Construction method of pre assembled unit of bolt sphere grid

NASA Astrophysics Data System (ADS)

Hu, L. W.; Guo, F. L.; Wang, J. L.; Bu, F. M.

2018-03-01

The traditional construction of bolt sphere grid has many disadvantages, such as high cost, large amount of work at high altitude and long construction period, in order to make up for these shortcomings, in this paper, a new and applicable construction method is explored: setting up local scaffolding, installing the bolt sphere grid starting frame on the local scaffolding, then the pre assembled unit of bolt sphere grid is assembled on the ground, using small hoisting equipment to lift pre assembled unit to high altitude and install. Compared with the traditional installation method, the construction method has strong practicability and high economic efficiency, and has achieved good social and economic benefits.

Rotational superstructure in van der Waals heterostructure of self-assembled C 60 monolayer on the WSe 2 surface

DOE PAGES

Santos, Elton J. G.; Scullion, Declan; Chu, Ximo S.; ...

2017-08-23

Hybrid van der Waals (vdW) heterostructures composed of two-dimensional (2D) layered materials and self-assembled organic molecules are promising systems for electronic and optoelectronic applications with enhanced properties and performance. Control of molecular assembly is therefore paramount to fundamentally understand the nucleation, ordering, alignment, and electronic interaction of organic molecules with 2D materials. Here, we report the formation and detailed study of highly ordered, crystalline monolayers of C 60 molecules self-assembled on the surface of WSe 2 in well-ordered arrays with large grain sizes (~5 μm). Using high-resolution scanning tunneling microscopy (STM), we observe a periodic 2 × 2 superstructure inmore » the C 60 monolayer and identify four distinct molecular appearances. Using vdW-corrected ab initio density functional theory (DFT) simulations, we determine that the interplay between vdW and Coulomb interactions as well as adsorbate–adsorbate and adsorbate–substrate interactions results in specific rotational arrangements of the molecules forming the superstructure. The orbital ordering through the relative positions of bonds in adjacent molecules creates a charge redistribution that links the molecule units in a long-range network. Furthermore, this rotational superstructure extends throughout the self-assembled monolayer and opens a pathway towards engineering aligned hybrid organic/inorganic vdW heterostructures with 2D layered materials in a precise and controlled way.« less

Rotational superstructure in van der Waals heterostructure of self-assembled C 60 monolayer on the WSe 2 surface

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

Santos, Elton J. G.; Scullion, Declan; Chu, Ximo S.

Hybrid van der Waals (vdW) heterostructures composed of two-dimensional (2D) layered materials and self-assembled organic molecules are promising systems for electronic and optoelectronic applications with enhanced properties and performance. Control of molecular assembly is therefore paramount to fundamentally understand the nucleation, ordering, alignment, and electronic interaction of organic molecules with 2D materials. Here, we report the formation and detailed study of highly ordered, crystalline monolayers of C 60 molecules self-assembled on the surface of WSe 2 in well-ordered arrays with large grain sizes (~5 μm). Using high-resolution scanning tunneling microscopy (STM), we observe a periodic 2 × 2 superstructure inmore » the C 60 monolayer and identify four distinct molecular appearances. Using vdW-corrected ab initio density functional theory (DFT) simulations, we determine that the interplay between vdW and Coulomb interactions as well as adsorbate–adsorbate and adsorbate–substrate interactions results in specific rotational arrangements of the molecules forming the superstructure. The orbital ordering through the relative positions of bonds in adjacent molecules creates a charge redistribution that links the molecule units in a long-range network. Furthermore, this rotational superstructure extends throughout the self-assembled monolayer and opens a pathway towards engineering aligned hybrid organic/inorganic vdW heterostructures with 2D layered materials in a precise and controlled way.« less

Precise Truss Assembly using Commodity Parts and Low Precision Welding

NASA Technical Reports Server (NTRS)

Komendera, Erik; Reishus, Dustin; Dorsey, John T.; Doggett, William R.; Correll, Nikolaus

2013-01-01

We describe an Intelligent Precision Jigging Robot (IPJR), which allows high precision assembly of commodity parts with low-precision bonding. We present preliminary experiments in 2D that are motivated by the problem of assembling a space telescope optical bench on orbit using inexpensive, stock hardware and low-precision welding. An IPJR is a robot that acts as the precise "jigging", holding parts of a local assembly site in place while an external low precision assembly agent cuts and welds members. The prototype presented in this paper allows an assembly agent (in this case, a human using only low precision tools), to assemble a 2D truss made of wooden dowels to a precision on the order of millimeters over a span on the order of meters. We report the challenges of designing the IPJR hardware and software, analyze the error in assembly, document the test results over several experiments including a large-scale ring structure, and describe future work to implement the IPJR in 3D and with micron precision.

Morphology, directed self-assembly and pattern transfer from a high molecular weight polystyrene-block-poly(dimethylsiloxane) block copolymer film

NASA Astrophysics Data System (ADS)

Cheng, Li-Chen; Bai, Wubin; Fernandez Martin, Eduardo; Tu, Kun-Hua; Ntetsikas, Konstantinos; Liontos, George; Avgeropoulos, Apostolos; Ross, C. A.

2017-04-01

The self-assembly of block copolymers with large feature sizes is inherently challenging as the large kinetic barrier arising from chain entanglement of high molecular weight (MW) polymers limits the extent over which long-range ordered microdomains can be achieved. Here, we illustrate the evolution of thin film morphology from a diblock copolymer of polystyrene-block-poly(dimethylsiloxane) exhibiting total number average MW of 123 kg mol-1, and demonstrate the formation of layers of well-ordered cylindrical microdomains under appropriate conditions of binary solvent mix ratio, commensurate film thickness, and solvent vapor annealing time. Directed self-assembly of the block copolymer within lithographically patterned trenches occurs with alignment of cylinders parallel to the sidewalls. Fabrication of ordered cobalt nanowire arrays by pattern transfer was also implemented, and their magnetic properties and domain wall behavior were characterized.

Mixed non-covalent assemblies of ethynyl nile red and ethynyl pyrene along oligonucleotide templates.

PubMed

Ensslen, Philipp; Fritz, Yannic; Wagenknecht, Hans-Achim

2015-01-14

Ethynyl pyrene and ethynyl nile red as modifications at the 5-position of 2'-deoxyuridines self-assemble non-covalently and specifically along oligo-2'-deoxyadenosines as templates. Oligo-2'-deoxyadenosines of the lengths (dA)10-(dA)20 are able to retain nearly exactly as many ethynyl nile red units in solution as binding sites are available on these templates. In contrast, in the presence of oligo-2'-thymidines the ethynyl nile red moieties are similarly insoluble to those in the absence of any oligonucleotide and yield an aggregate. The mixed assemblies of both chromophores are highly ordered, show left-handed chirality and yield dual fluorescence. The strong excitonic coupling indicates assemblies with a high degree of order. These results show that DNA represents an important supramolecular scaffold for the templated, helical and non-covalent arrangement not only for one type of chromophore but also for mixtures of two different chromophores.

A Robust and Engineerable Self-Assembling Protein Template for the Synthesis and Patterning of Ordered Nanoparticle Arrays

NASA Technical Reports Server (NTRS)

McMillan, R. Andrew; Howard, Jeanie; Zaluzec, Nestor J.; Kagawa, Hiromi K.; Li, Yi-Fen; Paavola, Chad D.; Trent, Jonathan D.

2004-01-01

Self-assembling biomolecules that form highly ordered structures have attracted interest as potential alternatives to conventional lithographic processes for patterning materials. Here we introduce a general technique for patterning materials on the nanoscale using genetically modified protein cage structures called chaperonins that self-assemble into crystalline templates. Constrained chemical synthesis of transition metal nanoparticles is specific to templates genetically functionalized with poly-Histidine sequences. These arrays of materials are ordered by the nanoscale structure of the crystallized protein. This system may be easily adapted to pattern a variety of materials given the rapidly growing list of peptide sequences selected by screening for specificity for inorganic materials.

High performance superconducting devices enabled by three dimensionally ordered nanodots and/or nanorods

DOEpatents

Goyal, Amit

2013-09-17

Novel articles and methods to fabricate same with self-assembled nanodots and/or nanorods of a single or multicomponent material within another single or multicomponent material for use in electrical, electronic, magnetic, electromagnetic and electrooptical devices is disclosed. Self-assembled nanodots and/or nanorods are ordered arrays wherein ordering occurs due to strain minimization during growth of the materials. A simple method to accomplish this when depositing in-situ films is also disclosed. Device applications of resulting materials are in areas of superconductivity, photovoltaics, ferroelectrics, magnetoresistance, high density storage, solid state lighting, non-volatile memory, photoluminescence, thermoelectrics and in quantum dot lasers.

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

High performance electrical, magnetic, electromagnetic and electrooptical devices enabled by three dimensionally ordered nanodots and nanorods

DOEpatents

Goyal, Amit , Kang; Sukill, [Knoxville, TN

2012-02-21

Novel articles and methods to fabricate same with self-assembled nanodots and/or nanorods of a single or multicomponent material within another single or multicomponent material for use in electrical, electronic, magnetic, electromagnetic and electrooptical devices is disclosed. Self-assembled nanodots and/or nanorods are ordered arrays wherein ordering occurs due to strain minimization during growth of the materials. A simple method to accomplish this when depositing in-situ films is also disclosed. Device applications of resulting materials are in areas of superconductivity, photovoltaics, ferroelectrics, magnetoresistance, high density storage, solid state lighting, non-volatile memory, photoluminescence, thermoelectrics and in quantum dot lasers.

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.

Fast assembly of ordered block copolymer nanostructures through microwave annealing.

PubMed

Zhang, Xiaojiang; Harris, Kenneth D; Wu, Nathanael L Y; Murphy, Jeffrey N; Buriak, Jillian M

2010-11-23

Block copolymer self-assembly is an innovative technology capable of patterning technologically relevant substrates with nanoscale precision for a range of applications from integrated circuit fabrication to tissue interfacing, for example. In this article, we demonstrate a microwave-based method of rapidly inducing order in block copolymer structures. The technique involves the usage of a commercial microwave reactor to anneal block copolymer films in the presence of appropriate solvents, and we explore the effect of various parameters over the polymer assembly speed and defect density. The approach is applied to the commonly used poly(styrene)-b-poly(methyl methacrylate) (PS-b-PMMA) and poly(styrene)-b-poly(2-vinylpyridine) (PS-b-P2VP) families of block copolymers, and it is found that the substrate resistivity, solvent environment, and anneal temperature all critically influence the self-assembly process. For selected systems, highly ordered patterns were achieved in less than 3 min. In addition, we establish the compatibility of the technique with directed assembly by graphoepitaxy.

Highly ductile multilayered films by layer-by-layer assembly of oppositely charged polyurethanes for biomedical applications.

PubMed

Podsiadlo, Paul; Qin, Ming; Cuddihy, Meghan; Zhu, Jian; Critchley, Kevin; Kheng, Eugene; Kaushik, Amit K; Qi, Ying; Kim, Hyoung-Sug; Noh, Si-Tae; Arruda, Ellen M; Waas, Anthony M; Kotov, Nicholas A

2009-12-15

Multilayered thin films prepared with the layer-by-layer (LBL) assembly technique are typically "brittle" composites, while many applications such as flexible electronics or biomedical devices would greatly benefit from ductile, and tough nanostructured coatings. Here we present the preparation of highly ductile multilayered films via LBL assembly of oppositely charged polyurethanes. Free-standing films were found to be robust, strong, and tough with ultimate strains as high as 680% and toughness of approximately 30 MJ/m(3). These results are at least 2 orders of magnitude greater than most LBL materials presented until today. In addition to enhanced ductility, the films showed first-order biocompatibility with animal and human cells. Multilayered structures incorporating polyurethanes open up a new research avenue into the preparation of multifunctional nanostructured films with great potential in biomedical applications.

Ultrafast Self-Assembly of Sub-10 nm Block Copolymer Nanostructures by Solvent-Free High-Temperature Laser Annealing.

PubMed

Jiang, Jing; Jacobs, Alan G; Wenning, Brandon; Liedel, Clemens; Thompson, Michael O; Ober, Christopher K

2017-09-20

Laser spike annealing was applied to PS-b-PDMS diblock copolymers to induce short-time (millisecond time scale), high-temperature (300 to 700 °C) microphase segregation and directed self-assembly of sub-10 nm features. Conditions were identified that enabled uniform microphase separation in the time frame of tens of milliseconds. Microphase ordering improved with increased temperature and annealing time, whereas phase separation contrast was lost for very short annealing times at high temperature. PMMA brush underlayers aided ordering under otherwise identical laser annealing conditions. Good long-range order for sub-10 nm cylinder morphology was achieved using graphoepitaxy coupled with a 20 ms dwell laser spike anneal above 440 °C.

Precision lens assembly with alignment turning system

NASA Astrophysics Data System (ADS)

Ho, Cheng-Fang; Huang, Chien-Yao; Lin, Yi-Hao; Kuo, Hui-Jean; Kuo, Ching-Hsiang; Hsu, Wei-Yao; Chen, Fong-Zhi

2017-10-01

The poker chip assembly with high precision lens barrels is widely applied to ultra-high performance optical system. ITRC applies the poker chip assembly technology to the high numerical aperture objective lenses and lithography projection lenses because of its high efficiency assembly process. In order to achieve high precision lens cell for poker chip assembly, an alignment turning system (ATS) is developed. The ATS includes measurement, alignment and turning modules. The measurement module is equipped with a non-contact displacement sensor (NCDS) and an autocollimator (ACM). The NCDS and ACM are used to measure centration errors of the top and the bottom surface of a lens respectively; then the amount of adjustment of displacement and tilt with respect to the rotational axis of the turning machine for the alignment module can be determined. After measurement, alignment and turning processes on the ATS, the centration error of a lens cell with 200 mm in diameter can be controlled within 10 arcsec. Furthermore, a poker chip assembly lens cell with three sub-cells is demonstrated, each sub-cells are measured and accomplished with alignment and turning processes. The lens assembly test for five times by each three technicians; the average transmission centration error of assembly lens is 12.45 arcsec. The results show that ATS can achieve high assembly efficiency for precision optical systems.

Self-assembly of ordered nanostructures

NASA Astrophysics Data System (ADS)

Yin, Jinsong

2000-10-01

Several different kinds of nanostructure materials were studied in this thesis: self-assembled monodispersive nanocrystals, photonic crystals, ordered mesoporous silica and hierarchically ordered nanostructured materials. Tetrahedral nanocrystals of CoO, with edge-lengths of 4.4 +/- 0.2 nm, were synthesized at high purity and monodispersity. The size, shape and phase selections of the nanocrystals were performed using a novel magnetic field separation technique. These nanocrystals behave like molecules, forming a face-centered cubic self-assembly of nanocrystal superlattices. In-situ behavior of self-assembled CoO nanocrystal arrays was also analyzed using transmission electron microscopy and associated techniques. The surface passivation layer started to evaporate/decompose at temperatures as low as ˜200°C, but the exposed cores of nanocrystals preserved the geometrical configuration of the assembly due to the strong adhesion of the carbon substrate. As the temperature is further increased from 300 to 600°C, the intrinsic crystal structure of the CoO nanoparticles experiences a replacement reaction, resulting in the formation of cobalt carbides. Two-dimensional self-assembling of cobalt nanocrystals with an average particle size of 9.2 nm and polydispersity of 9% is processed. Phtonic crystals were processed by a template-assisted method. Ordered self-assembly of pores of titania nanocrystals formed a face-centered cubic packing structure. The walls of the pores were made of anatase nanocrystals of ˜8 nm in diameter. Cobalt can be doped into the walls of the pores by solution infiltration of cobalt carbonyl. Cobalt titanium oxide may be formed on the internal surface of the ordered pore structure. This type of structure is likely to be an excellent supporting material for catalysis. The experimental results suggest that transition metal elements can be incorporated into porous titania without blocking the interconnected pores. Hierarchically ordered nanostructured materials with high porosity at dual length-scale were prepared by a single annealing procedure. The plasma energy of this porous materials shifts about 1.2 eV to lower energy, compared to the fully densed silica spheres. This type of material is expected to have not only large surface area for catalysis, but also low dielectric constant for low-loss dielectric applications.

Facile "modular assembly" for fast construction of a highly oriented crystalline MOF nanofilm.

PubMed

Xu, Gang; Yamada, Teppei; Otsubo, Kazuya; Sakaida, Shun; Kitagawa, Hiroshi

2012-10-10

The preparation of crystalline, ordered thin films of metal-organic frameworks (MOFs) will be a critical process for MOF-based nanodevices in the future. MOF thin films with perfect orientation and excellent crystallinity were formed with novel nanosheet-structured components, Cu-TCPP [TCPP = 5,10,15,20-tetrakis(4-carboxyphenyl)porphyrin], by a new "modular assembly" strategy. The modular assembly process involves two steps: a "modularization" step is used to synthesize highly crystalline "modules" with a nanosized structure that can be conveniently assembled into a thin film in the following "assembly" step. With this method, MOF thin films can easily be set up on different substrates at very high speed with controllable thickness. This new approach also enabled us to prepare highly oriented crystalline thin films of MOFs that cannot be prepared in thin-film form by traditional techniques.

Rapid cloning of genes in hexaploid wheat using cultivar-specific long-range chromosome assembly.

PubMed

Thind, Anupriya Kaur; Wicker, Thomas; Šimková, Hana; Fossati, Dario; Moullet, Odile; Brabant, Cécile; Vrána, Jan; Doležel, Jaroslav; Krattinger, Simon G

2017-08-01

Cereal crops such as wheat and maize have large repeat-rich genomes that make cloning of individual genes challenging. Moreover, gene order and gene sequences often differ substantially between cultivars of the same crop species. A major bottleneck for gene cloning in cereals is the generation of high-quality sequence information from a cultivar of interest. In order to accelerate gene cloning from any cropping line, we report 'targeted chromosome-based cloning via long-range assembly' (TACCA). TACCA combines lossless genome-complexity reduction via chromosome flow sorting with Chicago long-range linkage to assemble complex genomes. We applied TACCA to produce a high-quality (N50 of 9.76 Mb) de novo chromosome assembly of the wheat line CH Campala Lr22a in only 4 months. Using this assembly we cloned the broad-spectrum Lr22a leaf-rust resistance gene, using molecular marker information and ethyl methanesulfonate (EMS) mutants, and found that Lr22a encodes an intracellular immune receptor homologous to the Arabidopsis thaliana RPM1 protein.

Precise Truss Assembly Using Commodity Parts and Low Precision Welding

NASA Technical Reports Server (NTRS)

Komendera, Erik; Reishus, Dustin; Dorsey, John T.; Doggett, W. R.; Correll, Nikolaus

2014-01-01

Hardware and software design and system integration for an intelligent precision jigging robot (IPJR), which allows high precision assembly using commodity parts and low-precision bonding, is described. Preliminary 2D experiments that are motivated by the problem of assembling space telescope optical benches and very large manipulators on orbit using inexpensive, stock hardware and low-precision welding are also described. An IPJR is a robot that acts as the precise "jigging", holding parts of a local structure assembly site in place, while an external low precision assembly agent cuts and welds members. The prototype presented in this paper allows an assembly agent (for this prototype, a human using only low precision tools), to assemble a 2D truss made of wooden dowels to a precision on the order of millimeters over a span on the order of meters. The analysis of the assembly error and the results of building a square structure and a ring structure are discussed. Options for future work, to extend the IPJR paradigm to building in 3D structures at micron precision are also summarized.

Large-Scale Automated Production of Highly Ordered Ultralong Hydroxyapatite Nanowires and Construction of Various Fire-Resistant Flexible Ordered Architectures.

PubMed

Chen, Feng; Zhu, Ying-Jie

2016-12-27

Practical applications of nanostructured materials have been largely limited by the difficulties in controllable and scaled-up synthesis, large-sized highly ordered self-assembly, and macroscopic processing of nanostructures. Hydroxyapatite (HAP), the major inorganic component of human bone and tooth, is an important biomaterial with high biocompatibility, bioactivity, and high thermal stability. Large-sized highly ordered HAP nanostructures are of great significance for applications in various fields and for understanding the formation mechanisms of bone and tooth. However, the synthesis of large-sized highly ordered HAP nanostructures remains a great challenge, especially for the preparation of large-sized highly ordered ultralong HAP nanowires because ultralong HAP nanowires are easily tangled and aggregated. Herein, we report our three main research findings: (1) the large-scale synthesis of highly flexible ultralong HAP nanowires with lengths up to >100 μm and aspect ratios up to >10000; (2) the demonstration of a strategy for the rapid automated production of highly flexible, fire-resistant, large-sized, self-assembled highly ordered ultralong HAP nanowires (SHOUHNs) at room temperature; and (3) the successful construction of various flexible fire-resistant HAP ordered architectures using the SHOUHNs, such as high-strength highly flexible nanostructured ropes (nanoropes), highly flexible textiles, and 3-D printed well-defined highly ordered patterns. The SHOUHNs are successively formed from the nanoscale to the microscale then to the macroscale, and the ordering direction of the ordered HAP structure is controllable. These ordered HAP architectures made from the SHOUHNs, such as highly flexible textiles, may be engineered into advanced functional products for applications in various fields, for example, fireproof clothing.

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

Stochastic dynamics of virus capsid formation: direct versus hierarchical self-assembly

PubMed Central

2012-01-01

Background In order to replicate within their cellular host, many viruses have developed self-assembly strategies for their capsids which are sufficiently robust as to be reconstituted in vitro. Mathematical models for virus self-assembly usually assume that the bonds leading to cluster formation have constant reactivity over the time course of assembly (direct assembly). In some cases, however, binding sites between the capsomers have been reported to be activated during the self-assembly process (hierarchical assembly). Results In order to study possible advantages of such hierarchical schemes for icosahedral virus capsid assembly, we use Brownian dynamics simulations of a patchy particle model that allows us to switch binding sites on and off during assembly. For T1 viruses, we implement a hierarchical assembly scheme where inter-capsomer bonds become active only if a complete pentamer has been assembled. We find direct assembly to be favorable for reversible bonds allowing for repeated structural reorganizations, while hierarchical assembly is favorable for strong bonds with small dissociation rate, as this situation is less prone to kinetic trapping. However, at the same time it is more vulnerable to monomer starvation during the final phase. Increasing the number of initial monomers does have only a weak effect on these general features. The differences between the two assembly schemes become more pronounced for more complex virus geometries, as shown here for T3 viruses, which assemble through homogeneous pentamers and heterogeneous hexamers in the hierarchical scheme. In order to complement the simulations for this more complicated case, we introduce a master equation approach that agrees well with the simulation results. Conclusions Our analysis shows for which molecular parameters hierarchical assembly schemes can outperform direct ones and suggests that viruses with high bond stability might prefer hierarchical assembly schemes. These insights increase our physical understanding of an essential biological process, with many interesting potential applications in medicine and materials science. PMID:23244740

Hierarchical nanoparticle assemblies formed by decorating breath figures.

PubMed

Böker, Alexander; Lin, Yao; Chiapperini, Kristen; Horowitz, Reina; Thompson, Mike; Carreon, Vincent; Xu, Ting; Abetz, Clarissa; Skaff, Habib; Dinsmore, A D; Emrick, Todd; Russell, Thomas P

2004-05-01

The combination of two self-assembly processes on different length scales leads to the formation of hierarchically structured nanoparticle arrays. Here, the formation of spherical cavities, or 'breath figures'-made by the condensation of micrometre-sized water droplets on the surface of a polymer solution-that self-assemble into a well-ordered hexagonal array, is combined with the self-assembly of CdSe nanoparticles at the polymer solution-water droplet interface. Complete evaporation of the solvent and water confines the particle assembly to an array of spherical cavities and allows for ex situ investigation. Fluorescence confocal, transmission electron and scanning electron microscope images show the preferential segregation of the CdSe nanoparticles to the polymer solution-water interface where they form a 5-7-nm-thick layer, thus functionalizing the walls of the holes. This process opens a new route to fabricating highly functionalized ordered microarrays of nanoparticles, potentially useful in sensory, separation membrane or catalytic applications.

Coevolutionary constraints in the sequence-space of macromolecular complexes reflect their self-assembly pathways.

PubMed

Mallik, Saurav; Kundu, Sudip

2017-07-01

Is the order in which biomolecular subunits self-assemble into functional macromolecular complexes imprinted in their sequence-space? Here, we demonstrate that the temporal order of macromolecular complex self-assembly can be efficiently captured using the landscape of residue-level coevolutionary constraints. This predictive power of coevolutionary constraints is irrespective of the structural, functional, and phylogenetic classification of the complex and of the stoichiometry and quaternary arrangement of the constituent monomers. Combining this result with a number of structural attributes estimated from the crystal structure data, we find indications that stronger coevolutionary constraints at interfaces formed early in the assembly hierarchy probably promotes coordinated fixation of mutations that leads to high-affinity binding with higher surface area, increased surface complementarity and elevated number of molecular contacts, compared to those that form late in the assembly. Proteins 2017; 85:1183-1189. © 2017 Wiley Periodicals, Inc. © 2017 Wiley Periodicals, Inc.

Postassembly chemical modification of a highly ordered organosilane multilayer: new insights into the structure, bonding, and dynamics of self-assembling silane monolayers.

PubMed

Wen, Ke; Maoz, Rivka; Cohen, Hagai; Sagiv, Jacob; Gibaud, Alain; Desert, Anne; Ocko, Benjamin M

2008-03-01

Experimental evidence derived from a comprehensive study of a self-assembled organosilane multilayer film system undergoing a process of postassembly chemical modification that affects interlayer-located polar groups of the constituent molecules while preserving its overall molecular architecture allows a quantitative evaluation of both the degree of intralayer polymerization and that of interlayer covalent bonding of the silane headgroups in a highly ordered layer assembly of this type. The investigated system consists of a layer-by-layer assembled multilayer of a bifunctional n-alkyl silane with terminal alcohol group that is in situ converted, via a wet chemical oxidation process conducted on the entire multilayer, to the corresponding carboxylic acid function. A combined chemical-structural analysis of data furnished by four different techniques, Fourier transform infrared spectroscopy (FTIR), synchrotron X-ray scattering, X-ray photoelectron spectroscopy (XPS), and contact angle measurements, demonstrates that the highly ordered 3D molecular arrangement of the initial alcohol-silane multilayer stack is well preserved upon virtually quantitative conversion of the alcohol to carboxylic acid and the concomitant irreversible cleavage of interlayer covalent bonds. Thus, the correlation of quantitative chemical and structural data obtained from such unreacted and fully reacted film samples offers an unprecedented experimental framework within which it becomes possible to differentiate between intralayer and interlayer covalent bonding. In addition, the use of a sufficiently thick multilayer effectively eliminates the interfering contributions of the underlying silicon oxide substrate to both the X-ray scattering and XPS data. The present findings contribute a firm experimental basis to the elucidation of the self-assembly mechanism, the molecular organization, and the modes and dynamics of intra- and interlayer bonding prevailing in highly ordered organosilane films; with further implications for the rational exploitation of some of the unique options such supramolecular surface entities can offer in the advancement of a chemical nanofabrication methodology.

Self-organization of a self-assembled supramolecular rectangle, square, and three-dimensional cage on Au111 surfaces.

PubMed

Yuan, Qun-Hui; Wan, Li-Jun; Jude, Hershel; Stang, Peter J

2005-11-23

The structure and conformation of three self-assembled supramolecular species, a rectangle, a square, and a three-dimensional cage, on Au111 surfaces were investigated by scanning tunneling microscopy. These supramolecular assemblies adsorb on Au111 surfaces and self-organize to form highly ordered adlayers with distinct conformations that are consistent with their chemical structures. The faces of the supramolecular rectangle and square lie flat on the surface, preserving their rectangle and square conformations, respectively. The three-dimensional cage also forms well-ordered adlayers on the gold surface, forming regular molecular rows of assemblies. When the rectangle and cage were mixed together, the assemblies separated into individual domains, and no mixed adlayers were observed. These results provide direct evidence of the noncrystalline solid-state structures of these assemblies and information about how they self-organize on Au111 surfaces, which is of importance in the potential manufacturing of functional nanostructures and devices.

End Groups of Functionalized Siloxane Oligomers Direct Block-Copolymeric or Liquid-Crystalline Self-Assembly Behavior

PubMed Central

2016-01-01

Monodisperse oligodimethylsiloxanes end-functionalized with the hydrogen-bonding ureidopyrimidinone (UPy) motif undergo phase separation between their aromatic end groups and dimethylsiloxane midblocks to form ordered nanostructures with domain spacings of <5 nm. The self-assembly behavior of these well-defined oligomers resembles that of high degree of polymerization (N)–high block interaction parameter (χ) linear diblock copolymers despite their small size. Specifically, the phase morphology varies from lamellar to hexagonal to body-centered cubic with increasing asymmetry in molecular volume fraction. Mixing molecules with different molecular weights to give dispersity >1.13 results in disorder, showing importance of molecular monodispersity for ultrasmall ordered phase separation. In contrast, oligodimethylsiloxanes end-functionalized with an O-benzylated UPy derivative self-assemble into lamellar nanostructures regardless of volume fraction because of the strong preference of the end groups to aggregate in a planar geometry. Thus, these molecules display more classically liquid-crystalline self-assembly behavior where the lamellar bilayer thickness is determined by the siloxane midblock. Here the lamellar nanostructure is tolerant to molecular polydispersity. We show the importance of end groups in high χ–low N block molecules, where block-copolymer-like self-assembly in our UPy-functionalized oligodimethylsiloxanes relies upon the dominance of phase separation effects over directional end group aggregation. PMID:27054381

Improving the goat long-read assembly with optical mapping

USDA-ARS?s Scientific Manuscript database

Reference genome assemblies provide important context in genetics by standardizing the order of genes and providing a universal set of coordinates for individual nucleotides. Often due to the high complexity of genic regions and higher copy number of genes involved in immune function, immunity-relat...

Ordered CdSe nanoparticles within self-assembled block copolymer domains on surfaces.

PubMed

Zou, Shan; Hong, Rui; Emrick, Todd; Walker, Gilbert C

2007-02-13

Hierarchical, high-density, ordered patterns were fabricated on Si substrates by self-assembly of CdSe nanoparticles within approximately 20-nm-thick diblock copolymer films in a controlled manner. Surface-modified CdSe nanoparticles formed well-defined structures within microphase-separated polystyrene-b-poly(2-vinylpyridine) (PS-b-P2VP) domains. Trioctylphosphine oxide (TOPO)-coated CdSe nanoparticles were incorporated into PS domains and polyethylene glycol-coated CdSe nanoparticles were located primarily in the P2VP domains. Nearly close-packed CdSe nanoparticles were clearly identified within the highly ordered patterns on Si substrates by scanning electron microscopy (SEM). Contact angle measurements together with SEM results indicate that TOPO-CdSe nanoparticles were partially placed at the air/copolymer interface.

Coupling Considerations in Assembly Language

DTIC Science & Technology

2018-01-05

report discusses coupling issues arising in assembly language source code, as contrasted to similar issues arising in high order language (HOL...Warfare Center Weapons Division (NAWCWD) require compliance with DO-178B and DO-178C, which contain guidelines relating to data and control coupling. The...considered unknown, but its effect on development and maintenance will serve as indicators on whether the coupling measure is high or low. Both

Ultrathin gold nanoribbons synthesized within the interior cavity of a self-assembled peptide nanoarchitecture.

PubMed

Tomizaki, Kin-ya; Wakizaka, Shota; Yamaguchi, Yuichi; Kobayashi, Akitsugu; Imai, Takahito

2014-01-28

There is increasing interest in gold nanocrystals due to their unique physical, chemical, and biocompatible properties. In order to develop a template-assisted method for the fabrication of gold nanocrystals, we demonstrate here the de novo design and synthesis of a β-sheet-forming nonapeptide (RU006: Ac-AIAKAXKIA-NH2, X = L-2-naphthylalanine) which undergoes self-assembly to form disk-like nanoarchitectures approximately 100 nm wide and 2.5 nm high. These self-assemblies tend to form a network of higher-order assemblies in ultrapure water. Using RU006 as a template molecule, we fabricated ultrathin gold nanoribbons 50-100 nm wide, 2.5 nm high, and micrometers long without external reductants. Furthermore, in order to determine the mechanism of ultrathin gold nanoribbon formation, we synthesized four different RU006 analogues. On the basis of the results obtained using RU006 and these analogues, we propose the following mechanism for the self-assembly of RU006. First, RU006 forms a network by the cooperative association of disk-like assemblies in the presence of AuCl4(-) ions that are encapsulated and concentrated within the interior cavity of the network architectures. This is followed by electron transfer from the naphthalene rings to Au(III), resulting in slow growth to form ultrathin gold nanoribbons along the template network architectures under ambient conditions. The resulting ribbons retain the dimensions of the cavity of the template architecture. Our approach will allow the construction of diverse template architectural morphologies and will find applications in the construction of a variety of metallic nanoarchitectures.

Augmenting Chinese hamster genome assembly by identifying regions of high confidence.

PubMed

Vishwanathan, Nandita; Bandyopadhyay, Arpan A; Fu, Hsu-Yuan; Sharma, Mohit; Johnson, Kathryn C; Mudge, Joann; Ramaraj, Thiruvarangan; Onsongo, Getiria; Silverstein, Kevin A T; Jacob, Nitya M; Le, Huong; Karypis, George; Hu, Wei-Shou

2016-09-01

Chinese hamster Ovary (CHO) cell lines are the dominant industrial workhorses for therapeutic recombinant protein production. The availability of genome sequence of Chinese hamster and CHO cells will spur further genome and RNA sequencing of producing cell lines. However, the mammalian genomes assembled using shot-gun sequencing data still contain regions of uncertain quality due to assembly errors. Identifying high confidence regions in the assembled genome will facilitate its use for cell engineering and genome engineering. We assembled two independent drafts of Chinese hamster genome by de novo assembly from shotgun sequencing reads and by re-scaffolding and gap-filling the draft genome from NCBI for improved scaffold lengths and gap fractions. We then used the two independent assemblies to identify high confidence regions using two different approaches. First, the two independent assemblies were compared at the sequence level to identify their consensus regions as "high confidence regions" which accounts for at least 78 % of the assembled genome. Further, a genome wide comparison of the Chinese hamster scaffolds with mouse chromosomes revealed scaffolds with large blocks of collinearity, which were also compiled as high-quality scaffolds. Genome scale collinearity was complemented with EST based synteny which also revealed conserved gene order compared to mouse. As cell line sequencing becomes more commonly practiced, the approaches reported here are useful for assessing the quality of assembly and potentially facilitate the engineering of cell lines. Copyright © 2016 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Large-scale self-assembled zirconium phosphate smectic layers via a simple spray-coating process

NASA Astrophysics Data System (ADS)

Wong, Minhao; Ishige, Ryohei; White, Kevin L.; Li, Peng; Kim, Daehak; Krishnamoorti, Ramanan; Gunther, Robert; Higuchi, Takeshi; Jinnai, Hiroshi; Takahara, Atsushi; Nishimura, Riichi; Sue, Hung-Jue

2014-04-01

The large-scale assembly of asymmetric colloidal particles is used in creating high-performance fibres. A similar concept is extended to the manufacturing of thin films of self-assembled two-dimensional crystal-type materials with enhanced and tunable properties. Here we present a spray-coating method to manufacture thin, flexible and transparent epoxy films containing zirconium phosphate nanoplatelets self-assembled into a lamellar arrangement aligned parallel to the substrate. The self-assembled mesophase of zirconium phosphate nanoplatelets is stabilized by epoxy pre-polymer and exhibits rheology favourable towards large-scale manufacturing. The thermally cured film forms a mechanically robust coating and shows excellent gas barrier properties at both low- and high humidity levels as a result of the highly aligned and overlapping arrangement of nanoplatelets. This work shows that the large-scale ordering of high aspect ratio nanoplatelets is easier to achieve than previously thought and may have implications in the technological applications for similar materials.

Mobility of human immunodeficiency virus type 1 Pr55Gag in living cells.

PubMed

Gomez, Candace Y; Hope, Thomas J

2006-09-01

Human immunodeficiency virus type 1 (HIV-1) assembly requires the converging of thousands of structural proteins on cellular membranes to form a tightly packed immature virion. The Gag polyprotein contains all of the determinants important for viral assembly and must move around in the cell in order to form particles. This work has focused on Gag mobility in order to provide more insights into the dynamics of particle assembly. Key to these studies was the use of several fluorescently labeled Gag derivatives. We used fluorescence recovery after photobleaching as well as photoactivation to determine Gag mobility. Upon expression, Gag can be localized diffusely in the cytoplasm, associated with the plasma membrane, or in virus-like particles (VLPs). Here we show that Gag VLPs are primarily localized in the plasma membrane and do not colocalize with CD63. We have shown using full-length Gag as well as truncation mutants fused to green fluorescent protein that Gag is highly mobile in live cells when it is not assembled into VLPs. Results also showed that this mobility is highly dependent upon cholesterol. When cholesterol is depleted from cells expressing Gag, mobility is significantly decreased. Once cholesterol was replenished, Gag mobility returned to wild-type levels. Taken together, results from these mobility studies suggest that Gag is highly mobile and that as the assembly process proceeds, mobility decreases. These studies also suggest that Gag assembly must occur in cholesterol-rich domains in the plasma membrane.

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

Assembling Ordered Nanorod Superstructures and Their Application as Microcavity Lasers

NASA Astrophysics Data System (ADS)

Liu, Pai; Singh, Shalini; Guo, Yina; Wang, Jian-Jun; Xu, Hongxing; Silien, Christophe; Liu, Ning; Ryan, Kevin M.

2017-03-01

Herein we report the formation of multi-layered arrays of vertically aligned and close packed semiconductor nanorods in perfect registry at a substrate using electric field assisted assembly. The collective properties of these CdSexS1-x nanorod emitters are harnessed by demonstrating a relatively low amplified spontaneous emission (ASE) threshold and a high net optical gain at medium pump intensity. The importance of order in the system is highlighted where a lower ASE threshold is observed compared to disordered samples.

Optical assembly of microparticles into highly ordered structures using Ince-Gaussian beams

NASA Astrophysics Data System (ADS)

Woerdemann, Mike; Alpmann, Christina; Denz, Cornelia

2011-03-01

Ince-Gaussian (IG) beams are a third complete family of solutions of the paraxial Helmholtz equation. While many applications of Hermite-Gaussian and Laguerre-Gaussian beams have been demonstrated for manipulation of microparticles, the potential of the more general class of IG beams has not yet been exploited at all. We describe the unique properties of IG beams with respect to optical trapping applications, demonstrate a flexible experimental realization of arbitrary IG beams and prove the concept by creating two- and three-dimensional, highly ordered assemblies of typical microparticles. The concept is universal and can easily be integrated into existing holographic optical tweezers setups.

High performance devices enabled by epitaxial, preferentially oriented, nanodots and/or nanorods

DOEpatents

Goyal, Amit [Knoxville, TN

2011-10-11

Novel articles and methods to fabricate same with self-assembled nanodots and/or nanorods of a single or multicomponent material within another single or multicomponent material for use in electrical, electronic, magnetic, electromagnetic, superconducting and electrooptical devices is disclosed. Self-assembled nanodots and/or nanorods are ordered arrays wherein ordering occurs due to strain minimization during growth of the materials. A simple method to accomplish this when depositing in-situ films is also disclosed. Device applications of resulting materials are in areas of superconductivity, photovoltaics, ferroelectrics, magnetoresistance, high density storage, solid state lighting, non-volatile memory, photoluminescence, thermoelectrics and in quantum dot lasers.

In situ grazing incidence small-angle X-ray scattering investigation of polystyrene nanoparticle spray deposition onto silicon.

