol ligands yield high gauge sensitivity. Temperature-dependent resistance measurements are explained using the 'regular island array model' that extracts transport parameters, i.e., the tunneling decay constant β and the Coulomb charging energy E(C). This reveals that the Au@CIT nanoparticle assemblies exhibit a behavior characteristic of a strong-coupling regime, whereas those of Au@BSPP, Au@TDSP, Au@MPA and Au@MUDA nanoparticles manifest a weak-coupling regime. A comparison of the parameters extracted from the two methods indicates that the most sensitive gauges in the weak-coupling regime feature the highest β. Moreover, the E(C) values of these 14 nm NPs cannot be neglected in determining the β values.

Electron transport in gold colloidal nanoparticle-based strain gauges

NASA Astrophysics Data System (ADS)

Moreira, Helena; Grisolia, Jérémie; Sangeetha, Neralagatta M.; Decorde, Nicolas; Farcau, Cosmin; Viallet, Benoit; Chen, Ke; Viau, Guillaume; Ressier, Laurence

2013-03-01

A systematic approach for understanding the electron transport mechanisms in resistive strain gauges based on assemblies of gold colloidal nanoparticles (NPs) protected by organic ligands is described. The strain gauges were fabricated from parallel micrometer wide wires made of 14 nm gold (Au) colloidal NPs on polyethylene terephthalate substrates, elaborated by convective self-assembly. Electron transport in such devices occurs by inter-particle electron tunneling through the tunnel barrier imposed by the organic ligands protecting the NPs. This tunnel barrier was varied by changing the nature of organic ligands coating the nanoparticles: citrate (CIT), phosphines (BSPP, TDSP) and thiols (MPA, MUDA). Electro-mechanical tests indicate that only the gold NPs protected by phosphine and thiol ligands yield high gauge sensitivity. Temperature-dependent resistance measurements are explained using the ‘regular island array model’ that extracts transport parameters, i.e., the tunneling decay constant β and the Coulomb charging energy EC. This reveals that the Au@CIT nanoparticle assemblies exhibit a behavior characteristic of a strong-coupling regime, whereas those of Au@BSPP, Au@TDSP, Au@MPA and Au@MUDA nanoparticles manifest a weak-coupling regime. A comparison of the parameters extracted from the two methods indicates that the most sensitive gauges in the weak-coupling regime feature the highest β. Moreover, the EC values of these 14 nm NPs cannot be neglected in determining the β values.

Final Scientific/Technical Report -- Single-Junction Organic Solar Cells with >15% Efficiency

DOE Office of Scientific and Technical Information (OSTI.GOV)

Starkenburg, Daken; Weldeab, Asmerom; Fagnani, Dan

Organic solar cells have the potential to offer low-cost solar energy conversion due to low material costs and compatibility with low-temperature and high throughput manufacturing processes. This project aims to further improve the efficiency of organic solar cells by applying a previously demonstrated molecular self-assembly approach to longer-wavelength light-absorbing organic materials. The team at the University of Florida designed and synthesized a series of low-bandgap organic semiconductors with functional hydrogen-bonding groups, studied their assembly characteristics and optoelectronic properties in solid-state thin film, and fabricated organic solar cells using solution processing. These new organic materials absorb light up 800 nm wavelength,more » and provide a maximum open-circuit voltage of 1.05 V in the resulted solar cells. The results further confirmed the effectiveness in this approach to guide the assembly of organic semiconductors in thin films to yield higher photovoltaic performance for solar energy conversion. Through this project, we have gained important understanding on designing, synthesizing, and processing organic semiconductors that contain appropriately functionalized groups to control the morphology of the organic photoactive layer in solar cells. Such fundamental knowledge could be used to further develop new functional organic materials to achieve higher photovoltaic performance, and contribute to the eventual commercialization of the organic solar cell technology.« less

Latest Results of ILC High-Gradient R&D 9-cell Cavities at JLAB

DOE Office of Scientific and Technical Information (OSTI.GOV)

Geng, Rongli

2008-02-11

It has been over a year since JLAB started processing and testing ILC 9-cell cavities in the frame work of ILC high-gradient cavity R&D, aiming at the goal of a 35 MV/m gradient at a Q of 1E10 with a yield of 90%. The necessary cavity processing steps include field flatness tuning, electropolishing (EP), hydrogen out-gassing under vacuum, high-pressure water rinsing, clean room assembly, and low temperature bake. These are followed by RF test at 2 Kelvin. Ultrasonic cleaning with Micro-90, an effective post-EP rinsing recipe discovered at JLAB, is routinely used. Seven industry manufactured 9-cell TESLAshape cavities are processedmore » and tested repeatedly. So far, 33 EP cycles are accumulated, corresponding to more than 65 hours of active EP time. An emphasis put on RF testing is to discern cavity quench characteristics, including its nature and its location. Often times, the cavity performance is limited by thermal-magnetic quench instead of field emission. The quench field in some cavities is lower than 20 MV/m and remains unchanged despite repeated EP, implying material and/or fabrication defects. The quench field in some other cavities is high but changes unpredictably after repeated EP, suggesting processing induced defects. Based on our experience and results, several areas are identified where improvement is needed to improve cavity performance as well as yield.« less

Metal-Assisted Channel Stabilization: Disposition of a Single Histidine on the N-terminus of Alamethicin Yields Channels with Extraordinarily Long Lifetimes

PubMed Central

Noshiro, Daisuke; Asami, Koji; Futaki, Shiroh

2010-01-01

Abstract Alamethicin, a member of the peptaibol family of antibiotics, is a typical channel-forming peptide with a helical structure. The self-assembly of the peptide in the membranes yields voltage-dependent channels. In this study, three alamethicin analogs possessing a charged residue (His, Lys, or Glu) on their N-termini were designed with the expectation of stabilizing the transmembrane structure. A slight elongation of channel lifetime was observed for the Lys and Glu analogs. On the other hand, extensive stabilization of certain channel open states was observed for the His analog. This stabilization was predominantly observed in the presence of metal ions such as Zn2+, suggesting that metal coordination with His facilitates the formation of a supramolecular assembly in the membranes. Channel stability was greatly diminished by acetylation of the N-terminal amino group, indicating that the N-terminal amino group also plays an important role in metal coordination. PMID:20441743

Synthesis and biomedical applications of functional poly(α-hydroxy acids) via ring-opening polymerization of O-carboxyanhydrides.

PubMed

Yin, Qian; Yin, Lichen; Wang, Hua; Cheng, Jianjun

2015-07-21

Poly(α-hydroxy acids) (PAHAs) are a class of biodegradable and biocompatible polymers that are widely used in numerous applications. One drawback of these conventional polymers, however, is their lack of side-chain functionalities, which makes it difficult to conjugate active moieties to PAHA or to fine-tune the physical and chemical properties of PAHA-derived materials through side-chain modifications. Thus, extensive efforts have been devoted to the development of methodology that allows facile preparation of PAHAs with controlled molecular weights and a variety of functionalities for widespread utilities. However, it is highly challenging to introduce functional groups into conventional PAHAs derived from ring-opening polymerization (ROP) of lactides and glycolides to yield functional PAHAs with favorable properties, such as tunable hydrophilicity/hydrophobicity, facile postpolymerization modification, and well-defined physicochemical properties. Amino acids are excellent resources for functional polymers because of their low cost, availability, and structural as well as stereochemical diversity. Nevertheless, the synthesis of functional PAHAs using amino acids as building blocks has been rarely reported because of the difficulty of preparing large-scale monomers and poor yields during the synthesis. The synthesis of functionalized PAHAs from O-carboxyanhydrides (OCAs), a class of five-membered cyclic anhydrides derived from amino acids, has proven to be one of the most promising strategies and has thus attracted tremendous interest recently. In this Account, we highlight the recent progress in our group on the synthesis of functional PAHAs via ROP of OCAs and their self-assembly and biomedical applications. New synthetic methodologies that allow the facile preparation of PAHAs with controlled molecular weights and various functionalities through ROP of OCAs are reviewed and evaluated. The in vivo stability, side-chain functionalities, and/or trigger responsiveness of several functional PAHAs are evaluated. Their biomedical applications in drug and gene delivery are also discussed. The ready availability of starting materials from renewable resources and the facile postmodification strategies such as azide-alkyne cycloaddition and the thiol-yne "click" reaction have enabled the production of a multitude of PAHAs with controlled molecular weights, narrow polydispersity, high terminal group fidelities, and structural diversities that are amenable for self-assembly and bioapplications. We anticipate that this new generation of PAHAs and their self-assembled nanosystems as biomaterials will open up exciting new opportunities and have widespread utilities for biological applications.

Encapsulation of enzyme via one-step template-free formation of stable organic-inorganic capsules: A simple and efficient method for immobilizing enzyme with high activity and recyclability.

PubMed

Huang, Renliang; Wu, Mengyun; Goldman, Mark J; Li, Zhi

2015-06-01

Enzyme encapsulation is a simple, gentle, and general method for immobilizing enzyme, but it often suffers from one or more problems regarding enzyme loading efficiency, enzyme leakage, mechanical stability, and recyclability. Here we report a novel, simple, and efficient method for enzyme encapsulation to overcome these problems by forming stable organic-inorganic hybrid capsules. A new, facile, one-step, and template-free synthesis of organic-inorganic capsules in aqueous phase were developed based on PEI-induced simultaneous interfacial self-assembly of Fmoc-FF and polycondensation of silicate. Addition of an aqueous solution of Fmoc-FF and sodium silicate into an aqueous solution of PEI gave a new class of organic-inorganic hybrid capsules (FPSi) with multi-layered structure in high yield. The capsules are mechanically stable due to the incorporation of inorganic silica. Direct encapsulation of enzyme such as epoxide hydrolase SpEH and BSA along with the formation of the organic-inorganic capsules gave high yield of enzyme-containing capsules (∼1.2 mm in diameter), >90% enzyme loading efficiency, high specific enzyme loading (158 mg protein g(-1) carrier), and low enzyme leakage (<3% after 48 h incubation). FPSi-SpEH capsules catalyzed the hydrolysis of cyclohexene oxide to give (1R, 2R)-cyclohexane-1,2-diol in high yield and concentration, with high specific activity (6.94 U mg(-1) protein) and the same high enantioselectivity as the free enzyme. The immobilized SpEH demonstrated also excellent operational stability and recyclability: retaining 87% productivity after 20 cycles with a total reaction time of 80 h. The new enzyme encapsulation method is efficient, practical, and also better than other reported encapsulation methods. © 2015 Wiley Periodicals, Inc.