PubMed

Herzog, Gerd; Benecke, Gunthard; Buffet, Adeline; Heidmann, Berit; Perlich, Jan; Risch, Johannes F H; Santoro, Gonzalo; Schwartzkopf, Matthias; Yu, Shun; Wurth, Wilfried; Roth, Stephan V

2013-09-10

We investigated the spray deposition and subsequent self-assembly during drying of a polystyrene nanoparticle dispersion with in situ grazing incidence small-angle X-ray scattering at high time resolution. During the fast deposition of the dispersion and the subsequent evaporation of the solvent, different transient stages of nanoparticle assembly can be identified. In the first stage, the solvent starts to evaporate without ordering of the nanoparticles. During the second stage, large-scale structures imposed by the breakup of the liquid film are observable. In this stage, the solvent evaporates further and nanoparticle ordering starts. In the late third drying stage, the nanoparticles self-assemble into the final layer structure.

John H. Dillon Medal Lecture: Magnetic Field Directed Self-Assembly of Block Copolymers and Surfactant Mesophases

NASA Astrophysics Data System (ADS)

Osuji, Chinedum

2015-03-01

Molecular self-assembly of block copolymers and small molecule surfactants gives rise to a rich phase behavior as a function of temperature, composition, and other variables. We consider the directed self-assembly of such soft mesophases using magnetic fields, principally through the use of in situ x-ray scattering studies. Field alignment is predicated on a sufficiently large product of magnetic anisotropy and grain size to produce magnetostatic interactions which are substantive relative to thermal forces. We examine the role of field strength on the phase behavior and alignment dynamics of a series of soft mesophases, outlining the possibility to readily create highly ordered functional materials over macroscopic length scales. We show that magnetic fields as large as 10 T have little discernable impact on the stability of block copolymer systems considered, with shifts in order-disorder transition temperatures of roughly 5 mK or smaller. Consequently, directed self-assembly in these systems proceeds by nucleation of randomly aligned grains which thereafter rotate into registry with the field. We highlight the tradeoff between decreasing mobility and increasing anisotropic field interaction that dictates alignment kinetics while transiting from a high temperature disordered state to an ordered system at lower temperatures. NSF support through DMR-0847534 is gratefully acknowledged.

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.

Self-Assembly of Narrowly Dispersed Brush Diblock Copolymers with Domain Spacing more than 100 nm

NASA Astrophysics Data System (ADS)

Gu, Weiyin; Sveinbjornsson, Benjamin; Hong, Sung Woo; Grubbs, Robert; Russell, Thomas

2012-02-01

Self-assembled structures of high molecular weight (MW), narrow molecular weight distribution brush block copolymers containing polylactic acid (PLA) and polystyrene (PS) side chains with similar MWs were studied in both the melt and thin films. The polynorbornene-backbone-based brush diblock copolymers containing approximately equal volume fractions of each block self-assembled into highly ordered lamellae with domain spacing over 100 nm, as revealed by SAXS, GISAXS and AFM. The domain size increased approximately linearly with backbone length, which indicated an extended conformation of the backbone in the ordered state. The length of side chains also played a significant role in terms of controlling the domain size. As the degree of polymerization (DP) increased, the symmetric brush diblock copolymers with longer side chains tended to form larger lamellar microdomains in comparison to those that have the same DP but shorter side chains.

General Model for Retroviral Capsid Pattern Recognition by TRIM5 Proteins.

PubMed

Wagner, Jonathan M; Christensen, Devin E; Bhattacharya, Akash; Dawidziak, Daria M; Roganowicz, Marcin D; Wan, Yueping; Pumroy, Ruth A; Demeler, Borries; Ivanov, Dmitri N; Ganser-Pornillos, Barbie K; Sundquist, Wesley I; Pornillos, Owen

2018-02-15

Restriction factors are intrinsic cellular defense proteins that have evolved to block microbial infections. Retroviruses such as HIV-1 are restricted by TRIM5 proteins, which recognize the viral capsid shell that surrounds, organizes, and protects the viral genome. TRIM5α uses a SPRY domain to bind capsids with low intrinsic affinity ( K D of >1 mM) and therefore requires higher-order assembly into a hexagonal lattice to generate sufficient avidity for productive capsid recognition. TRIMCyp, on the other hand, binds HIV-1 capsids through a cyclophilin A domain, which has a well-defined binding site and higher affinity ( K D of ∼10 μM) for isolated capsid subunits. Therefore, it has been argued that TRIMCyp proteins have dispensed with the need for higher-order assembly to function as antiviral factors. Here, we show that, consistent with its high degree of sequence similarity with TRIM5α, the TRIMCyp B-box 2 domain shares the same ability to self-associate and facilitate assembly of a TRIMCyp hexagonal lattice that can wrap about the HIV-1 capsid. We also show that under stringent experimental conditions, TRIMCyp-mediated restriction of HIV-1 is indeed dependent on higher-order assembly. Both forms of TRIM5 therefore use the same mechanism of avidity-driven capsid pattern recognition. IMPORTANCE Rhesus macaques and owl monkeys are highly resistant to HIV-1 infection due to the activity of TRIM5 restriction factors. The rhesus macaque TRIM5α protein blocks HIV-1 through a mechanism that requires self-assembly of a hexagonal TRIM5α lattice around the invading viral core. Lattice assembly amplifies very weak interactions between the TRIM5α SPRY domain and the HIV-1 capsid. Assembly also promotes dimerization of the TRIM5α RING E3 ligase domain, resulting in synthesis of polyubiquitin chains that mediate downstream steps of restriction. In contrast to rhesus TRIM5α, the owl monkey TRIM5 homolog, TRIMCyp, binds isolated HIV-1 CA subunits much more tightly through its cyclophilin A domain and therefore was thought to act independently of higher-order assembly. Here, we show that TRIMCyp shares the assembly properties of TRIM5α and that both forms of TRIM5 use the same mechanism of hexagonal lattice formation to promote viral recognition and restriction. Copyright © 2018 American Society for Microbiology.

Using Polarized Spectroscopy to Investigate Order in Thin-Films of Ionic Self-Assembled Materials Based on Azo-Dyes

PubMed Central

Ahmad, Mariam; Andersen, Frederik; Brend Bech, Ári; Bendixen, H. Krestian L.; Nawrocki, Patrick R.; Bloch, Anders J.; Bora, Ilkay; Bukhari, Tahreem A.; Bærentsen, Nicolai V.; Carstensen, Jens; Chima, Smeeah; Colberg, Helene; Dahm, Rasmus T.; Daniels, Joshua A.; Dinckan, Nermin; El Idrissi, Mohamed; Erlandsen, Ricci; Førster, Marc; Ghauri, Yasmin; Gold, Mikkel; Hansen, Andreas; Hansen, Kenn; Helmsøe-Zinck, Mathias; Henriksen, Mathias; Hoffmann, Sophus V.; Hyllested, Louise O. H.; Jensen, Casper; Kallenbach, Amalie S.; Kaur, Kirandip; Khan, Suheb R.; Kjær, Emil T. S.; Kristiansen, Bjørn; Langvad, Sylvester; Lund, Philip M.; Munk, Chastine F.; Møller, Theis; Nehme, Ola M. Z.; Nejrup, Mathilde Rove; Nexø, Louise; Nielsen, Simon Skødt Holm; Niemeier, Nicolai; Nikolajsen, Lasse V.; Nøhr, Peter C. T.; Skaarup Ovesen, Jacob; Paustian, Lucas; Pedersen, Adam S.; Petersen, Mathias K.; Poulsen, Camilla M.; Praeger-Jahnsen, Louis; Qureshi, L. Sonia; Schiermacher, Louise S.; Simris, Martin B.; Smith, Gorm; Smith, Heidi N.; Sonne, Alexander K.; Zenulovic, Marko R.; Winther Sørensen, Alma; Vogt, Emil; Væring, Andreas; Westermann, Jonas; Özcan, Sevin B.

2018-01-01

Three series of ionic self-assembled materials based on anionic azo-dyes and cationic benzalkonium surfactants were synthesized and thin films were prepared by spin-casting. These thin films appear isotropic when investigated with polarized optical microscopy, although they are highly anisotropic. Here, three series of homologous materials were studied to rationalize this observation. Investigating thin films of ordered molecular materials relies to a large extent on advanced experimental methods and large research infrastructure. A statement that in particular is true for thin films with nanoscopic order, where X-ray reflectometry, X-ray and neutron scattering, electron microscopy and atom force microscopy (AFM) has to be used to elucidate film morphology and the underlying molecular structure. Here, the thin films were investigated using AFM, optical microscopy and polarized absorption spectroscopy. It was shown that by using numerical method for treating the polarized absorption spectroscopy data, the molecular structure can be elucidated. Further, it was shown that polarized optical spectroscopy is a general tool that allows determination of the molecular order in thin films. Finally, it was found that full control of thermal history and rigorous control of the ionic self-assembly conditions are required to reproducibly make these materials of high nanoscopic order. Similarly, the conditions for spin-casting are shown to be determining for the overall thin film morphology, while molecular order is maintained. PMID:29462883

Using Polarized Spectroscopy to Investigate Order in Thin-Films of Ionic Self-Assembled Materials Based on Azo-Dyes.

PubMed

Kühnel, Miguel R Carro-Temboury Martin; Ahmad, Mariam; Andersen, Frederik; Bech, Ári Brend; Bendixen, H Krestian L; Nawrocki, Patrick R; Bloch, Anders J; Bora, Ilkay; Bukhari, Tahreem A; Bærentsen, Nicolai V; Carstensen, Jens; Chima, Smeeah; Colberg, Helene; Dahm, Rasmus T; Daniels, Joshua A; Dinckan, Nermin; Idrissi, Mohamed El; Erlandsen, Ricci; Førster, Marc; Ghauri, Yasmin; Gold, Mikkel; Hansen, Andreas; Hansen, Kenn; Helmsøe-Zinck, Mathias; Henriksen, Mathias; Hoffmann, Sophus V; Hyllested, Louise O H; Jensen, Casper; Kallenbach, Amalie S; Kaur, Kirandip; Khan, Suheb R; Kjær, Emil T S; Kristiansen, Bjørn; Langvad, Sylvester; Lund, Philip M; Munk, Chastine F; Møller, Theis; Nehme, Ola M Z; Nejrup, Mathilde Rove; Nexø, Louise; Nielsen, Simon Skødt Holm; Niemeier, Nicolai; Nikolajsen, Lasse V; Nøhr, Peter C T; Orlowski, Dominik B; Overgaard, Marc; Ovesen, Jacob Skaarup; Paustian, Lucas; Pedersen, Adam S; Petersen, Mathias K; Poulsen, Camilla M; Praeger-Jahnsen, Louis; Qureshi, L Sonia; Ree, Nicolai; Schiermacher, Louise S; Simris, Martin B; Smith, Gorm; Smith, Heidi N; Sonne, Alexander K; Zenulovic, Marko R; Sørensen, Alma Winther; Sørensen, Karina; Vogt, Emil; Væring, Andreas; Westermann, Jonas; Özcan, Sevin B; Sørensen, Thomas Just

2018-02-15

Three series of ionic self-assembled materials based on anionic azo-dyes and cationic benzalkonium surfactants were synthesized and thin films were prepared by spin-casting. These thin films appear isotropic when investigated with polarized optical microscopy, although they are highly anisotropic. Here, three series of homologous materials were studied to rationalize this observation. Investigating thin films of ordered molecular materials relies to a large extent on advanced experimental methods and large research infrastructure. A statement that in particular is true for thin films with nanoscopic order, where X-ray reflectometry, X-ray and neutron scattering, electron microscopy and atom force microscopy (AFM) has to be used to elucidate film morphology and the underlying molecular structure. Here, the thin films were investigated using AFM, optical microscopy and polarized absorption spectroscopy. It was shown that by using numerical method for treating the polarized absorption spectroscopy data, the molecular structure can be elucidated. Further, it was shown that polarized optical spectroscopy is a general tool that allows determination of the molecular order in thin films. Finally, it was found that full control of thermal history and rigorous control of the ionic self-assembly conditions are required to reproducibly make these materials of high nanoscopic order. Similarly, the conditions for spin-casting are shown to be determining for the overall thin film morphology, while molecular order is maintained.

Programmable assembly of nanoarchitectures using genetically engineered viruses.

PubMed

Huang, Yu; Chiang, Chung-Yi; Lee, Soo Kwan; Gao, Yan; Hu, Evelyn L; De Yoreo, James; Belcher, Angela M

2005-07-01

Biological systems possess inherent molecular recognition and self-assembly capabilities and are attractive templates for constructing complex material structures with molecular precision. Here we report the assembly of various nanoachitectures including nanoparticle arrays, hetero-nanoparticle architectures, and nanowires utilizing highly engineered M13 bacteriophage as templates. The genome of M13 phage can be rationally engineered to produce viral particles with distinct substrate-specific peptides expressed on the filamentous capsid and the ends, providing a generic template for programmable assembly of complex nanostructures. Phage clones with gold-binding motifs on the capsid and streptavidin-binding motifs at one end are created and used to assemble Au and CdSe nanocrytals into ordered one-dimensional arrays and more complex geometries. Initial studies show such nanoparticle arrays can further function as templates to nucleate highly conductive nanowires that are important for addressing/interconnecting individual nanostructures.

High Order in a Self-Assembled Iridium(III) Complex Gelator Towards Nanostructured IrO2 Thin Films.

PubMed

Scarpelli, Francesca; Ionescu, Andreea; Aiello, Iolinda; La Deda, Massimo; Crispini, Alessandra; Ghedini, Mauro; Brunelli, Elvira; Sesti, Settimio; Godbert, Nicolas

2017-10-18

The preparation and characterization of a new metallogelator based on the Ir III discrete cyclometalated complex [(ppy) 2 Ir(bpy)](CH 3 CH 2 OCH 2 CO 2 ) are reported, where H(ppy) is 2-phenylpiridine and bpy is 2,2'-bipyridine, which is used as an ancillary ligand. The compound is able to self-assemble in water in a range of concentrations between 3 % and 6 % w/w, creating a luminescent ordered supramolecular gel. The gel and xerogel architectures were investigated through polarized optical microscopy (POM), SEM and TEM microscopies coupled with powder X-ray diffraction. The gel supramolecular organization is characterized by columnar tetragonal strands, already present at high dilution conditions, of cations surrounded by counteranions. These strands, in turn, are self-assembled in an oblique columnar cell upon gelification. The xerogel thin films obtained upon complete dehydration maintained the gel supramolecular order and can be used as a precursor for the preparation of nanostructured IrO 2 thin films. © 2017 Wiley-VCH Verlag GmbH & Co. KGaA, Weinheim.

Charge Stabilized Crystalline Colloidal Arrays As Templates For Fabrication of Non-Close-Packed Inverted Photonic Crystals

PubMed Central

Bohn, Justin J.; Ben-Moshe, Matti; Tikhonov, Alexander; Qu, Dan; Lamont, Daniel N.

2010-01-01

We developed a straightforward method to form non close-packed highly ordered fcc direct and inverse opal silica photonic crystals. We utilize an electrostatically self assembled crystalline colloidal array (CCA) template formed by monodisperse, highly charged polystyrene particles. We then polymerize a hydrogel around the CCA (PCCA) and condense the silica to form a highly ordered silica impregnated (siPCCA) photonic crystal. Heating at 450 °C removes the organic polymer leaving a silica inverse opal structure. By altering the colloidal particle concentration we independently control the particle spacing and the wall thickness of the inverse opal photonic crystals. This allows us to control the optical dielectric constant modulation in order to optimize the diffraction; the dielectric constant modulation is controlled independently of the photonic crystal periodicity. These fcc photonic crystals are better ordered than typical close-packed photonic crystals because their self assembly utilizes soft electrostatic repulsive potentials. We show that colloidal particle size and charge polydispersity has modest impact on ordering, in contrast to that for close-packed crystals. PMID:20163800

Role of Histone Acetylation in the Assembly and Modulation of Chromatin Structures

PubMed Central

Annunziato, Anthony T.; Hansen, Jeffrey C.

2000-01-01

The acetylation of the core histone N-terminal “tail” domains is now recognized as a highly conserved mechanism for regulating chromatin functional states. The following article examines possible roles of acetylation in two critically important cellular processes: replication-coupled nucleosome assembly, and reversible transitions in chromatin higher order structure. After a description of the acetylation of newly synthesized histones, and of the likely acetyltransferases involved, an overview of histone octamer assembly is presented. Our current understanding of the factors thought to assemble chromatin in vivo is then described. Genetic and biochemical investigations of the function the histone tails, and their acetylation, in nucleosome assembly are detailed, followed by an analysis of the importance of histone deacetylation in the maturation of newly replicated chromatin. In the final section the involvement of the histone tail domains in chromatin higher order structures is addressed, along with the role of histone acetylation in chromatin folding. Suggestions for future research are offered in the concluding remarks. PMID:11097424

Development of an Advanced Recycle Filter Tank Assembly for the ISS Urine Processor Assembly

NASA Technical Reports Server (NTRS)

Link, Dwight E., Jr.; Carter, Donald Layne; Higbie, Scott

2010-01-01

Recovering water from urine is a process that is critical to supporting larger crews for extended missions aboard the International Space Station. Urine is collected, preserved, and stored for processing into water and a concentrated brine solution that is highly toxic and must be contained to avoid exposure to the crew. The brine solution is collected in an accumulator tank, called a Recycle Filter Tank Assembly (RFTA) that must be replaced monthly and disposed in order to continue urine processing operations. In order to reduce resupply requirements, a new accumulator tank is being developed that can be emptied on orbit into existing ISS waste tanks. The new tank, called the Advanced Recycle Filter Tank Assembly (ARFTA) is a metal bellows tank that is designed to collect concentrated brine solution and empty by applying pressure to the bellows. This paper discusses the requirements and design of the ARFTA as well as integration into the urine processor assembly.

Reference quality assembly of the 3.5-Gb genome of Capsicum annuum from a single linked-read library.

PubMed

Hulse-Kemp, Amanda M; Maheshwari, Shamoni; Stoffel, Kevin; Hill, Theresa A; Jaffe, David; Williams, Stephen R; Weisenfeld, Neil; Ramakrishnan, Srividya; Kumar, Vijay; Shah, Preyas; Schatz, Michael C; Church, Deanna M; Van Deynze, Allen

2018-01-01

Linked-Read sequencing technology has recently been employed successfully for de novo assembly of human genomes, however, the utility of this technology for complex plant genomes is unproven. We evaluated the technology for this purpose by sequencing the 3.5-gigabase (Gb) diploid pepper ( Capsicum annuum ) genome with a single Linked-Read library. Plant genomes, including pepper, are characterized by long, highly similar repetitive sequences. Accordingly, significant effort is used to ensure that the sequenced plant is highly homozygous and the resulting assembly is a haploid consensus. With a phased assembly approach, we targeted a heterozygous F 1 derived from a wide cross to assess the ability to derive both haplotypes and characterize a pungency gene with a large insertion/deletion. The Supernova software generated a highly ordered, more contiguous sequence assembly than all currently available C. annuum reference genomes. Over 83% of the final assembly was anchored and oriented using four publicly available  de novo linkage maps. A comparison of the annotation of conserved eukaryotic genes indicated the completeness of assembly. The validity of the phased assembly is further demonstrated with the complete recovery of both 2.5-Kb insertion/deletion haplotypes of the PUN1 locus in the F 1 sample that represents pungent and nonpungent peppers, as well as nearly full recovery of the BUSCO2 gene set within each of the two haplotypes. The most contiguous pepper genome assembly to date has been generated which demonstrates that Linked-Read library technology provides a tool to de novo assemble complex highly repetitive heterozygous plant genomes. This technology can provide an opportunity to cost-effectively develop high-quality genome assemblies for other complex plants and compare structural and gene differences through accurate haplotype reconstruction.

Hierarchical and Helical Self-assembly of ADP-ribosyl Cyclase into Large-scale Protein Microtubes

PubMed Central

Liu, Qun; Kriksunov, Irina A.; Wang, Zhongwu; Graeff, Richard; Lee, Hon Cheung; Hao, Quan

2013-01-01

Proteins are macromolecules with characteristic structures and biological functions. It is extremely challenging to obtain protein microtube structures through self-assembly as proteins are very complex and flexible. Here we present a strategy showing how a specific protein, ADP-ribosyl cyclase, helically self-assembles from monomers into hexagonal nanochains and further to highly ordered crystalline microtubes. The structures of protein nanochains and consequently self-assembled superlattice were determined by X-ray crystallography at 4.5 Å resolution and imaged by Scanning Electron Microscopy. The protein initially forms into dimers that have a fixed size of 5.6 nm, and then, helically self-assembles into 35.6 nm long hexagonal nanochains. One such nanochain consists of six dimers (12 monomers) that stack in order by a pseudo P61 screw axis. Seven nanochains produce a series of largescale assemblies, nanorods, forming the building blocks for microrods. A proposed aging process of microrods results in the formation of hollow microstructures. Synthesis and characterization of large scale self-assembled protein microtubes may pave a new pathway, capable of not only understanding the self-assembly dynamics of biological materials, but also directing design and fabrication of multifunctional nanobuilding blocks with particular applications in biomedical engineering. PMID:18956900

ABACAS: algorithm-based automatic contiguation of assembled sequences

PubMed Central

Assefa, Samuel; Keane, Thomas M.; Otto, Thomas D.; Newbold, Chris; Berriman, Matthew

2009-01-01

Summary: Due to the availability of new sequencing technologies, we are now increasingly interested in sequencing closely related strains of existing finished genomes. Recently a number of de novo and mapping-based assemblers have been developed to produce high quality draft genomes from new sequencing technology reads. New tools are necessary to take contigs from a draft assembly through to a fully contiguated genome sequence. ABACAS is intended as a tool to rapidly contiguate (align, order, orientate), visualize and design primers to close gaps on shotgun assembled contigs based on a reference sequence. The input to ABACAS is a set of contigs which will be aligned to the reference genome, ordered and orientated, visualized in the ACT comparative browser, and optimal primer sequences are automatically generated. Availability and Implementation: ABACAS is implemented in Perl and is freely available for download from http://abacas.sourceforge.net Contact: sa4@sanger.ac.uk PMID:19497936

A microsphere assembly method with laser microwelding for fabrication of three-dimensional periodic structures

NASA Astrophysics Data System (ADS)

Takagi, Kenta; Omote, Masanori; Kawasaki, Akira

2010-03-01

The orderly build-up of monosized microspheres with sizes of hundreds of micrometres enabled us to develop three-dimensional (3D) photonic crystal devices for terahertz electromagnetic waves. We designed and manufactured an original 3D particle assembly system capable of fabricating arbitrary periodic structures from these spherical particles. This method employs a pick-and-place assembling approach with robotic manipulation and interparticle laser microwelding in order to incorporate a contrivance for highly accurate arraying: an operation that compensates the size deviation of raw monosized particles. Pre-examination of particles of various materials revealed that interparticle laser welding must be achieved with local melting by suppressing heat diffusion from the welding area. By optimizing the assembly conditions, we succeeded in fabricating an accurate periodic structure with a diamond lattice from 400 µm polyethylene composite particles. This structure demonstrated a photonic bandgap in the terahertz frequency range.

Layer-by-layer self-assembly in the development of electrochemical energy conversion and storage devices from fuel cells to supercapacitors.

PubMed

Xiang, Yan; Lu, Shanfu; Jiang, San Ping

2012-11-07

As one of the most effective synthesis tools, layer-by-layer (LbL) self-assembly technology can provide a strong non-covalent integration and accurate assembly between homo- or hetero-phase compounds or oppositely charged polyelectrolytes, resulting in highly-ordered nanoscale structures or patterns with excellent functionalities and activities. It has been widely used in the developments of novel materials and nanostructures or patterns from nanotechnologies to medical fields. However, the application of LbL self-assembly in the development of highly efficient electrocatalysts, specific functionalized membranes for proton exchange membrane fuel cells (PEMFCs) and electrode materials for supercapacitors is a relatively new phenomenon. In this review, the application of LbL self-assembly in the development and synthesis of key materials of PEMFCs including polyelectrolyte multilayered proton-exchange membranes, methanol-blocking Nafion membranes, highly uniform and efficient Pt-based electrocatalysts, self-assembled polyelectrolyte functionalized carbon nanotubes (CNTs) and graphenes will be reviewed. The application of LbL self-assembly for the development of multilayer nanostructured materials for use in electrochemical supercapacitors will also be reviewed and discussed (250 references).

A component modes projection and assembly model reduction methodology for articulated, multi-flexible body structures

NASA Technical Reports Server (NTRS)

Lee, Allan Y.; Tsuha, Walter S.

1993-01-01

A two-stage model reduction methodology, combining the classical Component Mode Synthesis (CMS) method and the newly developed Enhanced Projection and Assembly (EP&A) method, is proposed in this research. The first stage of this methodology, called the COmponent Modes Projection and Assembly model REduction (COMPARE) method, involves the generation of CMS mode sets, such as the MacNeal-Rubin mode sets. These mode sets are then used to reduce the order of each component model in the Rayleigh-Ritz sense. The resultant component models are then combined to generate reduced-order system models at various system configurations. A composite mode set which retains important system modes at all system configurations is then selected from these reduced-order system models. In the second stage, the EP&A model reduction method is employed to reduce further the order of the system model generated in the first stage. The effectiveness of the COMPARE methodology has been successfully demonstrated on a high-order, finite-element model of the cruise-configured Galileo spacecraft.

Modeling the assembly order of multimeric heteroprotein complexes

PubMed Central

Esquivel-Rodriguez, Juan; Terashi, Genki; Christoffer, Charles; Shin, Woong-Hee

2018-01-01

Protein-protein interactions are the cornerstone of numerous biological processes. Although an increasing number of protein complex structures have been determined using experimental methods, relatively fewer studies have been performed to determine the assembly order of complexes. In addition to the insights into the molecular mechanisms of biological function provided by the structure of a complex, knowing the assembly order is important for understanding the process of complex formation. Assembly order is also practically useful for constructing subcomplexes as a step toward solving the entire complex experimentally, designing artificial protein complexes, and developing drugs that interrupt a critical step in the complex assembly. There are several experimental methods for determining the assembly order of complexes; however, these techniques are resource-intensive. Here, we present a computational method that predicts the assembly order of protein complexes by building the complex structure. The method, named Path-LzerD, uses a multimeric protein docking algorithm that assembles a protein complex structure from individual subunit structures and predicts assembly order by observing the simulated assembly process of the complex. Benchmarked on a dataset of complexes with experimental evidence of assembly order, Path-LZerD was successful in predicting the assembly pathway for the majority of the cases. Moreover, when compared with a simple approach that infers the assembly path from the buried surface area of subunits in the native complex, Path-LZerD has the strong advantage that it can be used for cases where the complex structure is not known. The path prediction accuracy decreased when starting from unbound monomers, particularly for larger complexes of five or more subunits, for which only a part of the assembly path was correctly identified. As the first method of its kind, Path-LZerD opens a new area of computational protein structure modeling and will be an indispensable approach for studying protein complexes. PMID:29329283

Modeling the assembly order of multimeric heteroprotein complexes.

PubMed

Peterson, Lenna X; Togawa, Yoichiro; Esquivel-Rodriguez, Juan; Terashi, Genki; Christoffer, Charles; Roy, Amitava; Shin, Woong-Hee; Kihara, Daisuke

2018-01-01

Protein-protein interactions are the cornerstone of numerous biological processes. Although an increasing number of protein complex structures have been determined using experimental methods, relatively fewer studies have been performed to determine the assembly order of complexes. In addition to the insights into the molecular mechanisms of biological function provided by the structure of a complex, knowing the assembly order is important for understanding the process of complex formation. Assembly order is also practically useful for constructing subcomplexes as a step toward solving the entire complex experimentally, designing artificial protein complexes, and developing drugs that interrupt a critical step in the complex assembly. There are several experimental methods for determining the assembly order of complexes; however, these techniques are resource-intensive. Here, we present a computational method that predicts the assembly order of protein complexes by building the complex structure. The method, named Path-LzerD, uses a multimeric protein docking algorithm that assembles a protein complex structure from individual subunit structures and predicts assembly order by observing the simulated assembly process of the complex. Benchmarked on a dataset of complexes with experimental evidence of assembly order, Path-LZerD was successful in predicting the assembly pathway for the majority of the cases. Moreover, when compared with a simple approach that infers the assembly path from the buried surface area of subunits in the native complex, Path-LZerD has the strong advantage that it can be used for cases where the complex structure is not known. The path prediction accuracy decreased when starting from unbound monomers, particularly for larger complexes of five or more subunits, for which only a part of the assembly path was correctly identified. As the first method of its kind, Path-LZerD opens a new area of computational protein structure modeling and will be an indispensable approach for studying protein complexes.

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

Surface-Directed Assembly of Sequence-Defined Synthetic Polymers into Networks of Hexagonally Patterned Nanoribbons with Controlled Functionalities

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

Chen, Chun-Long; Zuckermann, Ronald N.; DeYoreo, James J.

The exquisite self-assembly of proteins and peptides in nature into highly ordered functional materials has inspired innovative approaches to biomimetic materials design and synthesis. Here we report the assembly of peptoids—a class of highly stable sequence-defined synthetic polymers—into biomimetic materials on mica surfaces. The assembling 12-mer peptoid contains alternating acidic and aromatic residues, and the presence of Ca2+ cations creates peptoid-peptoid and peptoid-mica interactions that drive assembly. In situ atomic force microscopy (AFM) shows that peptoids first assemble into discrete nanoparticles, these particles then transform into hexagonally-patterned nanoribbons on mica surfaces. AFM-based dynamic force spectroscopy (DFS) studies show that peptoid-micamore » interactions are much stronger than peptoidpeptoid interactions in the presence of Ca2+, illuminating the physical parameters that drive peptoid assembly. We further demonstrate the display of functional groups at the N-terminus of assembling peptoid sequence to produce biomimetic materials with similar hierarchical structures. This research demonstrates that surface-directed peptoid assembly can be used as a robust platform to develop biomimetic coating materials for applications.« less

Self-Assembly of Heterogeneously Shaped Nanoparticles into Plasmonic Metamolecules on DNA Origami.

PubMed

Liu, Wenyan; Li, Ling; Yang, Shuo; Gao, Jie; Wang, Risheng

2017-10-12

Fabrication of plasmonic metamolecules (PMs) with rationally designed complexity is one of the major goals of nanotechnology. Most self-assembled PMs, however, have been constructed using single-component systems. The corresponding plasmonic assemblies still suffer from the lack of complexity, which is required to achieve a high degree of functionality. Here, we report a general applicable strategy that can realize a series of high-ordered hetero-PMs using bottom-up DNA self-assembly. DNA-functionalized differently shaped nanoparticles were deliberately arranged in prescribed positions on 3D triangular DNA origami frames to form various hetero-PMs. Importantly, we showed that the optical properties of assembled PMs could be facially tuned by selectively regulating the position of each component. This method provides a promising pathway for manufacturing more complex and advanced materials by integrating diverse nanocomponents with particular properties. © 2017 Wiley-VCH Verlag GmbH & Co. KGaA, Weinheim.

Rapid Growth of Acetylated Aβ(16-20) into Macroscopic Crystals.

PubMed

Bortolini, Christian; Klausen, Lasse Hyldgaard; Hoffmann, Søren Vrønning; Jones, Nykola C; Saadeh, Daniela; Wang, Zegao; Knowles, Tuomas P J; Dong, Mingdong

2018-05-22

Aberrant assembly of the amyloid-β (Aβ) is responsible for the development of Alzheimer's disease, but can also be exploited to obtain highly functional biomaterials. The short Aβ fragment, KLVFF (Aβ 16-20 ), is crucial for Aβ assembly and considered to be an Aβ aggregation inhibitor. Here, we show that acetylation of KLVFF turns it into an extremely fast self-assembling molecule, reaching macroscopic ( i.e., mm) size in seconds. We show that KLVFF is metastable and that the self-assembly can be directed toward a crystalline or fibrillar phase simply through chemical modification, via acetylation or amidation of the peptide. Amidated KLVFF can form amyloid fibrils; we observed folding events of such fibrils occurring in as little as 60 ms. The ability of single KLVFF molecules to rapidly assemble as highly ordered macroscopic structures makes it a promising candidate for applications as a rapid-forming templating material.

Self-Assembly Driven Aggregation-Induced Emission of Copper Nanoclusters: A Novel Technology for Lighting.

PubMed

Liu, Yi; Yao, Dong; Zhang, Hao

2018-04-18

Because of the specific properties including HOMO-LUMO electronic transition, size-dependent fluorescent emission, and intense light absorption, metal nanoclusters (NCs) have been considered to be one of the most competitive color conversion materials in light-emitting diodes (LEDs). However, the monotonous emission color and the low emission stability and intensity of individual metal NCs strongly limit their universal application. Inspired by the concept of "aggregation-induced emission" (AIE), the utilization of highly ordered metal NC assemblies opens a door to resolve these problems. After self-assembly, the emission stability and intensity of metal NC assemblies are enhanced. At the same time, the emission color of metal NC assemblies become tunable. We termed this process as self-assembly driven AIE of metal NCs. In this review, we use Cu NCs as the example to convey the concept that the compact and ordered arrangement can efficiently improve the metal NCs' emission stability, tunability, and intensity. We first introduce the synthesis of 2D Cu NC self-assemblies and their emissions. We further summarize some of the factors that can affect the emissions of 2D Cu NC self-assemblies. We then discuss the utilization of 2D Cu NC self-assemblies as color conversion materials for LEDs. At last, we outline current challenges and our perspectives on the development of this area.

Large surface-enhanced Raman scattering from self-assembled gold nanosphere monolayers

NASA Astrophysics Data System (ADS)

Fontana, Jake; Livenere, John; Bezares, Francisco J.; Caldwell, Joshua D.; Rendell, Ronald; Ratna, Banahalli R.

2013-05-01

We demonstrate an average surface-enhanced Raman scattering enhancement on the order of 108 from benzenethiol molecules using self-assembled, macroscopic, and tunable gold nanosphere monolayers on non-templated substrates. The self-assembly of the nanosphere monolayers uses a simple and efficient technique that allows for the creation of a high-density, chemically functionalized gold nanosphere monolayers with enhancement factors comparable to those produced using top-down fabrication techniques. These films may provide an approach for the future development of portable chemical/biological sensors.

Tuning peptide self-assembly by an in-tether chiral center

PubMed Central

Hu, Kuan; Xiong, Wei; Li, Hu; Zhang, Pei-Yu; Yin, Feng; Zhang, Qianling; Jiang, Fan; Li, Zigang

2018-01-01

The self-assembly of peptides into ordered nanostructures is important for understanding both peptide molecular interactions and nanotechnological applications. However, because of the complexity and various self-assembling pathways of peptide molecules, design of self-assembling helical peptides with high controllability and tunability is challenging. We report a new self-assembling mode that uses in-tether chiral center-induced helical peptides as a platform for tunable peptide self-assembly with good controllability. It was found that self-assembling behavior was governed by in-tether substitutional groups, where chirality determined the formation of helical structures and aromaticity provided the driving force for self-assembly. Both factors were essential for peptide self-assembly to occur. Experiments and theoretical calculations indicate long-range crystal-like packing in the self-assembly, which was stabilized by a synergy of interpeptide π-π and π-sulfur interactions and hydrogen bond networks. In addition, the self-assembled peptide nanomaterials were demonstrated to be promising candidate materials for applications in biocompatible electrochemical supercapacitors.

Improving draft genome contiguity with reference-derived in silico mate-pair libraries.

PubMed

Grau, José Horacio; Hackl, Thomas; Koepfli, Klaus-Peter; Hofreiter, Michael

2018-05-01

Contiguous genome assemblies are a highly valued biological resource because of the higher number of completely annotated genes and genomic elements that are usable compared to fragmented draft genomes. Nonetheless, contiguity is difficult to obtain if only low coverage data and/or only distantly related reference genome assemblies are available. In order to improve genome contiguity, we have developed Cross-Species Scaffolding-a new pipeline that imports long-range distance information directly into the de novo assembly process by constructing mate-pair libraries in silico. We show how genome assembly metrics and gene prediction dramatically improve with our pipeline by assembling two primate genomes solely based on ∼30x coverage of shotgun sequencing data.

Self-assembly of conjugated oligomers and polymers at the interface: structure and properties.

PubMed

Xu, Lirong; Yang, Liu; Lei, Shengbin

2012-08-07

In this review, we give a brief account on the recent scanning tunneling microscopy investigation of interfacial structures and properties of π-conjugated semiconducting oligomers and polymers, either at the solid-air (including solid-vacuum) or at the solid-liquid interface. The structural aspects of the self-assembly of both oligomers and polymers are highlighted. Conjugated oligomers can form well ordered supramolecular assemblies either at the air-solid or liquid-solid interface, thanks to the relatively high mobility and structural uniformity in comparison with polymers. The backbone structure, substitution of side chains and functional groups can affect the assembling behavior significantly, which offers the opportunity to tune the supramolecular structure of these conjugated oligomers at the interface. For conjugated polymers, the large molecular weight limits the mobility on the surface and the distribution in size also prevents the formation of long range ordered supramolecular assembly. The submolecular resolution obtained on the assembling monolayers enables a detailed investigation of the chain folding at the interface, both the structural details and the effect on electronic properties. Besides the ability in studying the assembling structures at the interfaces, STM also provides a reasonable way to evaluate the distribution of the molecular weight of conjugated polymers by statistic of the contour length of the adsorbed polymer chains. Both conjugated oligomers and polymers can form composite assemblies with other materials. The ordered assembly of oligomers can act as a template to controllably disperse other molecules such as coronene or fullerene. These investigations open a new avenue to fine tune the assembling structure at the interface and in turn the properties of the composite materials. To summarize scanning tunneling microscopy has demonstrated its surprising ability in the investigation of the assembling structures and properties of conjugated oligomers and polymers. The information obtained could benefit the understanding of the elements affecting the film morphology and helps the optimization of device performance.

Using optical mapping data for the improvement of vertebrate genome assemblies.

PubMed

Howe, Kerstin; Wood, Jonathan M D

2015-01-01

Optical mapping is a technology that gathers long-range information on genome sequences similar to ordered restriction digest maps. Because it is not subject to cloning, amplification, hybridisation or sequencing bias, it is ideally suited to the improvement of fragmented genome assemblies that can no longer be improved by classical methods. In addition, its low cost and rapid turnaround make it equally useful during the scaffolding process of de novo assembly from high throughput sequencing reads. We describe how optical mapping has been used in practice to produce high quality vertebrate genome assemblies. In particular, we detail the efforts undertaken by the Genome Reference Consortium (GRC), which maintains the reference genomes for human, mouse, zebrafish and chicken, and uses different optical mapping platforms for genome curation.

Ordering pathway of block copolymers under dynamic thermal gradients studied by in situ GISAXS

DOE PAGES

Samant, Saumil; Strzalka, Joseph; Yager, Kevin G.; ...

2016-10-31

Dynamic thermal gradient-based processes for directed self-assembly of block copolymer (BCP) thin films such as cold zone annealing (CZA) have demonstrated much potential for rapidly fabricating highly ordered patterns of BCP domains with facile orientation control. As a demonstration, hexagonally packed predominantly vertical cylindrical morphology, technologically relevant for applications such as membranes and lithography, was achieved in 1 μm thick cylinder-forming PS-b-PMMA (cBCP) films by applying sharp thermal gradients (CZA-Sharp) at optimum sample sweep rates. A thorough understanding of the molecular level mechanisms and pathways of the BCP ordering that occur during this CZA-S process is presented, useful to fullymore » exploit the potential of CZA-S for large-scale BCP-based device fabrication. To that end, we developed a customized CZA-S assembly to probe the dynamic structure evolution and ordering of the PS-b-PMMA cBCP film in situ as it undergoes the CZA-S process using the grazing incidence small-angle X-ray scattering (GISAXS) technique. Four distinct regimes of BCP ordering were observed within the gradient that include microphase separation from an “as cast” unordered state (Regime I), evolution of vertical cylinders under a thermally imposed strain gradient (Regime II), reorientation of a fraction of cylinders due to preferential substrate interactions (Regime III), and finally grain-coarsening on the cooling edge (Regime IV). The ordering pathway in the different regimes is further described within the framework of an energy landscape. A novel aspect of this study is the identification of a grain-coarsening regime on the cooling edge of the gradient, previously obscure in zone annealing studies of BCPs. Furthermore, such insights into the development of highly ordered BCP nanostructures under template-free thermal gradient fields can potentially have important ramifications in the field of BCP-directed self-assembly and self-assembling polymer systems more broadly.« less

Pathway-engineering for highly-aligned block copolymer arrays

DOE PAGES

Choo, Youngwoo; Majewski, Paweł W.; Fukuto, Masafumi; ...

2017-12-06

While kinetic aspects of self-assembly can hinder ordering, non-equilibirum effects can also be exploited to enforce a particular kind of order. We develop a pathway-engineering approach, using it to select a particular arrangement of a block copolymer cylinder phase.

Pathway-engineering for highly-aligned block copolymer arrays

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

Choo, Youngwoo; Majewski, Paweł W.; Fukuto, Masafumi

While kinetic aspects of self-assembly can hinder ordering, non-equilibirum effects can also be exploited to enforce a particular kind of order. We develop a pathway-engineering approach, using it to select a particular arrangement of a block copolymer cylinder phase.

Fabrication of sophisticated two-dimensional organic nanoarchitectures thought hydrogen bond mediated molecular self assembly

NASA Astrophysics Data System (ADS)

Silly, Fabien

2012-02-01

Complex supramolecular two-dimensional (2D) networks are attracting considerable interest as highly ordered functional materials for applications in nanotechnology. The challenge consists in tailoring the ordering of one or more molecular species into specific architectures over an extended length scale with molecular precision. Highly organized supramolecular arrays can be obtained through self-assembly of complementary molecules which can interlock via intermolecular interactions. Molecules forming hydrogen bonds (H-bonds) are especially interesting building blocks for creating sophisticated organic architectures due to high selectivity and directionality of these bindings. We used scanning tunnelling microscopy to investigate at the atomic scale the formation of H-bonded 2D organic nanoarchitectures on surfaces. We mixed perylene derivatives having rectangular shape with melamine and DNA base having triangular and non symmetric shape respectively. We observe that molecule substituents play a key role in formation of the multicomponent H-bonded architectures. We show that the 2D self-assembly of these molecules can be tailored by adjusting the temperature and molecular ratio. We used these stimuli to successfully create numerous close-packed and porous 2D multicomponent structures.

Electrochemical Functionalization of Graphene at the Nanoscale with Self-Assembling Diazonium Salts.

PubMed

Xia, Zhenyuan; Leonardi, Francesca; Gobbi, Marco; Liu, Yi; Bellani, Vittorio; Liscio, Andrea; Kovtun, Alessandro; Li, Rongjin; Feng, Xinliang; Orgiu, Emanuele; Samorì, Paolo; Treossi, Emanuele; Palermo, Vincenzo

2016-07-26

We describe a fast and versatile method to functionalize high-quality graphene with organic molecules by exploiting the synergistic effect of supramolecular and covalent chemistry. With this goal, we designed and synthesized molecules comprising a long aliphatic chain and an aryl diazonium salt. Thanks to the long chain, these molecules physisorb from solution onto CVD graphene or bulk graphite, self-assembling in an ordered monolayer. The sample is successively transferred into an aqueous electrolyte, to block any reorganization or desorption of the monolayer. An electrochemical impulse is used to transform the diazonium group into a radical capable of grafting covalently to the substrate and transforming the physisorption into a covalent chemisorption. During covalent grafting in water, the molecules retain the ordered packing formed upon self-assembly. Our two-step approach is characterized by the independent control over the processes of immobilization of molecules on the substrate and their covalent tethering, enabling fast (t < 10 s) covalent functionalization of graphene. This strategy is highly versatile and works with many carbon-based materials including graphene deposited on silicon, plastic, and quartz as well as highly oriented pyrolytic graphite.

Creating Quasi Two-Dimensional Cluster-Assembled Materials through Self-Assembly of a Janus Polyoxometalate-Silsesquioxane Co-Cluster.

PubMed

Wu, Han; Zhang, Yu-Qi; Hu, Min-Biao; Ren, Li-Jun; Lin, Yue; Wang, Wei

2017-05-30

Clusters are an important class of nanoscale molecules or superatoms that exhibit an amazing diversity in structure, chemical composition, shape, and functionality. Assembling two types of clusters is creating emerging cluster-assembled materials (CAMs). In this paper, we report an effective approach to produce quasi two-dimensional (2D) CAMs of two types of spherelike clusters, polyhedral oligomeric silsesquioxanes (POSS), and polyoxometalates (POM). To avoid macrophase separation between the two clusters, they are covalently linked to form a POM-POSS cocluster with Janus characteristics and a dumbbell shape. This Janus characteristics enables the cocluster to self-assemble into diverse nanoaggregates, as conventional amphiphilic molecules and macromolecules do, in selective solvents. In our study, we obtained micelles, vesicles, nanosheets, and nanoribbons by tuning the n-hexane content in mixed solvents of acetone and n-hexane. Ordered packing of clusters in the nanosheets and nanoribbons were directly visualized using high-angle annular dark-field scanning transmission electron microscopy (HAADF-STEM) technique. We infer that the increase of packing order results in the vesicle-to-sheet transition and the change in packing mode causes the sheet-to-ribbon transitions. Our findings have verified the effectivity of creating quasi 2D cluster-assembled materials though the cocluster self-assembly as a new approach to produce novel CAMs.

Radiation hybrid maps of D-genome of Aegilops tauschii and their application in sequence assembly of large and complex plant genomes

USDA-ARS?s Scientific Manuscript database

The large and complex genome of bread wheat (Triticum aestivum L., ~17 Gb) requires high-resolution genome maps saturated with ordered markers to assist in anchoring and orienting BAC contigs/ sequence scaffolds for whole genome sequence assembly. Radiation hybrid (RH) mapping has proven to be an e...

Next-generation sequencing of mixed genomic DNA allows efficient assembly of rearranged mitochondrial genomes in Amolops chunganensis and Quasipaa boulengeri

PubMed Central

Yuan, Siqi; Zheng, Yuchi; Zeng, Xiaomao

2016-01-01

Recent improvements in next-generation sequencing (NGS) technologies can facilitate the obtainment of mitochondrial genomes. However, it is not clear whether NGS could be effectively used to reconstruct the mitogenome with high gene rearrangement. These high rearrangements would cause amplification failure, and/or assembly and alignment errors. Here, we choose two frogs with rearranged gene order, Amolops chunganensis and Quasipaa boulengeri, to test whether gene rearrangements affect the mitogenome assembly and alignment by using NGS. The mitogenomes with gene rearrangements are sequenced through Illumina MiSeq genomic sequencing and assembled effectively by Trinity v2.1.0 and SOAPdenovo2. Gene order and contents in the mitogenome of A. chunganensis and Q. boulengeri are typical neobatrachian pattern except for rearrangements at the position of “WANCY” tRNA genes cluster. Further, the mitogenome of Q. boulengeri is characterized with a tandem duplication of trnM. Moreover, we utilize 13 protein-coding genes of A. chunganensis, Q. boulengeri and other neobatrachians to reconstruct the phylogenetic tree for evaluating mitochondrial sequence authenticity of A. chunganensis and Q. boulengeri. In this work, we provide nearly complete mitochondrial genomes of A. chunganensis and Q. boulengeri. PMID:27994980

Mesoscopic self-organization of a self-assembled supramolecular rectangle on highly oriented pyrolytic graphite and Au(111) surfaces.

PubMed

Gong, Jian-Ru; Wan, Li-Jun; Yuan, Qun-Hui; Bai, Chun-Li; Jude, Hershel; Stang, Peter J

2005-01-25

A self-assembled supramolecular metallacyclic rectangle was investigated with scanning tunneling microscopy on highly oriented pyrolytic graphite and Au(111) surfaces. The rectangles spontaneously adsorb on both surfaces and self-organize into well ordered adlayers. On highly oriented pyrolytic graphite, the long edge of the rectangle stands on the surface, forming a 2D molecular network. In contrast, the face of the rectangle lays flat on the Au(111) surface, forming linear chains. The structures and intramolecular features obtained through high-resolution scanning tunneling microscopy imaging are discussed.

Self-assembly of polyelectrolyte surfactant complexes using large scale MD simulation

NASA Astrophysics Data System (ADS)

Goswami, Monojoy; Sumpter, Bobby

2014-03-01

Polyelectrolytes (PE) and surfactants are known to form interesting structures with varied properties in aqueous solutions. The morphological details of the PE-surfactant complexes depend on a combination of polymer backbone, electrostatic interactions and hydrophobic interactions. We study the self-assembly of cationic PE and anionic surfactants complexes in dilute condition. The importance of such complexes of PE with oppositely charged surfactants can be found in biological systems, such as immobilization of enzymes in polyelectrolyte complexes or nonspecific association of DNA with protein. Many useful properties of PE surfactant complexes come from the highly ordered structures of surfactant self-assembly inside the PE aggregate which has applications in industry. We do large scale molecular dynamics simulation using LAMMPS to understand the structure and dynamics of PE-surfactant systems. Our investigation shows highly ordered pearl-necklace structures that have been observed experimentally in biological systems. We investigate many different properties of PE-surfactant complexation for different parameter ranges that are useful for pharmaceutical, engineering and biological applications.

3D superstructures with an orthorhombic lattice assembled by colloidal PbS quantum dots.

PubMed

Ushakova, Elena V; Cherevkov, Sergei A; Litvin, Aleksandr P; Parfenov, Peter S; Kasatkin, Igor A; Fedorov, Anatoly V; Gun'ko, Yurii K; Baranov, Alexander V

2018-05-03

We report a new type of metamaterial comprising a highly ordered 3D network of 3-7 nm lead sulfide quantum dots self-assembled in an organic matrix formed by amphiphilic ligands (oleic acid molecules). The obtained 3D superstructures possess an orthorhombic lattice with the distance between the nanocrystals as large as 10-40 nm. Analysis of self-assembly and destruction of the superstructures in time performed by a SAXS technique shows that their morphology depends on the quantity of amphiphilic ligands and width of the quantum dot size and its distribution. Formation of the superstructures is discussed in terms of a model describing the lyotropic crystal formation by micelles from three-phase mixtures. The results show that the organic molecules possessing surfactant properties and capable of forming micelles with nanoparticles as a micelle core can be utilized as building blocks for the creation of novel metamaterials based on a highly ordered 3D network of semiconductors, metals or magnetic nanoparticles.

Characterization and kinetics of surface functionalization and binding of biologically and chemically significant molecules

NASA Astrophysics Data System (ADS)

Steiner, Rachel

The purpose of this project is to investigate intermolecular interactions of organic molecular assemblies. By understanding the structure and physical interactions in these assemblies, we gain insights into practical applications for nanoscale systems built upon these surface structures. It is possible for organic chemists to create many forms of modified organic molecules, functionalizing them with specific reactive end groups. Through surface functionalization, enabling covalent or highly associative binding, it is possible to create ordered molecular assemblies of these molecules. Scientists can study the nature of this structure and the intermolecular interactions through spectroscopic, optical, and scattering experiments. To understand the self-assembly process in molecular systems, we preliminarily created monolayer films on silica substrates with a variety of organic molecules. In particular, we functionalized silica substrates with hydroxyl groups and covalently bound acid chloride functionalized aromatic compounds, with and without an underlying adhesion layer of 3-aminopropyltriethoxysilane. We characterized the monolayer assemblies with ellipsometry, UV-vis absorption spectroscopy, FTIR spectroscopy, and fluorescence/photoemission spectroscopy, obtaining a quantitative measure of the molecular surface coverage. In order to understand the nature of these molecular assemblies, we also pursued an in-depth kinetic study to control and optimize the monolayer formation process. Through use of UV-vis spectroscopy, we determined that the monolayer formation can best be modeled with diffusion-limited Langmuir kinetics. Specifically, we concluded that for anthracene acid chloride in dichloromethane the average diffusion coefficient was 1.6x10-7 cm2/sec. Additionally, we find we are able to achieve surface coverages of approximately 2x1014 molecules/cm2. Having established the ability to create ordered molecular assemblies, through surface functionalization, enabling covalent or highly associative binding, we continued to explore the field of molecular assemblies by studying the binding and structure of molecules to carbon nanostructures. Previous studies have shown that alkyl side chains and aromatic compounds, such as pyrene, will bind non-covalently to the sidewalls of carbon nanotubes through pi-pi interactions. We explored functionalization of carbon nanotubes and graphene by using microscopy to examine the adsorption of biomolecules onto nanotube sidewalls and graphene.

Emerging Insights into Directed Assembly: Taking Examples from Nature to Design Synthetic Processes

NASA Astrophysics Data System (ADS)

de Pablo, Juan J.

There is considerable interest in controlling the assembly of polymeric material in order to create highly ordered materials for applications. Such materials are often trapped in metastable, non-equilibrium states, and the processes through which they assemble become an important aspect of the materials design strategy. An example is provided by di-block copolymer directed self-assembly, where a decade of work has shown that, through careful choice of process variables, it is possible to create ordered structures whose degree of perfection meets the constraints of commercial semiconductor manufacturing. As impactful as that work has been, it has focused on relatively simple materials neutral polymers, consisting of two or at most three blocks. Furthermore, the samples that have been produced have been limited to relatively thin films, and the assembly has been carried out on ideal, two-dimensional substrates. The question that arises now is whether one can translate those achievements to polymeric materials having a richer sequence, to monomers that include charges, to three-dimensional substrates, or to active systems that are in a permanent non-equilibrium state. Building on discoveries from the biophysics literature, this presentation will review recent work from our group and others that explains how nature has evolved to direct the assembly of nucleic acids into intricate, fully three-dimensional macroscopic functional materials that are not only active, but also responsive to external cues. We will discuss how principles from polymer physics serve to explain those assemblies, and how one might design a new generation of synthetic systems that incorporate some of those principles.

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.

Assembly of large-area, highly ordered, crack-free inverse opal films

PubMed Central

Hatton, Benjamin; Mishchenko, Lidiya; Davis, Stan; Sandhage, Kenneth H.; Aizenberg, Joanna

2010-01-01

Whereas considerable interest exists in self-assembly of well-ordered, porous “inverse opal” structures for optical, electronic, and (bio)chemical applications, uncontrolled defect formation has limited the scale-up and practicality of such approaches. Here we demonstrate a new method for assembling highly ordered, crack-free inverse opal films over a centimeter scale. Multilayered composite colloidal crystal films have been generated via evaporative deposition of polymeric colloidal spheres suspended within a hydrolyzed silicate sol-gel precursor solution. The coassembly of a sacrificial colloidal template with a matrix material avoids the need for liquid infiltration into the preassembled colloidal crystal and minimizes the associated cracking and inhomogeneities of the resulting inverse opal films. We discuss the underlying mechanisms that may account for the formation of large-area defect-free films, their unique preferential growth along the 〈110〉 direction and unusual fracture behavior. We demonstrate that this coassembly approach allows the fabrication of hierarchical structures not achievable by conventional methods, such as multilayered films and deposition onto patterned or curved surfaces. These robust SiO2 inverse opals can be transformed into various materials that retain the morphology and order of the original films, as exemplified by the reactive conversion into Si or TiO2 replicas. We show that colloidal coassembly is available for a range of organometallic sol-gel and polymer matrix precursors, and represents a simple, low-cost, scalable method for generating high-quality, chemically tailorable inverse opal films for a variety of applications. PMID:20484675

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.

Self assembled 12-tungstophosphoric acid-silica mesoporous nanocomposites as proton exchange membranes for direct alcohol fuel cells.

PubMed

Tang, Haolin; Pan, Mu; Jiang, San Ping

2011-05-21

A highly ordered inorganic electrolyte based on 12-tungstophosphoric acid (H(3)PW(12)O(40), abbreviated as HPW or PWA)-silica mesoporous nanocomposite was synthesized through a facile one-step self-assembly between the positively charged silica precursor and negatively charged PW(12)O(40)(3-) species. The self-assembled HPW-silica nanocomposites were characterized by small-angle XRD, TEM, nitrogen adsorption-desorption isotherms, ion exchange capacity, proton conductivity and solid-state (31)P NMR. The results show that highly ordered and uniform nanoarrays with long-range order are formed when the HPW content in the nanocomposites is equal to or lower than 25 wt%. The mesoporous structures/textures were clearly presented, with nanochannels of 3.2-3.5 nm in diameter. The (31)P NMR results indicates that there are (≡SiOH(2)(+))(H(2)PW(12)O(40)(-)) species in the HPW-silica nanocomposites. A HPW-silica (25/75 w/o) nanocomposite gave an activation energy of 13.0 kJ mol(-1) and proton conductivity of 0.076 S cm(-1) at 100 °C and 100 RH%, and an activation energy of 26.1 kJ mol(-1) and proton conductivity of 0.05 S cm(-1) at 200 °C with no external humidification. A fuel cell based on a 165 μm thick HPW-silica nanocomposite membrane achieved a maximum power output of 128.5 and 112.0 mW cm(-2) for methanol and ethanol fuels, respectively, at 200 °C. The high proton conductivity and good performance demonstrate the excellent water retention capability and great potential of the highly ordered HPW-silica mesoporous nanocomposites as high-temperature proton exchange membranes for direct alcohol fuel cells (DAFCs).

Self-assembly of mesoscopically ordered chromatic polydiacetylene/silica nanocomposites

NASA Technical Reports Server (NTRS)

Lu, Y.; Yang, Y.; Sellinger, A.; Lu, M.; Huang, J.; Fan, H.; Haddad, R.; Lopez, G.; Burns, A. R.; Sasaki, D. Y.;

High Resistivity Lipid Bilayers Assembled on Polyelectrolyte Multilayer Cushions: An Impedance Study.

PubMed

Diamanti, Eleftheria; Gregurec, Danijela; Rodríguez-Presa, María José; Gervasi, Claudio A; Azzaroni, Omar; Moya, Sergio E

2016-06-28

Supported membranes on top of polymer cushions are interesting models of biomembranes as cell membranes are supported on a polymer network of proteins and sugars. In this work lipid vesicles formed by a mixture of 30% 1,2-dioleoyl-sn-glycero-3-phosphocholine (DOPC) and 70% 1,2-dioleoyl-sn-glycero-3-phospho-l-serine (DOPS) are assembled on top of a polyelectrolyte multilayer (PEM) cushion of poly(allylamine hydrochloride) (PAH) and poly(styrene sodium sulfonate) (PSS). The assembly results in the formation of a bilayer on top of the PEM as proven by means of the quartz crystal microbalance with dissipation technique (QCM-D) and by cryo-transmission electron microscopy (cryo-TEM). The electrical properties of the bilayer are studied by electrochemical impedance spectroscopy (EIS). The bilayer supported on the PEMs shows a high resistance, on the order of 10(7) Ω cm(2), which is indicative of a continuous, dense bilayer. Such resistance is comparable with the resistance of black lipid membranes. This is the first time that such values are obtained for lipid bilayers supported on PEMs. The assembly of polyelectrolytes on top of a lipid bilayer decreases the resistance of the bilayer up to 2 orders of magnitude. The assembly of the polyelectrolytes on the lipids induces defects or pores in the bilayer which in turn prompts a decrease in the measured resistance.

Multicomponent self-assembly as a tool to harness new properties from peptides and proteins in material design.

PubMed

Okesola, Babatunde O; Mata, Alvaro

2018-05-21

Nature is enriched with a wide variety of complex, synergistic, and highly functional protein-based multicomponent assemblies. As such, nature has served as a source of inspiration for using multicomponent self-assembly as a platform to create highly ordered, complex, and dynamic protein and peptide-based nanostructures. Such an assembly system relies on the initial interaction of distinct individual building blocks leading to the formation of a complex that subsequently assembles into supramolecular architectures. This approach not only serves as a powerful platform for gaining insight into how proteins co-assemble in nature but also offers huge opportunities to harness new properties not inherent in the individual building blocks. In the past decades, various multicomponent self-assembly strategies have been used to extract synergistic properties from proteins and peptides. This review highlights the updates in the field of multicomponent self-assembly of proteins and peptides and summarizes various strategies, including covalent conjugation, ligand-receptor interactions, templated/directed assembly and non-specific co-assembly, for driving the self-assembly of multiple proteins and peptide-based building blocks into functional materials. In particular, we focus on peptide- or protein-containing multicomponent systems that, upon self-assembly, enable the emergence of new properties or phenomena. The ultimate goal of this review is to highlight the importance of multicomponent self-assembly in protein and peptide engineering, and to advocate its growth in the fields of materials science and nanotechnology.

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

Samant, Saumil; Strzalka, Joseph; Yager, Kevin G.

Dynamic thermal gradient-based processes for directed self-assembly of block copolymer (BCP) thin films such as cold zone annealing (CZA) have demonstrated much potential for rapidly fabricating highly ordered patterns of BCP domains with facile orientation control. As a demonstration, hexagonally packed predominantly vertical cylindrical morphology, technologically relevant for applications such as membranes and lithography, was achieved in 1 μm thick cylinder-forming PS-b-PMMA (cBCP) films by applying sharp thermal gradients (CZA-Sharp) at optimum sample sweep rates. A thorough understanding of the molecular level mechanisms and pathways of the BCP ordering that occur during this CZA-S process is presented, useful to fullymore » exploit the potential of CZA-S for large-scale BCP-based device fabrication. To that end, we developed a customized CZA-S assembly to probe the dynamic structure evolution and ordering of the PS-b-PMMA cBCP film in situ as it undergoes the CZA-S process using the grazing incidence small-angle X-ray scattering (GISAXS) technique. Four distinct regimes of BCP ordering were observed within the gradient that include microphase separation from an “as cast” unordered state (Regime I), evolution of vertical cylinders under a thermally imposed strain gradient (Regime II), reorientation of a fraction of cylinders due to preferential substrate interactions (Regime III), and finally grain-coarsening on the cooling edge (Regime IV). The ordering pathway in the different regimes is further described within the framework of an energy landscape. A novel aspect of this study is the identification of a grain-coarsening regime on the cooling edge of the gradient, previously obscure in zone annealing studies of BCPs. Furthermore, such insights into the development of highly ordered BCP nanostructures under template-free thermal gradient fields can potentially have important ramifications in the field of BCP-directed self-assembly and self-assembling polymer systems more broadly.« less

Toward high throughput optical metamaterial assemblies.

PubMed

Fontana, Jake; Ratna, Banahalli R

2015-11-01

Optical metamaterials have unique engineered optical properties. These properties arise from the careful organization of plasmonic elements. Transitioning these properties from laboratory experiments to functional materials may lead to disruptive technologies for controlling light. A significant issue impeding the realization of optical metamaterial devices is the need for robust and efficient assembly strategies to govern the order of the nanometer-sized elements while enabling macroscopic throughput. This mini-review critically highlights recent approaches and challenges in creating these artificial materials. As the ability to assemble optical metamaterials improves, new unforeseen opportunities may arise for revolutionary optical devices.

The development of alignment turning system for precision len cells

NASA Astrophysics Data System (ADS)

Huang, Chien-Yao; Ho, Cheng-Fang; Wang, Jung-Hsing; Chung, Chien-Kai; Chen, Jun-Cheng; Chang, Keng-Shou; Kuo, Ching-Hsiang; Hsu, Wei-Yao; Chen, Fong-Zhi

2017-08-01

In general, the drop-in and cell-mounted assembly are used for standard and high performance optical system respectively. The optical performance is limited by the residual centration error and position accuracy of the conventional assembly. Recently, the poker chip assembly with high precision lens barrels that can overcome the limitation of conventional assembly is widely applied to ultra-high performance optical system. ITRC also develops the poker chip assembly solution for high numerical aperture objective lenses and lithography projection lenses. In order to achieve high precision lens cell for poker chip assembly, an alignment turning system (ATS) is developed. The ATS includes measurement, alignment and turning modules. The measurement module including a non-contact displacement sensor and an autocollimator can measure centration errors of the top and the bottom surface of a lens respectively. The alignment module comprising tilt and translation stages can align the optical axis of the lens to the rotating axis of the vertical lathe. The key specifications of the ATS are maximum lens diameter, 400mm, and radial and axial runout of the rotary table < 2 μm. The cutting performances of the ATS are surface roughness Ra < 1 μm, flatness < 2 μm, and parallelism < 5 μm. After measurement, alignment and turning processes on our ATS, the centration error of a lens cell with 200mm in diameter can be controlled in 10 arcsec. This paper also presents the thermal expansion of the hydrostatic rotating table. A poker chip assembly lens cell with three sub-cells is accomplished with average transmission centration error in 12.45 arcsec by fresh technicians. The results show that ATS can achieve high assembly efficiency for precision optical systems.

Fabrication of Si3N4 nanowire membranes: free standing disordered nanopapers and aligned nanowire assemblies

NASA Astrophysics Data System (ADS)

Liu, Haitao; Fang, Minghao; Huang, Zhaohui; Huang, Juntong; Liu, Yan-gai; Wu, Xiaowen

2016-08-01

Herein, ultralong silicon nitride nanowires were synthesized via a chemical vapor deposition method by using the low-cost quartz and silicon powder as raw materials. Simple processes were used for the fabrication of disordered and ordered nanowire membranes of pure silicon nitride nanowires. The nanowires in the disordered nanopapers are intertwined with each other to form a paper-like structure which exhibit excellent flame retardancy and mechanical properties. Fourier-transform infrared spectroscopy and thermal gravity analysis were employed to characterize the refractory performance of the disordered nanopapers. Highly ordered nanowire membranes were also assembled through a three-phase assembly approach which make the Si3N4 nanowires have potential use in textured ceramics and semiconductor field. Moreover, the surface nanowires can also be modified to be hydrophobic; this characteristic make the as-prepared nanowires have the potential to be assembled by the more effective Langmuir-Blodgett method and also make the disordered nanopapers possess a super-hydrophobic surface.

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.

Crystal structure of a small heat-shock protein from Xylella fastidiosa reveals a distinct high-order structure.

PubMed

Fonseca, Emanuella Maria Barreto; Scorsato, Valéria; Dos Santos, Marcelo Leite; Júnior, Atilio Tomazini; Tada, Susely Ferraz Siqueira; Dos Santos, Clelton Aparecido; de Toledo, Marcelo Augusto Szymanski; de Souza, Anete Pereira; Polikarpov, Igor; Aparicio, Ricardo

2017-04-01

Citrus variegated chlorosis is a disease that attacks economically important citrus plantations and is caused by the plant-pathogenic bacterium Xylella fastidiosa. In this work, the structure of a small heat-shock protein from X. fastidiosa (XfsHSP17.9) is reported. The high-order structures of small heat-shock proteins from other organisms are arranged in the forms of double-disc, hollow-sphere or spherical assemblies. Unexpectedly, the structure reported here reveals a high-order architecture forming a nearly square cavity.

Nanocrystalline Precursors for the Co-Assembly of Crack-Free Metal Oxide Inverse Opals.

PubMed

Phillips, Katherine R; Shirman, Tanya; Shirman, Elijah; Shneidman, Anna V; Kay, Theresa M; Aizenberg, Joanna

2018-05-01

Inorganic microstructured materials are ubiquitous in nature. However, their formation in artificial self-assembly systems is challenging as it involves a complex interplay of competing forces during and after assembly. For example, colloidal assembly requires fine-tuning of factors such as the size and surface charge of the particles and electrolyte strength of the solvent to enable successful self-assembly and minimize crack formation. Co-assembly of templating colloidal particles together with a sol-gel matrix precursor material helps to release stresses that accumulate during drying and solidification, as previously shown for the formation of high-quality inverse opal (IO) films out of amorphous silica. Expanding this methodology to crystalline materials would result in microscale architectures with enhanced photonic, electronic, and catalytic properties. This work describes tailoring the crystallinity of metal oxide precursors that enable the formation of highly ordered, large-area (mm 2 ) crack-free titania, zirconia, and alumina IO films. The same bioinspired approach can be applied to other crystalline materials as well as structures beyond IOs. © 2018 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Toward tunable doping in graphene FETs by molecular self-assembled monolayers

NASA Astrophysics Data System (ADS)

Li, Bing; Klekachev, Alexander V.; Cantoro, Mirco; Huyghebaert, Cedric; Stesmans, André; Asselberghs, Inge; de Gendt, Stefan; de Feyter, Steven

2013-09-01

In this paper, we report the formation of self-assembled monolayers (SAMs) of oleylamine (OA) on highly oriented pyrolytic graphite (HOPG) and graphene surfaces and demonstrate the potential of using such organic SAMs to tailor the electronic properties of graphene. Molecular resolution Atomic Force Microscopy (AFM) and Scanning Tunneling Microscopy (STM) images reveal the detailed molecular ordering. The electrical measurements show that OA strongly interacts with graphene leading to n-doping effects in graphene devices. The doping levels are tunable by varying the OA deposition conditions. Importantly, neither hole nor electron mobilities are decreased by the OA modification. As a benefit from this noncovalent modification strategy, the pristine characteristics of the device are recoverable upon OA removal. From this study, one can envision the possibility to correlate the graphene-based device performance with the molecular structure and supramolecular ordering of the organic dopant.In this paper, we report the formation of self-assembled monolayers (SAMs) of oleylamine (OA) on highly oriented pyrolytic graphite (HOPG) and graphene surfaces and demonstrate the potential of using such organic SAMs to tailor the electronic properties of graphene. Molecular resolution Atomic Force Microscopy (AFM) and Scanning Tunneling Microscopy (STM) images reveal the detailed molecular ordering. The electrical measurements show that OA strongly interacts with graphene leading to n-doping effects in graphene devices. The doping levels are tunable by varying the OA deposition conditions. Importantly, neither hole nor electron mobilities are decreased by the OA modification. As a benefit from this noncovalent modification strategy, the pristine characteristics of the device are recoverable upon OA removal. From this study, one can envision the possibility to correlate the graphene-based device performance with the molecular structure and supramolecular ordering of the organic dopant. Electronic supplementary information (ESI) available: AFM images of self-assembled monolayers of OA on HOPG; AFM height image of the graphene surface on a SiC substrate; high resolution STM image of a self-assembled monolayer of OA on HOPG; transfer curves of a graphene FET with and without baking steps; transfer curves of a graphene FET under high vacuum conditions; transfer curves of a graphene FET and its Raman response before and after OA treatment; transfer curves of a graphene FET before and after rinsing with n-hexane. See DOI: 10.1039/c3nr01255g

Nanomagnetism study of highly-ordered iron oxide nanocrystal assemblies fabricated by the Langmuir-Blodgett technique.

PubMed

Zhang, HaiTao; Bao, NiNa; Yuan, Du; Ding, Jun

2013-09-21

Iron oxide nanocrystals are ideal building blocks for the construction of flexible nanodevices whose performance can be modulated by controlling the morphology of isolated particles and their organizational form. This work demonstrates the fabrication of high quality Langmuir-Blodgett (LB) nanocrystal assemblies with limited overlapping and higher coverage by systemically and combinatorially optimizing the parameters of compression pressure and quantity of spread nanocrystals. Monodispersed iron oxide nanocrystals with a diameter of 11.8 nm were synthesized by thermal decomposition of Fe(CO)5 in trioctylamine with the presence of oleic acid. Multilayer nanocrystal assemblies were obtained through a layer-by-layer (LBL) process by repeating the transfer procedure after their hydrophilicity had been improved via treatment in a UV-ozone oven. The quality of nanocrystal assemblies was investigated by UV-vis spectrometry and scanning electron microscopy. The nanomagnetism for the nanostructures of different combination manners was studied systemically by a superconducting quantum interference device (SQUID). A lower superparamagnetic blocking temperature was found in the monolayer Fe3O4 nanocrystal assembly. The superparamagnetic blocking temperature in magnetic nanocrystal assemblies could be tuned through modifying the interparticle interactions among the interlayer and intralayers by controlling the layer number of the assemblies.

Preparations, Properties, and Applications of Periodic Nano Arrays using Anodized Aluminum Oxide and Di-block Copolymer

NASA Astrophysics Data System (ADS)

Noh, Kunbae

2011-12-01

Self-ordered arrangements observed in various materials systems such as anodic aluminum oxide, polystyrene nanoparticles, and block copolymer are of great interest in terms of providing new opportunities in nanofabrication field where lithographic techniques are broadly used in general. Investigations on self-assembled nano arrays to understand how to obtain periodic nano arrays in an efficient yet inexpensive way, and how to realize advanced material and device systems thereof, can lead to significant impacts on science and technology for many forefront device applications. In this thesis, various aspects of periodic nano-arrays have been discussed including novel preparations, properties and applications of anodized aluminum oxide (AAO) and PS-b-P4VP (S4VP) di-block copolymer self-assembly. First, long-range ordered AAO arrays have been demonstrated. Nanoimprint lithography (NIL) process allowed a faithful pattern transfer of the imprint mold pattern onto Al thin film, and interesting self-healing and pattern tripling phenomena were observed, which could be applicable towards fabrication of the NIL master mold having highly dense pattern over large area, useful for fabrication of a large-area substrate for predictable positioning of arrayed devices. Second, S4VP diblock copolymer self-assembly and S4VP directed AAO self-assembly have been demonstrated in the Al thin film on Si substrate. Such a novel combination of two dissimilar self-assembly techniques demonstrated a potential as a versatile tool for nanopatterning formation on a Si substrate, capable of being integrated into Si process technology. As exemplary applications, vertically aligned Ni nanowires have been synthesized into an S4VP-guided AAO membrane on a Si substrate in addition to anti-dot structured [Co/Pd]n magnetic multilayer using S4VP self assembly. Third, a highly hexagonally ordered, vertically parallel aluminum oxide nanotube array was successfully fabricated via hard anodization technique. The Al2O3 nanotube arrays so fabricated exhibit a uniform and reproducible dimension, and a quite high aspect ratio of greater than ˜1,000. Such high-aspect-ratio, mechanically robust, large-surface-area nanotube array structure can be useful for many technical applications. As a potential application in biomedical research, drug storage/controlled drug release from such AAO nanotubes was investigated, and the advantageous potential of using AAO nanotubes for biological implant surface coatings alternative to TiO2 nanotubes has been discussed.

Macroporous 'bubble' graphene film via template-directed ordered-assembly for high rate supercapacitors.

PubMed

Chen, Cheng-Meng; Zhang, Qiang; Huang, Chun-Hsien; Zhao, Xiao-Chen; Zhang, Bing-Sen; Kong, Qing-Qiang; Wang, Mao-Zhang; Yang, Yong-Gang; Cai, Rong; Sheng Su, Dang

2012-07-21

A three-dimensional bubble graphene film, with controllable and uniform macropores and tailorable microstructure, was fabricated by a facile hard templating strategy and exhibit extraordinary electrochemical capacitance with high rate capability (1.0 V s(-1)).

Vibration Monitoring Using Fiber Optic Sensors in a Lead-Bismuth Eutectic Cooled Nuclear Fuel Assembly †

PubMed Central

De Pauw, Ben; Lamberti, Alfredo; Ertveldt, Julien; Rezayat, Ali; van Tichelen, Katrien; Vanlanduit, Steve; Berghmans, Francis

2016-01-01

Excessive fuel assembly vibrations in nuclear reactor cores should be avoided in order not to compromise the lifetime of the assembly and in order to prevent the occurrence of safety hazards. This issue is particularly relevant to new reactor designs that use liquid metal coolants, such as, for example, a molten lead-bismuth eutectic. The flow of molten heavy metal around and through the fuel assembly may cause the latter to vibrate and hence suffer degradation as a result of, for example, fretting wear or mechanical fatigue. In this paper, we demonstrate the use of optical fiber sensors to measure the fuel assembly vibration in a lead-bismuth eutectic cooled installation which can be used as input to assess vibration-related safety hazards. We show that the vibration characteristics of the fuel pins in the fuel assembly can be experimentally determined with minimal intrusiveness and with high precision owing to the small dimensions and properties of the sensors. In particular, we were able to record local strain level differences of about 0.2 μϵ allowing us to reliably estimate the vibration amplitudes and modal parameters of the fuel assembly based on optical fiber sensor readings during different stages of the operation of the facility, including the onset of the coolant circulation and steady-state operation. PMID:27110782

First de novo whole genome sequencing and assembly of the pink-footed goose.

PubMed

Pujolar, J M; Dalén, L; Olsen, R A; Hansen, M M; Madsen, J

2018-03-01

Annotated genomes can provide new perspectives on the biology of species. We present the first de novo whole genome sequencing for the pink-footed goose. In order to obtain a high-quality de novo assembly the strategy used was to combine one short insert paired-end library with two mate-pair libraries. The pink-footed goose genome was assembled de novo using three different assemblers and an assembly evaluation was subsequently performed in order to choose the best assembler. For our data, ALLPATHS-LG performed the best, since the assembly produced covers most of the genome, while introducing the fewest errors. A total of 26,134 genes were annotated, with bird species accounting for virtually all BLAST hits. We also estimated the substitution rate in the pink-footed goose, which can be of use in future demographic studies, by using a comparative approach with the genome of the chicken, the mallard and the swan goose. A substitution rate of 1.38×10 -7 per nucleotide per generation was obtained when comparing the genomes of the two closely-related goose species (the pink-footed and the swan goose). Altogether, we provide a valuable tool for future genomic studies aiming at particular genes and regions of the pink-footed goose genome as well as other bird species. Copyright © 2017 Elsevier Inc. All rights reserved.

Millisecond ordering of block-copolymer films via photo-thermal gradients

DOE PAGES

Majewski, Pawel W.; Yager, Kevin G.

2015-03-12

For the promise of self-assembly to be realized, processing techniques must be developed that simultaneously enable control of the nanoscale morphology, rapid assembly, and, ideally, the ability to pattern the nanostructure. Here, we demonstrate how photo-thermal gradients can be used to control the ordering of block-copolymer thin films. Highly localized laser heating leads to intense thermal gradients, which induce a thermophoretic force on morphological defects. This increases the ordering kinetics by at least 3 orders-of-magnitude, compared to conventional oven annealing. By simultaneously exploiting the thermal gradients to induce shear fields, we demonstrate uniaxial alignment of a block-copolymer film in lessmore » than a second. Finally, we provide examples of how control of the incident light-field can be used to generate prescribed configurations of block-copolymer nanoscale patterns.« less

An improved filtering algorithm for big read datasets and its application to single-cell assembly.

PubMed

Wedemeyer, Axel; Kliemann, Lasse; Srivastav, Anand; Schielke, Christian; Reusch, Thorsten B; Rosenstiel, Philip

2017-07-03

For single-cell or metagenomic sequencing projects, it is necessary to sequence with a very high mean coverage in order to make sure that all parts of the sample DNA get covered by the reads produced. This leads to huge datasets with lots of redundant data. A filtering of this data prior to assembly is advisable. Brown et al. (2012) presented the algorithm Diginorm for this purpose, which filters reads based on the abundance of their k-mers. We present Bignorm, a faster and quality-conscious read filtering algorithm. An important new algorithmic feature is the use of phred quality scores together with a detailed analysis of the k-mer counts to decide which reads to keep. We qualify and recommend parameters for our new read filtering algorithm. Guided by these parameters, we remove in terms of median 97.15% of the reads while keeping the mean phred score of the filtered dataset high. Using the SDAdes assembler, we produce assemblies of high quality from these filtered datasets in a fraction of the time needed for an assembly from the datasets filtered with Diginorm. We conclude that read filtering is a practical and efficient method for reducing read data and for speeding up the assembly process. This applies not only for single cell assembly, as shown in this paper, but also to other projects with high mean coverage datasets like metagenomic sequencing projects. Our Bignorm algorithm allows assemblies of competitive quality in comparison to Diginorm, while being much faster. Bignorm is available for download at https://git.informatik.uni-kiel.de/axw/Bignorm .