A Hybrid Approach for the Automated Finishing of Bacterial Genomes

PubMed Central

Robins, William P.; Chin, Chen-Shan; Webster, Dale; Paxinos, Ellen; Hsu, David; Ashby, Meredith; Wang, Susana; Peluso, Paul; Sebra, Robert; Sorenson, Jon; Bullard, James; Yen, Jackie; Valdovino, Marie; Mollova, Emilia; Luong, Khai; Lin, Steven; LaMay, Brianna; Joshi, Amruta; Rowe, Lori; Frace, Michael; Tarr, Cheryl L.; Turnsek, Maryann; Davis, Brigid M; Kasarskis, Andrew; Mekalanos, John J.; Waldor, Matthew K.; Schadt, Eric E.

2013-01-01

Dramatic improvements in DNA sequencing technology have revolutionized our ability to characterize most genomic diversity. However, accurate resolution of large structural events has remained challenging due to the comparatively shorter read lengths of second-generation technologies. Emerging third-generation sequencing technologies, which yield markedly increased read length on rapid time scales and for low cost, have the potential to address assembly limitations. Here we combine sequencing data from second- and third-generation DNA sequencing technologies to assemble the two-chromosome genome of a recent Haitian cholera outbreak strain into two nearly finished contigs at > 99.9% accuracy. Complex regions with clinically significant structure were completely resolved. In separate control assemblies on experimental and simulated data for the canonical N16961 reference we obtain 14 and 8 scaffolds greater than 1kb, respectively, correcting several errors in the underlying source data. This work provides a blueprint for the next generation of rapid microbial identification and full-genome assembly. PMID:22750883

Octanol-assisted liposome assembly on chip

PubMed Central

Deshpande, Siddharth; Caspi, Yaron; Meijering, Anna E. C.; Dekker, Cees

2016-01-01

Liposomes are versatile supramolecular assemblies widely used in basic and applied sciences. Here we present a novel microfluidics-based method, octanol-assisted liposome assembly (OLA), to form monodisperse, cell-sized (5–20 μm), unilamellar liposomes with excellent encapsulation efficiency. Akin to bubble blowing, an inner aqueous phase and a surrounding lipid-carrying 1-octanol phase is pinched off by outer fluid streams. Such hydrodynamic flow focusing results in double-emulsion droplets that spontaneously develop a side-connected 1-octanol pocket. Owing to interfacial energy minimization, the pocket splits off to yield fully assembled solvent-free liposomes within minutes. This solves the long-standing fundamental problem of prolonged presence of residual oil in the liposome bilayer. We demonstrate the unilamellarity of liposomes with functional α-haemolysin protein pores in the membrane and validate the biocompatibility by inner leaflet localization of bacterial divisome proteins (FtsZ and ZipA). OLA offers a versatile platform for future analytical tools, delivery systems, nanoreactors and synthetic cells. PMID:26794442

Octanol-assisted liposome assembly on chip.

PubMed

Deshpande, Siddharth; Caspi, Yaron; Meijering, Anna E C; Dekker, Cees

2016-01-22

Liposomes are versatile supramolecular assemblies widely used in basic and applied sciences. Here we present a novel microfluidics-based method, octanol-assisted liposome assembly (OLA), to form monodisperse, cell-sized (5-20 μm), unilamellar liposomes with excellent encapsulation efficiency. Akin to bubble blowing, an inner aqueous phase and a surrounding lipid-carrying 1-octanol phase is pinched off by outer fluid streams. Such hydrodynamic flow focusing results in double-emulsion droplets that spontaneously develop a side-connected 1-octanol pocket. Owing to interfacial energy minimization, the pocket splits off to yield fully assembled solvent-free liposomes within minutes. This solves the long-standing fundamental problem of prolonged presence of residual oil in the liposome bilayer. We demonstrate the unilamellarity of liposomes with functional α-haemolysin protein pores in the membrane and validate the biocompatibility by inner leaflet localization of bacterial divisome proteins (FtsZ and ZipA). OLA offers a versatile platform for future analytical tools, delivery systems, nanoreactors and synthetic cells.

Octanol-assisted liposome assembly on chip

NASA Astrophysics Data System (ADS)

Deshpande, Siddharth; Caspi, Yaron; Meijering, Anna E. C.; Dekker, Cees

2016-01-01

Liposomes are versatile supramolecular assemblies widely used in basic and applied sciences. Here we present a novel microfluidics-based method, octanol-assisted liposome assembly (OLA), to form monodisperse, cell-sized (5-20 μm), unilamellar liposomes with excellent encapsulation efficiency. Akin to bubble blowing, an inner aqueous phase and a surrounding lipid-carrying 1-octanol phase is pinched off by outer fluid streams. Such hydrodynamic flow focusing results in double-emulsion droplets that spontaneously develop a side-connected 1-octanol pocket. Owing to interfacial energy minimization, the pocket splits off to yield fully assembled solvent-free liposomes within minutes. This solves the long-standing fundamental problem of prolonged presence of residual oil in the liposome bilayer. We demonstrate the unilamellarity of liposomes with functional α-haemolysin protein pores in the membrane and validate the biocompatibility by inner leaflet localization of bacterial divisome proteins (FtsZ and ZipA). OLA offers a versatile platform for future analytical tools, delivery systems, nanoreactors and synthetic cells.

Responsive and Hybrid Nanostructures through Self-Assembly of Polymeric Macroions, Inorganic Nanoclusters and Dyes

NASA Astrophysics Data System (ADS)

Groehn, Franziska; Duering, Jasmin; Moldenhauer, Daniel; Interdisciplinary CenterMolecular Materials Team

2013-03-01

Recently we have introduced a novel type of self-assembled ``nano-objects'' in solution: From the association of macroions and multivalent counterions well-defined and stable structures in the shape of spheres, rod, rings, hollow spheres and networks can form in solution. Using light-addressable counterions, it is possible to switch the particle size through UV irradiation. Building blocks can be of organic or inorganic nature: Using gold or cadmium sulphide nanoclusters results in hybrid assemblies which also functionally combine nanoparticle and dye. Thermodynamic studies in combination with a detailed structural characterization yield insight into driving forces and structural control in the self-assembly process. Crucial is the delicate interplay of ionic, π - π , and Hamaker interaction. The concept is particularly attractive, as it relies on general physical effects - that is the combination of different non-covalent interactions - and hence is very versatile. Great potential of the structures presented lies in areas such as catalysis and energy conversion.

Asymmetric van der Waals Forces Drive Orientation of Compositionally Anisotropic Nanocylinders within Smectic Arrays: Experiment and Simulation

PubMed Central

Smith, Benjamin D.; Fichthorn, Kristen A.; Kirby, David J.; Quimby, Lisa M.; Triplett, Derek A.; González, Pedro; Hernández, Darimar; Keating, Christine D.

2014-01-01

Understanding how micro- and nanoparticles interact is important for achieving bottom-up assembly of desired structures. Here, we examine the self-assembly of two-component, compositionally asymmetric nanocylinders that sediment from solution onto a solid surface. These particles spontaneously formed smectic arrays. Within the rows of an array, nanocylinders tended to assemble such that neighboring particles had the same orientation of their segments. As a probe of interparticle interactions, we classified nanocylinder alignments by measuring the segment orientations of many sets of neighboring particles. Monte Carlo simulations incorporating an exact expression for the van der Waals (vdW) energy indicate that differences in the vdW interactions, even when small, are the key factor in producing observed segment alignment. These results point to asymmetrical vdW interactions as a potentially powerful means of controlling orientation in multicomponent cylinder arrays, and suggest that designing for these interactions could yield new ways to control self-assembly. PMID:24308771

Evaluation of Isoprene Chain Extension from PEO Macromolecular Chain Transfer Agents for the Preparation of Dual, Invertible Block Copolymer Nanoassemblies.

PubMed

Bartels, Jeremy W; Cauët, Solène I; Billings, Peter L; Lin, Lily Yun; Zhu, Jiahua; Fidge, Christopher; Pochan, Darrin J; Wooley, Karen L

2010-09-14

Two RAFT-capable PEO macro-CTAs, 2 and 5 kDa, were prepared and used for the polymerization of isoprene which yielded well-defined block copolymers of varied lengths and compositions. GPC analysis of the PEO macro-CTAs and block copolymers showed remaining unreacted PEO macro-CTA. Mathematical deconvolution of the GPC chromatograms allowed for the estimation of the blocking efficiency, about 50% for the 5 kDa PEO macro-CTA and 64% for the 2 kDa CTA. Self assembly of the block copolymers in both water and decane was investigated and the resulting regular and inverse assemblies, respectively, were analyzed with DLS, AFM, and TEM to ascertain their dimensions and properties. Assembly of PEO-b-PIp block copolymers in aqueous solution resulted in well-defined micelles of varying sizes while the assembly in hydrophobic, organic solvent resulted in the formation of different morphologies including large aggregates and well-defined cylindrical and spherical structures.

Whole transcriptome analysis using next-generation sequencing of model species Setaria viridis to support C4 photosynthesis research.

PubMed

Xu, Jiajia; Li, Yuanyuan; Ma, Xiuling; Ding, Jianfeng; Wang, Kai; Wang, Sisi; Tian, Ye; Zhang, Hui; Zhu, Xin-Guang

2013-09-01

Setaria viridis is an emerging model species for genetic studies of C4 photosynthesis. Many basic molecular resources need to be developed to support for this species. In this paper, we performed a comprehensive transcriptome analysis from multiple developmental stages and tissues of S. viridis using next-generation sequencing technologies. Sequencing of the transcriptome from multiple tissues across three developmental stages (seed germination, vegetative growth, and reproduction) yielded a total of 71 million single end 100 bp long reads. Reference-based assembly using Setaria italica genome as a reference generated 42,754 transcripts. De novo assembly generated 60,751 transcripts. In addition, 9,576 and 7,056 potential simple sequence repeats (SSRs) covering S. viridis genome were identified when using the reference based assembled transcripts and the de novo assembled transcripts, respectively. This identified transcripts and SSR provided by this study can be used for both reverse and forward genetic studies based on S. viridis.

A Simple And Rapid Minicircle DNA Vector Manufacturing System

PubMed Central

Kay, Mark A; He, Cheng-Yi; Chen, Zhi-Ying

2010-01-01

Minicircle DNA vectors consisting of a circular expression cassette devoid of the bacterial plasmid DNA backbone provides several advantages including sustained transgene expression in quiescent cells/tissues. Their use has been limited by labor-intensive production. We report on a strategy for making multiple genetic modifications in E.coli to construct a producer strain that stably expresses a set of inducible minicircle-assembly enzymes, the øC31-integrase and I-SceI homing-endonuclease. This bacterial strain is capable of producing highly purified minicircle yields in the same time frame as routine plasmid DNA. It is now feasible for minicircle DNA vectors to replace routine plasmids in mammalian transgene expression studies. PMID:21102455

An efficient optical-electrochemical dual probe for highly sensitive recognition of dopamine based on terbium complex functionalized reduced graphene oxide.