Cryogenic Fiber Optic Assemblies for Spaceflight Environments: Design, Manufacturing, Testing, and Integration

NASA Technical Reports Server (NTRS)

Thomes, W. Joe; Ott, Melanie N.; Chuska, Richard; Switzer, Robert; Onuma, Eleanya; Blair, Diana; Frese, Erich; Matyseck, Marc

2016-01-01

Fiber optic assemblies have been used on spaceflight missions for many years as an enabling technology for routing, transmitting, and detecting optical signals. Due to the overwhelming success of NASA in implementing fiber optic assemblies on spaceflight science-based instruments, system scientists increasingly request fibers that perform in extreme environments while still maintaining very high optical transmission, stability, and reliability. Many new applications require fiber optic assemblies that will operate down to cryogenic temperatures as low as 20 Kelvin. In order for the fiber assemblies to operate with little loss in optical throughput at these extreme temperatures requires a system level approach all the way from how the fiber assembly is manufactured to how it is held, routed, and integrated. The NASA Goddard Code 562 Photonics Group has been designing, manufacturing, testing, and integrating fiber optics for spaceflight and other high reliability applications for nearly 20 years. Design techniques and lessons learned over the years are consistently applied to developing new fiber optic assemblies that meet these demanding environments. System level trades, fiber assembly design methods, manufacturing, testing, and integration will be discussed. Specific recent examples of ground support equipment for the James Webb Space Telescope (JWST); the Ice, Cloud and Land Elevation Satellite-2 (ICESat-2); and others will be included.

Cryogenic fiber optic assemblies for spaceflight environments: design, manufacturing, testing, and integration

NASA Astrophysics Data System (ADS)

Thomes, W. Joe; Ott, Melanie N.; Chuska, Richard; Switzer, Robert; Onuma, Eleanya; Blair, Diana; Frese, Erich; Matyseck, Marc

2016-09-01

Fiber optic assemblies have been used on spaceflight missions for many years as an enabling technology for routing, transmitting, and detecting optical signals. Due to the overwhelming success of NASA in implementing fiber optic assemblies on spaceflight science-based instruments, system scientists increasingly request fibers that perform in extreme environments while still maintaining very high optical transmission, stability, and reliability. Many new applications require fiber optic assemblies that will operate down to cryogenic temperatures as low as 20 Kelvin. In order for the fiber assemblies to operate with little loss in optical throughput at these extreme temperatures requires a system level approach all the way from how the fiber assembly is manufactured to how it is held, routed, and integrated. The NASA Goddard Code 562 Photonics Group has been designing, manufacturing, testing, and integrating fiber optics for spaceflight and other high reliability applications for nearly 20 years. Design techniques and lessons learned over the years are consistently applied to developing new fiber optic assemblies that meet these demanding environments. System level trades, fiber assembly design methods, manufacturing, testing, and integration will be discussed. Specific recent examples of ground support equipment for the James Webb Space Telescope (JWST); the Ice, Cloud and Land Elevation Satellite-2 (ICESat- 2); and others will be included.

Hierarchical assembly of Sm2Co7/Co magnetic nanoparticles into highly stable and uniform nanospheres.

PubMed

Saravanan, P; Sreedhar, B; Mishra, D; Perumal, A; Chandrasekaran, V

2011-04-01

Hierarchical assembly of colloidal Sm2Co7/Co clusters in the form of nanospheres has been processed through a polyol process. The SmCo nanospheres are found to be robust, uniform ( 100 nm) and tend to self-assemble in the form of ordered superstructures. Each nanosphere consists of large number of discrete fine particles ( 6.0 nm), having two-phase structure of both Sm2Co7 and Co-phases. Upon annealing, these phases transform into Sm2Co17 phase with very high magnetization (169 emu/g). A possible mechanism on the formation of nanospheres from the individual Sm2Co2o7 and Co nanoparticles is also discussed.

Assembly techniques for ultra-low mass drift chambers

NASA Astrophysics Data System (ADS)

Assiro, R.; Cascella, M.; Grancagnolo, F.; L'Erario, A.; Miccoli, A.; Rella, S.; Spedicato, M.; Tassielli, G.

2014-03-01

We presents a novel technique for the fast assembly of next generation ultra low mass drift chambers offering space point resolution of the order of 100 μm and high tolerance to pile-up. The chamber design has been developed keeping in mind the requirements for the search of rare processes: high resolutions (order of 100-200 KeV/c) for particles momenta in a range (50-100 MeV/c) totally dominated by the multiple scattering contribution (e.g., muon and kaon decay experiment such as MEG at PSI and Mu2e and ORKA at Fermilab). We describe a novel wiring strategy enabling the semiautomatic wiring of a complete layer with a high degree of control over wire tension and position. We also present feed-through-less wire anchoring system. These techniques have been already implemented at INFN-Lecce in the construction of a prototype drift chamber to be soon tested with cosmic rays and particle beams.

Disruption of Chemoreceptor Signaling Arrays by High Levels of CheW, the Receptor-Kinase Coupling Protein

PubMed Central

Cardozo, Marcos J.; Massazza, Diego A.; Parkinson, John S.; Studdert, Claudia A.

2017-01-01

Summary During chemotactic signaling by Escherichia coli, the small cytoplasmic CheW protein couples the histidine kinase CheA to chemoreceptor control. Although essential for assembly and operation of receptor signaling complexes, CheW in stoichiometric excess disrupts chemotactic behavior. To explore the mechanism of the CheW excess effect, we measured the physiological consequences of high cellular levels of wild-type CheW and of several CheW variants with reduced or enhanced binding affinities for receptor molecules. We found that high levels of CheW interfered with trimer assembly, prevented CheA activation, blocked cluster formation, disrupted chemotactic ability, and elevated receptor methylation levels. The severity of these effects paralleled the receptor binding affinities of the CheW variants. Because trimer formation may be an obligate step in the assembly of ternary signaling complexes and higher-order receptor arrays, we suggest that all CheW excess effects stem from disruption of trimer assembly. We propose that the CheW-binding sites in receptor dimers overlap their trimer contact sites and that high levels of CheW saturate the receptor binding sites, preventing trimer assembly. The CheW-trapped receptor dimers seem to be improved substrates for methyltransferase reactions, but cannot activate CheA or assemble into clusters, processes that are essential for chemotactic signaling. PMID:20487303

Cluster synthesis and direct ordering of rare-earth transition-metal nanomagnets.

PubMed

Balasubramanian, Balamurugan; Skomski, Ralph; Li, Xingzhong; Valloppilly, Shah R; Shield, Jeffrey E; Hadjipanayis, George C; Sellmyer, David J

2011-04-13

Rare-earth transition-metal (R-TM) alloys show superior permanent magnetic properties in the bulk, but the synthesis and application of R-TM nanoparticles remains a challenge due to the requirement of high-temperature annealing above about 800 °C for alloy formation and subsequent crystalline ordering. Here we report a single-step method to produce highly ordered R-TM nanoparticles such as YCo(5) and Y(2)Co(17), without high-temperature thermal annealing by employing a cluster-deposition system and investigate their structural and magnetic properties. The direct ordering is highly desirable to create and assemble R-TM nanoparticle building blocks for future permanent-magnet and other significant applications.

Free-standing, well-aligned ordered mesoporous carbon nanofibers on current collectors for high-power micro-supercapacitors.

PubMed

Kang, Eunae; Jeon, Gumhye; Kim, Jin Kon

2013-07-21

The mesoporous carbon nanofiber arrays that stand on carbon-gold double-layer current collectors are synthesized by self-assembly of a PS-b-PEO copolymer and resol in AAO templates for a high-power micro-supercapacitor at high current densities.

Improvement of the Threespine Stickleback Genome Using a Hi-C-Based Proximity-Guided Assembly.

PubMed

Peichel, Catherine L; Sullivan, Shawn T; Liachko, Ivan; White, Michael A

2017-09-01

Scaffolding genomes into complete chromosome assemblies remains challenging even with the rapidly increasing sequence coverage generated by current next-generation sequence technologies. Even with scaffolding information, many genome assemblies remain incomplete. The genome of the threespine stickleback (Gasterosteus aculeatus), a fish model system in evolutionary genetics and genomics, is not completely assembled despite scaffolding with high-density linkage maps. Here, we first test the ability of a Hi-C based proximity-guided assembly (PGA) to perform a de novo genome assembly from relatively short contigs. Using Hi-C based PGA, we generated complete chromosome assemblies from a distribution of short contigs (20-100 kb). We found that 96.40% of contigs were correctly assigned to linkage groups (LGs), with ordering nearly identical to the previous genome assembly. Using available bacterial artificial chromosome (BAC) end sequences, we provide evidence that some of the few discrepancies between the Hi-C assembly and the existing assembly are due to structural variation between the populations used for the 2 assemblies or errors in the existing assembly. This Hi-C assembly also allowed us to improve the existing assembly, assigning over 60% (13.35 Mb) of the previously unassigned (~21.7 Mb) contigs to LGs. Together, our results highlight the potential of the Hi-C based PGA method to be used in combination with short read data to perform relatively inexpensive de novo genome assemblies. This approach will be particularly useful in organisms in which it is difficult to perform linkage mapping or to obtain high molecular weight DNA required for other scaffolding methods. © The American Genetic Association 2017. All rights reserved. For permissions, please e-mail: journals.permissions@oup.com.

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

Hu, Y.; Chen, D; Park, S

High-density arrays of highly ordered ferritin nanocages are fabricated through the guided assembly of thiol-modified ferritin on prepatterned gold nanodots, which are prepared by block copolymer micelle lithography. One and only one ferritin nanocage is anchored to each gold nanodot, as confirmed by scanning electron and scanning force microscopy.

A facile one-pot self-assembly approach to incorporate SnOx nanoparticles in ordered mesoporous carbon with soft templating for fuel cells.

PubMed

Huang, Yingqiang; Zhai, Zhicheng; Luo, Zhigang; Liu, Yingju; Liang, Zhurong; Fang, Yueping

2014-04-04

Unique SnO(x) (x = 1,2)/ordered mesoporous carbon nanocomposites (denoted as SnO(x)/OMC) are firstly synthesized through a 'one-pot' synthesis together with the soft template self-assembly approach. The obtained SnO(x)/OMC nanocomposites with various SnO(x) contents exhibit uniform pore sizes between 3.9 and 4.2 nm, high specific surface areas between 497 and 595 m(2) g(-1), and high pore volumes between 0.39 and 0.48 cm(3) g(-1). With loading of Pt, Pt-SnO(x)/OMC with relatively low SnO(x) content exhibits superior electrocatalytic performance, long-term durability, and resistance to CO poisoning for methanol oxidation, as compared to Pt/OMC, PtRu/C and Pt-SnO(x)/C, which may be attributed not only to the synergetic effect of embedded SnO(x), but also to the highly ordered mesostructure with high specific surface areas and large pore volumes affording plenty of surface area for support of Pt nanoparticles. This work supplies an efficient way to synthesize novel ordered mesoporous carbon self-supported metallic oxide as catalyst support and its further potential application to reduce the cost of catalysts in direct methanol fuel cells.

A facile one-pot self-assembly approach to incorporate SnOx nanoparticles in ordered mesoporous carbon with soft templating for fuel cells

NASA Astrophysics Data System (ADS)

Huang, Yingqiang; Zhai, Zhicheng; Luo, Zhigang; Liu, Yingju; Liang, Zhurong; Fang, Yueping

2014-04-01

Unique SnOx (x = 1,2)/ordered mesoporous carbon nanocomposites (denoted as SnOx/OMC) are firstly synthesized through a ‘one-pot’ synthesis together with the soft template self-assembly approach. The obtained SnOx/OMC nanocomposites with various SnOx contents exhibit uniform pore sizes between 3.9 and 4.2 nm, high specific surface areas between 497 and 595 m2 g-1, and high pore volumes between 0.39 and 0.48 cm3 g-1. With loading of Pt, Pt-SnOx/OMC with relatively low SnOx content exhibits superior electrocatalytic performance, long-term durability, and resistance to CO poisoning for methanol oxidation, as compared to Pt/OMC, PtRu/C and Pt-SnOx/C, which may be attributed not only to the synergetic effect of embedded SnOx, but also to the highly ordered mesostructure with high specific surface areas and large pore volumes affording plenty of surface area for support of Pt nanoparticles. This work supplies an efficient way to synthesize novel ordered mesoporous carbon self-supported metallic oxide as catalyst support and its further potential application to reduce the cost of catalysts in direct methanol fuel cells.

Strength of Neisseria meningitidis binding to endothelial cells requires highly-ordered CD147/β2-adrenoceptor clusters assembled by alpha-actinin-4

PubMed Central

Maïssa, Nawal; Covarelli, Valentina; Janel, Sébastien; Durel, Beatrice; Simpson, Nandi; Bernard, Sandra C.; Pardo-Lopez, Liliana; Bouzinba-Ségard, Haniaa; Faure, Camille; Scott, Mark G.H.; Coureuil, Mathieu; Morand, Philippe C.; Lafont, Frank; Nassif, Xavier; Marullo, Stefano; Bourdoulous, Sandrine

2017-01-01

Neisseria meningitidis (meningococcus) is an invasive bacterial pathogen that colonizes human vessels, causing thrombotic lesions and meningitis. Establishment of tight interactions with endothelial cells is crucial for meningococci to resist haemodynamic forces. Two endothelial receptors, CD147 and the β2-adrenergic receptor (β2AR), are sequentially engaged by meningococci to adhere and promote signalling events leading to vascular colonization, but their spatiotemporal coordination is unknown. Here we report that CD147 and β2AR form constitutive hetero-oligomeric complexes. The scaffolding protein α-actinin-4 directly binds to the cytosolic tail of CD147 and governs the assembly of CD147–β2AR complexes in highly ordered clusters at bacterial adhesion sites. This multimolecular assembly process increases the binding strength of meningococci to endothelial cells under shear stress, and creates molecular platforms for the elongation of membrane protrusions surrounding adherent bacteria. Thus, the specific organization of cellular receptors has major impacts on host–pathogen interaction. PMID:28569760

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 Self- and Directed Assembly of Nanowires

NASA Astrophysics Data System (ADS)

Smith, Benjamin David

This thesis explores the self- and directed assembly of nanowires. Specifically, we examine the driving forces behind nanowire self-assembly and the macro-structures that are formed. Particle-dense, oriented nanowire structures show promise in the fields of photonics, energy, sensing, catalysis, and electronics. Arrays of spherical particles have already found uses in electronic inks, sensing arrays, and many other commercial applications; but, it is a challenge to create specific arrays of morphologically and/or compositionally anisotropic particles. The following chapters illuminate the interactions that drive the assembly of anisotropic particles in high density solutions in the absence of applied fields or solution drying. Special emphasis is placed on the structures that are formed. The properties of micro- and nanoparticles and their assembly are introduced in Chapter 1. In particular, the properties of shape and material anisotropic particles are highlighted, while challenges in producing desired arrays are discussed. In this thesis, metallic nanowires of increasing complexity were used to examine the self-assembly behavior of both shape and material anisotropic particles. Nanowires were synthesized through templated electrodeposition. In this process, porous alumina membranes served as a template in which metal salts were reduced to form particles. Upon template dissolution, billions of nominally identical particles were released. We specifically focused on segmented, metallic nanowires 2-13 mum in length and 180 to 350 nm in diameter. Since these particles have strong van der Waals (VDWs) attractions, an electrostatically repulsive coating was necessary to prevent aggregation; we used small molecule, DNA, or amorphous silica coatings. Nanowires and their coatings were characterized by electron microscopy. In order to study self-assembly behavior, particle-dense aqueous suspensions were placed within an assembly chamber defined by a silicone spacer. The nanowires rapidly sedimented due to gravity onto a glass cover slip to concentrate and form a dense film. Particles and assemblies were imaged using inverted optical microscopy. We quantitatively analyzed the images and movies captured in order to track and classify particles and classify the overall arrays formed. We then correlated how particle characteristics, e.g., materials, size, segmentation, etc. changed the ordering and alignment observed. With that knowledge, we hope to be able to form new and interesting structures. We began our studies by examining the assembly of single component nanowires. Chapter 2 describes this work, in which solid Au nanowires measuring 2-7 mum in length and 290 nm in diameter self-assembled into smectic rows. By both experiment and theory, we determined that these rows formed due to a balance of electrostatic repulsions and van der Waals attractions. Final assemblies were stable for at least several days. Monte Carlo methods were used to simulate assemblies and showed structures that mirrored those experimentally observed. Simulations indicated that the smectic phase was preferred over others, i.e., nematic, when an additional small charge was added to the ends of the nanowires. Our particles have rough tips, which might create these additional electrostatic repulsions. To increase the particle and array complexity, two-component, metallic nanowire assembly was explored in Chapter 3. We examined numerous types of nanowires by changing the segment length, ratio, and material, the nanowire length, the surface coating, and the presence of small third segments. These segmented nanowires were generally Au-Ag and also ordered into smectic rows. Segmented wires arranged in rows, however, can be aligned in two possible ways with respect to a neighboring particle. The Au segments on neighboring particles can be oriented in the same direction or opposed to each other. Orientation was quantified in terms of an order parameter that took into account alignment with respect to nearest neighbor particles. All experiments showed order parameters indicating a slight preference for orientational ordering that was relatively insensitive to segment size, nanowire size, and nanowire coating. Monte Carlo simulations pointed towards this alignment as a consequence of small differences in the van der Waals attractions between the segments. Experimentally, ordering might to be limited by the large size of the nanowires, which results in kinetically trapped structures. In an attempt to obtain better ordering within rows, silica coated nanowires with partial Au cores were made. The synthesis involved silica-coating the nanowires and selectively etching a Ag segment. These particles have extremely different VDWs attractions between their segments, as the Au cores are much more attractive than the solvent-filled etched ends. The assembly of these partially etched nanowires (PENs) is detailed in Chapters 4, 5, and 6. When allowed to self-assemble, we observed the formation of either vertically or horizontally oriented arrays depending on PEN composition. The formation of vertically oriented arrays of anisotropic particles is important, since not many methods to produce these structures are currently available for particles of this size. We examined the effects of PEN length, PEN diameter, and the size, number, and location of the core segments. Our findings showed a large etched segment at one end (which resulted in a large offset in the center of mass and concentrated the VDWs attractions to one end of the particle) resulted in the best columnar assemblies. These vertically orientated arrays formed in a two part process. First, after PENs sedimented, they fell flat and oriented parallel to the surface. These PENs then sampled many orientations, including rotating out of the surface plane. When higher surface concentrations of particles built as more PENs fell to the surface of the cover slip, neighboring particles stabilized vertical orientations. Second, particles fell oriented vertically and when the surface concentrations were high, they retained this orientation upon reaching the substrate. Since vertically aligned PENs supported each other, assembly into vertical arrays was highly dependent on the surface concentration. But, oriented arrays could be easily formed on larger or smaller substrates, provided a particle concentration scaled to the substrate were used. The mixing of these particles to form heterogeneous arrays was examined. The overall array structure favored that of particles which sedimented more quickly and/or were present in higher amounts. The semi-automated counting of PENs in images by software is used heavily in Chapters 4 and 5. Appendix A describes the use, development, and validation of macros within Image-Pro. The structure, syntax, and use are specifically examined for three nanowire counting macros. The counting results; including: number of particles in an image, number of horizontally vs. vertically oriented PENs, and PENs in microwells; are compared with manual hand counts. Chapter 7 examines the overall conclusions and future directions for this research. By combining our assembly techniques with known directing forces (e.g., electric or magnetic fields) more specific alignment and/or positioning could be achieved. We have also begun to explore directing assembly through lithographic microwells. Further work needs to explore the integration of arrays into devices and the use of functional materials. Then, high density, oriented arrays could be created for photonic, energy, sensing, catalytic, and electronic applications.

Allosteric Control of Icosahedral Capsid Assembly

PubMed Central

Lazaro, Guillermo R.

2017-01-01

During the lifecycle of a virus, viral proteins and other components self-assemble to form an ordered protein shell called a capsid. This assembly process is subject to multiple competing constraints, including the need to form a thermostable shell while avoiding kinetic traps. It has been proposed that viral assembly satisfies these constraints through allosteric regulation, including the interconversion of capsid proteins among conformations with different propensities for assembly. In this article we use computational and theoretical modeling to explore how such allostery affects the assembly of icosahedral shells. We simulate assembly under a wide range of protein concentrations, protein binding affinities, and two different mechanisms of allosteric control. We find that, above a threshold strength of allosteric control, assembly becomes robust over a broad range of subunit binding affinities and concentrations, allowing the formation of highly thermostable capsids. Our results suggest that allostery can significantly shift the range of protein binding affinities that lead to successful assembly, and thus should be accounted for in models that are used to estimate interaction parameters from experimental data. PMID:27117092

Unusually large unit cell of lipid bicontinuous cubic phase: towards nature's length scales

NASA Astrophysics Data System (ADS)

Kim, Hojun; Leal, Cecilia

Lipid bicontinuous cubic phases are of great interest for drug delivery, protein crystallization, biosensing, and templates for directing hard material assembly. Structural modulations of lipid mesophases regarding phase identity and unit cell size are often necessary to augment loading and gain pore size control. One important example is the need for unit cells large enough to guide the crystallization of bigger proteins without distortion of the templating phase. In nature, bicontinuous cubic constructs achieve unit cell dimensions as high as 300 nm. However, the largest unit cell of lipid mesophases synthesized in the lab is an order of magnitude lower. In fact, it has been predicted theoretically that lipid bicontinuous cubic phases of unit cell dimensions exceeding 30 nm could not exist, as high membrane fluctuations would damp liquid crystalline order. Here we report non-equilibrium assembly methods of synthesizing metastable bicontinuous cubic phases with unit cell dimensions as high as 70 nm. The phases are stable for very long periods and become increasingly ordered as time goes by without changes to unit cell dimensions. We acknowledge the funding source as a NIH.

Scalable Directed Assembly of Highly Crystalline 2,7-Dioctyl[1]benzothieno[3,2- b][1]benzothiophene (C8-BTBT) Films.

PubMed

Chai, Zhimin; Abbasi, Salman A; Busnaina, Ahmed A

2018-05-30

Assembly of organic semiconductors with ordered crystal structure has been actively pursued for electronics applications such as organic field-effect transistors (OFETs). Among various film deposition methods, solution-based film growth from small molecule semiconductors is preferable because of its low material and energy consumption, low cost, and scalability. Here, we show scalable and controllable directed assembly of highly crystalline 2,7-dioctyl[1]benzothieno[3,2- b][1]benzothiophene (C8-BTBT) films via a dip-coating process. Self-aligned stripe patterns with tunable thickness and morphology over a centimeter scale are obtained by adjusting two governing parameters: the pulling speed of a substrate and the solution concentration. OFETs are fabricated using the C8-BTBT films assembled at various conditions. A field-effect hole mobility up to 3.99 cm 2 V -1 s -1 is obtained. Owing to the highly scalable crystalline film formation, the dip-coating directed assembly process could be a great candidate for manufacturing next-generation electronics. Meanwhile, the film formation mechanism discussed in this paper could provide a general guideline to prepare other organic semiconducting films from small molecule solutions.

Application of Bottlebrush Block Copolymers as Photonic Crystals.

PubMed

Liberman-Martin, Allegra L; Chu, Crystal K; Grubbs, Robert H

2017-07-01

Brush block copolymers are a class of comb polymers that feature polymeric side chains densely grafted to a linear backbone. These polymers display interesting properties due to their dense functionality, low entanglement, and ability to rapidly self-assemble to highly ordered nanostructures. The ability to prepare brush polymers with precise structures has been enabled by advancements in controlled polymerization techniques. This Feature Article highlights the development of brush block copolymers as photonic crystals that can reflect visible to near-infrared wavelengths of light. Fabrication of these materials relies on polymer self-assembly processes to achieve nanoscale ordering, which allows for the rapid preparation of photonic crystals from common organic chemical feedstocks. The characteristic physical properties of brush block copolymers are discussed, along with methods for their preparation. Strategies to induce self-assembly at ambient temperatures and the use of blending techniques to tune photonic properties are emphasized. © 2017 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Crystal structure of human proteasome assembly chaperone PAC4 involved in proteasome formation.

PubMed

Kurimoto, Eiji; Satoh, Tadashi; Ito, Yuri; Ishihara, Eri; Okamoto, Kenta; Yagi-Utsumi, Maho; Tanaka, Keiji; Kato, Koichi

2017-05-01

The 26S proteasome is a large protein complex, responsible for degradation of ubiquinated proteins in eukaryotic cells. Eukaryotic proteasome formation is a highly ordered process that is assisted by several assembly chaperones. The assembly of its catalytic 20S core particle depends on at least five proteasome-specific chaperones, i.e., proteasome-assembling chaperons 1-4 (PAC1-4) and proteasome maturation protein (POMP). The orthologues of yeast assembly chaperones have been structurally characterized, whereas most mammalian assembly chaperones are not. In the present study, we determined a crystal structure of human PAC4 at 1.90-Å resolution. Our crystallographic data identify a hydrophobic surface that is surrounded by charged residues. The hydrophobic surface is complementary to that of its binding partner, PAC3. The surface also exhibits charge complementarity with the proteasomal α4-5 subunits. This will provide insights into human proteasome-assembling chaperones as potential anticancer drug targets. © 2017 The Protein Society.

Layered host-guest long-afterglow ultrathin nanosheets: high-efficiency phosphorescence energy transfer at 2D confined interface.

PubMed

Gao, Rui; Yan, Dongpeng

2017-01-01

Tuning and optimizing the efficiency of light energy transfer play an important role in meeting modern challenges of minimizing energy loss and developing high-performance optoelectronic materials. However, attempts to fabricate systems giving highly efficient energy transfer between luminescent donor and acceptor have achieved limited success to date. Herein, we present a strategy towards phosphorescence energy transfer at a 2D orderly crystalline interface. We first show that new ultrathin nanosheet materials giving long-afterglow luminescence can be obtained by assembling aromatic guests into a layered double hydroxide host. Furthermore, we demonstrate that co-assembly of these long-lived energy donors with an energy acceptor in the same host generates an ordered arrangement of phosphorescent donor-acceptor pairs spatially confined within the 2D nanogallery, which affords energy transfer efficiency as high as 99.7%. Therefore, this work offers an alternative route to develop new types of long-afterglow nanohybrids and efficient light transfer systems with potential energy, illumination and sensor applications.

Self-assembly of block copolymers on topographically patterned polymeric substrates

DOEpatents

Russell, Thomas P.; Park, Soojin; Lee, Dong Hyun; Xu, Ting

2016-05-10

Highly-ordered block copolymer films are prepared by a method that includes forming a polymeric replica of a topographically patterned crystalline surface, forming a block copolymer film on the topographically patterned surface of the polymeric replica, and annealing the block copolymer film. The resulting structures can be used in a variety of different applications, including the fabrication of high density data storage media. The ability to use flexible polymers to form the polymeric replica facilitates industrial-scale processes utilizing the highly-ordered block copolymer films.

Research on the Development Prospect of Assembled Passive Building Based on Green Development Concept

NASA Astrophysics Data System (ADS)

Lixin, Zhang; Ju, Ma; Baohui, He

2018-02-01

In recent years, the vigorous development of the construction industry has brought about serious problems of environmental pollution and resource consumption. In order to reduce the negative impact that the construction industry has on the natural environment,this paper, from the perspective of environmental protection, studies the pollution and high consumption problems existing in the production and use of traditional construction industry, compares and analyzes the green and energy-saving advantages in the construction and using phase of assembled passive building, and at the same time, combined with our country is vigorously promoting the assembled passive building and the green development, concluded that the assembled passive building is the new development direction of China’s construction industry.

Nano-assembly and Controlled Release Kinetics of Nanoelements from Nanoporous Templates

NASA Astrophysics Data System (ADS)

Gultepe, E.; Nagesha, D.; McNulty, J.; Sridhar, S.

2008-03-01

Nanotemplates and nanoparticles have potential for use in the area of nanomanufacturing and biomedical applications. We are using highly ordered nanoporous alumina as a template for drug delivery and to assemble nanoelements such as latex beads and single wall carbon nanotubes (SWNT) by the means of electrophoresis and/or dielectrophoresis. The results of 100% assembly of latex beads and controlled elution of drugs from nanoporous templates will be discussed. Vertically assembled SWNT and with the I-V characteristic as 3D interconnects, will also be presented. We have developed a variety of platforms incorporating superparamagnetic iron oxide nanoparticles for targeted delivery, magnetic hyperthermia and as a contrast agent for magnetic resonance imaging. The results of cell studies on these platforms will be discussed.

Triconstituent co-assembly to ordered mesostructured polymer-silica and carbon-silica nanocomposites and large-pore mesoporous carbons with high surface areas.

PubMed

Liu, Ruili; Shi, Yifeng; Wan, Ying; Meng, Yan; Zhang, Fuqiang; Gu, Dong; Chen, Zhenxia; Tu, Bo; Zhao, Dongyuan

2006-09-06

Highly ordered mesoporous polymer-silica and carbon-silica nanocomposites with interpenetrating networks have been successfully synthesized by the evaporation-induced triconstituent co-assembly method, wherein soluble resol polymer is used as an organic precursor, prehydrolyzed TEOS is used as an inorganic precursor, and triblock copolymer F127 is used as a template. It is proposed for the first time that ordered mesoporous nanocomposites have "reinforced concrete"-structured frameworks. By adjusting the initial mass ratios of TEOS to resol, we determined the obtained nanocomposites possess continuous composition with the ratios ranging from zero to infinity for the two constituents that are "homogeneously" dispersed inside the pore walls. The presence of silicates in nanocomposites dramatically inhibits framework shrinkage during the calcination, resulting in highly ordered large-pore mesoporous carbon-silica nanocomposites. Combustion in air or etching in HF solution can remove carbon or silica from the carbon-silica nanocomposites and yield ordered mesoporous pure silica or carbon frameworks. The process generates plenty of small pores in carbon or/and silica pore walls. Ordered mesoporous carbons can then be obtained with large pore sizes of approximately 6.7 nm, pore volumes of approximately 2.0 cm(3)/g, and high surface areas of approximately 2470 m(2)/g. The pore structures and textures can be controlled by varying the sizes and polymerization degrees of two constituent precursors. Accordingly, by simply tuning the aging time of TEOS, ordered mesoporous carbons with evident bimodal pores at 2.6 and 5.8 nm can be synthesized.

Magnetic-Field-Assisted Assembly of Ordered Multifunctional Ceramic Nanocomposites for Extreme Environments

DTIC Science & Technology

2016-04-01

SUBJECT TERMS carbon nanotubes, composite, electromagnetic shielding , extreme environments, magnetism , fibers, woven composite, boron nitride...AFRL-AFOSR-VA-TR-2016-0158 Magnetic -Field-Assisted Assembly of Ordered Multifunctional Ceramic Nanocomposites for Extreme Environments Konstantin...From - To) 15 Sep 2012 to 14 Nov 2017 4. TITLE AND SUBTITLE Magnetic -Field-Assisted Assembly of Ordered Multifunctional Ceramic Nanocomposites for

Hierarchical Materials Design by Pattern Transfer Printing of Self-Assembled Binary Nanocrystal Superlattices

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

Paik, Taejong; Yun, Hongseok; Fleury, Blaise

We demonstrate the fabrication of hierarchical materials by controlling the structure of highly ordered binary nanocrystal superlattices (BNSLs) on multiple length scales. Combinations of magnetic, plasmonic, semiconducting, and insulating colloidal nanocrystal (NC) building blocks are self-assembled into BNSL membranes via the liquid–interfacial assembly technique. Free-standing BNSL membranes are transferred onto topographically structured poly(dimethylsiloxane) molds via the Langmuir–Schaefer technique and then deposited in patterns onto substrates via transfer printing. BNSLs with different structural motifs are successfully patterned into various meso- and microstructures such as lines, circles, and even three-dimensional grids across large-area substrates. A combination of electron microscopy and grazing incidencemore » small-angle X-ray scattering (GISAXS) measurements confirm the ordering of NC building blocks in meso- and micropatterned BNSLs. This technique demonstrates structural diversity in the design of hierarchical materials by assembling BNSLs from NC building blocks of different composition and size by patterning BNSLs into various size and shape superstructures of interest for a broad range of applications.« less

Real-time analysis of self-assembled nucleobases by Venturi easy ambient sonic-spray ionization mass spectrometry.

PubMed

Na, Na; Shi, Ruixia; Long, Zi; Lu, Xin; Jiang, Fubin; Ouyang, Jin

2014-10-01

In this study, the real-time analysis of self-assembled nucleobases was employed by Venturi easy ambient sonic-spray ionization mass spectrometry (V-EASI-MS). With the analysis of three nucleobases including 6-methyluracil (6MU), uracil (U) and thymine (T) as examples, different orders of clusters centered with different metal ions were recorded in both positive and negative modes. Compared with the results obtained by traditional electrospray ionization mass spectrometry (ESI-MS) under the same condition, more clusters with high orders, such as [6MU7+Na](+), [6MU15+2NH4](2+), [6MU10+Na](+), [T7+Na](+), and [T15+2NH4](2+) were detected by V-EASI-MS, which demonstrated the soft ionization ability of V-EASI for studying the non-covalent interaction in a self-assembly process. Furthermore, with the injection of K(+) to the system by a syringe pumping, the real-time monitoring of the formation of nucleobases clusters was achieved by the direct extraction of samples from the system under the Venturi effect. Therefore, the effect of cations on the formation of clusters during self-assembly of nucleobases was demonstrated, which was in accordance with the reports. Free of high voltage, heating or radiation during the ionization, this technique is much soft and suitable for obtaining the real-time information of the self-assembly system, which also makes it quite convenient for extraction samples from the reaction system. This "easy and soft" ionization technique has provided a potential pathway for monitoring and controlling the self-assembly processes. Copyright © 2014 Elsevier B.V. All rights reserved.

Mitochondrial ribosome assembly in health and disease

PubMed Central

De Silva, Dasmanthie; Tu, Ya-Ting; Amunts, Alexey; Fontanesi, Flavia; Barrientos, Antoni

2015-01-01

The ribosome is a structurally and functionally conserved macromolecular machine universally responsible for catalyzing protein synthesis. Within eukaryotic cells, mitochondria contain their own ribosomes (mitoribosomes), which synthesize a handful of proteins, all essential for the biogenesis of the oxidative phosphorylation system. High-resolution cryo-EM structures of the yeast, porcine and human mitoribosomal subunits and of the entire human mitoribosome have uncovered a wealth of new information to illustrate their evolutionary divergence from their bacterial ancestors and their adaptation to synthesis of highly hydrophobic membrane proteins. With such structural data becoming available, one of the most important remaining questions is that of the mitoribosome assembly pathway and factors involved. The regulation of mitoribosome biogenesis is paramount to mitochondrial respiration, and thus to cell viability, growth and differentiation. Moreover, mutations affecting the rRNA and protein components produce severe human mitochondrial disorders. Despite its biological and biomedical significance, knowledge on mitoribosome biogenesis and its deviations from the much-studied bacterial ribosome assembly processes is scarce, especially the order of rRNA processing and assembly events and the regulatory factors required to achieve fully functional particles. This article focuses on summarizing the current available information on mitoribosome assembly pathway, factors that form the mitoribosome assembly machinery, and the effect of defective mitoribosome assembly on human health. PMID:26030272

Impact of Linear Alkyl Length on the Assembly of Twisted Perylene Bisimides: From Molecular Arrangement to Nanostructures.

PubMed

Guo, Zongxia; Wang, Kun; Yu, Ping; Wang, Xiangnan; Lan, Shusha; Sun, Kai; Yi, Yuanping; Li, Zhibo

2017-11-02

The effect of the length of linear alkyl chains substituted at imine positions on the assembly of tetrachlorinated perylene bisimides (1: PBI with -C 6 H 13 ; 2: PBI with -C 12 H 25 ) has been investigated. Solvent-induced assembly was performed in solutions of THF and methanol with varying volume ratios. Morphological (SEM, AFM, and TEM) and spectral (UV/Vis, fluorescence, FTIR, and XRD) methods were used to characterize the assembled nanostructures and the molecular arrangement in the aggregates. It was found that uniform structures could be obtained for both molecules in solutions with a high ratio of methanol. PBI 1 formed rigid nanosheets, whereas 2 assembled into longer nanostripes with a high ratio of length to width. On combining the morphological data with the spectral data, it was suggested that π-π stacking predominated in assemblies of 1, and the synergetic effect of van der Waals interactions from the long alkyl chains and π-π stacking between neighboring building blocks facilitated the growth of the long-range-ordered nanostructures of 2. By changing the linear chain length, the hierarchical assembly of PBIs modified on bay positions could be manipulated effectively. © 2017 Wiley-VCH Verlag GmbH & Co. KGaA, Weinheim.

Changes in Dimensionality and Fractal Scaling Suggest Soft-Assembled Dynamics in Human EEG

PubMed Central

Wiltshire, Travis J.; Euler, Matthew J.; McKinney, Ty L.; Butner, Jonathan E.

2017-01-01

Humans are high-dimensional, complex systems consisting of many components that must coordinate in order to perform even the simplest of activities. Many behavioral studies, especially in the movement sciences, have advanced the notion of soft-assembly to describe how systems with many components coordinate to perform specific functions while also exhibiting the potential to re-structure and then perform other functions as task demands change. Consistent with this notion, within cognitive neuroscience it is increasingly accepted that the brain flexibly coordinates the networks needed to cope with changing task demands. However, evaluation of various indices of soft-assembly has so far been absent from neurophysiological research. To begin addressing this gap, we investigated task-related changes in two distinct indices of soft-assembly using the established phenomenon of EEG repetition suppression. In a repetition priming task, we assessed evidence for changes in the correlation dimension and fractal scaling exponents during stimulus-locked event-related potentials, as a function of stimulus onset and familiarity, and relative to spontaneous non-task-related activity. Consistent with predictions derived from soft-assembly, results indicated decreases in dimensionality and increases in fractal scaling exponents from resting to pre-stimulus states and following stimulus onset. However, contrary to predictions, familiarity tended to increase dimensionality estimates. Overall, the findings support the view from soft-assembly that neural dynamics should become increasingly ordered as external task demands increase, and support the broader application of soft-assembly logic in understanding human behavior and electrophysiology. PMID:28919862

Hierachical assembly of collagen mimetic peptides into biofunctional materials

NASA Astrophysics Data System (ADS)

Gleaton, Jeremy W.

Collagen is a remarkably strong and prevalent protein distributed throughout nature and as such, collagen is an ideal material for a variety of medical applications. Research efforts for the development of synthetic collagen biomaterials is an area of rapid growth. Here we present two methods for the assembly of collagen mimetic peptides (CMPs). The initial approach prompts assembly of CMPs which contain modifications for metal ion-triggered assembly. Hierarchical assembly into triple helices, followed by formation of disks via hydrophobic interactions has been demonstrated. Metal-ion mediated assembly of these disks, using iron (II)-bipyrdine interactions, has been shown to form micron-sized cages. The nature of the final structures that form depends on the number of bipyridine moieties incorporated into the CMP. These hollow spheres encapsulate a range of molecular weight fluorescently labeled dextrans. Furthermore, they demonstrate a time dependent release of contents under a variety of thermal conditions. The second approach assembles CMPs via the copper-catalyzed alkyne-azide cycloaddition (CuAAC) and the strain-promoted alkyne-azide cycloaddition (SPAAC) reactions. CMPs that incorporate the unnatural amino acids L-propargylglycine and L-azidolysine form triple helices and demonstrate higher order assembly when reacted via CuAAC. Reaction of the alkyne/azide modified CMPs under CuAAC conditions was found to produce an crosslinked 3-dimensional network. Moreover, we demonstrate that polymers, such as, PEG, can be reacted with alkyne and azide CMP triple helices via CuAAC and SPAAC. This designed covalent CMP chemistry allows for high flexibility in integrating various chemical cues, such as cell growth and differentiation within the higher order structures.

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.

Application of X-Ray Computer Tomography for Observing the Central Void Formations and the Fuel Pin Deformations of Irradiated FBR Fuel Assemblies

NASA Astrophysics Data System (ADS)

Katsuyama, Kozo; Nagamine, Tsuyoshi; Furuya, Hirotaka

2010-10-01

In order to observe the structural change in the interior of irradiated fuel assemblies, a non-destructive post-irradiation examination (PIE) technique using X-ray computer tomography (X-ray CT) was developed. This X-ray CT technique was applied to observe the central void formations and fuel pin deformations of fuel assemblies which had been irradiated at high linear heat rating. The central void sizes in all fuel pins were measured on five cross sections of the core fuel column as a parameter for evaluating fuel thermal performance. In addition, the fuel pin deformations were analyzed from X-ray CT images obtained along the axial direction of a fuel assembly at the same separation interval. A dependence of void size on the linear heat rating was seen in the fuel assembly irradiated at high linear heat rating. In addition, significant undulations of the fuel pin were observed along the axial direction, coinciding with the wrapping wire pitch in the core fuel column. Application of the developed technique should provide enhanced resolution of measurements and simplify fuel PIEs.