PubMed

Zhou, Zhan; Wang, Qianming

2014-05-07

A novel organic-inorganic hybrid sensor based on diethylenetriaminepentaacetic acid (DTPA) modified reduced graphene oxide (RGO-DTPA) chelated with terbium ions allows detection of dopamine (DA) through an emission enhancement effect. Its luminescence, peaking at 545 nm, has been improved by a factor of 25 in the presence of DA (detection limit = 80 nM). In addition, this covalently bonded terbium complex functionalized reduced graphene oxide (RGO-DTPA-Tb) can be successfully assembled on a glassy carbon electrode. The assay performed through differential pulse voltammetry (DPV) yielded obvious peak separation between DA and excessive amounts of the interfering ascorbic acid (AA).

Aerodynamic effects of moveable sidewall nozzle geometry and rotor exit restriction on the performance of a radial turbine

NASA Technical Reports Server (NTRS)

Rogo, C.; Hajek, T.; Roelke, R.

1983-01-01

Attention is given to the experimental results obtained with a high work capacity radial inflow turbine of known performance, whose baseline configuration was modified to accept a variety of movable nozzle sidewall, diffusing or accelerating rotor inlet ramp, and rotor exit restriction ring combinations. The performance of this variable geometry turbine was measured at constant speed and pressure ratio for 31 different test configurations, yielding test data over a nozzle area range from 50 to 100 percent of maximum depending on the movement of the nozzle assembly's forward and rearward sidewalls. Performance comparisons with data for a variable stagger angle vane concept indicate the present system's viability.

Polarized emission from CsPbBr3 nanowire embedded-electrospun PU fibers

NASA Astrophysics Data System (ADS)

Güner, Tuğrul; Topçu, Gökhan; Savacı, Umut; Genç, Aziz; Turan, Servet; Sari, Emre; Demir, Mustafa M.

2018-04-01

Interest in all-inorganic halide perovskites has been increasing dramatically due to their high quantum yield, band gap tunability, and ease of fabrication in compositional and geometric diversity. In this study, we synthesized several hundreds of nanometer long and ˜4 nm thick CsPbBr 3 nanowires (NWs). They were then integrated into electrospun polyurethane (PU) fibers to examine the polarization behavior of the composite fiber assembly. Aligned electrospun fibers containing CsPbBr 3 NWs showed a remarkable increase in the degree of polarization from 0.17-0.30. This combination of NWs and PU fibers provides a promising composite material for various applications such as optoelectronic devices and solar cells.

Adaptive Injection-locking Oscillator Array for RF Spectrum Analysis

DOE Office of Scientific and Technical Information (OSTI.GOV)

Leung, Daniel

2011-04-19

A highly parallel radio frequency receiver using an array of injection-locking oscillators for on-chip, rapid estimation of signal amplitudes and frequencies is considered. The oscillators are tuned to different natural frequencies, and variable gain amplifiers are used to provide negative feedback to adapt the locking band-width with the input signal to yield a combined measure of input signal amplitude and frequency detuning. To further this effort, an array of 16 two-stage differential ring oscillators and 16 Gilbert-cell mixers is designed for 40-400 MHz operation. The injection-locking oscillator array is assembled on a custom printed-circuit board. Control and calibration is achievedmore » by on-board microcontroller.« less

DOE Office of Scientific and Technical Information (OSTI.GOV)

Bushuev, A. V.; Kozhin, A. F., E-mail: alexfkozhin@yandex.ru; Aleeva, T. B.

An active neutron method for measuring the residual mass of {sup 235}U in spent fuel assemblies (FAs) of the IRT MEPhI research reactor is presented. The special measuring stand design and uniform irradiation of the fuel with neutrons along the entire length of the active part of the FA provide high accuracy of determination of the residual {sup 235}U content. AmLi neutron sources yield a higher effect/background ratio than other types of sources and do not induce the fission of {sup 238}U. The proposed method of transfer of the isotope source in accordance with a given algorithm may be usedmore » in experiments where the studied object needs to be irradiated with a uniform fluence.« less

Super-microporous solid base MgO-ZrO2 composite and their application in biodiesel production

NASA Astrophysics Data System (ADS)

Su, Jiaojiao; Li, Yongfeng; Wang, Huigang; Yan, Xiaoliang; Pan, Dahai; Fan, Binbin; Li, Ruifeng

2016-10-01

The super-microporous microcrystalline MgO-ZrO2 nanomaterials (pore size 1-2 nm) was prepared successfully via a facile one-pot evaporation-induced self-assembly (EISA) method and employed in the transesterification of soybean oil and methanol. X-ray diffraction, transmission electron microscope, temperature programmed desorption of CO2, and N2 adsorption porosimetry were employed to characterize the nanocomposites. Nitrogen sorption isotherms revealed that these materials had large surface areas of more than 200 m2/g. Moreover, the sample with a Mg/Zr molar ratio of 0.5 and calcined at 400 °C showed high biodiesel yield (around 99% at 150 °C).