Assembly planning based on subassembly extraction

NASA Technical Reports Server (NTRS)

Lee, Sukhan; Shin, Yeong Gil

1990-01-01

A method is presented for the automatic determination of assembly partial orders from a liaison graph representation of an assembly through the extraction of preferred subassemblies. In particular, the authors show how to select a set of tentative subassemblies by decomposing a liaison graph into a set of subgraphs based on feasibility and difficulty of disassembly, how to evaluate each of the tentative subassemblies in terms of assembly cost using the subassembly selection indices, and how to construct a hierarchical partial order graph (HPOG) as an assembly plan. The method provides an approach to assembly planning by identifying spatial parallelism in assembly as a means of constructing temporal relationships among assembly operations and solves the problem of finding a cost-effective assembly plan in a flexible environment. A case study of the assembly planning of a mechanical assembly is presented.

Chemically programmed self-sorting of gelator networks.

PubMed

Morris, Kyle L; Chen, Lin; Raeburn, Jaclyn; Sellick, Owen R; Cotanda, Pepa; Paul, Alison; Griffiths, Peter C; King, Stephen M; O'Reilly, Rachel K; Serpell, Louise C; Adams, Dave J

2013-01-01

Controlling the order and spatial distribution of self-assembly in multicomponent supramolecular systems could underpin exciting new functional materials, but it is extremely challenging. When a solution of different components self-assembles, the molecules can either coassemble, or self-sort, where a preference for like-like intermolecular interactions results in coexisting, homomolecular assemblies. A challenge is to produce generic and controlled 'one-pot' fabrication methods to form separate ordered assemblies from 'cocktails' of two or more self-assembling species, which might have relatively similar molecular structures and chemistry. Self-sorting in supramolecular gel phases is hence rare. Here we report the first example of the pH-controlled self-sorting of gelators to form self-assembled networks in water. Uniquely, the order of assembly can be predefined. The assembly of each component is preprogrammed by the pK(a) of the gelator. This pH-programming method will enable higher level, complex structures to be formed that cannot be accessed by simple thermal gelation.

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.

Organic materials as templates for the formation of mesoporous inorganic materials and ordered inorganic nanocomposites

NASA Astrophysics Data System (ADS)

Ziegler, Christopher R.

Hierarchically structured inorganic materials are everywhere in nature. From unicellular aquatic algae such as diatoms to the bones and/or cartilage that comprise the skeletal systems of vertebrates. Complex mechanisms involving site-specific chemistries and precision kinetics are responsible for the formation of such structures. In the synthetic realm, reproduction of even the most basic hierarchical structure effortlessly produced in nature is difficult. However, through the utilization of self-assembling structures or "templates", such as polymers or amphiphilic surfactants, combined with some favorable interaction between a chosen inorganic, the potential exists to imprint an inorganic material with a morphology dictated via synthetic molecular self-assembly. In doing so, a very basic hierarchical structure is formed on the angstrom and nanometer scales. The work presented herein utilizes the self-assembly of either surfactants or block copolymers with the desired inorganic or inorganic precursor to form templated inorganic structures. Specifically, mesoporous silica spheres and copolymer directed calcium phosphate-polymer composites were formed through the co-assembly of an organic template and a precursor to form the desired mesostructured inorganic. For the case of the mesoporous silica spheres, a silica precursor was mixed with cetyltrimethylammonium bromide and cysteamine, a highly effective biomimetic catalyst for the conversion of alkoxysilanes to silica. Through charge-based interactions between anionic silica species and the micelle-forming cationic surfactant, ordered silica structures resulted. The incorporation of a novel, effective catalyst was found to form highly condensed silica spheres for potential application as catalyst supports or an encapsulation media. Ordered calcium phosphate-polymer composites were formed using two routes. Both routes take advantage of hydrogen bonding and ionic interactions between the calcium and phosphate precursors and the self-assembling copolymer template. Some evidence suggests that the copolymer morphology remained in the composite despite the known tendency for calcium phosphates to form highly elongated crystalline structures with time, as is commonly the case for synthetic hydroxyapatites. Such materials have obvious application as bone grafts and bone coatings due, in part, to the osteoconductive nature of calcium phosphate as well as to the mesoporosity generated through the cooperative assembly of the block copolymer and the inorganic. Future work, including potential experiments to determine osteoconductivity of as-prepared composites, is also presented herein.

Water ordering controls the dynamic equilibrium of micelle-fibre formation in self-assembly of peptide amphiphiles.

PubMed

Deshmukh, Sanket A; Solomon, Lee A; Kamath, Ganesh; Fry, H Christopher; Sankaranarayanan, Subramanian K R S

2016-08-24

Understanding the role of water in governing the kinetics of the self-assembly processes of amphiphilic peptides remains elusive. Here, we use a multistage atomistic-coarse-grained approach, complemented by circular dichroism/infrared spectroscopy and dynamic light scattering experiments to highlight the dual nature of water in driving the self-assembly of peptide amphiphiles (PAs). We show computationally that water cage formation and breakage near the hydrophobic groups control the fusion dynamics and aggregation of PAs in the micellar stage. Simulations also suggest that enhanced structural ordering of vicinal water near the hydrophilic amino acids shifts the equilibrium towards the fibre phase and stimulates structure and order during the PA assembly into nanofibres. Experiments validate our simulation findings; the measured infrared O-H bond stretching frequency is reminiscent of an ice-like bond which suggests that the solvated water becomes increasingly ordered with time in the assembled peptide network, thus shedding light on the role of water in a self-assembly process.

From micelle supramolecular assemblies in selective solvents to isoporous membranes.

PubMed

Nunes, Suzana P; Karunakaran, Madhavan; Pradeep, Neelakanda; Behzad, Ali Reza; Hooghan, Bobby; Sougrat, Rachid; He, Haoze; Peinemann, Klaus-Viktor

2011-08-16

The supramolecular assembly of PS-b-P4VP copolymer micelles induced by selective solvent mixtures was used to manufacture isoporous membranes. Micelle order in solution was confirmed by cryo-scanning electron microscopy in casting solutions, leading to ordered pore morphology. When dioxane, a solvent that interacts poorly with the micelle corona, was added to the solution, polymer-polymer segment contact was preferential, increasing the intermicelle contact. Immersion in water gave rise to asymmetric porous membranes with exceptional pore uniformity and high porosity. The introduction of a small number of carbon nanotubes to the casting solution improved the membrane stability and the reversibility of the gate response in the presence of different pH values.

Reliability of spring interconnects for high channel-count polyimide electrode arrays

NASA Astrophysics Data System (ADS)

Khan, Sharif; Ordonez, Juan Sebastian; Stieglitz, Thomas

2018-05-01

Active neural implants with a high channel-count need robust and reliable operational assembly for the targeted environment in order to be classified as viable fully implantable systems. The discrete functionality of the electrode array and the implant electronics is vital for intact assembly. A critical interface exists at the interconnection sites between the electrode array and the implant electronics, especially in hybrid assemblies (e.g. retinal implants) where electrodes and electronics are not on the same substrate. Since the interconnects in such assemblies cannot be hermetically sealed, reliable protection against the physiological environment is essential for delivering high insulation resistance and low defusibility of salt ions, which are limited in complexity by current assembly techniques. This work reports on a combination of spring-type interconnects on a polyimide array with silicone rubber gasket insulation for chronically active implantable systems. The spring design of the interconnects on the backend of the electrode array compensates for the uniform thickness of the sandwiched gasket during bonding in assembly and relieves the propagation of extrinsic stresses to the bulk polyimide substrate. The contact resistance of the microflex-bonded spring interconnects with the underlying metallized ceramic test vehicles and insulation through the gasket between adjacent contacts was investigated against the MIL883 standard. The contact and insulation resistances remained stable in the exhausting environmental conditions.

Method and system rapid piece handling

DOEpatents

Spletzer, Barry L.

1996-01-01

The advent of high-speed fabric cutters has made necessary the development of automated techniques for the collection and sorting of garment pieces into collated piles of pieces ready for assembly. The present invention enables a new method for such handling and sorting of garment parts, and to apparatus capable of carrying out this new method. The common thread is the application of computer-controlled shuttling bins, capable of picking up a desired piece of fabric and dropping it in collated order for assembly. Such apparatus with appropriate computer control relieves the bottleneck now presented by the sorting and collation procedure, thus greatly increasing the overall rate at which garments can be assembled.

Fabrication Equipment for Periodic Material Assemblies and Ph Assemblies and Photonic Crystals (DURIP FY06)

DTIC Science & Technology

2008-04-29

An exhaust hood is necessary for binder removal. Cooling requires a fan at a second speed setpoint . Firing profiles need to be precisely...29,935.06 from Ohio match. Plasmalab 80 Plus Compact etching system (left) and heater/ chiller unit (right). CAHN TherMax 500 High Pressure TGA...the current research is aimed to optimize parameters of the structure, in order to improve the resonant properties of the periodic layered structures

Long-range single domain array of a 5 nm pattern of supramolecules via solvent annealing in a double-sandwich cell.

PubMed

Kwon, Kiok; Park, Kangho; Jung, Hee-Tae

2018-05-10

In nanotechnology and microelectronics research, the generation of an ultradense, single-grain nanostructure with a long-range lateral order is challenging. In this paper, we report upon a new solvent-annealing method using a double-sandwich confinement to promote the formation of a large-area, single-domain array (>0.3 × 0.3 mm2) of supramolecular cylinders with a small feature size (4.7 nm). The in situ GISAXS experiment result shows the ordering process during solvent evaporation. The diffusion of the solvent molecules led to the disassembly of the supramolecules confined between the top and bottom surfaces and their subsequent mobilization, thereby producing a highly ordered hexagonal array of supramolecular materials under the double-sandwich confinement upon solvent evaporation. In addition, two key factors were found to be crucial in this process for generating highly-ordered supramolecular building blocks: (i) the presence of a top coat during solvent evaporation to provide a geometric confinement template, and (ii) the control of the solvent evaporation rate during the solvent evaporation step to provide the dendrimer sufficient time to self-assemble into the highly ordered state over a large area. Our developed approach, which can be extended to be used for a large family of supramolecules, is of critical importance in providing a new bottom-up lithographic method based on supramolecular self-assembly.

Automation or De-automation

NASA Astrophysics Data System (ADS)

Gorlach, Igor; Wessel, Oliver

2008-09-01

In the global automotive industry, for decades, vehicle manufacturers have continually increased the level of automation of production systems in order to be competitive. However, there is a new trend to decrease the level of automation, especially in final car assembly, for reasons of economy and flexibility. In this research, the final car assembly lines at three production sites of Volkswagen are analysed in order to determine the best level of automation for each, in terms of manufacturing costs, productivity, quality and flexibility. The case study is based on the methodology proposed by the Fraunhofer Institute. The results of the analysis indicate that fully automated assembly systems are not necessarily the best option in terms of cost, productivity and quality combined, which is attributed to high complexity of final car assembly systems; some de-automation is therefore recommended. On the other hand, the analysis shows that low automation can result in poor product quality due to reasons related to plant location, such as inadequate workers' skills, motivation, etc. Hence, the automation strategy should be formulated on the basis of analysis of all relevant aspects of the manufacturing process, such as costs, quality, productivity and flexibility in relation to the local context. A more balanced combination of automated and manual assembly operations provides better utilisation of equipment, reduces production costs and improves throughput.

A universal approach to fabricate ordered colloidal crystals arrays based on electrostatic self-assembly.

PubMed

Zhang, Xun; Zhang, Junhu; Zhu, Difu; Li, Xiao; Zhang, Xuemin; Wang, Tieqiang; Yang, Bai

2010-12-07

We present a novel and simple method to fabricate two-dimensional (2D) poly(styrene sulfate) (PSS, negatively charged) colloidal crystals on a positively charged substrate. Our strategy contains two separate steps: one is the three-dimensional (3D) assembly of PSS particles in ethanol, and the other is electrostatic adsorption in water. First, 3D assembly in ethanol phase eliminates electrostatic attractions between colloids and the substrate. As a result, high-quality colloidal crystals are easily generated, for electrostatic attractions are unfavorable for the movement of colloidal particles during convective self-assembly. Subsequently, top layers of colloidal spheres are washed away in the water phase, whereas well-packed PSS colloids that are in contact with the substrate are tightly linked due to electrostatic interactions, resulting in the formation of ordered arrays of 2D colloidal spheres. Cycling these processes leads to the layer-by-layer assembly of 3D colloidal crystals with controllable layers. In addition, this strategy can be extended to the fabrication of patterned 2D colloidal crystals on patterned polyelectrolyte surfaces, not only on planar substrates but also on nonplanar substrates. This straightforward method may open up new possibilities for practical use of colloidal crystals of excellent quality, various patterns, and controllable fashions.

DNA nanotechnology: a future perspective

PubMed Central

2013-01-01

In addition to its genetic function, DNA is one of the most distinct and smart self-assembling nanomaterials. DNA nanotechnology exploits the predictable self-assembly of DNA oligonucleotides to design and assemble innovative and highly discrete nanostructures. Highly ordered DNA motifs are capable of providing an ultra-fine framework for the next generation of nanofabrications. The majority of these applications are based upon the complementarity of DNA base pairing: adenine with thymine, and guanine with cytosine. DNA provides an intelligent route for the creation of nanoarchitectures with programmable and predictable patterns. DNA strands twist along one helix for a number of bases before switching to the other helix by passing through a crossover junction. The association of two crossovers keeps the helices parallel and holds them tightly together, allowing the assembly of bigger structures. Because of the DNA molecule's unique and novel characteristics, it can easily be applied in a vast variety of multidisciplinary research areas like biomedicine, computer science, nano/optoelectronics, and bionanotechnology. PMID:23497147

Self-assembling layers created by membrane proteins on gold.

PubMed

Shah, D S; Thomas, M B; Phillips, S; Cisneros, D A; Le Brun, A P; Holt, S A; Lakey, J H

2007-06-01

Membrane systems are based on several types of organization. First, amphiphilic lipids are able to create monolayer and bilayer structures which may be flat, vesicular or micellar. Into these structures membrane proteins can be inserted which use the membrane to provide signals for lateral and orientational organization. Furthermore, the proteins are the product of highly specific self-assembly otherwise known as folding, which mostly places individual atoms at precise places in three dimensions. These structures all have dimensions in the nanoscale, except for the size of membrane planes which may extend for millimetres in large liposomes or centimetres on planar surfaces such as monolayers at the air/water interface. Membrane systems can be assembled on to surfaces to create supported bilayers and these have uses in biosensors and in electrical measurements using modified ion channels. The supported systems also allow for measurements using spectroscopy, surface plasmon resonance and atomic force microscopy. By combining the roles of lipids and proteins, highly ordered and specific structures can be self-assembled in aqueous solution at the nanoscale.

High-Definition Self-Assemblies driven by the Hydrophobic Effect: Synthesis and Properties of a Supramolecular Nano-Capsule

PubMed Central

Liu, Simin

2008-01-01

High definition self-assemblies, those that possess order at the molecular level, are most commonly made from subunits possessing metals and metal coordination sites, or groups capable of partaking in hydrogen bonding. In other words, enthalpy is the driving force behind the free energy of assembly. The hydrophobic effect engenders the possibility of (nominally) relying not on enthalpy but entropy to drive assembly. Towards this idea, we describe how template molecules can trigger the dimerization of a cavitand in aqueous solution, and in doing so are encapsulated within the resulting capsule. Although not held together by (enthalpically) strong and directional non-covalent forces, these capsules possess considerable thermodynamic and kinetic stability. As a result, they display unusual and even unique properties. We discuss some of these, including the use of the capsule as a nano-scale reaction chamber and how they can bring about the separation of hydrocarbon gases. PMID:18685753

Programmable DNA scaffolds for spatially-ordered protein assembly.

PubMed

Chandrasekaran, Arun Richard

2016-02-28

Ever since the notion of using DNA as a material was realized, it has been employed in the construction of complex structures that facilitate the assembly of nanoparticles or macromolecules with nanometer-scale precision. Specifically, tiles fashioned from DNA strands and DNA origami sheets have been shown to be suitable as scaffolds for immobilizing proteins with excellent control over their spatial positioning. Supramolecular assembly of proteins into periodic arrays in one or more dimensions is one of the most challenging aspects in the design of scaffolds for biomolecular investigations and macromolecular crystallization. This review provides a brief overview of how various biomolecular interactions with high degree of specificity such as streptavidin-biotin, antigen-antibody, and aptamer-protein interactions have been used to fabricate linear and multidimensional assemblies of structurally intact and functional proteins. The use of DNA-binding proteins as adaptors, polyamide recognition on DNA scaffolds and oligonucleotide linkers for protein assembly are also discussed.

Mechanisms of Size Control and Polymorphism in Viral Capsid Assembly

PubMed Central

Elrad, Oren M.; Hagan, Michael F.

2009-01-01

We simulate the assembly dynamics of icosahedral capsids from subunits that interconvert between different conformations (or quasi-equivalent states). The simulations identify mechanisms by which subunits form empty capsids with only one morphology, but adaptively assemble into different icosahedral morphologies around nanoparticle cargoes with varying sizes, as seen in recent experiments with brome mosaic virus (BMV) capsid proteins. Adaptive cargo encapsidation requires moderate cargo-subunit interaction strengths; stronger interactions frustrate assembly by stabilizing intermediates with incommensurate curvature. We compare simulation results to experiments with cowpea chlorotic mottle virus empty capsids and BMV capsids assembled on functionalized nanoparticles, and suggest new cargo encapsidation experiments. Finally, we find that both empty and templated capsids maintain the precise spatial ordering of subunit conformations seen in the crystal structure even if interactions that preserve this arrangement are favored by as little as the thermal energy, consistent with experimental observations that different subunit conformations are highly similar. PMID:18950240

Unique nucleotide sequence-guided assembly of repetitive DNA parts for synthetic biology applications

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

Torella, JP; Lienert, F; Boehm, CR

2014-08-07

Recombination-based DNA construction methods, such as Gibson assembly, have made it possible to easily and simultaneously assemble multiple DNA parts, and they hold promise for the development and optimization of metabolic pathways and functional genetic circuits. Over time, however, these pathways and circuits have become more complex, and the increasing need for standardization and insulation of genetic parts has resulted in sequence redundancies-for example, repeated terminator and insulator sequences-that complicate recombination-based assembly. We and others have recently developed DNA assembly methods, which we refer to collectively as unique nucleotide sequence (UNS)-guided assembly, in which individual DNA parts are flanked withmore » UNSs to facilitate the ordered, recombination-based assembly of repetitive sequences. Here we present a detailed protocol for UNS-guided assembly that enables researchers to convert multiple DNA parts into sequenced, correctly assembled constructs, or into high-quality combinatorial libraries in only 2-3 d. If the DNA parts must be generated from scratch, an additional 2-5 d are necessary. This protocol requires no specialized equipment and can easily be implemented by a student with experience in basic cloning techniques.« less

Unique nucleotide sequence (UNS)-guided assembly of repetitive DNA parts for synthetic biology applications

PubMed Central

Torella, Joseph P.; Lienert, Florian; Boehm, Christian R.; Chen, Jan-Hung; Way, Jeffrey C.; Silver, Pamela A.

2016-01-01

Recombination-based DNA construction methods, such as Gibson assembly, have made it possible to easily and simultaneously assemble multiple DNA parts and hold promise for the development and optimization of metabolic pathways and functional genetic circuits. Over time, however, these pathways and circuits have become more complex, and the increasing need for standardization and insulation of genetic parts has resulted in sequence redundancies — for example repeated terminator and insulator sequences — that complicate recombination-based assembly. We and others have recently developed DNA assembly methods that we refer to collectively as unique nucleotide sequence (UNS)-guided assembly, in which individual DNA parts are flanked with UNSs to facilitate the ordered, recombination-based assembly of repetitive sequences. Here we present a detailed protocol for UNS-guided assembly that enables researchers to convert multiple DNA parts into sequenced, correctly-assembled constructs, or into high-quality combinatorial libraries in only 2–3 days. If the DNA parts must be generated from scratch, an additional 2–5 days are necessary. This protocol requires no specialized equipment and can easily be implemented by a student with experience in basic cloning techniques. PMID:25101822

Detail design of the surface tension propellant management device for the Intelsat VII communication satellite

NASA Astrophysics Data System (ADS)

Giacalone, Philip L.

1993-06-01

The design of the Intelsat VII surface tension propellant management device (PMD) (an all-welded assembly consisting of about 100 individual components) was developed using a modular design approach that allowed the complex PMD assembly to be divided into smaller modules. The modular approach reduces manufacturing-related technical and schedule risks and allows many components and assemblies to be processed in parallel, while also facilitating the incorporation of quality assurance tests at all critical PMD subassembly levels. The baseline PMD assembly is made from titanium and stainless steel materials. In order to obtain a 100 percent titanium PMD, a new, state-of-the-art fine mesh titanium screen material was developed, tested, and qualified for use as an alternaltive to the stainless steel screen material. The Ti based screen material demonstrated a high level of bubble point performance. It was integrated into a PMD assembly and was successfully qualification tested at the tank assembly level.

Water Ordering Controls the Dynamic Equilibrium of Micelle-Fiber Formation in Self-Assembly of Peptide Amphiphiles

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

Deshmukh, Sanket; Solomon, Lee A.; Kamath, Ganesh

Understanding the role of water in governing the kinetics of the self-assembly processes of amphiphilic peptides has still remained elusive. Here, using a multi-stage atomistic-coarse-grained approach, complemented by circular dichroism/infra-red spectroscopy and dynamic light scattering experiments, we highlight the dual nature of water in dictating the mechanism and dynamics of self-assembly of peptide amphiphiles (PAs). Our computational study shows that (i) Water cage formation and breakage near the hydrophobic groups controls the fusion dynamics and aggregation of PAs in the micellar stage, and (ii) Enhanced structural ordering of vicinal water near the hydrophilic amino acids shifts the equilibrium towards themore » fiber phase and stimulates structure and order in the PAs when they assemble into a hexagonal nanofiber architecture. Finally, spectroscopy and microscopy studies authenticate our computational observation that water ordering near the PAs increases with increase in time. The measured infra-red O-H bond stretch frequency reminiscent of ice-like suggests that the solvated water becomes increasingly solid-like with increased structural order in the assembled peptide network – thus shedding light on the role of water in a self-assembly process.« less

Water Ordering Controls the Dynamic Equilibrium of Micelle-Fiber Formation in Self-Assembly of Peptide Amphiphiles

DOE PAGES

Deshmukh, Sanket; Solomon, Lee A.; Kamath, Ganesh; ...

2016-08-24

Understanding the role of water in governing the kinetics of the self-assembly processes of amphiphilic peptides has still remained elusive. Here, using a multi-stage atomistic-coarse-grained approach, complemented by circular dichroism/infra-red spectroscopy and dynamic light scattering experiments, we highlight the dual nature of water in dictating the mechanism and dynamics of self-assembly of peptide amphiphiles (PAs). Our computational study shows that (i) Water cage formation and breakage near the hydrophobic groups controls the fusion dynamics and aggregation of PAs in the micellar stage, and (ii) Enhanced structural ordering of vicinal water near the hydrophilic amino acids shifts the equilibrium towards themore » fiber phase and stimulates structure and order in the PAs when they assemble into a hexagonal nanofiber architecture. Finally, spectroscopy and microscopy studies authenticate our computational observation that water ordering near the PAs increases with increase in time. The measured infra-red O-H bond stretch frequency reminiscent of ice-like suggests that the solvated water becomes increasingly solid-like with increased structural order in the assembled peptide network – thus shedding light on the role of water in a self-assembly process.« less

Functionalized graphene nanomaterials: new insight into direct exfoliation of graphite with supramolecular polymers

NASA Astrophysics Data System (ADS)

Cheng, Chih-Chia; Chang, Feng-Chih; Wang, Jui-Hsu; Chen, Jem-Kun; Yen, Ying-Chieh; Lee, Duu-Jong

2015-12-01

A novel urea-cytosine end-capped polypropylene glycol (UrCy-PPG) can self-assemble into a long-range ordered lamellar microstructure on the surface of graphene, due to the strong specific interactions between UrCy-PPG and graphene. In addition, the graphene composite produced exhibits a high conductivity (~1093 S m-1) with a dramatic thermo-responsive ON/OFF resistance-switching behavior (10 consecutive cycles).A novel urea-cytosine end-capped polypropylene glycol (UrCy-PPG) can self-assemble into a long-range ordered lamellar microstructure on the surface of graphene, due to the strong specific interactions between UrCy-PPG and graphene. In addition, the graphene composite produced exhibits a high conductivity (~1093 S m-1) with a dramatic thermo-responsive ON/OFF resistance-switching behavior (10 consecutive cycles). Electronic supplementary information (ESI) available. See DOI: 10.1039/c5nr07076g

High-speed superresolution imaging of the proteins in fission yeast clathrin-mediated endocytic actin patches

PubMed Central

Arasada, Rajesh; Sayyad, Wasim A.; Berro, Julien; Pollard, Thomas D.

2018-01-01

To internalize nutrients and cell surface receptors via clathrin-mediated endocytosis, cells assemble at least 50 proteins, including clathrin, clathrin-interacting proteins, actin filaments, and actin binding proteins, in a highly ordered and regulated manner. The molecular mechanism by which actin filament polymerization deforms the cell membrane is unknown, largely due to lack of knowledge about the organization of the regulatory proteins and actin filaments. We used high-speed superresolution localization microscopy of live fission yeast cells to improve the spatial resolution to ∼35 nm with 1-s temporal resolution. The nucleation promoting factors Wsp1p (WASp) and Myo1p (myosin-I) define two independent pathways that recruit Arp2/3 complex, which assembles two zones of actin filaments. Myo1p concentrates at the site of endocytosis and initiates a zone of actin filaments assembled by Arp2/3 complex. Wsp1p appears simultaneously at this site but subsequently moves away from the cell surface as it stimulates Arp2/3 complex to assemble a second zone of actin filaments. Cells lacking either nucleation-promoting factor assemble only one, stationary, zone of actin filaments. These observations support our two-zone hypothesis to explain endocytic tubule elongation and vesicle scission in fission yeast. PMID:29212877

Tunable and rapid self-assembly of block copolymers using mixed solvent vapors.

PubMed

Park, Woon Ik; Tong, Sheng; Liu, Yuzi; Jung, Il Woong; Roelofs, Andreas; Hong, Seungbum

2014-12-21

Pattern generation of well-controlled block copolymers (BCPs) with a high Flory-Huggins interaction parameter (χ) is important for applications in sub-20 nm nanolithography. We used mixed solvents of dimethylformamide (DMF) and toluene to control the morphology as well as the time to achieve the targeted morphology via self-assembly of BCPs. By precisely controlling the volume ratio of DMF and toluene, well-ordered line, honeycomb, circular hole, and lamellar nanostructures were obtained from a cylinder-forming poly(styrene-b-2-vinylpyridine) (PS-b-P2VP) BCP with high χ. Furthermore, a well-aligned 12 nm line pattern was successfully achieved in the guiding template within one minute using the mixed solvents. This practical method may also be applicable to self-assembly of other BCPs, providing more opportunities for the next-generation sub-10 nm lithography applications.

Influence of functionalized silicones on hair fiber-fiber interactions and on the relationship with the macroscopic behavior of hair assembly.

PubMed

Dussaud, Anne; Fieschi-Corso, Lara

2009-01-01

It is well established that silicones alter hair surface properties and that silicones have a significant impact on the macroscopic behavior of hair assembly, such as visual appearance, combing performance and manageability of the hair. In order to fine-tune the chemistry of functionlized silicones for specific consumer benefits and hair types, we investigated the influence of silicones on hair fiber-fiber interactions and their correlation to hair volume. The incline plane fiber loop method, implemented with a high-precision motorized rotary stage, was used to quantify the fiber-fiber interactions. Low load static friction was studied as a function of polymer molecular weight, dose and chemical architecture. This information was related to the macroscopic behavior of hair assembly, using virgin curly hair in high humidity.

Long-read sequence assembly of the firefly Pyrocoelia pectoralis genome

PubMed Central

Fu, Xinhua; Li, Jingjing; Tian, Yu; Quan, Weipeng; Zhang, Shu; Liu, Qian; Liang, Fan; Zhu, Xinlei; Zhang, Liangsheng

2017-01-01

Abstract Background Fireflies are a family of insects within the beetle order Coleoptera, or winged beetles, and they are one of the most well-known and loved insect species because of their bioluminescence. However, the firefly is in danger of extinction because of the massive destruction of its living environment. In order to improve the understanding of fireflies and protect them effectively, we sequenced the whole genome of the terrestrial firefly Pyrocoelia pectoralis. Findings Here, we developed a highly reliable genome resource for the terrestrial firefly Pyrocoelia pectoralis (E. Oliv., 1883; Coleoptera: Lampyridae) using single molecule real time (SMRT) sequencing on the PacBio Sequel platform. In total, 57.8 Gb of long reads were generated and assembled into a 760.4-Mb genome, which is close to the estimated genome size and covered 98.7% complete and 0.7% partial insect Benchmarking Universal Single-Copy Orthologs. The k-mer analysis showed that this genome is highly heterozygous. However, our long-read assembly demonstrates continuousness with a contig N50 length of 3.04 Mb and the longest contig length of 13.69 Mb. Furthermore, 135 589 SSRs and 341 Mb of repeat sequences were detected. A total of 23 092 genes were predicted; 88.44% of genes were annotated with one or more related functions. Conclusions We assembled a high-quality firefly genome, which will not only provide insights into the conservation and biodiversity of fireflies, but also provide a wealth of information to study the mechanisms of their sexual communication, bio-luminescence, and evolution. PMID:29186486

Design of ferrocene-dipeptide bioorganometallic conjugates to induce chirality-organized structures.

PubMed

Moriuchi, Toshiyuki; Hirao, Toshikazu

2010-07-20

The highly ordered molecular assemblies in proteins can have a variety of functions, as observed in enzymes, receptors, and the like. Synthetic scientists are constructing bioinspired systems by harnessing the self-assembling properties of short peptides. Secondary structures such as alpha-helices, beta-sheets, and beta-turns are important in protein folding, which is mostly directed and stabilized by hydrogen bonding and the hydrophobic interactions of side chains. The design of secondary structure mimics that are composed of short peptides has attracted much attention, both for gaining fundamental insight into the factors affecting protein folding and for developing pharmacologically useful compounds, artificial receptors, asymmetric catalysts, and new materials. Ferrocenes are an organometallic scaffold with a central reverse-turn unit based on the inter-ring spacing of about 3.3 A, which is a suitable distance for hydrogen bonding between attached peptide strands. The conjugation of organometallic compounds with biomolecules such as amino acids, peptides, and DNA should provide novel systems that reflect properties of both the ferrocene and the biologically derived moieties. In this Account, we focus on recent advances in the design of ferrocene-peptide bioconjugates, which help illustrate the peptidomimetic basis for protein folding and the means of constructing highly ordered molecular assemblies. Ferrocene-peptide bioconjugates are constructed to form chirality-organized structures in both solid and solution states. The ferrocene serves as a reliable organometallic scaffold for the construction of protein secondary structures via intramolecular hydrogen bonding: the attached dipeptide strands are constrained within the appropriate dimensions. The introduction of the chiral dipeptide chains into the ferrocene scaffold induces the conformational enantiomerization of the ferrocenyl moiety; the chirality-organized structure results from intramolecular hydrogen bonding. The configuration and sequence of the amino acids are instrumental in the process. Regulation of the directionality and specificity of hydrogen bonding is a key component in the design of various molecular assemblies. Ferrocene-peptide bioconjugates also have a strong tendency to self-assemble through the contributions of available hydrogen-bonding donors in the solid state. Some ferrocene-peptide bioconjugates bearing only one dipeptide chain exhibit a helically ordered molecular assembly through a network of intermolecular (rather than intramolecular) hydrogen bonds. The propensity to form the chiral helicity appears to be controlled by the chirality of the dipeptide chains. Organization of host molecules is a useful strategy for forming artificial receptors. The conformationally regulated ferrocene-peptide bioconjugate provides the chirality-organized binding site for size-selective and chiral recognition of dicarboxylic acids through multipoint hydrogen bonds. Metal ions serve a variety of purposes in proteins, including structural stabilization for biological function. The complexation of ferrocene-peptide bioconjugates with palladium(II) compounds not only stabilizes the chirality conformational regulation but also induces conformational regulation of the dipeptide chain through complexation and intramolecular chirality organization. Construction of the chirality-organized ferrocene-peptide bioconjugates is also achieved by metal-directed assembly. These varied examples amply demonstrate the value of ferrocene-peptide bioconjugates in asserting architectural control over highly ordered molecular assemblies.

Cobalt ion-coordinated self-assembly synthesis of nitrogen-doped ordered mesoporous carbon nanosheets for efficiently catalyzing oxygen reduction.

PubMed

Wang, Haitao; Wang, Wei; Asif, Muhammad; Yu, Yang; Wang, Zhengyun; Wang, Junlei; Liu, Hongfang; Xiao, Junwu

2017-10-19

The design and synthesis of a promising porous carbon-based electrocatalyst with an ordered and uninterrupted porous structure for oxygen reduction reaction (ORR) is still a significant challenge. Herein, an efficient catalyst based on cobalt-embedded nitrogen-doped ordered mesoporous carbon nanosheets (Co/N-OMCNS) is successfully prepared through a two-step procedure (cobalt ion-coordinated self-assembly and carbonization process) using 3-aminophenol as a nitrogen source, cobalt acetate as a cobalt source and Pluronic F127 as a mesoporous template. This work indicates that the formation of a two dimensional nanosheet structure is directly related to the extent of the cobalt ion coordination interaction. Moreover, the critical roles of pyrolysis temperature in nitrogen doping and ORR catalytic activity are also investigated. Benefiting from the high surface area and graphitic degree, high contents of graphitic N and pyridinic N, ordered interconnected mesoporous carbon framework, as well as synergetic interaction between the cobalt nanoparticles and protective nitrogen doped graphitic carbon layer, the resultant optimal catalyst Co/N-OMCNS-800 (pyrolyzed at 800 °C) exhibits comparable ORR catalytic activity to Pt/C, superior tolerance to methanol crossover and stability.

Gyroid Nickel Nanostructures from Diblock Copolymer Supramolecules

PubMed Central

Vukovic, Ivana; Punzhin, Sergey; Voet, Vincent S. D.; Vukovic, Zorica; de Hosson, Jeff Th. M.; ten Brinke, Gerrit; Loos, Katja

2014-01-01

Nanoporous metal foams possess a unique combination of properties - they are catalytically active, thermally and electrically conductive, and furthermore, have high porosity, high surface-to-volume and strength-to-weight ratio. Unfortunately, common approaches for preparation of metallic nanostructures render materials with highly disordered architecture, which might have an adverse effect on their mechanical properties. Block copolymers have the ability to self-assemble into ordered nanostructures and can be applied as templates for the preparation of well-ordered metal nanofoams. Here we describe the application of a block copolymer-based supramolecular complex - polystyrene-block-poly(4-vinylpyridine)(pentadecylphenol) PS-b-P4VP(PDP) - as a precursor for well-ordered nickel nanofoam. The supramolecular complexes exhibit a phase behavior similar to conventional block copolymers and can self-assemble into the bicontinuous gyroid morphology with two PS networks placed in a P4VP(PDP) matrix. PDP can be dissolved in ethanol leading to the formation of a porous structure that can be backfilled with metal. Using electroless plating technique, nickel can be inserted into the template's channels. Finally, the remaining polymer can be removed via pyrolysis from the polymer/inorganic nanohybrid resulting in nanoporous nickel foam with inverse gyroid morphology. PMID:24797367

Gyroid nickel nanostructures from diblock copolymer supramolecules.

PubMed

Vukovic, Ivana; Punzhin, Sergey; Voet, Vincent S D; Vukovic, Zorica; de Hosson, Jeff Th M; ten Brinke, Gerrit; Loos, Katja

2014-04-28

Nanoporous metal foams possess a unique combination of properties - they are catalytically active, thermally and electrically conductive, and furthermore, have high porosity, high surface-to-volume and strength-to-weight ratio. Unfortunately, common approaches for preparation of metallic nanostructures render materials with highly disordered architecture, which might have an adverse effect on their mechanical properties. Block copolymers have the ability to self-assemble into ordered nanostructures and can be applied as templates for the preparation of well-ordered metal nanofoams. Here we describe the application of a block copolymer-based supramolecular complex - polystyrene-block-poly(4-vinylpyridine)(pentadecylphenol) PS-b-P4VP(PDP) - as a precursor for well-ordered nickel nanofoam. The supramolecular complexes exhibit a phase behavior similar to conventional block copolymers and can self-assemble into the bicontinuous gyroid morphology with two PS networks placed in a P4VP(PDP) matrix. PDP can be dissolved in ethanol leading to the formation of a porous structure that can be backfilled with metal. Using electroless plating technique, nickel can be inserted into the template's channels. Finally, the remaining polymer can be removed via pyrolysis from the polymer/inorganic nanohybrid resulting in nanoporous nickel foam with inverse gyroid morphology.

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.

Assembling the bacterial segrosome.

PubMed

Hayes, Finbarr; Barillà, Daniela

2006-05-01

Genome segregation in prokaryotes is a highly ordered process that integrates with DNA replication, cytokinesis and other fundamental facets of the bacterial cell cycle. The segrosome is the nucleoprotein complex that mediates DNA segregation in bacteria, its assembly and organization is best understood for plasmid partition. The recent elucidation of structures of the ParB plasmid segregation protein bound to centromeric DNA, and of the tertiary structures of other segregation proteins, are key milestones in the path to deciphering the molecular basis of bacterial DNA segregation.

High performance and durability of order-structured cathode catalyst layer based on TiO2@PANI core-shell nanowire arrays

NASA Astrophysics Data System (ADS)

Chen, Ming; Wang, Meng; Yang, Zhaoyi; Wang, Xindong

2017-06-01

In this paper, an order-structured cathode catalyst layer consisting of Pt-TiO2@PANI core-shell nanowire arrays that in situ grown on commercial gas diffusion layer (GDL) are prepared and applied to membrane electrode assembly (MEA) of proton exchange membrane fuel cell (PEMFC). In order to prepare the TiO2@PANI core-shell nanowire arrays with suitable porosity and prominent conductivity, the morphologies of the TiO2 nanoarray and electrochemical polymerization process of aniline are schematically investigated. The MEA with order-structured cathode catalyst layer is assembled in the single cell to evaluate the electrochemical performance and durability of PEMFC. As a result, the PEMFC with order-structured cathode catalyst layer shows higher peak power density (773.54 mW cm-2) than conventional PEMFC (699.30 mW cm-2). Electrochemically active surface area (ECSA) and charge transfer impedance (Rct) are measured before and after accelerated degradation test (ADT), and the corresponding experimental results indicate the novel cathode structure exhibits a better stability with respect to conventional cathode. The enhanced electrochemical performance and durability toward PEMFC can be ascribed to the order-structured cathode nanoarray structure with high specific surface area increases the utilization of catalyst and reduces the tortuosity of transport pathways, and the synergistic effect between TiO2@PANI support and Pt nanoparticles promotes the high efficiency of electrochemical reaction and improves the stability of catalyst. This research provides a facile and controllable method to prepare order-structured membrane electrode with lower Pt loading for PEMFC in the future.

Dynamics of self-assembled cytosine nucleobases on graphene

NASA Astrophysics Data System (ADS)

Saikia, Nabanita; Johnson, Floyd; Waters, Kevin; Pandey, Ravindra

2018-05-01

Molecular self-assembly of cytosine (C n ) bases on graphene was investigated using molecular dynamics methods. For free-standing C n bases, simulation conditions (gas versus aqueous) determine the nature of self-assembly; the bases prefer to aggregate in the gas phase and are stabilized by intermolecular H-bonds, while in the aqueous phase, the water molecules disrupt base-base interactions, which facilitate the formation of π-stacked domains. The substrate-induced effects, on the other hand, find the polarity and donor-acceptor sites of the bases to govern the assembly process. For example, in the gas phase, the assembly of C n bases on graphene displays short-range ordered linear arrays stabilized by the intermolecular H-bonds. In the aqueous phase, however, there are two distinct configurations for the C n bases assembly on graphene. For the first case corresponding to low surface coverage, the bases are dispersed on graphene and are isolated. The second configuration archetype is disordered linear arrays assembled with medium and high surface coverage. The simulation results establish the role of H-bonding, vdW π-stacking, and the influence of graphene surface towards the self-assembly. The ability to regulate the assembly into well-defined patterns can aid in the design of self-assembled nanostructures for the next-generation DNA based biosensors and nanoelectronic devices.

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.

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.

Electrochemical Control of Peptide Self-Organization on Atomically Flat Solid Surfaces: A Case Study with Graphite.

PubMed

Seki, Takakazu; So, Christopher R; Page, Tamon R; Starkebaum, David; Hayamizu, Yuhei; Sarikaya, Mehmet

2018-02-06

The nanoscale self-organization of biomolecules, such as proteins and peptides, on solid surfaces under controlled conditions is an important issue in establishing functional bio/solid soft interfaces for bioassays, biosensors, and biofuel cells. Electrostatic interaction between proteins and surfaces is one of the most essential parameters in the adsorption and self-assembly of proteins on solid surfaces. Although the adsorption of proteins has been studied with respect to the electrochemical surface potential, the self-assembly of proteins or peptides forming well-organized nanostructures templated by lattice structure of the solid surfaces has not been studied in the relation to the surface potential. In this work, we utilize graphite-binding peptides (GrBPs) selected by the phage display method to investigate the relationship between the electrochemical potential of the highly ordered pyrolytic graphite (HOPG) and peptide self-organization forming long-range-ordered structures. Under modulated electrical bias, graphite-binding peptides form various ordered structures, such as well-ordered nanowires, dendritic structures, wavy wires, amorphous (disordered) structures, and islands. A systematic investigation of the correlation between peptide sequence and self-organizational characteristics reveals that the presence of the bias-sensitive amino acid modules in the peptide sequence has a significant effect on not only surface coverage but also on the morphological features of self-assembled structures. Our results show a new method to control peptide self-assembly by means of applied electrochemical bias as well as peptide design-rules for the construction of functional soft bio/solid interfaces that could be integrated in a wide range of practical implementations.

Highly-ordered supportless three-dimensional nanowire networks with tunable complexity and interwire connectivity for device integration.

PubMed

Rauber, Markus; Alber, Ina; Müller, Sven; Neumann, Reinhard; Picht, Oliver; Roth, Christina; Schökel, Alexander; Toimil-Molares, Maria Eugenia; Ensinger, Wolfgang

2011-06-08

The fabrication of three-dimensional assemblies consisting of large quantities of nanowires is of great technological importance for various applications including (electro-)catalysis, sensitive sensing, and improvement of electronic devices. Because the spatial distribution of the nanostructured material can strongly influence the properties, architectural design is required in order to use assembled nanowires to their full potential. In addition, special effort has to be dedicated to the development of efficient methods that allow precise control over structural parameters of the nanoscale building blocks as a means of tuning their characteristics. This paper reports the direct synthesis of highly ordered large-area nanowire networks by a method based on hard templates using electrodeposition within nanochannels of ion track-etched polymer membranes. Control over the complexity of the networks and the dimensions of the integrated nanostructures are achieved by a modified template fabrication. The networks possess high surface area and excellent transport properties, turning them into a promising electrocatalyst material as demonstrated by cyclic voltammetry studies on platinum nanowire networks catalyzing methanol oxidation. Our method opens up a new general route for interconnecting nanowires to stable macroscopic network structures of very high integration level that allow easy handling of nanowires while maintaining their connectivity.

Individualized FAC on bottom tab subassemblies to minimize adhesive gap between emitter and optics

NASA Astrophysics Data System (ADS)

Sauer, Sebastian; Müller, Tobias; Haag, Sebastian; Beleke, Andreas; Zontar, Daniel; Baum, Christoph; Brecher, Christian

2017-02-01

High Power Diode Laser (HPDL) systems with short focal length fast-axis collimators (FAC) require submicron assembly precision. Conventional FAC-Lens assembly processes require adhesive gaps of 50 microns or more in order to compensate for component tolerances (e.g. deviation of back focal length) and previous assembly steps. In order to control volumetric shrinkage of fast-curing UV-adhesives shrinkage compensation is mandatory. The novel approach described in this paper aims to minimize the impact of volumetric shrinkage due to the adhesive gap between HPDL edge emitters and FAC-Lens. Firstly, the FAC is actively aligned to the edge emitter without adhesives or bottom tab. The relative position and orientation of FAC to emitter are measured and stored. Consecutively, an individual subassembly of FAC and bottom tab is assembled on Fraunhofer IPT's mounting station with a precision of +/-1 micron. Translational and lateral offsets can be compensated, so that a narrow and uniform glue gap for the consecutive bonding process of bottom tab to heatsink applies (Figure 4). Accordingly, FAC and bottom tab are mounted to the heatsink without major shrinkage compensation. Fraunhofer IPT's department assembly of optical systems and automation has made several publications regarding active alignment of FAC lenses [SPIE LASE 8241-12], volumetric shrinkage compensation [SPIE LASE 9730-28] and FAC on bottom tab assembly [SPIE LASE 9727-31] in automated production environments. The approach described in this paper combines these and is the logical continuation of that work towards higher quality of HPDLs.

Assembly of the epithelial Na+ channel evaluated using sucrose gradient sedimentation analysis.

PubMed

Cheng, C; Prince, L S; Snyder, P M; Welsh, M J

1998-08-28

Three subunits, alpha, beta, and gamma, contribute to the formation of the epithelial Na+ channel. To investigate the oligomeric assembly of the channel complex, we used sucrose gradient sedimentation analysis to determine the sedimentation properties of individual subunits and heteromultimers comprised of multiple subunits. When the alpha subunit was expressed alone, it first formed an oligomeric complex with a sedimentation coefficient of 11 S, and then generated a higher order multimer of 25 S. In contrast, individual beta and gamma subunits predominately assembled into 11 S complexes. We obtained similar results with expression in cells and in vitro. When we co-expressed beta with alpha or with alpha plus gamma, the beta subunit assembled into a 25 S complex. Glycosylation of the alpha subunit was not required for assembly into a 25 S complex. We found that the alpha subunit formed intra-chain disulfide bonds. Although such bonds were not required to generate an oligomeric complex, under nonreducing conditions the alpha subunit formed a complex that migrated more homogeneously at 25 S. This suggests that intra-chain disulfide bonds may stabilize the complex. These data suggest that the epithelial Na+ channel subunits form high order oligomeric complexes and that the alpha subunit contains the information that facilitates such formation. Interestingly, the ability of the alpha, but not the beta or gamma, subunit to assemble into a 25 S homomeric complex correlates with the ability of these subunits to generate functional channels when expressed alone.

Multifunctional Self-Assembled Monolayers for Organic Field-Effect Transistors

NASA Astrophysics Data System (ADS)

Cernetic, Nathan

Organic field effect transistors (OFETs) have the potential to reach commercialization for a wide variety of applications such as active matrix display circuitry, chemical and biological sensing, radio-frequency identification devices and flexible electronics. In order to be commercially competitive with already at-market amorphous silicon devices, OFETs need to approach similar performance levels. Significant progress has been made in developing high performance organic semiconductors and dielectric materials. Additionally, a common route to improve the performance metric of OFETs is via interface modification at the critical dielectric/semiconductor and electrode/semiconductor interface which often play a significant role in charge transport properties. These metal oxide interfaces are typically modified with rationally designed multifunctional self-assembled monolayers. As means toward improving the performance metrics of OFETs, rationally designed multifunctional self-assembled monolayers are used to explore the relationship between surface energy, SAM order, and SAM dipole on OFET performance. The studies presented within are (1) development of a multifunctional SAM capable of simultaneously modifying dielectric and metal surface while maintaining compatibility with solution processed techniques (2) exploration of the relationship between SAM dipole and anchor group on graphene transistors, and (3) development of self-assembled monolayer field-effect transistor in which the traditional thick organic semiconductor is replaced by a rationally designed self-assembled monolayer semiconductor. The findings presented within represent advancement in the understanding of the influence of self-assembled monolayers on OFETs as well as progress towards rationally designed monolayer transistors.

Self-assembly and modular functionalization of three-dimensional crystals from oppositely charged proteins

NASA Astrophysics Data System (ADS)

Liljeström, Ville; Mikkilä, Joona; Kostiainen, Mauri A.

2014-07-01

Multicomponent crystals and nanoparticle superlattices are a powerful approach to integrate different materials into ordered nanostructures. Well-developed, especially DNA-based, methods for their preparation exist, yet most techniques concentrate on molecular and synthetic nanoparticle systems in non-biocompatible environment. Here we describe the self-assembly and characterization of binary solids that consist of crystalline arrays of native biomacromolecules. We electrostatically assembled cowpea chlorotic mottle virus particles and avidin proteins into heterogeneous crystals, where the virus particles adopt a non-close-packed body-centred cubic arrangement held together by avidin. Importantly, the whole preparation process takes place at room temperature in a mild aqueous medium allowing the processing of delicate biological building blocks into ordered structures with lattice constants in the nanometre range. Furthermore, the use of avidin-biotin interaction allows highly selective pre- or post-functionalization of the protein crystals in a modular way with different types of functional units, such as fluorescent dyes, enzymes and plasmonic nanoparticles.

Self-assembly of dodecaphenyl POSS thin films

NASA Astrophysics Data System (ADS)

Handke, Bartosz; Klita, Łukasz; Niemiec, Wiktor

2017-12-01

The self-assembly abilities of Dodecaphenyl Polyhedral Oligomeric Silsesquioxane thin films on Si(1 0 0) surfaces were studied. Due to their thermal properties - relatively low sublimation temperature and preservation of molecular structure - cage type silsesquioxanes are ideal material for the preparation of a thin films by Physical Vapor Deposition. The Ultra-High Vacuum environment and the deposition precision of the PVD method enable the study of early stages of thin film growth and its molecular organization. X-ray Reflectivity and Atomic Force Microscopy measurements allow to pursuit size-effects in the structure of thin films with thickness ranges from less than a single molecular layer up to several tens of layers. Thermal treatment of the thin films triggered phase change: from a poorly ordered polycrystalline film into a well-ordered multilayer structure. Self-assembly of the layers is the effect of the π-stacking of phenyl rings, which force molecules to arrange in a superlattice, forming stacks of alternating organic-inorganic layers.

Kinetic Effects on Self-Assembly and Function of Protein-Polymer Bioconjugates in Thin Films Prepared by Flow Coating.

PubMed

Chang, Dongsook; Huang, Aaron; Olsen, Bradley D

2017-01-01

The self-assembly of nanostructured globular protein arrays in thin films is demonstrated using protein-polymer block copolymers based on a model protein mCherry and the polymer poly(oligoethylene glycol acrylate) (POEGA). Conjugates are flow coated into thin films on a poly(ethylene oxide) grafted Si surface, forming self-assembled cylindrical nanostructures with POEGA domains selectively segregating to the air-film interface. Long-range order and preferential arrangement of parallel cylinders templated by selective surfaces are demonstrated by controlling relative humidity. Long-range order increases with coating speed when the film thicknesses are kept constant, due to reduced nucleation per unit area of drying film. Fluorescence emission spectra of mCherry in films prepared at <25% relative humidity shows a small shift suggesting that proteins are more perturbed at low humidity than high humidity or the solution state. © 2016 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Encapsulation of Polymer Colloids in a Sol-Gel Matrix. Direct-Writing of Coassembling Organic-Inorganic Hybrid Photonic Crystals.

PubMed

Mikosch, Annabel; Kuehne, Alexander J C

2016-03-22

The spontaneous self-assembly of polymer colloids into ordered arrangements provides a facile strategy for the creation of photonic crystals. However, these structures often suffer from defects and insufficient cohesion, which result in flaking and delamination from the substrate. A coassembly process has been developed for convective assembly, resulting in large-area encapsulated colloidal crystals. However, to generate patterns or discrete deposits in designated places, convective assembly is not suitable. Here we experimentally develop conditions for direct-writing of coassembling monodisperse dye-doped polystyrene particles with a sol-gel precursor to form solid encapsulated photonic crystals. In a simple procedure the colloids are formulated in a sol-gel precursor solution, drop-cast on a flat substrate, and dried. We here establish the optimal parameters to form reproducible highly ordered photonic crystals with good optical performance. The obtained photonic crystals interact with light in the visible spectrum with a narrow optical stop-gap.

Inter and Intra Molecular Phase Separation Environment Effects on PI-PEO Block Copolymers for Batteries and Fuel Cells

NASA Technical Reports Server (NTRS)

Xue, Chen-Chen; Meador, Mary Ann B.; Eby, R. K.; Cheng, Stephen Z. D.; Ge, Jason J.; Cubon, Valerie A.

2002-01-01

Rod-coil molecules have been introduced as a novel type of block copolymers with unique microstructure due to their ability to self-assemble to various ordered morphologies on a nanometer length scale. These molecules, comprised two homo polymers joined together at one end, microphase separate into ordered, periodic arrays of spheres, cylinders in the bulk state and or solution. To get ordered structure in a reasonable scale, additional force field are applied, such as mechanical shearing, electric field and magnetic field. Recently, progress has made it a possible to develop a new class of polyimides (PI)-Polyethylene oxide (PEO) that are soluble in polar organic solvents. The solvent-soluble PI-PEO has a wide variety of applications in microelectronics, since these PI-PEO films exhibit a high degree of thermal and chemical stability. In this paper, we report the self-assembled ordered structure of PI-PEO molecules formed from concentrate solution.

Design and testing of the Space Station Freedom Propellant Tank Assembly

NASA Technical Reports Server (NTRS)

Dudley, D. D.; Thonet, T. A.; Goforth, A. M.

1992-01-01

Propellant storage and management functions for the Propulsion Module of the U.S. Space Station Freedom are provided by the Propellant Tank Assembly (PTA). The PTA consists of a surface-tension type propellant acquisition device contained within a welded titanium pressure vessel. The PTA design concept was selected with high reliability and low program risk as primary goals in order to meet stringent NASA structural, expulsion, fracture control and reliability requirements. The PTA design makes use of Shuttle Orbital Maneuvering System and Peacekeeper Propellant Storage Assembly design and analysis techniques. This paper summarizes the PTA design solution and discusses the underlying detailed analyses. In addition, design verification and qualification test activities are discussed.

Self-assembly and structural relaxation in a model ionomer melt

DOE PAGES

Goswami, Monojoy; Borreguero, Jose M.; Sumpter, Bobby G.

2015-02-26

Molecular dynamics simulations are used to understand the self-assembly and structural relaxation in ionomer melts containing less than 10% degree of ionization on the backbone. We study the self-assembly of charged sites and counterions that show structural ordering and agglomeration with a range of structures that can be achieved by changing the dielectric constant of the medium. The intermediate scattering function shows a decoupling of charge and counterion relaxation at longer length scales for only high dielectric constant and at shorter length scales for all dielectric constants. Finally, the slow structural decay of counterions in the strongly correlated ionomer systemmore » closely resembles transport properties of semi-flexible polymers.« less

Fabrication and Metrology of High-Precision Foil Mirror Mounting Elements

NASA Technical Reports Server (NTRS)

Schattenburg, Mark L.

2002-01-01

During the period of this Cooperative Agreement, MIT (Massachusetts Institute of Technology) developed advanced methods for applying silicon microstructures for the precision assembly of foil x-ray optics in support of the Constellation-X Spectroscopy X-ray Telescope (SXT) development effort at Goddard Space Flight Center (GSFC). MIT developed improved methods for fabricating and characterizing the precision silicon micro-combs. MIT also developed and characterized assembly tools and several types of metrology tools in order to characterize and reduce the errors associated with precision assembly of foil optics. Results of this effort were published and presented to the scientific community and the GSFC SXT team. A bibliography of papers and presentations is offered.

Structural Determination of Biomolecules in Microfluidic Systems

NASA Astrophysics Data System (ADS)

Butler, John C.; Menard, Etienne; Rogers, John A.; Wong, Gerard C. L.

2004-03-01

Supramolecular biological complexes are often too large to be crystallized for structural studies. Here, we explore the use of microfluidic arrays to order a model self-assembled cytoskeletal system. Filamentous actin (F-actin) is a negatively charged protein rod and is a key structural component in the eukaryotic cytoskeleton. In this context, F-actin can self-assemble with actin binding proteins (ABP) in a highly regulated manner to dynamically form structures for a wide range of biomechanical functions. In this work, we will systematically study the action of 3 types of actin binding proteins (a-actinin, fimbrin, cofilin) on the self-assembled structures of F-actin that have been aligned in microfluidic arrays.

The sarcomeric cytoskeleton: from molecules to motion.

PubMed

Gautel, Mathias; Djinović-Carugo, Kristina

2016-01-01

Highly ordered organisation of striated muscle is the prerequisite for the fast and unidirectional development of force and motion during heart and skeletal muscle contraction. A group of proteins, summarised as the sarcomeric cytoskeleton, is essential for the ordered assembly of actin and myosin filaments into sarcomeres, by combining architectural, mechanical and signalling functions. This review discusses recent cell biological, biophysical and structural insight into the regulated assembly of sarcomeric cytoskeleton proteins and their roles in dissipating mechanical forces in order to maintain sarcomere integrity during passive extension and active contraction. α-Actinin crosslinks in the Z-disk show a pivot-and-rod structure that anchors both titin and actin filaments. In contrast, the myosin crosslinks formed by myomesin in the M-band are of a ball-and-spring type and may be crucial in providing stable yet elastic connections during active contractions, especially eccentric exercise. © 2016. Published by The Company of Biologists Ltd.

Construction and Annotation of a High Density SNP Linkage Map of the Atlantic Salmon (Salmo salar) Genome.

PubMed

Tsai, Hsin Y; Robledo, Diego; Lowe, Natalie R; Bekaert, Michael; Taggart, John B; Bron, James E; Houston, Ross D

2016-07-07

High density linkage maps are useful tools for fine-scale mapping of quantitative trait loci, and characterization of the recombination landscape of a species' genome. Genomic resources for Atlantic salmon (Salmo salar) include a well-assembled reference genome, and high density single nucleotide polymorphism (SNP) arrays. Our aim was to create a high density linkage map, and to align it with the reference genome assembly. Over 96,000 SNPs were mapped and ordered on the 29 salmon linkage groups using a pedigreed population comprising 622 fish from 60 nuclear families, all genotyped with the 'ssalar01' high density SNP array. The number of SNPs per group showed a high positive correlation with physical chromosome length (r = 0.95). While the order of markers on the genetic and physical maps was generally consistent, areas of discrepancy were identified. Approximately 6.5% of the previously unmapped reference genome sequence was assigned to chromosomes using the linkage map. Male recombination rate was lower than females across the vast majority of the genome, but with a notable peak in subtelomeric regions. Finally, using RNA-Seq data to annotate the reference genome, the mapped SNPs were categorized according to their predicted function, including annotation of ∼2500 putative nonsynonymous variants. The highest density SNP linkage map for any salmonid species has been created, annotated, and integrated with the Atlantic salmon reference genome assembly. This map highlights the marked heterochiasmy of salmon, and provides a useful resource for salmonid genetics and genomics research. Copyright © 2016 Tsai et al.

Numerical calculations of temperature dependence of dielectric constant for an ordered assembly of BaTiO3 nanocubes with small tilt angles

NASA Astrophysics Data System (ADS)

Yasui, Kyuichi; Mimura, Ken-ichi; Izu, Noriya; Kato, Kazumi

2018-03-01

The dielectric constant of an ordered assembly of BaTiO3 nanocubes is numerically calculated as a function of temperature assuming a distribution of tilt angles of attached nanocubes. As the phase transition temperature from the tetragonal crystal structure to the cubic crystal structure of a BaTiO3 nanocube decreases as the tilt angle increases, the temperature at the peak of the dielectric constant of an ordered assembly is considerably lower than the Curie temperature of a free-standing BaTiO3 crystal. The peak of the dielectric constant as a function of temperature for an ordered assembly becomes considerably broader than that for a single crystal owing to the contribution of nanocubes with various tilt angles.

High pressure, high current, low inductance, high reliability sealed terminals

DOEpatents

Hsu, John S [Oak Ridge, TN; McKeever, John W [Oak Ridge, TN

2010-03-23

The invention is a terminal assembly having a casing with at least one delivery tapered-cone conductor and at least one return tapered-cone conductor routed there-through. The delivery and return tapered-cone conductors are electrically isolated from each other and positioned in the annuluses of ordered concentric cones at an off-normal angle. The tapered cone conductor service can be AC phase conductors and DC link conductors. The center core has at least one service conduit of gate signal leads, diagnostic signal wires, and refrigerant tubing routed there-through. A seal material is in direct contact with the casing inner surface, the tapered-cone conductors, and the service conduits thereby hermetically filling the interstitial space in the casing interior core and center core. The assembly provides simultaneous high-current, high-pressure, low-inductance, and high-reliability service.

ENDF/B-VII.0 Data Testing Using 1,172 Critical Assemblies

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

Plechaty, E F; Cullen, D E

2007-10-01

In order to test the ENDF/B-VII.0 neutron data library [1], 1,172 critical assemblies from [2] have been calculated using the Monte Carlo transport code TART [3]. TART's 'best' physics was used for all of these calculations; this included continuous energy cross sections, delayed neutrons in their spectrum that is slower than prompt neutrons, unresolved resonance region self-shielding, the thermal scattering (free atom for all materials plus thermal scattering law data S({alpha},{beta}) when available). In this first pass through the assemblies the objective was to 'quickly' test the validity of the ENDF/B-VII.0 data [1], the assembly models as defined in [2]more » and coded for use with TART, and TART's physics treatment [3] of these assemblies. With TART we have the option of running criticality problems until K-eff has been calculated to an acceptable input accuracy. In order to 'quickly' calculate all of these assemblies K-eff was calculated in each case to +/- 0.002. For these calculations the assemblies were divided into ten types based on fuel (mixed, Pu239, U233, U235) and median fission energy (Fast, Midi, Slow). A table is provided that shows a summary of these results. This is followed be details for every assembly, and statistical information about the distribution of K-eff for each type of assembly. After a review of these results to eliminate any obvious errors in ENDF/B data, assembly models, or TART physics, all assemblies will be run again to a higher precision. Only after this second run is finished will we have highly precise results. Until then the results presently here should only be interpreted as approximate values of K-eff with a standard deviation of +/- 0.002; for such a large number of assemblies we expected the results to be approximately normal, with a spread out to several times the standard deviation; see the calculated statistical distributions and their comparisons to a normal distribution.« less

An assembly system based on industrial robot with binocular stereo vision

NASA Astrophysics Data System (ADS)

Tang, Hong; Xiao, Nanfeng

2017-01-01

This paper proposes an electronic part and component assembly system based on an industrial robot with binocular stereo vision. Firstly, binocular stereo vision with a visual attention mechanism model is used to get quickly the image regions which contain the electronic parts and components. Secondly, a deep neural network is adopted to recognize the features of the electronic parts and components. Thirdly, in order to control the end-effector of the industrial robot to grasp the electronic parts and components, a genetic algorithm (GA) is proposed to compute the transition matrix and the inverse kinematics of the industrial robot (end-effector), which plays a key role in bridging the binocular stereo vision and the industrial robot. Finally, the proposed assembly system is tested in LED component assembly experiments, and the results denote that it has high efficiency and good applicability.

Preparation and high-resolution microscopy of gold cluster labeled nucleic acid conjugates and nanodevices

PubMed Central

Powell, Richard D.; Hainfeld, James F.

2013-01-01

Nanogold and undecagold are covalently linked gold cluster labels which enable the identification and localization of biological components with molecular precision and resolution. They can be prepared with different reactivities, which means they can be conjugated to a wide variety of molecules, including nucleic acids, at specific, unique sites. The location of these sites can be synthetically programmed in order to preserve the binding affinity of the conjugate and impart novel characteristics and useful functionality. Methods for the conjugation of undecagold and Nanogold to DNA and RNA are discussed, and applications of labeled conjugates to the high-resolution microscopic identification of binding sites and characterization of biological macromolecular assemblies are described. In addition to providing insights into their molecular structure and function, high-resolution microscopic methods also show how Nanogold and undecagold conjugates can be synthetically assembled, or self-assemble, into supramolecular materials to which the gold cluster labels impart useful functionality. PMID:20869258

Functional nanocomposites prepared by self-assembly and polymerization of diacetylene surfactants and silicic acid

NASA Technical Reports Server (NTRS)

Yang, Yi; Lu, Yunfeng; Lu, Mengcheng; Huang, Jinman; Haddad, Raid; Xomeritakis, George; Liu, Nanguo; Malanoski, Anthony P.; Sturmayr, Dietmar; Fan, Hongyou;

A post-assembly genome-improvement toolkit (PAGIT) to obtain annotated genomes from contigs.

PubMed

Swain, Martin T; Tsai, Isheng J; Assefa, Samual A; Newbold, Chris; Berriman, Matthew; Otto, Thomas D

2012-06-07

Genome projects now produce draft assemblies within weeks owing to advanced high-throughput sequencing technologies. For milestone projects such as Escherichia coli or Homo sapiens, teams of scientists were employed to manually curate and finish these genomes to a high standard. Nowadays, this is not feasible for most projects, and the quality of genomes is generally of a much lower standard. This protocol describes software (PAGIT) that is used to improve the quality of draft genomes. It offers flexible functionality to close gaps in scaffolds, correct base errors in the consensus sequence and exploit reference genomes (if available) in order to improve scaffolding and generating annotations. The protocol is most accessible for bacterial and small eukaryotic genomes (up to 300 Mb), such as pathogenic bacteria, malaria and parasitic worms. Applying PAGIT to an E. coli assembly takes ∼24 h: it doubles the average contig size and annotates over 4,300 gene models.

Wavefront Sensing Analysis of Grazing Incidence Optical Systems

NASA Technical Reports Server (NTRS)

Rohrbach, Scott; Saha, Timo

2012-01-01

Wavefront sensing is a process by which optical system errors are deduced from the aberrations in the image of an ideal source. The method has been used successfully in near-normal incidence, but not for grazing incidence systems. This innovation highlights the ability to examine out-of-focus images from grazing incidence telescopes (typically operating in the x-ray wavelengths, but integrated using optical wavelengths) and determine the lower-order deformations. This is important because as a metrology tool, this method would allow the integration of high angular resolution optics without the use of normal incidence interferometry, which requires direct access to the front surface of each mirror. Measuring the surface figure of mirror segments in a highly nested x-ray telescope mirror assembly is difficult due to the tight packing of elements and blockage of all but the innermost elements to normal incidence light. While this can be done on an individual basis in a metrology mount, once the element is installed and permanently bonded into the assembly, it is impossible to verify the figure of each element and ensure that the necessary imaging quality will be maintained. By examining on-axis images of an ideal point source, one can gauge the low-order figure errors of individual elements, even when integrated into an assembly. This technique is known as wavefront sensing (WFS). By shining collimated light down the optical axis of the telescope and looking at out-of-focus images, the blur due to low-order figure errors of individual elements can be seen, and the figure error necessary to produce that blur can be calculated. The method avoids the problem of requiring normal incidence access to the surface of each mirror segment. Mirror figure errors span a wide range of spatial frequencies, from the lowest-order bending to the highest order micro-roughness. While all of these can be measured in normal incidence, only the lowest-order contributors can be determined through this WFS technique.

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.

Long-read sequencing improves assembly of Trichinella genomes 10-fold, revealing substantial synteny between lineages diverged over 7 million years.

PubMed

Thompson, Peter C; Zarlenga, Dante S; Liu, Ming-Yuan; Rosenthal, Benjamin M

2017-09-01

Genome assemblies can form the basis of comparative analyses fostering insight into the evolutionary genetics of a parasite's pathogenicity, host-pathogen interactions, environmental constraints and invasion biology; however, the length and complexity of many parasite genomes has hampered the development of well-resolved assemblies. In order to improve Trichinella genome assemblies, the genome of the sylvatic encapsulated species Trichinella murrelli was sequenced using third-generation, long-read technology and, using syntenic comparisons, scaffolded to a reference genome assembly of Trichinella spiralis, markedly improving both. A high-quality draft assembly for T. murrelli was achieved that totalled 63·2 Mbp, half of which was condensed into 26 contigs each longer than 571 000 bp. When compared with previous assemblies for parasites in the genus, ours required 10-fold fewer contigs, which were five times longer, on average. Better assembly across repetitive regions also enabled resolution of 8 Mbp of previously indeterminate sequence. Furthermore, syntenic comparisons identified widespread scaffold misassemblies in the T. spiralis reference genome. The two new assemblies, organized for the first time into three chromosomal scaffolds, will be valuable resources for future studies linking phenotypic traits within each species to their underlying genetic bases.

Liquid crystal templating as an approach to spatially and temporally organise soft matter.

PubMed

van der Asdonk, Pim; Kouwer, Paul H J

2017-10-02

Chemistry quickly moves from a molecular science to a systems science. This requires spatial and temporal control over the organisation of molecules and molecular assemblies. Whilst Nature almost by default (transiently) organises her components at multiple different length scales, scientists struggle to realise even relatively straightforward patterns. In the past decades, supramolecular chemistry has taught us the rules to precisely engineer molecular assembly at the nanometre scale. At higher length scales, however, we are bound to top-down nanotechnology techniques to realise order. For soft, biological matter, many of these top-down techniques come with serious limitations since the molecules generally show low susceptibilities to the applied stimuli. A new method is based on liquid crystal templating. In this hierarchical approach, a liquid crystalline host serves as the scaffold to order polymers or assemblies. Being a liquid crystal, the host material can be ordered at many different length scales and on top of that, is highly susceptible to many external stimuli, which can even be used to manipulate the liquid crystal organisation in time. As a result, we anticipate large control over the organisation of the materials inside the liquid crystalline host. Recently, liquid crystal templating was also realised in water. This suddenly makes this tool highly applicable to start organising more delicate biological materials or even small organisms. We review the scope and limitations of liquid crystal templating and look out to where the technique may lead us.

Formation of monodisperse mesoporous silica microparticles via spray-drying.

PubMed

Waldron, Kathryn; Wu, Winston Duo; Wu, Zhangxiong; Liu, Wenjie; Selomulya, Cordelia; Zhao, Dongyuan; Chen, Xiao Dong

2014-03-15

In this work, a protocol to synthesize monodisperse mesoporous silica microparticles via a unique microfluidic jet spray-drying route is reported for the first time. The microparticles demonstrated highly ordered hexagonal mesostructures with surface areas ranging from ~900 up to 1500 m(2)/g and pore volumes from ~0.6 to 0.8 cm(3)/g. The particle size could be easily controlled from ~50 to 100 μm from the same diameter nozzle via changing the initial solute content, or changing the drying temperature. The ratio of the surfactant (CTAB) and silica (TEOS), and the amount of water in the precursor were found to affect the degree of ordering of mesopores by promoting either the self-assembly of the surfactant-silica micelles or the condensation of the silica as two competing processes in evaporation induced self-assembly. The drying rate and the curvature of particles also affected the self-assembly of the mesostructure. The particle mesostructure is not influenced by the inlet drying temperature in the range of 92-160 °C, with even a relatively low temperature of 92 °C producing highly ordered mesoporous microparticles. The spray-drying derived mesoporous silica microparticles, while of larger sizes and more rapidly synthesized, showed a comparable performance with the conventional mesoporous silica MCM-41 in controlled release of a dye, Rhodamine B, indicating that these spray dried microparticles could be used for the immobilisation and controlled release of small molecules. Copyright © 2013 Elsevier Inc. All rights reserved.

Fluctuation Effects on Propagating Waves of Self-Assembly in Organosilane Monolayers.

NASA Astrophysics Data System (ADS)

Douglas, Jack

2008-03-01

Wavefronts associated with reaction--diffusion and self-assembly processes are ubiquitous in the natural world. For example, propagating fronts arise in crystallization and diverse other thermodynamic ordering processes, in polymerization fronts involved in cell movement and division, as well as in the competitive social interactions and population dynamics of animals at much larger scales. Although it is often claimed that self-sustaining or autocatalytic front propagation is well described by mean-field ``reaction-- diffusion'' or ``phase field'' ordering models, it has recently become appreciated from simulations and theoretical arguments that fluctuation effects in lower spatial dimensions can lead to appreciable deviations from the classical mean-field theory (MFT) of this type of front propagation. The present work explores these fluctuation effects in a real physical system. In particular, we consider a high-resolution near-edge x-ray absorption fine structure spectroscopy (NEXAFS) study of the spontaneous frontal self-assembly of organosilane (OS) molecules into self-assembled monolayer (SAM) surface-energy gradients on oxidized silicon wafers. We find that these layers organize from the wafer edge as propagating wavefronts having well defined velocities. In accordance with two-dimensional simulations of this type of front propagation that take fluctuation effects into account, we find that the interfacial widths w(t) of these SAM self-assembly fronts exhibit a power-law broadening of in time w(t) ˜ t^β, rather than the constant width predicted by MFT. Moreover, the observed exponent values accord rather well with previous simulation and theoretical estimates. These observations have significant implications for diverse types of ordering fronts that occur under confinement conditions in biological or materials-processing contexts.

Meraculous: De Novo Genome Assembly with Short Paired-End Reads

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

Chapman, Jarrod A.; Ho, Isaac; Sunkara, Sirisha

2011-08-18

We describe a new algorithm, meraculous, for whole genome assembly of deep paired-end short reads, and apply it to the assembly of a dataset of paired 75-bp Illumina reads derived from the 15.4 megabase genome of the haploid yeast Pichia stipitis. More than 95% of the genome is recovered, with no errors; half the assembled sequence is in contigs longer than 101 kilobases and in scaffolds longer than 269 kilobases. Incorporating fosmid ends recovers entire chromosomes. Meraculous relies on an efficient and conservative traversal of the subgraph of the k-mer (deBruijn) graph of oligonucleotides with unique high quality extensions inmore » the dataset, avoiding an explicit error correction step as used in other short-read assemblers. A novel memory-efficient hashing scheme is introduced. The resulting contigs are ordered and oriented using paired reads separated by ~280 bp or ~3.2 kbp, and many gaps between contigs can be closed using paired-end placements. Practical issues with the dataset are described, and prospects for assembling larger genomes are discussed.« less

Nano-soldering of magnetically aligned three-dimensional nanowire networks.

PubMed

Gao, Fan; Gu, Zhiyong

2010-03-19

It is extremely challenging to fabricate 3D integrated nanostructures and hybrid nanoelectronic devices. In this paper, we report a simple and efficient method to simultaneously assemble and solder nanowires into ordered 3D and electrically conductive nanowire networks. Nano-solders such as tin were fabricated onto both ends of multi-segmented nanowires by a template-assisted electrodeposition method. These nanowires were then self-assembled and soldered into large-scale 3D network structures by magnetic field assisted assembly in a liquid medium with a high boiling point. The formation of junctions/interconnects between the nanowires and the scale of the assembly were dependent on the solder reflow temperature and the strength of the magnetic field. The size of the assembled nanowire networks ranged from tens of microns to millimeters. The electrical characteristics of the 3D nanowire networks were measured by regular current-voltage (I-V) measurements using a probe station with micropositioners. Nano-solders, when combined with assembling techniques, can be used to efficiently connect and join nanowires with low contact resistance, which are very well suited for sensor integration as well as nanoelectronic device fabrication.

Ionic liquid-induced aggregate formation and their applications.

PubMed

Dutta, Rupam; Kundu, Sangita; Sarkar, Nilmoni

2018-06-01

In the last two decades, researchers have extensively studied highly stable and ordered supramolecular assembly formation using oppositely charged surfactants. Thereafter, surface-active ionic liquids (SAILs), a special class of room temperature ionic liquids (RTILs), replace the surfactants to form various supramolecular aggregates. Therefore, in the last decade, the building blocks of the supramolecular aggregates (micelle, mixed micelle, and vesicular assemblies) have changed from oppositely charged surfactant/surfactant pair to surfactant/SAIL and SAIL/SAIL pair. It is also found that various biomolecules can also interact with SAILs to construct biologically important supramolecular assemblies. The very latest addition to this combination of ion pairs is the dye molecules having a long hydrophobic chain part along with a hydrophilic ionic head group. Thus, dye/surfactant or dye/SAIL pair also produces different assemblies through electrostatic, hydrophobic, and π-π stacking interactions. Vesicles are one of the important self-assemblies which mimic cellular membranes, and thus have biological application as a drug carrier. Moreover, vesicles can act as a suitable microreactor for nanoparticle synthesis.

Templated bilayer self-assembly of fully conjugated π-expanded macrocyclic oligothiophenes complexed with fullerenes

PubMed Central

Cojal González, José D.; Iyoda, Masahiko; Rabe, Jürgen P.

2017-01-01

Fully conjugated macrocyclic oligothiophenes exhibit a combination of highly attractive structural, optical and electronic properties, and multifunctional molecular thin film architectures thereof are envisioned. However, control over the self-assembly of such systems becomes increasingly challenging, the more complex the target structures are. Here we show a robust self-assembly based on hierarchical non-covalent interactions. A self-assembled monolayer of hydrogen-bonded trimesic acid at the interface between an organic solution and graphite provides host-sites for the epitaxial ordering of Saturn-like complexes of fullerenes with oligothiophene macrocycles in mono- and bilayers. STM tomography verifies the formation of the templated layers. Molecular dynamics simulations corroborate the conformational stability and assign the adsorption sites of the adlayers. Scanning tunnelling spectroscopy determines their rectification characteristics. Current–voltage characteristics reveal the modification of the rectifying properties of the macrocycles by the formation of donor–acceptor complexes in a densely packed all-self-assembled supramolecular nanostructure. PMID:28281557

Programming Hierarchical Self-Assembly of Patchy Particles into Colloidal Crystals via Colloidal Molecules.

PubMed

Morphew, Daniel; Shaw, James; Avins, Christopher; Chakrabarti, Dwaipayan

2018-03-27

Colloidal self-assembly is a promising bottom-up route to a wide variety of three-dimensional structures, from clusters to crystals. Programming hierarchical self-assembly of colloidal building blocks, which can give rise to structures ordered at multiple levels to rival biological complexity, poses a multiscale design problem. Here we explore a generic design principle that exploits a hierarchy of interaction strengths and employ this design principle in computer simulations to demonstrate the hierarchical self-assembly of triblock patchy colloidal particles into two distinct colloidal crystals. We obtain cubic diamond and body-centered cubic crystals via distinct clusters of uniform size and shape, namely, tetrahedra and octahedra, respectively. Such a conceptual design framework has the potential to reliably encode hierarchical self-assembly of colloidal particles into a high level of sophistication. Moreover, the design framework underpins a bottom-up route to cubic diamond colloidal crystals, which have remained elusive despite being much sought after for their attractive photonic applications.

Templated bilayer self-assembly of fully conjugated π-expanded macrocyclic oligothiophenes complexed with fullerenes

NASA Astrophysics Data System (ADS)

Cojal González, José D.; Iyoda, Masahiko; Rabe, Jürgen P.

2017-03-01

Fully conjugated macrocyclic oligothiophenes exhibit a combination of highly attractive structural, optical and electronic properties, and multifunctional molecular thin film architectures thereof are envisioned. However, control over the self-assembly of such systems becomes increasingly challenging, the more complex the target structures are. Here we show a robust self-assembly based on hierarchical non-covalent interactions. A self-assembled monolayer of hydrogen-bonded trimesic acid at the interface between an organic solution and graphite provides host-sites for the epitaxial ordering of Saturn-like complexes of fullerenes with oligothiophene macrocycles in mono- and bilayers. STM tomography verifies the formation of the templated layers. Molecular dynamics simulations corroborate the conformational stability and assign the adsorption sites of the adlayers. Scanning tunnelling spectroscopy determines their rectification characteristics. Current-voltage characteristics reveal the modification of the rectifying properties of the macrocycles by the formation of donor-acceptor complexes in a densely packed all-self-assembled supramolecular nanostructure.