Electrochromic Behavior of Ionically Self-Assembled Thin Films

NASA Astrophysics Data System (ADS)

Janik, J. A.; Heflin, J. R.; Marciu, D.; Miller, M. B.; Davis, R. M.

2001-03-01

Ionically self-assembled monolayers (ISAMs), fabricated by alternate adsorption of cationic and anionic components, yield exceptionally homogeneous thin films with sub-nanometer control of the thickness and relative special location of the component materials. Using organic electrochromic materials such as polyaniline, we report studies of electrochromic responses in ISAM films. Reversible changes in the absorption spectrum are observed with the application of voltages on the order of 1.0 V. Measurements are made using both liquid electrolytes and in all-solid state devices incorporating solid polyelectrolytes such as poly(2-acylamido 2-methyl propane sulfonic acid) (PAMPS).

Light-assisted templated self assembly using photonic crystal slabs.

PubMed

Mejia, Camilo A; Dutt, Avik; Povinelli, Michelle L

2011-06-06

We explore a technique which we term light-assisted templated self-assembly. We calculate the optical forces on colloidal particles over a photonic crystal slab. We show that exciting a guided resonance mode of the slab yields a resonantly-enhanced, attractive optical force. We calculate the lateral optical forces above the slab and predict that stably trapped periodic patterns of particles are dependent on wavelength and polarization. Tuning the wavelength or polarization of the light source may thus allow the formation and reconfiguration of patterns. We expect that this technique may be used to design all-optically reconfigurable photonic devices.

Controlling transformations in the assembly of polyoxometalate clusters: {Mo11V7}, {Mo17V8} and {Mo72V30}.

PubMed

Miras, Haralampos N; Ochoa, M Nieves Corella; Long, De-Liang; Cronin, Leroy

2010-11-21

The reaction of molybdate with vanadium(V) in the presence of sulfite anions is explored showing how, via cation control, stepwise assembly through the {Mo(11)V(7)} cluster yields a {M(25)} cluster-based compound, [Mo(VI)(11)V(V)(5)V(IV)(2)O(52)(μ(9)-SO(3))(Mo(VI)(6)V(V)O(22))](10-) (1a), which was first discovered using cryospray mass spectrometry, whereas switching the cation away from ammonium allows the direct formation of the spherical 'Keplerate' {Mo(72)V(30)} cluster.

Photochemical CVD of Ru on functionalized self-assembled monolayers from organometallic precursors

NASA Astrophysics Data System (ADS)

Johnson, Kelsea R.; Arevalo Rodriguez, Paul; Brewer, Christopher R.; Brannaka, Joseph A.; Shi, Zhiwei; Yang, Jing; Salazar, Bryan; McElwee-White, Lisa; Walker, Amy V.

2017-02-01

Chemical vapor deposition (CVD) is an attractive technique for the metallization of organic thin films because it is selective and the thickness of the deposited film can easily be controlled. However, thermal CVD processes often require high temperatures which are generally incompatible with organic films. In this paper, we perform proof-of-concept studies of photochemical CVD to metallize organic thin films. In this method, a precursor undergoes photolytic decomposition to generate thermally labile intermediates prior to adsorption on the sample. Three readily available Ru precursors, CpRu(CO)2Me, (η3-allyl)Ru(CO)3Br, and (COT)Ru(CO)3, were employed to investigate the role of precursor quantum yield, ligand chemistry, and the Ru oxidation state on the deposition. To investigate the role of the substrate chemistry on deposition, carboxylic acid-, hydroxyl-, and methyl-terminated self-assembled monolayers were used. The data indicate that moderate quantum yields for ligand loss (φ ≥ 0.4) are required for ruthenium deposition, and the deposition is wavelength dependent. Second, anionic polyhapto ligands such as cyclopentadienyl and allyl are more difficult to remove than carbonyls, halides, and alkyls. Third, in contrast to the atomic layer deposition, acid-base reactions between the precursor and the substrate are more effective for deposition than nucleophilic reactions. Finally, the data suggest that selective deposition can be achieved on organic thin films by judicious choice of precursor and functional groups present on the substrate. These studies thus provide guidelines for the rational design of new precursors specifically for selective photochemical CVD on organic substrates.

Explosive Joining for Nuclear-Reactor Repair

NASA Technical Reports Server (NTRS)

Bement, L. J.; Bailey, J. W.

1983-01-01

In explosive joining technique, adapter flange from fuel channel machined to incorporate a V-notch interface. Ribbon explosive, 1/2 inch (1.3 cm) in width, drives V-notched wall of adapter into bellows assembly, producing atomic-level metallurgical bond. Ribbon charge yields joint with double parent metal strength.

Assembly of highly repetitive genomes using short reads: the genome of discrete typing unit III Trypanosoma cruzi strain 231.