Highly crystalline inverse opal transition metal oxides via a combined assembly of soft and hard chemistries.

PubMed

Orilall, M Christopher; Abrams, Neal M; Lee, Jinwoo; DiSalvo, Francis J; Wiesner, Ulrich

2008-07-16

A combined assembly of soft and hard chemistries is employed to generate highly crystalline three-dimensionally ordered macroporous (3DOM) niobia (Nb2O5) and titania (TiO2) structures by colloidal crystal templating. Polystyrene spheres with sp2 hybridized carbon are used in a reverse-template infiltration technique based on the aqueous liquid phase deposition of the metal oxide in the interstitial spaces of a colloidal assembly. Heating under inert atmosphere as high as 900 degrees C converts the polymer into sturdy carbon that acts as a scaffold and keeps the macropores open while the oxides crystallize. Using X-ray diffraction it is demonstrated that for both oxides this approach leads to highly crystalline materials while heat treatments to lower temperatures commonly used for polymer colloidal templating, in particular for niobia, results in only weakly crystallized materials. Furthermore it is demonstrated that heat treatment directly to higher temperatures without generating the carbon scaffold leads to a collapse of the macrostructure. The approach should in principle be applicable to other 3DOM materials that require heat treatments to higher temperatures.

Structural assemblies of the di- and oligomeric G-protein coupled receptor TGR5 in live cells: an MFIS-FRET and integrative modelling study

NASA Astrophysics Data System (ADS)

Greife, Annemarie; Felekyan, Suren; Ma, Qijun; Gertzen, Christoph G. W.; Spomer, Lina; Dimura, Mykola; Peulen, Thomas O.; Wöhler, Christina; Häussinger, Dieter; Gohlke, Holger; Keitel, Verena; Seidel, Claus A. M.

2016-11-01

TGR5 is the first identified bile acid-sensing G-protein coupled receptor, which has emerged as a potential therapeutic target for metabolic disorders. So far, structural and multimerization properties are largely unknown for TGR5. We used a combined strategy applying cellular biology, Multiparameter Image Fluorescence Spectroscopy (MFIS) for quantitative FRET analysis, and integrative modelling to obtain structural information about dimerization and higher-order oligomerization assemblies of TGR5 wildtype (wt) and Y111 variants fused to fluorescent proteins. Residue 111 is located in transmembrane helix 3 within the highly conserved ERY motif. Co-immunoprecipitation and MFIS-FRET measurements with gradually increasing acceptor to donor concentrations showed that TGR5 wt forms higher-order oligomers, a process disrupted in TGR5 Y111A variants. From the concentration dependence of the MFIS-FRET data we conclude that higher-order oligomers - likely with a tetramer organization - are formed from dimers, the smallest unit suggested for TGR5 Y111A variants. Higher-order oligomers likely have a linear arrangement with interaction sites involving transmembrane helix 1 and helix 8 as well as transmembrane helix 5. The latter interaction is suggested to be disrupted by the Y111A mutation. The proposed model of TGR5 oligomer assembly broadens our view of possible oligomer patterns and affinities of class A GPCRs.

Highly crystalline covalent organic frameworks from flexible building blocks.

PubMed

Xu, Liqian; Ding, San-Yuan; Liu, Junmin; Sun, Junliang; Wang, Wei; Zheng, Qi-Yu

2016-03-28

Two novel 2D covalent organic frameworks (TPT-COF-1 and TPT-COF-2) were synthesized from the flexible 2,4,6-triaryloxy-1,3,5-triazine building blocks on a gram scale, which show high crystallinity and large surface area. The controllable formation of highly ordered frameworks is mainly attributed to the self-assembly Piedfort unit of 2,4,6-triaryloxy-1,3,5-triazine.

Molecular dynamics simulations reveal the assembly mechanism of polysaccharides in marine aerosols.

PubMed

Sun, Lu; Li, Xin; Hede, Thomas; Tu, Yaoquan; Leck, Caroline; Ågren, Hans

2014-12-21

The high Arctic marine environment has recently detected polymer gels in atmospheric aerosol particles and cloud water originating from the surface microlayer of the open leads within the pack ice area. These polysaccharide molecules are water insoluble but water solvated, highly surface-active and highly hydrated (99% water). In order to add to the understanding and to complement missing laboratory characterization of marine polymer gels we have in this work performed an atomistic study of the assembly process and interfacial properties of polysaccharides. Our study reveals a number of salient features of the microscopic process behind polysaccharide assembly into nanogels. With three- and four-repeating units the polysaccharides assemble into a cluster in 50 ns. The aggregates grow quicker by absorbing one or two polymers each time, depending on the unit length and the type of inter-bridging cation. Although both the hydrophobic and hydrophilic domains are contracted, the latter dominates distinctly upon the contraction of solvent accessible surface areas. The establishment of inter-chain hydrogen-bonds is the key to the assembly while ionic bridges can further promote aggregation. During the assembly of the more bent four-unit polymers, intra-chain hydrogen bonds are significantly diminished by Ca(2+). Meanwhile, the percentage of Ca(2+) acting as an ionic bridge is more eminent, highlighting the significance of Ca(2+) ions for longer-chain polysaccharides. The aggregates are able to enhance surface tension more in the presence of Ca(2+) than in the presence of Na(+) owing to their more compact structure. These conclusions all demonstrate that studies of the present kind provide insight into the self-assembly process and interfacial properties of marine gels. We hope this understanding will keep up the interest in the complex and the fascinating relationship between marine microbiology, atmospheric aerosols, clouds and climate.

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.

A dual-rating method for evaluating impact noise isolation of floor-ceiling assemblies.

PubMed

LoVerde, John J; Dong, D Wayland

2017-01-01

Impact Insulation Class (IIC), the single-number rating for evaluating the impact noise insulation of a floor-ceiling assembly, and the associated field testing ratings, are unsatisfactory because they do not have strong correlation with subjective reaction nor provide suitable detailed information for evaluation or design of floor-ceiling assemblies. Various proposals have been made for improving the method, but the data presented indicate that no single-number rating can adequately characterize the impact noise isolation of an assembly. For realistic impact noise sources and floor-ceiling assembly types, there are two frequency domains for impact noise, and the impact noise levels in the two domains can vary independently. Therefore, two ratings are required in order to satisfactorily evaluate the impact isolation provided by a floor-ceiling assembly. Two different ratings are introduced for measuring field impact isolation in the two frequency domains, using the existing impact source and measurement method. They are named low-frequency impact rating (LIR) and high-frequency impact rating (HIR). LIR and HIR are proposed to improve the current method for design and evaluation of floor-ceiling assemblies and also provide a better method for predicting subjective reaction.

Validation of the U.S. NRC NGNP evaluation model with the HTTR

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

Saller, T.; Seker, V.; Downar, T.

2012-07-01

The High Temperature Test Reactor (HTTR) was modeled with TRITON/PARCS. Traditional light water reactor (LWR) homogenization methods rely on the short mean free paths of neutrons in LWR. In gas-cooled, graphite-moderated reactors like the HTTR neutrons have much longer mean free paths and penetrate further into neighboring assemblies than in LWRs. Because of this, conventional lattice calculations with a single assembly may not be valid. In addition to difficulties caused by the longer mean free paths, the HTTR presents unique axial and radial heterogeneities that require additional modifications to the single assembly homogenization method. To handle these challenges, the homogenizationmore » domain is decreased while the computational domain is increased. Instead of homogenizing a single hexagonal fuel assembly, the assembly is split into six triangles on the radial plane and five blocks axially in order to account for the placement of burnable poisons. Furthermore, the radial domain is increased beyond a single fuel assembly to account for spectrum effects from neighboring fuel, reflector, and control rod assemblies. A series of five two-dimensional cases, each closer to the full core, were calculated to evaluate the effectiveness of the homogenization method and cross-sections. (authors)« less

Self-assembly of coiled coil peptides into nanoparticles vs 2-d plates: effects of assembly pathway

NASA Astrophysics Data System (ADS)

Kim, Kyunghee; Pochan, Darrin

Molecular solution assembly, or self-assembly, is a process by which ordered nanostructures or patterns are formed by non-covalent interactions during assembly. Biomimicry, the use of bioinspired molecules or biologically relevant materials, is an important area of self-assembly research with peptides serving a critical role as molecular tools. The morphology of peptide assemblies can be controlled by adjusting solution conditions such as the concentration of peptides, the temperature, and pH. Herein, spherical nanostructures, which have potential for creating an encapsulation system, are formed by self-assembly when coiled coil peptides are combined in solution. These peptides are homotrimeric and heterodimeric coiled-coil bundles and the homotrimer is connected with each of heterodimer through their external surfaces via disulfide bonds. The resultant covalent constructs could co-assemble into complementary trimeric hubs, respectively. The two peptide constructs are directly mixed and assembled in solution in order to produce either spherical particles or 2-d plates depending on the solution conditions and kinetic pathway of assembly. In particular, structural changes of the self-assembled peptides are explored by control of the thermal history of the assembly solution.

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.

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

Self-Assembling Block Copolymer Resist Mixtures towards Lithographic Resists for Sub-10 nm Features

NASA Astrophysics Data System (ADS)

Chandler, Curran; Daga, Vikram; Watkins, James

2009-03-01

Significant improvements in 193 nm photolithography have enabled the extension of device feature sizes beyond the 45 nm and 32 nm nodes, yet uncertainty lies beyond 22 nm features as no single replacement has emerged. Here we show that low molecular weight, nonionic block copolymer surfactant blends are capable of self-assembling into highly ordered domains with feature sizes on the order of 5 nm. These surfactants, most of which lack the required χN for microphase separation on their own, exhibit strong segregation and long-range order upon addition of a component capable of multi-point hydrogen bonding that is specific for one of the blocks in the copolymer. This has been demonstrated by our SAXS data for several Pluronic (PEO-b-PPO-b-PEO) and Brij (PEO-b-[CH2]nCH3) surfactants of various molecular weights and PEO volume fractions. Furthermore, we employ these highly-ordered systems as thin film, nanolithographic etch masks for the transfer of sub-10 nm patterns into silicon-based substrates. Small molecule, hydrogen bonding additives containing aromatic or silsesquioxane structure are also used to tune etch contrast between the blocks which is important for reducing line edge roughness (LER) of such small features.

Fabrication and performance analysis of a high-coupling-efficiency and convenient-integration optical transceiver

NASA Astrophysics Data System (ADS)

He, Hui-min; Liu, Feng-man; Xue, Hai-yun; Wu, Peng; Song, Man-gu; Sun, Yu; Cao, Li-qiang

2017-07-01

An optical transceiver with a novel optical subassembly structure is proposed in this paper, which achieves high coupling efficiency and low assembly difficulty. The proposed optical transceiver consumes 0.9 W power and retains a small size of 28 mm×16 mm×3 mm. The fabrication process of the silicon substrate and the assembly process of the optical transceiver are demonstrated in details. Moreover, the optical transceiver is measured in order to verify its transmission performance. The clear eye diagrams and the low bit error rate ( BER) less than 10-13 at 10 Gbit/s per channel show good transmission characteristics of the designed optical transceiver.

Cooperative light-induced molecular movements of highly ordered azobenzene self-assembled monolayers.

PubMed

Pace, Giuseppina; Ferri, Violetta; Grave, Christian; Elbing, Mark; von Hänisch, Carsten; Zharnikov, Michael; Mayor, Marcel; Rampi, Maria Anita; Samorì, Paolo

2007-06-12

Photochromic systems can convert light energy into mechanical energy, thus they can be used as building blocks for the fabrication of prototypes of molecular devices that are based on the photomechanical effect. Hitherto a controlled photochromic switch on surfaces has been achieved either on isolated chromophores or within assemblies of randomly arranged molecules. Here we show by scanning tunneling microscopy imaging the photochemical switching of a new terminally thiolated azobiphenyl rigid rod molecule. Interestingly, the switching of entire molecular 2D crystalline domains is observed, which is ruled by the interactions between nearest neighbors. This observation of azobenzene-based systems displaying collective switching might be of interest for applications in high-density data storage.

Protein-directed self-assembly of a fullerene crystal.

PubMed

Kim, Kook-Han; Ko, Dong-Kyun; Kim, Yong-Tae; Kim, Nam Hyeong; Paul, Jaydeep; Zhang, Shao-Qing; Murray, Christopher B; Acharya, Rudresh; DeGrado, William F; Kim, Yong Ho; Grigoryan, Gevorg

2016-04-26

Learning to engineer self-assembly would enable the precise organization of molecules by design to create matter with tailored properties. Here we demonstrate that proteins can direct the self-assembly of buckminsterfullerene (C60) into ordered superstructures. A previously engineered tetrameric helical bundle binds C60 in solution, rendering it water soluble. Two tetramers associate with one C60, promoting further organization revealed in a 1.67-Å crystal structure. Fullerene groups occupy periodic lattice sites, sandwiched between two Tyr residues from adjacent tetramers. Strikingly, the assembly exhibits high charge conductance, whereas both the protein-alone crystal and amorphous C60 are electrically insulating. The affinity of C60 for its crystal-binding site is estimated to be in the nanomolar range, with lattices of known protein crystals geometrically compatible with incorporating the motif. Taken together, these findings suggest a new means of organizing fullerene molecules into a rich variety of lattices to generate new properties by design.

Horizontal high speed stacking for batteries with prismatic cans

DOEpatents

Bartos, Andrew L.; Lin, Yhu-Tin; Turner, III, Raymond D.

2016-06-14

A system and method for stacking battery cells or related assembled components. Generally planar, rectangular (prismatic-shaped) battery cells are moved from an as-received generally vertical stacking orientation to a generally horizontal stacking orientation without the need for robotic pick-and-place equipment. The system includes numerous conveyor belts that work in cooperation with one another to deliver, rotate and stack the cells or their affiliated assemblies. The belts are outfitted with components to facilitate the cell transport and rotation. The coordinated movement between the belts and the components promote the orderly transport and rotation of the cells from a substantially vertical stacking orientation into a substantially horizontal stacking orientation. The approach of the present invention helps keep the stacked assemblies stable so that subsequent assembly steps--such as compressing the cells or attaching electrical leads or thermal management components--may proceed with a reduced chance of error.

Genome Partitioner: A web tool for multi-level partitioning of large-scale DNA constructs for synthetic biology applications.

PubMed

Christen, Matthias; Del Medico, Luca; Christen, Heinz; Christen, Beat

2017-01-01

Recent advances in lower-cost DNA synthesis techniques have enabled new innovations in the field of synthetic biology. Still, efficient design and higher-order assembly of genome-scale DNA constructs remains a labor-intensive process. Given the complexity, computer assisted design tools that fragment large DNA sequences into fabricable DNA blocks are needed to pave the way towards streamlined assembly of biological systems. Here, we present the Genome Partitioner software implemented as a web-based interface that permits multi-level partitioning of genome-scale DNA designs. Without the need for specialized computing skills, biologists can submit their DNA designs to a fully automated pipeline that generates the optimal retrosynthetic route for higher-order DNA assembly. To test the algorithm, we partitioned a 783 kb Caulobacter crescentus genome design. We validated the partitioning strategy by assembling a 20 kb test segment encompassing a difficult to synthesize DNA sequence. Successful assembly from 1 kb subblocks into the 20 kb segment highlights the effectiveness of the Genome Partitioner for reducing synthesis costs and timelines for higher-order DNA assembly. The Genome Partitioner is broadly applicable to translate DNA designs into ready to order sequences that can be assembled with standardized protocols, thus offering new opportunities to harness the diversity of microbial genomes for synthetic biology applications. The Genome Partitioner web tool can be accessed at https://christenlab.ethz.ch/GenomePartitioner.

Pre-transition effects mediate forces of assembly between transmembrane proteins

DOE PAGES

Katira, Sachi; Mandadapu, Kranthi K.; Vaikuntanathan, Suriyanarayanan; ...

2016-02-24

We present a mechanism for a generic, powerful force of assembly and mobility for transmembrane proteins in lipid bilayers. This force is a pre-transition (or pre-melting) effect for the first-order transition between ordered and disordered phases in the membrane. Using large-scale molecular simulation, we show that a protein with hydrophobic thickness equal to that of the disordered phase embedded in an ordered bilayer stabilizes a microscopic order-disorder interface. The stiffness of that interface is finite. When two such proteins approach each other, they assemble because assembly reduces the net interfacial energy. Analogous to the hydrophobic effect, we refer to thismore » phenomenon as the ‘orderphobic effect’. The effect is mediated by proximity to the order-disorder phase transition and the size and hydrophobic mismatch of the protein. Furthermore, the strength and range of forces arising from this effect are significantly larger than those that could arise from membrane elasticity for the membranes considered.« less

Pre-transition effects mediate forces of assembly between transmembrane proteins

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

Katira, Sachi; Mandadapu, Kranthi K.; Vaikuntanathan, Suriyanarayanan

We present a mechanism for a generic, powerful force of assembly and mobility for transmembrane proteins in lipid bilayers. This force is a pre-transition (or pre-melting) effect for the first-order transition between ordered and disordered phases in the membrane. Using large-scale molecular simulation, we show that a protein with hydrophobic thickness equal to that of the disordered phase embedded in an ordered bilayer stabilizes a microscopic order-disorder interface. The stiffness of that interface is finite. When two such proteins approach each other, they assemble because assembly reduces the net interfacial energy. Analogous to the hydrophobic effect, we refer to thismore » phenomenon as the ‘orderphobic effect’. The effect is mediated by proximity to the order-disorder phase transition and the size and hydrophobic mismatch of the protein. Furthermore, the strength and range of forces arising from this effect are significantly larger than those that could arise from membrane elasticity for the membranes considered.« less

Dynamics of dissipative self-assembly of particles interacting through oscillatory forces

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

Tagliazucchi, M.; Szleifer, I.

Dissipative self-assembly is the formation of ordered structures far from equilibrium, which continuously uptake energy and dissipate it into the environment. Due to its dynamical nature, dissipative self-assembly can lead to new phenomena and possibilities of self-organization that are unavailable to equilibrium systems. Understanding the dynamics of dissipative self-assembly is required in order to direct the assembly to structures of interest. In the present work, Brownian dynamics simulations and analytical theory were used to study the dynamics of self-assembly of a mixture of particles coated with weak acids and bases under continuous oscillations of the pH. The pH of themore » system modulates the charge of the particles and, therefore, the interparticle forces oscillate in time. This system produces a variety of self-assembled structures, including colloidal molecules, fibers and different types of crystalline lattices. The most important conclusions of our study are: (i) in the limit of fast oscillations, the whole dynamics (and not only those at the non-equilibrium steady state) of a system of particles interacting through time-oscillating interparticle forces can be described by an effective potential that is the time average of the time-dependent potential over one oscillation period; (ii) the oscillation period is critical to determine the order of the system. In some cases the order is favored by very fast oscillations while in others small oscillation frequencies increase the order. In the latter case, it is shown that slow oscillations remove kinetic traps and, thus, allow the system to evolve towards the most stable non-equilibrium steady state.« less

Rapid ordering of block copolymer thin films

NASA Astrophysics Data System (ADS)

Majewski, Pawel W.; Yager, Kevin G.

2016-10-01

Block-copolymers self-assemble into diverse morphologies, where nanoscale order can be finely tuned via block architecture and processing conditions. However, the ultimate usage of these materials in real-world applications may be hampered by the extremely long thermal annealing times—hours or days—required to achieve good order. Here, we provide an overview of the fundamentals of block-copolymer self-assembly kinetics, and review the techniques that have been demonstrated to influence, and enhance, these ordering kinetics. We discuss the inherent tradeoffs between oven annealing, solvent annealing, microwave annealing, zone annealing, and other directed self-assembly methods; including an assessment of spatial and temporal characteristics. We also review both real-space and reciprocal-space analysis techniques for quantifying order in these systems.

Directed Self-Assembly of Block Copolymers for High Breakdown Strength Polymer Film Capacitors.

PubMed

Samant, Saumil P; Grabowski, Christopher A; Kisslinger, Kim; Yager, Kevin G; Yuan, Guangcui; Satija, Sushil K; Durstock, Michael F; Raghavan, Dharmaraj; Karim, Alamgir

2016-03-01

Emerging needs for fast charge/discharge yet high-power, lightweight, and flexible electronics requires the use of polymer-film-based solid-state capacitors with high energy densities. Fast charge/discharge rates of film capacitors on the order of microseconds are not achievable with slower charging conventional batteries, supercapacitors and related hybrid technologies. However, the current energy densities of polymer film capacitors fall short of rising demand, and could be significantly enhanced by increasing the breakdown strength (EBD) and dielectric permittivity (εr) of the polymer films. Co-extruded two-homopolymer component multilayered films have demonstrated much promise in this regard showing higher EBD over that of component polymers. Multilayered films can also help incorporate functional features besides energy storage, such as enhanced optical, mechanical, thermal and barrier properties. In this work, we report accomplishing multilayer, multicomponent block copolymer dielectric films (BCDF) with soft-shear driven highly oriented self-assembled lamellar diblock copolymers (BCP) as a novel application of this important class of self-assembling materials. Results of a model PS-b-PMMA system show ∼50% enhancement in EBD of self-assembled multilayer lamellar BCP films compared to unordered as-cast films, indicating that the breakdown is highly sensitive to the nanostructure of the BCP. The enhancement in EBD is attributed to the "barrier effect", where the multiple interfaces between the lamellae block components act as barriers to the dielectric breakdown through the film. The increase in EBD corresponds to more than doubling the energy storage capacity using a straightforward directed self-assembly strategy. This approach opens a new nanomaterial paradigm for designing high energy density dielectric materials.

Directed self-assembly of block copolymers for high breakdown strength polymer film capacitors

DOE PAGES

Samant, Saumil P.; Grabowski, Christopher A.; Kisslinger, Kim; ...

2016-03-04

Emerging needs for fast charge/discharge yet high-power, lightweight, and flexible electronics requires the use of polymer-film-based solid-state capacitors with high energy densities. Fast charge/discharge rates of film capacitors on the order of microseconds are not achievable with slower charging conventional batteries, supercapacitors and related hybrid technologies. However, the current energy densities of polymer film capacitors fall short of rising demand, and could be significantly enhanced by increasing the breakdown strength (E BD) and dielectric permittivity (ε r) of the polymer films. Co-extruded two-homopolymer component multilayered films have demonstrated much promise in this regard showing higher E BD over that ofmore » component polymers. Multilayered films can also help incorporate functional features besides energy storage, such as enhanced optical, mechanical, thermal and barrier properties. In this work, we report accomplishing multilayer, multicomponent block copolymer dielectric films (BCDF) with soft-shear driven highly oriented self-assembled lamellar diblock copolymers (BCP) as a novel application of this important class of self-assembling materials. Results of a model PS- b-PMMA system show ~50% enhancement in E BD of self-assembled multilayer lamellar BCP films compared to unordered as-cast films, indicating that the breakdown is highly sensitive to the nanostructure of the BCP. The enhancement in E BD is attributed to the “barrier effect”, where the multiple interfaces between the lamellae block components act as barriers to the dielectric breakdown through the film. The increase in E BD corresponds to more than doubling the energy storage capacity using a straightforward directed self-assembly strategy. Lastly, this approach opens a new nanomaterial paradigm for designing high energy density dielectric materials.« less

Size and space controlled hexagonal arrays of superparamagnetic iron oxide nanodots: magnetic studies and application

PubMed Central

Ghoshal, Tandra; Maity, Tuhin; Senthamaraikannan, Ramsankar; Shaw, Matthew T.; Carolan, Patrick; Holmes, Justin D.; Roy, Saibal; Morris, Michael A.

2013-01-01

Highly dense hexagonally arranged iron oxide nanodots array were fabricated using PS-b-PEO self-assembled patterns. The copolymer molecular weight, composition and choice of annealing solvent/s allows dimensional and structural control of the nanopatterns at large scale. A mechanism is proposed to create scaffolds through degradation and/or modification of cylindrical domains. A methodology based on selective metal ion inclusion and subsequent processing was used to create iron oxide nanodots array. The nanodots have uniform size and shape and their placement mimics the original self-assembled nanopatterns. For the first time these precisely defined and size selective systems of ordered nanodots allow careful investigation of magnetic properties in dimensions from 50 nm to 10 nm, which delineate the nanodots are superparamagnetic, well-isolated and size monodispersed. This diameter/spacing controlled iron oxide nanodots systems were demonstrated as a resistant mask over silicon to fabricate densely packed, identical ordered, high aspect ratio silicon nanopillars and nanowire features. PMID:24072037

Directing self-assembly of gold nanoparticles in diblock copolymer scaffold

NASA Astrophysics Data System (ADS)

Li, Qifang; He, Jinbo; Glogowski, Elizabeth; Emrick, Todd; Russell, Thomas

2007-03-01

A versatile hierarchical approach for directing self -assembly of gold nanostructures with size 2-3nm in diblock copolymer scaffolds is found. Diblock copolymer polystyrene-b-poly(2-vinylpyridine) (PS-b-P2VP) is used to form a regular scaffold of highly anisotropic, stripe-like domains, and controlled differential wetting by dichloromethane and thermal annealing guides gold nanoparticles with half hydrophilic ligand to aggregate selectively along the scaffold, producing highly organized metal nanostructures. In as-cast block-copolymer and gold nanoparticles thin films, micelle structure and gold nanoparticles random distribution on scaffold are typically observed. However, samples annealed in dichloromethane exhibit well-defined short-range ordered nanostructure with gold nanoparticles located at the interface of PS and P2VP nanoscale domain. After annealing at 170 C, the gold nanoparticles at interface migrated into the middle of P2VP phase and exhibited long-range ordered hierarchical structures. Synergistic interactions between the gold nanoparticles and the PS-b-P2VP caused an orientation of the microdomains normal to the film surface.

Self-Assembled Array of Tethered Manganese Oxide Nanoparticles for the Next Generation of Energy Storage

DOE PAGES

Stevens, Tyler E.; Pearce, Charles J.; Whitten, Caleah N.; ...

2017-03-13

There are many challenges to overcome in order to create reliable electrochemical energy storage devices with not only high energy but also high power densities. Gaps exist in both battery and supercapacitor technologies, with neither one satisfying the need for both large power and energy densities in a single device. We report a process to create a self-assembled array of electrochemically active nanoparticles bound directly to a current collector using extremely short (2 nm or less) conductive tethers, in order to begin addressing these challenges (and others). The tethered array of nanoparticles, MnO in this case, bound directly to amore » gold current collector via short conducting linkages eliminates the need for fillers, resulting in a material which achieves 99.9% active material by mass (excluding the current collector). Our strategy is expected to be both scalable as well as effective for alternative tethers and metal oxide nanoparticles.« less

Magnetically-guided assembly of microfluidic fibers for ordered construction of diverse netlike modules

NASA Astrophysics Data System (ADS)

Li, Xingfu; Shi, Qing; Wang, Huaping; Sun, Tao; Huang, Qiang; Fukuda, Toshio

2017-12-01

In this paper, a magnetically-guided assembly method is proposed to methodically construct diverse modules with a microfiber-based network for promoting nutrient circulation and waste excretion of cell culture. The microfiber is smoothly spun from the microfluidic device via precise control of the volumetric flow rate, and superparamagnetic nanoparticles within the alginate solution of the microfluidic fiber enable its magnetic response. The magnetized device is used to effectively capture the microfiber using its powerful magnetic flux density and high magnetic field gradient. Subsequently, the dot-matrix magnetic flux density is used to distribute the microfibers in an orderly fashion that depends on the array structure of the magnetized device. Furthermore, the magnetic microfluidic fibers are spatially organized into desired locations and are cross-aligned to form highly interconnected netlike modules in a liquid environment. Therefore, the experimental results herein demonstrate the structural controllability and stability of various modules and establish the effectiveness of the proposed method.

Component model reduction via the projection and assembly method

NASA Technical Reports Server (NTRS)

Bernard, Douglas E.

1989-01-01

The problem of acquiring a simple but sufficiently accurate model of a dynamic system is made more difficult when the dynamic system of interest is a multibody system comprised of several components. A low order system model may be created by reducing the order of the component models and making use of various available multibody dynamics programs to assemble them into a system model. The difficulty is in choosing the reduced order component models to meet system level requirements. The projection and assembly method, proposed originally by Eke, solves this difficulty by forming the full order system model, performing model reduction at the the system level using system level requirements, and then projecting the desired modes onto the components for component level model reduction. The projection and assembly method is analyzed to show the conditions under which the desired modes are captured exactly; to the numerical precision of the algorithm.

Development of self-assembling nanowires containing electronically active oligothiophenes

NASA Astrophysics Data System (ADS)

Tsai, Wei-Wen

This dissertation discusses the development of conductive one-dimensional nanowires from self-assembling oligothiophene molecules. Self-assembly has been demonstrated to be a promising alternative approach towards high performance, solution processable, and low-cost organic electronics. One of the many challenges in this field is the control of supramolecular morphologies of ordered structures containing pi-conjugated moieties. This research demonstrated several successful strategies to achieve self assembly of conductive nanowires using synergistic interactions combining pi stacking and hydrogen bonding. The first approach used was to develop a hairpin-shaped sexithiophene molecule, which features two arms of the conjugated structure. The diamidocyclohexyl headgroup of this molecule successfully directs the self-assembly from hydrogen bonding among the amides, forming high-aspect-ratio one-dimensional nanowires with well-defined diameters of 3.0 +/- 0.3 nm. The molecular orientation in the nanostructures promotes formation of sexithiophene H and J aggregates that facilitate efficient charge transport. Organic field-effect transistors were fabricated to reveal improved intrinsic hole mobility from films of the nanostructures, 3.46 x 10-6 cm2V-1s-1, which is one order of magnitude higher than films cast from unassembled molecules. Bulk heterojunction solar cells were developed from this molecule and fullerenes utilizing solution-phase fabrication methods. Intimate mix of the molecule and phenyl-C61-butyric acid methyl ester creates structured interfaces for efficient exciton splitting. The charge carrier mobilities of each material are improved by self-assembly in solution and thermal-energy assisted phase separation.The photovoltaic devices achieved the highest open-circuit voltage of 0.62 V, short-circuit current of 1.79 mA/cm2, fill factor of 35%, and power conversion efficiency of 0.48%. Another strategy to one-dimensional nanowires studied here involved the modification of a class of peptide lipids. The tripeptide segments in the molecular structure promote beta-sheet formation in nonpolar organic solvents, which is the main driving force for their self-assembly into 1D nanowires. Left-handed helical nanowires were formed with diameters of 8.9 nm and pitches between 50--150 nm. Substitutions of oligothiophenes lead to unprecedented supercoiling phenomena manifested as the transformation from helical to coiled or curved nanowires. We proposed that the curving of the nanowires is the consequence of relaxation from torsionally strained nanohelices, a process similar to supercoiling of strained DNA double helix. This process is governed by the mismatch in intermolecular distances required for peptide beta-sheets vs. pi-pi interactions of the conjugated segments decorating the periphery of the nanowires. Circular dichroism revealed helical arrangements of the conjugated moieties in these peptide lipids manifesting supercoiling phenomena. Peptide lipids without helical arrangement of the conjugated segments only exhibit helical morphologies. The self-assembly process of peptide lipids also leads to hierarchical assemblies of energetically favored single, double, and triple-helical nanostructures with well-defined dimensions. Self-assembled nanowires from oligothiophene-substituted peptide lipids revealed increased conductivity of 1.39--1.41 x 10-5 S/cm, two orders of magnitude higher than unassembled films and one order of magnitude higher than unsubstituted peptide lipids. The role of the primary beta-helix in controlling supramolecular organization was investigated by varying the chirality of the tripeptide segments, GAA. Four diastereomers of a peptide lipid substituted with p-toluene carboxylates were compared using L or D-alanines. Molecules with all L residues self-assemble into left-handed helical nanofibers with a pitch of 160 +/- 30 nm. Substitution of one or two D-alanines leads to assemblies of cylindrical nanofibers without any twisting, left-handed helices with smaller pitches (40 +/- 6 nm), or aggregates without regular shapes. We believe these effects are steric in nature that changes the beta-sheet sub-structure within the nanofibers. These principles could be utilized as strategies to optimize the morphologies and properties of nanostructures based on these amphiphilic molecules.

Self-assembled polystyrene nanospheres for the evaluation of atomic force microscopy tip curvature radius

NASA Astrophysics Data System (ADS)

Colombi, P.; Alessandri, I.; Bergese, P.; Federici, S.; Depero, L. E.

2009-08-01

In this paper, self-assembled polystyrene nanospheres are proposed as a shape characterizer sample for SPM tips. Ordered arrays or 2D islands of polystyrene spheres may be prepared either by sedimentation or by crystallization of the colloidal spheres' suspension. The self-assembling mechanism guarantees high reproducibility; thus the characterizer sample can be 'freshly' prepared at each use, avoiding the problem of time and use deterioration and reducing the problem of sample structure fidelity that occurs when lithographic structures are employed. The spheres could also be deposited on the sample itself in order to speed up the characterization process in applications requiring frequent tip characterizations. We present numerical calculations of geometrical convoluted profiles on the proposed structures showing that, for a variety of different tip shapes, at the border between a couple of touching spheres the tip flanks do not come into contact with the spheres. Due to this behaviour, touching spheres are an optimum characterizer sample for SPM tip curvature radius characterization, enabling a straightforward procedure for calculating the curvature radius from the amplitude of tip oscillation along profiles connecting spheres' centres. The new procedure for the characterization of SPM probes was assessed exploiting different kinds of self-assembled structures and comparing results to those obtained by spiked structures and SEM observations.

Laser-directed 3D assembly of carbon nanotubes using two-photon polymerization (Conference Presentation)

NASA Astrophysics Data System (ADS)

Liu, Ying; Xiong, Wei; Jiang, Li Jia; Zhou, Yunshen; Li, Dawei; Jiang, Lan; Silvain, Jean-Francois; Lu, Yongfeng

2017-02-01

Precise assembly of carbon nanotubes (CNTs) in arbitrary 3D space with proper alignment is critically important and desirable for CNT applications but still remains as a long-standing challenge. Using the two-photon polymerization (TPP) technique, it is possible to fabricate 3D micro/nanoscale CNT/polymer architectures with proper CNT alignments in desired directions, which is expected to enable a broad range of applications of CNTs in functional devices. To unleash the full potential of CNTs, it is strategically important to develop TPP-compatible resins with high CNT concentrations for precise assembly of CNTs into 3D micro/nanostructures for functional device applications. We investigated a thiol grafting method in functionalizing multiwalled carbon nanotubes (MWNTs) to develop TPP-compatible MWNT-thiol-acrylate (MTA) composite resins. The composite resins developed had high MWNT concentrations up to 0.2 wt%, over one order of magnitude higher than previously published work. Significantly enhanced electrical and mechanical properties of the 3D micro/nanostructures were achieved. Precisely controlled MWNT assembly and strong anisotropic effects were confirmed. Microelectronic devices made of the MTA composite polymer were demonstrated. The nanofabrication method can achieve controlled assembly of MWNTs in 3D micro/nanostructures, enabling a broad range of CNT applications, including 3D electronics, integrated photonics, and micro/nanoelectromechanical systems (MEMS/NEMS).

Conformation-Directed Formation of Self-Healing Diblock Copolypeptide Hydrogels via Polyion Complexation.

PubMed

Sun, Yintao; Wollenberg, Alexander L; O'Shea, Timothy Mark; Cui, Yanxiang; Zhou, Z Hong; Sofroniew, Michael V; Deming, Timothy J

2017-10-25

Synthetic diblock copolypeptides were designed to incorporate oppositely charged ionic segments that form β-sheet-structured hydrogel assemblies via polyion complexation when mixed in aqueous media. The observed chain conformation directed assembly was found to be required for efficient hydrogel formation and provided distinct and useful properties to these hydrogels, including self-healing after deformation, microporous architecture, and stability against dilution in aqueous media. While many promising self-assembled materials have been prepared using disordered or liquid coacervate polyion complex (PIC) assemblies, the use of ordered chain conformations in PIC assemblies to direct formation of new supramolecular morphologies is unprecedented. The promising attributes and unique features of the β-sheet-structured PIC hydrogels described here highlight the potential of harnessing conformational order derived from PIC assembly to create new supramolecular materials.

Control of drug release through the in situ assembly of stimuli-responsive ordered mesoporous silica with magnetic particles.

PubMed

Zhu, Shenmin; Zhou, Zhengyang; Zhang, Di

2007-12-03

A site-selective controlled delivery system for controlled drug release is fabricated through the in situ assembly of stimuli-responsive ordered SBA-15 and magnetic particles. This approach is based on the formation of ordered mesoporous silica with magnetic particles formed from Fe(CO)5 via the surfactant-template sol-gel method and control of transport through polymerization of N-isopropyl acrylamide inside the pores. Hydrophobic Fe(CO)5 acts as a swelling agent as well as being the source of the magnetic particles. The obtained system demonstrates a high pore diameter (7.1 nm) and pore volume (0.41 cm(3) g(-1)), which improves drug storage for relatively large molecules. Controlled drug release through the porous network is demonstrated by measuring the uptake and release of ibuprofen (IBU). The delivery system displays a high IBU storage capacity of 71.5 wt %, which is almost twice as large as the highest value based on SBA-15 ever reported. In vitro testing of IBU loading and release exhibits a pronounced transition at around 32 degrees C, indicating a typical thermosensitive controlled release.

Solid-state synthesis of ordered mesoporous carbon catalysts via a mechanochemical assembly through coordination cross-linking

PubMed Central

Zhang, Pengfei; Wang, Li; Yang, Shize; Schott, Jennifer A.; Liu, Xiaofei; Mahurin, Shannon M.; Huang, Caili; Zhang, Yu; Fulvio, Pasquale F.; Chisholm, Matthew F.; Dai, Sheng

2017-01-01

Ordered mesoporous carbons (OMCs) have demonstrated great potential in catalysis, and as supercapacitors and adsorbents. Since the introduction of the organic–organic self-assembly approach in 2004/2005 until now, the direct synthesis of OMCs is still limited to the wet processing of phenol-formaldehyde polycondensation, which involves soluble toxic precursors, and acid or alkali catalysts, and requires multiple synthesis steps, thus restricting the widespread application of OMCs. Herein, we report a simple, general, scalable and sustainable solid-state synthesis of OMCs and nickel OMCs with uniform and tunable mesopores (∼4–10 nm), large pore volumes (up to 0.96 cm3 g−1) and high-surface areas exceeding 1,000 m2 g−1, based on a mechanochemical assembly between polyphenol-metal complexes and triblock co-polymers. Nickel nanoparticles (∼5.40 nm) confined in the cylindrical nanochannels show great thermal stability at 600 °C. Moreover, the nickel OMCs offer exceptional activity in the hydrogenation of bulky molecules (∼2 nm). PMID:28452357

Water-Rich Fluid Material Containing Orderly Condensed Proteins.

PubMed

Nojima, Tatsuya; Iyoda, Tomokazu

2017-01-24

A fluid material with high protein content (120-310 mg mL -1 ) was formed through the ordered self-assembly of native proteins segregated from water. This material is instantly prepared by the simple mixing of a protein solution with anionic and cationic surfactants. By changing the ratio of the surfactants based on the electrostatic characteristics of the target protein, we observed that the surfactants could function as a versatile molecular glue for protein assembly. Moreover, these protein assemblies could be disassembled back into an aqueous solution depending on the salt conditions. Owing to the water-retaining properties of the hydrophilic part of surfactants, the proteins in this material are in a water-rich environment, which maintains their native structure and function. The inclusion of water also provides functional extensibility to this material, as demonstrated by the preparation of an enzymatically active gel. We anticipate that the unique features of this material will permit the use of proteins not only in solution but also as elements of integrated functionalized materials. © 2017 Wiley-VCH Verlag GmbH & Co. KGaA, Weinheim.

Quaterrylene molecules on Ag(111): self-assembly behavior and voltage pulse induced trimer formation.