PubMed

Baptista, Rodrigo P; Reis-Cunha, Joao Luis; DeBarry, Jeremy D; Chiari, Egler; Kissinger, Jessica C; Bartholomeu, Daniella C; Macedo, Andrea M

2018-02-14

Next-generation sequencing (NGS) methods are low-cost high-throughput technologies that produce thousands to millions of sequence reads. Despite the high number of raw sequence reads, their short length, relative to Sanger, PacBio or Nanopore reads, complicates the assembly of genomic repeats. Many genome tools are available, but the assembly of highly repetitive genome sequences using only NGS short reads remains challenging. Genome assembly of organisms responsible for important neglected diseases such as Trypanosoma cruzi, the aetiological agent of Chagas disease, is known to be challenging because of their repetitive nature. Only three of six recognized discrete typing units (DTUs) of the parasite have their draft genomes published and therefore genome evolution analyses in the taxon are limited. In this study, we developed a computational workflow to assemble highly repetitive genomes via a combination of de novo and reference-based assembly strategies to better overcome the intrinsic limitations of each, based on Illumina reads. The highly repetitive genome of the human-infecting parasite T. cruzi 231 strain was used as a test subject. The combined-assembly approach shown in this study benefits from the reference-based assembly ability to resolve highly repetitive sequences and from the de novo capacity to assemble genome-specific regions, improving the quality of the assembly. The acceptable confidence obtained by analyzing our results showed that our combined approach is an attractive option to assemble highly repetitive genomes with NGS short reads. Phylogenomic analysis including the 231 strain, the first representative of DTU III whose genome was sequenced, was also performed and provides new insights into T. cruzi genome evolution.

SAW based micro- and acousto-fluidics in biomedicine

NASA Astrophysics Data System (ADS)

Ramasamy, Mouli; Varadan, Vijay K.

2017-04-01

Protein association starts with random collisions of individual proteins. Multiple collisions and rotational diffusion brings the molecules to a state of orientation. Majority of the protein associations are influenced by electrostatic interactions. To introduce: electrostatic rate enhancement, Brownian dynamics and transient complex theory has been traditionally used. Due to the recent advances in interdisciplinary sciences, an array of molecular assembly methods is being studied. Protein nanostructural assembly and macromolecular crowding are derived from the subsets of biochemistry to study protein-protein interactions and protein self-assembly. This paper tries to investigate the issue of enhancing the protein self-association rate, and bridging the gap between the simulations and experimental results. The methods proposed here include: electrostatic rate enhancement, macromolecular crowing, nanostructural protein assembly, microfluidics based approaches and magnetic force based approaches. Despite the suggestions of several methods, microfluidic and magnetic force based approaches seem to serve the need of protein assembly in a wider scale. Congruence of these approaches may also yield better results. Even though, these methods prove to be conceptually strong, to prevent the disagreement of theory and practice, a wide range of experiments is required. This proposal intends to study theoretical and experimental methods to successfully implement the aforementioned assembly strategies, and conclude with an extensive analysis of experimental data to address practical feasibility.

The assembly and use of continuous flow systems for chemical synthesis.

PubMed

Britton, Joshua; Jamison, Timothy F

2017-11-01

The adoption of and opportunities in continuous flow synthesis ('flow chemistry') have increased significantly over the past several years. Continuous flow systems provide improved reaction safety and accelerated reaction kinetics, and have synthesised several active pharmaceutical ingredients in automated reconfigurable systems. Although continuous flow platforms are commercially available, systems constructed 'in-lab' provide researchers with a flexible, versatile, and cost-effective alternative. Herein, we describe the assembly and use of a modular continuous flow apparatus from readily available and affordable parts in as little as 30 min. Once assembled, the synthesis of a sulfonamide by reacting 4-chlorobenzenesulfonyl chloride with dibenzylamine in a single reactor coil with an in-line quench is presented. This example reaction offers the opportunity to learn several important skills including reactor construction, charging of a back-pressure regulator, assembly of stainless-steel syringes, assembly of a continuous flow system with multiple junctions, and yield determination. From our extensive experience of single-step and multistep continuous flow synthesis, we also describe solutions to commonly encountered technical problems such as precipitation of solids ('clogging') and reactor failure. Following this protocol, a nonspecialist can assemble a continuous flow system from reactor coils, syringes, pumps, in-line liquid-liquid separators, drying columns, back-pressure regulators, static mixers, and packed-bed reactors.

Assessing pooled BAC and whole genome shotgun strategies for assembly of complex genomes

PubMed Central

2011-01-01

Background We investigate if pooling BAC clones and sequencing the pools can provide for more accurate assembly of genome sequences than the "whole genome shotgun" (WGS) approach. Furthermore, we quantify this accuracy increase. We compare the pooled BAC and WGS approaches using in silico simulations. Standard measures of assembly quality focus on assembly size and fragmentation, which are desirable for large whole genome assemblies. We propose additional measures enabling easy and visual comparison of assembly quality, such as rearrangements and redundant sequence content, relative to the known target sequence. Results The best assembly quality scores were obtained using 454 coverage of 15× linear and 5× paired (3kb insert size) reads (15L-5P) on Arabidopsis. This regime gave similarly good results on four additional plant genomes of very different GC and repeat contents. BAC pooling improved assembly scores over WGS assembly, coverage and redundancy scores improving the most. Conclusions BAC pooling works better than WGS, however, both require a physical map to order the scaffolds. Pool sizes up to 12Mbp work well, suggesting this pooling density to be effective in medium-scale re-sequencing applications such as targeted sequencing of QTL intervals for candidate gene discovery. Assuming the current Roche/454 Titanium sequencing limitations, a 12 Mbp region could be re-sequenced with a full plate of linear reads and a half plate of paired-end reads, yielding 15L-5P coverage after read pre-processing. Our simulation suggests that massively over-sequencing may not improve accuracy. Our scoring measures can be used generally to evaluate and compare results of simulated genome assemblies. PMID:21496274

Building polyhedra by self-assembly: theory and experiment.

PubMed

Kaplan, Ryan; Klobušický, Joseph; Pandey, Shivendra; Gracias, David H; Menon, Govind

2014-01-01

We investigate the utility of a mathematical framework based on discrete geometry to model biological and synthetic self-assembly. Our primary biological example is the self-assembly of icosahedral viruses; our synthetic example is surface-tension-driven self-folding polyhedra. In both instances, the process of self-assembly is modeled by decomposing the polyhedron into a set of partially formed intermediate states. The set of all intermediates is called the configuration space, pathways of assembly are modeled as paths in the configuration space, and the kinetics and yield of assembly are modeled by rate equations, Markov chains, or cost functions on the configuration space. We review an interesting interplay between biological function and mathematical structure in viruses in light of this framework. We discuss in particular: (i) tiling theory as a coarse-grained description of all-atom models; (ii) the building game-a growth model for the formation of polyhedra; and (iii) the application of these models to the self-assembly of the bacteriophage MS2. We then use a similar framework to model self-folding polyhedra. We use a discrete folding algorithm to compute a configuration space that idealizes surface-tension-driven self-folding and analyze pathways of assembly and dominant intermediates. These computations are then compared with experimental observations of a self-folding dodecahedron with side 300 μm. In both models, despite a combinatorial explosion in the size of the configuration space, a few pathways and intermediates dominate self-assembly. For self-folding polyhedra, the dominant intermediates have fewer degrees of freedom than comparable intermediates, and are thus more rigid. The concentration of assembly pathways on a few intermediates with distinguished geometric properties is biologically and physically important, and suggests deeper mathematical structure.

A Larger Chocolate Chip-Development of a 15K Theobroma cacao L. SNP Array to Create High-Density Linkage Maps.

PubMed

Livingstone, Donald; Stack, Conrad; Mustiga, Guiliana M; Rodezno, Dayana C; Suarez, Carmen; Amores, Freddy; Feltus, Frank A; Mockaitis, Keithanne; Cornejo, Omar E; Motamayor, Juan C

2017-01-01

Cacao ( Theobroma cacao L.) is an important cash crop in tropical regions around the world and has a rich agronomic history in South America. As a key component in the cosmetic and confectionary industries, millions of people worldwide use products made from cacao, ranging from shampoo to chocolate. An Illumina Infinity II array was created using 13,530 SNPs identified within a small diversity panel of cacao. Of these SNPs, 12,643 derive from variation within annotated cacao genes. The genotypes of 3,072 trees were obtained, including two mapping populations from Ecuador. High-density linkage maps for these two populations were generated and compared to the cacao genome assembly. Phenotypic data from these populations were combined with the linkage maps to identify the QTLs for yield and disease resistance.

Draft genome sequence of the rubber tree Hevea brasiliensis.

PubMed

Rahman, Ahmad Yamin Abdul; Usharraj, Abhilash O; Misra, Biswapriya B; Thottathil, Gincy P; Jayasekaran, Kandakumar; Feng, Yun; Hou, Shaobin; Ong, Su Yean; Ng, Fui Ling; Lee, Ling Sze; Tan, Hock Siew; Sakaff, Muhd Khairul Luqman Muhd; Teh, Beng Soon; Khoo, Bee Feong; Badai, Siti Suriawati; Aziz, Nurohaida Ab; Yuryev, Anton; Knudsen, Bjarne; Dionne-Laporte, Alexandre; Mchunu, Nokuthula P; Yu, Qingyi; Langston, Brennick J; Freitas, Tracey Allen K; Young, Aaron G; Chen, Rui; Wang, Lei; Najimudin, Nazalan; Saito, Jennifer A; Alam, Maqsudul

2013-02-02

Hevea brasiliensis, a member of the Euphorbiaceae family, is the major commercial source of natural rubber (NR). NR is a latex polymer with high elasticity, flexibility, and resilience that has played a critical role in the world economy since 1876. Here, we report the draft genome sequence of H. brasiliensis. The assembly spans ~1.1 Gb of the estimated 2.15 Gb haploid genome. Overall, ~78% of the genome was identified as repetitive DNA. Gene prediction shows 68,955 gene models, of which 12.7% are unique to Hevea. Most of the key genes associated with rubber biosynthesis, rubberwood formation, disease resistance, and allergenicity have been identified. The knowledge gained from this genome sequence will aid in the future development of high-yielding clones to keep up with the ever increasing need for natural rubber.

Draft genome sequence of the rubber tree Hevea brasiliensis

PubMed Central

2013-01-01

Background Hevea brasiliensis, a member of the Euphorbiaceae family, is the major commercial source of natural rubber (NR). NR is a latex polymer with high elasticity, flexibility, and resilience that has played a critical role in the world economy since 1876. Results Here, we report the draft genome sequence of H. brasiliensis. The assembly spans ~1.1 Gb of the estimated 2.15 Gb haploid genome. Overall, ~78% of the genome was identified as repetitive DNA. Gene prediction shows 68,955 gene models, of which 12.7% are unique to Hevea. Most of the key genes associated with rubber biosynthesis, rubberwood formation, disease resistance, and allergenicity have been identified. Conclusions The knowledge gained from this genome sequence will aid in the future development of high-yielding clones to keep up with the ever increasing need for natural rubber. PMID:23375136