PubMed

He, Yangyong; Cai, Zeying; Shao, Jian; Xu, Li; She, Limin; Zheng, Yue; Zhong, Dingyong

2018-05-03

The self-assembly behavior of quaterrylene (QR) molecules on Ag(111) surfaces has been investigated by scanning tunneling microscopy (STM) and density functional theory (DFT) calculations. It is found that the QR molecules are highly mobile on the Ag(111) surface at 78 K. No ordered assembled structure is formed on the surface with a sub-monolayer coverage up to 0.8 monolayer due to the intermolecular repulsive interactions, whereas ordered molecular structures are observed at one monolayer coverage. According to our DFT calculations, charge transfer occurs between the substrate and the adsorbed QR molecule. As a result, out-of-plane dipoles appear at the interface, which are ascribed to the repulsive dipole-dipole interactions between the QR molecules. Furthermore, due to the planar geometry, the QR molecules exhibit relatively low diffusion barriers on Ag(111). By applying a voltage pulse between the tunneling gap, immobilization and aggregation of QR molecules take place, resulting in the formation of a triangle-shaped trimer. Our work demonstrates the ability of manipulating intermolecular repulsive and attractive interactions at the single molecular level.

Self-assembly and nanosphere lithography for large-area plasmonic patterns on graphene.

PubMed

Lotito, Valeria; Zambelli, Tomaso

2015-06-01

Plasmonic structures on graphene can tailor its optical properties, which is essential for sensing and optoelectronic applications, e.g. for the enhancement of photoresponsivity of graphene photodetectors. Control over their structural and, hence, spectral properties can be attained by using electron beam lithography, which is not a viable solution for the definition of patterns over large areas. For the fabrication of large-area plasmonic nanostructures, we propose to use self-assembled monolayers of nanospheres as a mask for metal evaporation and etching processes. An optimized approach based on self-assembly at air/water interface with a properly designed apparatus allows the attainment of monolayers of hexagonally closely packed patterns with high long-range order and large area coverage; special strategies are devised in order to protect graphene against damage resulting from surface treatment and further processing steps such as reactive ion etching, which could potentially impair graphene properties. Therefore we demonstrate that nanosphere lithography is a cost-effective solution to create plasmonic patterns on graphene. Copyright © 2014 Elsevier Inc. All rights reserved.

RNA Seeds Higher Order Assembly of FUS Protein

PubMed Central

Schwartz, Jacob C.; Wang, Xueyin; Podell, Elaine R.; Cech, Thomas R.

2014-01-01

SUMMARY The abundant nuclear RNA-binding protein FUS binds the CTD of RNA polymerase II in an RNA-dependent manner, affecting Ser2 phosphorylation and transcription. Here we examine the mechanism of this process and find that RNA binding nucleates the formation of higher order FUS RNP assemblies that bind the CTD. Both the low-complexity domain and the RGG domain of FUS contribute to assembly. The assemblies appear fibrous by electron microscopy and have characteristics of beta-zipper structures. These results support the emerging view that the pathologic protein aggregation seen in neurodegenerative diseases such as ALS may occur by exaggeration of functionally important assemblies of RNA-binding proteins. PMID:24268778

The orderly nano array of truncated octahedra Cu2O nanocrystals with the enhancement of visible light photocatalytic activity

NASA Astrophysics Data System (ADS)

Wei, Xiaofeng; Pan, Jiaqi; Mei, Jie; Zheng, Yingying; Cui, Can; Li, Chaorong

2018-07-01

The orderly nano array is able to improve the light utilization efficiency and has been thought to be a promising way for advancing photocatalysis. The orderly nano array of truncated octahedra Cu2O nanocrystals have been successfully fabricated by the facile solution-based one-step reduction and self-assembly method. The results of XRD, SEM and TEM indicate that the Cu2O nano array is successfully assembled on the Si substrate. The photocatalytic activity of the Cu2O orderly nano array is investigated under visible light irradiation, and it is demonstrated to be significantly enhanced after the Cu2O is self-assembled orderly. Furthermore, the surface orderly structure of the nano array is considered as the main reason for the enhancement.

Augmenting Photoinduced Charge Transport in a Single-Component Gel System: Controlled In Situ Gel-Crystal Transformation at Room Temperature.

PubMed

Satapathy, Sitakanta; Prabakaran, Palani; Prasad, Edamana

2018-04-20

Smart single-component materials with versatile functions require pre-programming of a higher order molecular assembly. An electroactive supergelator (c=0.07 wt %) triphenylamine core-appended poly(aryl ether) dendron (TPAPAE) is described, where substantial dendritic effects improve the order and crystallinity by switching the local minima from self-assembled molecular wires to thermodynamically favorable global minima of ordered crystals, ripened within the fibers. Controlled in situ phase change at room temperature ultimately stabilized the mixed valence states in the single-component supramolecular assembly with photoluminescence and photoinduced charge transport amplified by two orders of magnitude. © 2018 Wiley-VCH Verlag GmbH & Co. KGaA, Weinheim.

Stimulus-Responsive Nanoparticles and Associated (Reversible) Polymorphism via Polymerization Induced Self-assembly (PISA).

PubMed

Pei, Yiwen; Lowe, Andrew B; Roth, Peter J

2017-01-01

Polymerization-induced self-assembly (PISA) is an extremely versatile method for the in situ preparation of soft-matter nanoparticles of defined size and morphologies at high concentrations, suitable for large-scale production. Recently, certain PISA-prepared nanoparticles have been shown to exhibit reversible polymorphism ("shape-shifting"), typically between micellar, worm-like, and vesicular phases (order-order transitions), in response to external stimuli including temperature, pH, electrolytes, and chemical modification. This review summarises the literature to date and describes molecular requirements for the design of stimulus-responsive nano-objects. Reversible pH-responsive behavior is rationalised in terms of increased solvation of reversibly ionized groups. Temperature-triggered order-order transitions, conversely, do not rely on inherently thermo-responsive polymers, but are explained based on interfacial LCST or UCST behavior that affects the volume fractions of the core and stabilizer blocks. Irreversible morphology transitions, on the other hand, can result from chemical post-modification of reactive PISA-made particles. Emerging applications and future research directions of this "smart" nanoparticle behavior are reviewed. © 2016 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Highly stable and self-repairing membrane-mimetic 2D nanomaterials assembled from lipid-like peptoids

DOE PAGES

Jin, Haibao; Jiao, Fang; Daily, Michael D.; ...

2016-07-12

Two-dimensional (2D) materials with molecular-scale thickness have attracted increasing interest for separation, electronic, catalytic, optical, energy and biomedical applications. Although extensive research on 2D materials, such as graphene and graphene oxide, has been performed in recent years, progress is limited on self-assembly of 2D materials from sequence-specific macromolecules, especially from synthetic sequences that could exhibit lipid-like self-assembly of bilayer sheets and mimic membrane proteins for functions. The creation of such new class of materials could enable development of highly stable biomimetic membranes that exhibit cell-membrane-like molecular transport with exceptional selectively and high transport rates. Here we demonstrate self-assembly of lipid-likemore » 12-mer peptoids into extremely stable, crystalline, flexible and free-standing 2D membrane materials. As with cell membranes, upon exposure to external stimuli, these materials exhibit changes in thickness, varying from 3.5 nm to 5.6 nm. We find that self-assembly occurs through a facile crystallization process, in which inter-peptoid hydrogen bonds and enhanced hydrophobic interactions drive the formation of a highly-ordered structure. Molecular simulation confirms this is the energetically favored structure. Displaying functional groups at arbitrary locations of membrane-forming peptoids produces membranes with similar structures. This research further shows that single-layer membranes can be coated onto substrate surfaces. Moreover, membranes with mechanically-induced defects can self-repair. Given that peptoids are sequence-specific and exhibit protein-like molecular recognition with enhanced stability, we anticipate our membranes to be a robust platform tailored to specific applications.« less

Highly stable and self-repairing membrane-mimetic 2D nanomaterials assembled from lipid-like peptoids

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

Jin, Haibao; Jiao, Fang; Daily, Michael D.

Two-dimensional (2D) materials with molecular-scale thickness have attracted increasing interest for separation, electronic, catalytic, optical, energy and biomedical applications. Although extensive research on 2D materials, such as graphene and graphene oxide, has been performed in recent years, progress is limited on self-assembly of 2D materials from sequence-specific macromolecules, especially from synthetic sequences that could exhibit lipid-like self-assembly of bilayer sheets and mimic membrane proteins for functions. The creation of such new class of materials could enable development of highly stable biomimetic membranes that exhibit cell-membrane-like molecular transport with exceptional selectively and high transport rates. Here we demonstrate self-assembly of lipid-likemore » 12-mer peptoids into extremely stable, crystalline, flexible and free-standing 2D membrane materials. As with cell membranes, upon exposure to external stimuli, these materials exhibit changes in thickness, varying from 3.5 nm to 5.6 nm. We find that self-assembly occurs through a facile crystallization process, in which inter-peptoid hydrogen bonds and enhanced hydrophobic interactions drive the formation of a highly-ordered structure. Molecular simulation confirms this is the energetically favored structure. Displaying functional groups at arbitrary locations of membrane-forming peptoids produces membranes with similar structures. This research further shows that single-layer membranes can be coated onto substrate surfaces. Moreover, membranes with mechanically-induced defects can self-repair. Given that peptoids are sequence-specific and exhibit protein-like molecular recognition with enhanced stability, we anticipate our membranes to be a robust platform tailored to specific applications.« less

Assembly of ordered contigs of cosmids selected with YACs of human chromosome 13

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

Fischer, S.G.; Cayanis, E.; Boukhgalter, B.

1994-06-01

The authors have developed an efficient method for assembling ordered cosmid contigs aligned to mega-YACs and midi-YACs (average insert sizes of 1.0 and 0.35 Mb, respectively) and used this general method to initiate high-resolution physical mapping of human chromosome 13 (Chr 13). Chr 13-enriched midi-YAC (mYAC) and mega-YAC (MYAC) sublibraries were obtained from corresponding CEPH total human YAC libraries by selecting colonies with inter-Alu PCR probes derived from Chr 13 monochromosomal cell hybrid DNA. These sublibraries were arrayed on filters at high density. In this approach, the MYAC 13 sublibrary is screened by hybridization with cytogenetically assigned Chr 13 DNAmore » probes to select one or a small subset of MYACs. Inter-Alu PCR products from each mYAC are then hybridized to the MYAC and mYAC sublibraries to identify overlapping YACs and to an arrayed Chr 13-specific cosmid library to select corresponding cosmids. The set of selected cosmids, gridded on filters at high density, is hybridized with inter-Alu PCR products from each of the overlapping YACs to identify subsets of cosmids and also with riboprobes from each cosmid of the arrayed set ({open_quotes}cosmid matrix cross-hybridization{close_quotes}). From these data, cosmid contigs are assembled by a specifically designed computer program. Application of this method generates cosmid contigs spanning the length of a MYAC with few gaps. To provide a high-resolution map, ends of cosmids are sequenced at preselected sites to position densely spaced sequence-tagged sites. 33 refs., 7 figs., 1 tab.« less

Self-Assembled, Iridescent, Crustacean-Mimetic Nanocomposites with Tailored Periodicity and Layered Cuticular Structure.

PubMed

Wang, Baochun; Walther, Andreas

2015-11-24

Natural high-performance materials inspire the pursuit of ordered hard/soft nanocomposite structures at high fractions of reinforcements and with balanced molecular interactions. Herein, we develop a facile, waterborne self-assembly pathway to mimic the multiscale cuticle structure of the crustacean armor by combining hard reinforcing cellulose nanocrystals (CNCs) with soft poly(vinyl alcohol) (PVA). We show iridescent CNC nanocomposites with cholesteric liquid-crystal structure, in which different helical pitches and photonic band gaps can be realized by varying the CNC/PVA ratio. We further show that multilayered crustacean-mimetic materials with tailored periodicity and layered cuticular structure can be obtained by sequential preparation pathways. The transition from a cholesteric to a disordered structure occurs for a critical polymer concentration. Correspondingly, we find a transition from stiff and strong mechanical behavior to materials with increasing ductility. Crack propagation studies using scanning electron microscopy visualize the different crack growth and toughening mechanisms inside cholesteric nanocomposites as a function of the interstitial polymer content for the first time. Different extents of crack deflection, layered delamination, ligament bridging, and constrained microcracking can be observed. Drawing of highly plasticized films sheds light on the mechanistic details of the transition from a cholesteric/chiral nematic to a nematic structure. The study demonstrates how self-assembly of biobased CNCs in combination with suitable polymers can be used to replicate a hierarchical biological structure and how future design of these ordered multifunctional nanocomposites can be optimized by understanding mechanistic details of deformation and fracture.

Error Modeling and Experimental Study of a Flexible Joint 6-UPUR Parallel Six-Axis Force Sensor.

PubMed

Zhao, Yanzhi; Cao, Yachao; Zhang, Caifeng; Zhang, Dan; Zhang, Jie

2017-09-29

By combining a parallel mechanism with integrated flexible joints, a large measurement range and high accuracy sensor is realized. However, the main errors of the sensor involve not only assembly errors, but also deformation errors of its flexible leg. Based on a flexible joint 6-UPUR (a kind of mechanism configuration where U-universal joint, P-prismatic joint, R-revolute joint) parallel six-axis force sensor developed during the prephase, assembly and deformation error modeling and analysis of the resulting sensors with a large measurement range and high accuracy are made in this paper. First, an assembly error model is established based on the imaginary kinematic joint method and the Denavit-Hartenberg (D-H) method. Next, a stiffness model is built to solve the stiffness matrix. The deformation error model of the sensor is obtained. Then, the first order kinematic influence coefficient matrix when the synthetic error is taken into account is solved. Finally, measurement and calibration experiments of the sensor composed of the hardware and software system are performed. Forced deformation of the force-measuring platform is detected by using laser interferometry and analyzed to verify the correctness of the synthetic error model. In addition, the first order kinematic influence coefficient matrix in actual circumstances is calculated. By comparing the condition numbers and square norms of the coefficient matrices, the conclusion is drawn theoretically that it is very important to take into account the synthetic error for design stage of the sensor and helpful to improve performance of the sensor in order to meet needs of actual working environments.

Error Modeling and Experimental Study of a Flexible Joint 6-UPUR Parallel Six-Axis Force Sensor

PubMed Central

Zhao, Yanzhi; Cao, Yachao; Zhang, Caifeng; Zhang, Dan; Zhang, Jie

2017-01-01

By combining a parallel mechanism with integrated flexible joints, a large measurement range and high accuracy sensor is realized. However, the main errors of the sensor involve not only assembly errors, but also deformation errors of its flexible leg. Based on a flexible joint 6-UPUR (a kind of mechanism configuration where U-universal joint, P-prismatic joint, R-revolute joint) parallel six-axis force sensor developed during the prephase, assembly and deformation error modeling and analysis of the resulting sensors with a large measurement range and high accuracy are made in this paper. First, an assembly error model is established based on the imaginary kinematic joint method and the Denavit-Hartenberg (D-H) method. Next, a stiffness model is built to solve the stiffness matrix. The deformation error model of the sensor is obtained. Then, the first order kinematic influence coefficient matrix when the synthetic error is taken into account is solved. Finally, measurement and calibration experiments of the sensor composed of the hardware and software system are performed. Forced deformation of the force-measuring platform is detected by using laser interferometry and analyzed to verify the correctness of the synthetic error model. In addition, the first order kinematic influence coefficient matrix in actual circumstances is calculated. By comparing the condition numbers and square norms of the coefficient matrices, the conclusion is drawn theoretically that it is very important to take into account the synthetic error for design stage of the sensor and helpful to improve performance of the sensor in order to meet needs of actual working environments. PMID:28961209

Single haplotype assembly of the human genome from a hydatidiform mole.

PubMed

Steinberg, Karyn Meltz; Schneider, Valerie A; Graves-Lindsay, Tina A; Fulton, Robert S; Agarwala, Richa; Huddleston, John; Shiryev, Sergey A; Morgulis, Aleksandr; Surti, Urvashi; Warren, Wesley C; Church, Deanna M; Eichler, Evan E; Wilson, Richard K

2014-12-01

A complete reference assembly is essential for accurately interpreting individual genomes and associating variation with phenotypes. While the current human reference genome sequence is of very high quality, gaps and misassemblies remain due to biological and technical complexities. Large repetitive sequences and complex allelic diversity are the two main drivers of assembly error. Although increasing the length of sequence reads and library fragments can improve assembly, even the longest available reads do not resolve all regions. In order to overcome the issue of allelic diversity, we used genomic DNA from an essentially haploid hydatidiform mole, CHM1. We utilized several resources from this DNA including a set of end-sequenced and indexed BAC clones and 100× Illumina whole-genome shotgun (WGS) sequence coverage. We used the WGS sequence and the GRCh37 reference assembly to create an assembly of the CHM1 genome. We subsequently incorporated 382 finished BAC clone sequences to generate a draft assembly, CHM1_1.1 (NCBI AssemblyDB GCA_000306695.2). Analysis of gene, repetitive element, and segmental duplication content show this assembly to be of excellent quality and contiguity. However, comparison to assembly-independent resources, such as BAC clone end sequences and PacBio long reads, indicate misassembled regions. Most of these regions are enriched for structural variation and segmental duplication, and can be resolved in the future. This publicly available assembly will be integrated into the Genome Reference Consortium curation framework for further improvement, with the ultimate goal being a completely finished gap-free assembly. © 2014 Steinberg et al.; Published by Cold Spring Harbor Laboratory Press.

Single haplotype assembly of the human genome from a hydatidiform mole

PubMed Central

Steinberg, Karyn Meltz; Schneider, Valerie A.; Graves-Lindsay, Tina A.; Fulton, Robert S.; Agarwala, Richa; Huddleston, John; Shiryev, Sergey A.; Morgulis, Aleksandr; Surti, Urvashi; Warren, Wesley C.; Church, Deanna M.; Eichler, Evan E.; Wilson, Richard K.

2014-01-01

A complete reference assembly is essential for accurately interpreting individual genomes and associating variation with phenotypes. While the current human reference genome sequence is of very high quality, gaps and misassemblies remain due to biological and technical complexities. Large repetitive sequences and complex allelic diversity are the two main drivers of assembly error. Although increasing the length of sequence reads and library fragments can improve assembly, even the longest available reads do not resolve all regions. In order to overcome the issue of allelic diversity, we used genomic DNA from an essentially haploid hydatidiform mole, CHM1. We utilized several resources from this DNA including a set of end-sequenced and indexed BAC clones and 100× Illumina whole-genome shotgun (WGS) sequence coverage. We used the WGS sequence and the GRCh37 reference assembly to create an assembly of the CHM1 genome. We subsequently incorporated 382 finished BAC clone sequences to generate a draft assembly, CHM1_1.1 (NCBI AssemblyDB GCA_000306695.2). Analysis of gene, repetitive element, and segmental duplication content show this assembly to be of excellent quality and contiguity. However, comparison to assembly-independent resources, such as BAC clone end sequences and PacBio long reads, indicate misassembled regions. Most of these regions are enriched for structural variation and segmental duplication, and can be resolved in the future. This publicly available assembly will be integrated into the Genome Reference Consortium curation framework for further improvement, with the ultimate goal being a completely finished gap-free assembly. PMID:25373144

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.

j5 v2.8.4

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

Hillson, Nathan

j5 automates and optimizes the design of the molecular biological process of cloning/constructing DNA. j5 enables users to benefit from (combinatorial) multi-part scar-less SLIC, Gibson, CPEC, Golden Gate assembly, or variants thereof, for which automation software does not currently exist, without the intense labor currently associated with the process. j5 inputs a list of the DNA sequences to be assembled, along with a Genbank, FASTA, jbei-seq, or SBOL v1.1 format sequence file for each DNA source. Given the list of DNA sequences to be assembled, j5 first determines the cost-minimizing assembly strategy for each part (direct synthesis, PCR/SOE, or oligo-embedding),more » designs DNA oligos with Primer3, adds flanking homology sequences (SLIC, Gibson, and CPEC; optimized with Primer3 for CPEC) or optimized overhang sequences (Golden Gate) to the oligos and direct synthesis pieces, and utilizes BLAST to check against oligo mis-priming and assembly piece incompatibility events. After identifying DNA oligos that are already contained within a local collection for reuse, the program estimates the total cost of direct synthesis and new oligos to be ordered. In the instance that j5 identifies putative assembly piece incompatibilities (multiple pieces with high flanking sequence homology), the program suggests hierarchical subassemblies where possible. The program outputs a comma-separated value (CSV) file, viewable via Excel or other spreadsheet software, that contains assembly design information (such as the PCR/SOE reactions to perform, their anticipated sizes and sequences, etc.) as well as a properly annotated genbank file containing the sequence resulting from the assembly, and appends the local oligo library with the oligos to be ordered j5 condenses multiple independent assembly projects into 96-well format for high-throughput liquid-handling robotics platforms, and generates configuration files for the PR-PR biology-friendly robot programming language. j5 thus provides a new way to design DNA assembly procedures much more productively and efficiently, not only in terms of time, but also in terms of cost. To a large extent, however, j5 does not allow people to do something that could not be done before by hand given enough time and effort. An exception to this is that, since the very act of using j5 to design the DNA assembly process standardizes the experimental details and workflow, j5 enables a single person to concurrently perform the independent DNA construction tasks of an entire group of researchers. Currently, this is not readily possible, since separate researchers employ disparate design strategies and workflows, and furthermore, their designs and workflows are very infrequently fully captured in an electronic format which is conducive to automation.« less

Rapid ordering of block copolymer thin films

DOE PAGES

Majewski, Pawel W.; Yager, Kevin G.

2016-08-18

Block-copolymers self-assemble into diverse morphologies, where nanoscale order can be finely tuned via block architecture and processing conditions. However, the ultimate usage of these materials in real-world applications may be hampered by the extremely long thermal annealing times—hours or days—required to achieve good order. Here, we provide an overview of the fundamentals of block-copolymer self-assembly kinetics, and review the techniques that have been demonstrated to influence, and enhance, these ordering kinetics. We discuss the inherent tradeoffs between oven annealing, solvent annealing, microwave annealing, zone annealing, and other directed self-assembly methods; including an assessment of spatial and temporal characteristics. Here, wemore » also review both real-space and reciprocal-space analysis techniques for quantifying order in these systems.« less

Communication: Microphase equilibrium and assembly dynamics.

PubMed

Zhuang, Yuan; Charbonneau, Patrick

2017-09-07

Despite many attempts, ordered equilibrium microphases have yet to be obtained in experimental colloidal suspensions. The recent computation of the equilibrium phase diagram of a microscopic, particle-based microphase former [Zhuang et al., Phys. Rev. Lett. 116, 098301 (2016)] has nonetheless found such mesoscale assemblies to be thermodynamically stable. Here, we consider their equilibrium and assembly dynamics. At intermediate densities above the order-disorder transition, we identify four different dynamical regimes and the structural changes that underlie the dynamical crossovers from one disordered regime to the next. Below the order-disorder transition, we also find that periodic lamellae are the most dynamically accessible of the periodic microphases. Our analysis thus offers a comprehensive view of the dynamics of disordered microphases and a route to the assembly of periodic microphases in a putative well-controlled, experimental system.

Debye ring diffraction elucidation of 2D photonic crystal self-assembly and ordering at the air-water interface.

PubMed

Smith, N L; Coukouma, A; Dubnik, S; Asher, S A

2017-12-06

We fabricate 2D photonic crystals (2DPC) by spreading a dispersion of charged colloidal particles (diameters = 409, 570, and 915 nm) onto the surface of electrolyte solutions using a needle tip flow method. When the interparticle electrostatic interaction potential is large, particles self-assemble into highly ordered hexagonal close packed (hcp) monolayers. Ordered 2DPC efficiently forward diffract monochromatic light to produce a Debye ring on a screen parallel to the 2DPC. The diameter of the Debye ring is inversely proportional to the 2DPC particle spacing, while the Debye ring brightness and thickness depends on the 2DPC ordering. The Debye ring thickness increases as the 2DPC order decreases. The Debye ring ordering measurements of 2DPC attached to glass slides track measurements of the 2D pair correlation function order parameter calculated from SEM micrographs. The Debye ring method was used to investigate the 2DPC particle spacing, and ordering at the air-solution interface of NaCl solutions, and for 2DPC arrays attached to glass slides. Surprisingly, the 2DPC ordering does not monotonically decrease as the salt concentration increases. This is because of chloride ion adsorption onto the anionic particle surfaces. This adsorption increases the particle surface charge and compensates for the decreased Debye length of the electric double layer when the NaCl concentration is below a critical value.

Templated Assembly of a Functional Ordered Protein Macromolecular Framework from P22 Virus-like Particles.

PubMed

McCoy, Kimberly; Uchida, Masaki; Lee, Byeongdu; Douglas, Trevor

2018-04-24

Bottom-up construction of mesoscale materials using biologically derived nanoscale building blocks enables engineering of desired physical properties using green production methods. Virus-like particles (VLPs) are exceptional building blocks due to their monodispersed sizes, geometric shapes, production ease, proteinaceous composition, and our ability to independently functionalize the interior and exterior interfaces. Here a VLP, derived from bacteriophage P22, is used as a building block for the fabrication of a protein macromolecular framework (PMF), a tightly linked 3D network of functional protein cages that exhibit long-range order and catalytic activity. Assembly of PMFs was electrostatically templated, using amine-terminated dendrimers, then locked into place with a ditopic cementing protein that binds to P22. Long-range order is preserved on removal of the dendrimer, leaving a framework material composed completely of protein. Encapsulation of β-glucosidase enzymes inside of P22 VLPs results in formation of stable, condensed-phase materials with high local concentration of enzymes generating catalytically active PMFs.

Bioinspired assembly of surface-roughened nanoplatelets.

PubMed

Lin, Tzung-Hua; Huang, Wei-Han; Jun, In-Kook; Jiang, Peng

2010-04-15

Here we report a novel electrophoretic deposition technology for assembling surface-roughened inorganic nanoplatelets into ordered multilayers that mimic the brick-and-mortar nanostructure found in the nacreous layer of mollusk shells. A thin layer of sol-gel silica is coated on smooth gibbsite nanoplatelets in order to increase the surface roughness to mimic the asperity of aragonite platelets found in nacres. To avoid the severe cracking caused by the shrinkage of sol-gel silica during drying, polyelectrolyte polyethyleneimine is used to reverse the surface charge of silica-coated-gibbsite nanoplatelets and increase the adherence and strength of the electrodeposited films. Polymer nanocomposites can then be made by infiltrating the interstitials of the aligned nanoplatelet multilayers with photocurable monomer followed by photopolymerization. The resulting self-standing films are highly transparent and exhibit nearly three times higher tensile strength and one-order-of-magnitude higher toughness than those of pure polymer. The measured tensile strength agrees with that predicted by a simple shear lag model. Published by Elsevier Inc.

Spontaneous formation of nanoparticle stripe patterns through dewetting

NASA Astrophysics Data System (ADS)

Huang, Jiaxing; Kim, Franklin; Tao, Andrea R.; Connor, Stephen; Yang, Peidong

2005-12-01

Significant advancement has been made in nanoparticle research, with synthetic techniques extending over a wide range of materials with good control over particle size and shape. A grand challenge is assembling and positioning the nanoparticles in desired locations to construct complex, higher-order functional structures. Controlled positioning of nanoparticles has been achieved in pre-defined templates fabricated by top-down approaches. A self-assembly method, however, is highly desirable because of its simplicity and compatibility with heterogeneous integration processes. Here we report on the spontaneous formation of ordered gold and silver nanoparticle stripe patterns on dewetting a dilute film of polymer-coated nanoparticles floating on a water surface. Well-aligned stripe patterns with tunable orientation, thickness and periodicity at the micrometre scale were obtained by transferring nanoparticles from a floating film onto a substrate in a dip-coating fashion. This facile technique opens up a new avenue for lithography-free patterning of nanoparticle arrays for various applications including, for example, multiplexed surface-enhanced Raman substrates and templated fabrication of higher-order nanostructures.

Bottom-Up Tri-gate Transistors and Submicrosecond Photodetectors from Guided CdS Nanowalls.

PubMed

Xu, Jinyou; Oksenberg, Eitan; Popovitz-Biro, Ronit; Rechav, Katya; Joselevich, Ernesto

2017-11-08

Tri-gate transistors offer better performance than planar transistors by exerting additional gate control over a channel from two lateral sides of semiconductor nanowalls (or "fins"). Here we report the bottom-up assembly of aligned CdS nanowalls by a simultaneous combination of horizontal catalytic vapor-liquid-solid growth and vertical facet-selective noncatalytic vapor-solid growth and their parallel integration into tri-gate transistors and photodetectors at wafer scale (cm 2 ) without postgrowth transfer or alignment steps. These tri-gate transistors act as enhancement-mode transistors with an on/off current ratio on the order of 10 8 , 4 orders of magnitude higher than the best results ever reported for planar enhancement-mode CdS transistors. The response time of the photodetector is reduced to the submicrosecond level, 1 order of magnitude shorter than the best results ever reported for photodetectors made of bottom-up semiconductor nanostructures. Guided semiconductor nanowalls open new opportunities for high-performance 3D nanodevices assembled from the bottom up.

Layer-by-layer assembly of two-dimensional materials into wafer-scale heterostructures

NASA Astrophysics Data System (ADS)

Kang, Kibum; Lee, Kan-Heng; Han, Yimo; Gao, Hui; Xie, Saien; Muller, David A.; Park, Jiwoong

2017-10-01

High-performance semiconductor films with vertical compositions that are designed to atomic-scale precision provide the foundation for modern integrated circuitry and novel materials discovery. One approach to realizing such films is sequential layer-by-layer assembly, whereby atomically thin two-dimensional building blocks are vertically stacked, and held together by van der Waals interactions. With this approach, graphene and transition-metal dichalcogenides--which represent one- and three-atom-thick two-dimensional building blocks, respectively--have been used to realize previously inaccessible heterostructures with interesting physical properties. However, no large-scale assembly method exists at present that maintains the intrinsic properties of these two-dimensional building blocks while producing pristine interlayer interfaces, thus limiting the layer-by-layer assembly method to small-scale proof-of-concept demonstrations. Here we report the generation of wafer-scale semiconductor films with a very high level of spatial uniformity and pristine interfaces. The vertical composition and properties of these films are designed at the atomic scale using layer-by-layer assembly of two-dimensional building blocks under vacuum. We fabricate several large-scale, high-quality heterostructure films and devices, including superlattice films with vertical compositions designed layer-by-layer, batch-fabricated tunnel device arrays with resistances that can be tuned over four orders of magnitude, band-engineered heterostructure tunnel diodes, and millimetre-scale ultrathin membranes and windows. The stacked films are detachable, suspendable and compatible with water or plastic surfaces, which will enable their integration with advanced optical and mechanical systems.

Layer-by-layer assembly of two-dimensional materials into wafer-scale heterostructures.

PubMed

Kang, Kibum; Lee, Kan-Heng; Han, Yimo; Gao, Hui; Xie, Saien; Muller, David A; Park, Jiwoong

2017-10-12

High-performance semiconductor films with vertical compositions that are designed to atomic-scale precision provide the foundation for modern integrated circuitry and novel materials discovery. One approach to realizing such films is sequential layer-by-layer assembly, whereby atomically thin two-dimensional building blocks are vertically stacked, and held together by van der Waals interactions. With this approach, graphene and transition-metal dichalcogenides-which represent one- and three-atom-thick two-dimensional building blocks, respectively-have been used to realize previously inaccessible heterostructures with interesting physical properties. However, no large-scale assembly method exists at present that maintains the intrinsic properties of these two-dimensional building blocks while producing pristine interlayer interfaces, thus limiting the layer-by-layer assembly method to small-scale proof-of-concept demonstrations. Here we report the generation of wafer-scale semiconductor films with a very high level of spatial uniformity and pristine interfaces. The vertical composition and properties of these films are designed at the atomic scale using layer-by-layer assembly of two-dimensional building blocks under vacuum. We fabricate several large-scale, high-quality heterostructure films and devices, including superlattice films with vertical compositions designed layer-by-layer, batch-fabricated tunnel device arrays with resistances that can be tuned over four orders of magnitude, band-engineered heterostructure tunnel diodes, and millimetre-scale ultrathin membranes and windows. The stacked films are detachable, suspendable and compatible with water or plastic surfaces, which will enable their integration with advanced optical and mechanical systems.

Genome Partitioner: A web tool for multi-level partitioning of large-scale DNA constructs for synthetic biology applications

PubMed Central

Del Medico, Luca; Christen, Heinz; Christen, Beat

2017-01-01

Recent advances in lower-cost DNA synthesis techniques have enabled new innovations in the field of synthetic biology. Still, efficient design and higher-order assembly of genome-scale DNA constructs remains a labor-intensive process. Given the complexity, computer assisted design tools that fragment large DNA sequences into fabricable DNA blocks are needed to pave the way towards streamlined assembly of biological systems. Here, we present the Genome Partitioner software implemented as a web-based interface that permits multi-level partitioning of genome-scale DNA designs. Without the need for specialized computing skills, biologists can submit their DNA designs to a fully automated pipeline that generates the optimal retrosynthetic route for higher-order DNA assembly. To test the algorithm, we partitioned a 783 kb Caulobacter crescentus genome design. We validated the partitioning strategy by assembling a 20 kb test segment encompassing a difficult to synthesize DNA sequence. Successful assembly from 1 kb subblocks into the 20 kb segment highlights the effectiveness of the Genome Partitioner for reducing synthesis costs and timelines for higher-order DNA assembly. The Genome Partitioner is broadly applicable to translate DNA designs into ready to order sequences that can be assembled with standardized protocols, thus offering new opportunities to harness the diversity of microbial genomes for synthetic biology applications. The Genome Partitioner web tool can be accessed at https://christenlab.ethz.ch/GenomePartitioner. PMID:28531174

Preparation and high-performance microwave absorption of hierarchical dendrite-like Co superstructures self-assembly of nanoflakes

NASA Astrophysics Data System (ADS)

Yu, Miao; Wang, Lirui; Yang, Pingan; Fu, Jie

2017-12-01

Dendritic-like Co superstructures based on the self-assembly of nanoflakes that could efficiently suppress the eddy current were successfully synthesized via a facile, rapid, and energy-saving chemical reduction method. Since crystal structure, size, and special geometrical morphology, magnetism have a vital influence on microwave absorption properties, the as-obtained products were characterized by x-ray diffraction, scanning electron microscopy, vibrating sample magnetometry, and vector network analysis. The prepared dendritic Co possesses abundant secondary branches that extend to the 3D space. Their dimensions, spacing, sheet-like blocks, and high-ordering microstructures all contribute to the penetration, scattering, and attenuation of EM waves. The composites present attractive microwave absorption performances in the X band, as well as in the whole S band (2-4 GHz). This work investigates the mechanism of absorption for the as-obtained Co, offers a promising strategy for the fabrication of hierarchical Co microstructure assemblies by multi-leaf flakes and introduces the application of dendritic-like Co as a highly efficient absorber in the S band and X band.

Highly conductive ribbons prepared by stick-slip assembly of organosoluble gold nanoparticles.

PubMed

Lawrence, Jimmy; Pham, Jonathan T; Lee, Dong Yun; Liu, Yujie; Crosby, Alfred J; Emrick, Todd

2014-02-25

Precisely positioning and assembling nanoparticles (NPs) into hierarchical nanostructures is opening opportunities in a wide variety of applications. Many techniques employed to produce hierarchical micrometer and nanoscale structures are limited by complex fabrication of templates and difficulties with scalability. Here we describe the fabrication and characterization of conductive nanoparticle ribbons prepared from surfactant-free organosoluble gold nanoparticles (Au NPs). We used a flow-coating technique in a controlled, stick-slip assembly to regulate the deposition of Au NPs into densely packed, multilayered structures. This affords centimeter-scale long, high-resolution Au NP ribbons with precise periodic spacing in a rapid manner, up to 2 orders-of-magnitude finer and faster than previously reported methods. These Au NP ribbons exhibit linear ohmic response, with conductivity that varies by changing the binding headgroup of the ligands. Controlling NP percolation during sintering (e.g., by adding polymer to retard rapid NP coalescence) enables the formation of highly conductive ribbons, similar to thermally sintered conductive adhesives. Hierarchical, conductive Au NP ribbons represent a promising platform to enable opportunities in sensing, optoelectronics, and electromechanical devices.

Self-assembled PCBM bilayers on graphene and HOPG examined by AFM and STM

NASA Astrophysics Data System (ADS)

Li, Yanlong; Chen, Chuanhui; Burton, John; Park, Kyungwha; Heflin, James R.; Tao, Chenggang

2018-05-01

In this work we report fabrication and characterization of phenyl-C61-butyric acid methyl ester (PCBM) bilayer structures on graphene and highly oriented pyrolytic graphite (HOPG). Through careful control of the PCBM solution concentration (from 0.1 to 2 mg ml-1) and the deposition conditions, we demonstrate that PCBM molecules self-assemble into bilayer structures on graphene and HOPG substrates. Interestingly, the PCBM bilayers are formed with two distinct heights on HOPG, but only one unique representative height on graphene. At elevated annealing temperatures, edge diffusion allows neighboring vacancies to merge into a more ordered structure. This is, to the best of our knowledge, the first experimental realization of PCBM bilayer structures on graphene. This work could provide valuable insight into fabrication of new hybrid, ordered structures for applications to organic solar cells.

Self-assembled PCBM bilayers on graphene and HOPG examined by AFM and STM.

PubMed

Li, Yanlong; Chen, Chuanhui; Burton, John; Park, Kyungwha; Heflin, James R; Tao, Chenggang

2018-05-04

In this work we report fabrication and characterization of phenyl-C61-butyric acid methyl ester (PCBM) bilayer structures on graphene and highly oriented pyrolytic graphite (HOPG). Through careful control of the PCBM solution concentration (from 0.1 to 2 mg ml -1 ) and the deposition conditions, we demonstrate that PCBM molecules self-assemble into bilayer structures on graphene and HOPG substrates. Interestingly, the PCBM bilayers are formed with two distinct heights on HOPG, but only one unique representative height on graphene. At elevated annealing temperatures, edge diffusion allows neighboring vacancies to merge into a more ordered structure. This is, to the best of our knowledge, the first experimental realization of PCBM bilayer structures on graphene. This work could provide valuable insight into fabrication of new hybrid, ordered structures for applications to organic solar cells.

Scar-less multi-part DNA assembly design automation

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

Hillson, Nathan J.

The present invention provides a method of a method of designing an implementation of a DNA assembly. In an exemplary embodiment, the method includes (1) receiving a list of DNA sequence fragments to be assembled together and an order in which to assemble the DNA sequence fragments, (2) designing DNA oligonucleotides (oligos) for each of the DNA sequence fragments, and (3) creating a plan for adding flanking homology sequences to each of the DNA oligos. In an exemplary embodiment, the method includes (1) receiving a list of DNA sequence fragments to be assembled together and an order in which tomore » assemble the DNA sequence fragments, (2) designing DNA oligonucleotides (oligos) for each of the DNA sequence fragments, and (3) creating a plan for adding optimized overhang sequences to each of the DNA oligos.« less

Monolayer Colloidal Crystals by Modified Air-Water Interface Self-Assembly Approach

PubMed Central

Ye, Xin; Huang, Jin; Zeng, Yong; Sun, Lai-Xi; Geng, Feng; Liu, Hong-Jie; Wang, Feng-Rui; Jiang, Xiao-Dong; Wu, Wei-Dong; Zheng, Wan-Guo

2017-01-01

Hexagonally ordered arrays of polystyrene (PS) microspheres were prepared by a modified air-water self-assembly method. A detailed analysis of the air-water interface self-assembly process was conducted. Several parameters affect the quality of the monolayer colloidal crystals, i.e., the colloidal microsphere concentration on the latex, the surfactant concentration, the polystyrene microsphere diameter, the microsphere polydispersity, and the degree of sphericity of polystyrene microspheres. An abrupt change in surface tension was used to improve the quality of the monolayer colloidal crystal. Three typical microstructures, i.e., a cone, a pillar, and a binary structure were prepared by reactive-ion etching using a high-quality colloidal crystal mask. This study provides insight into the production of microsphere templates with flexible structures for large-area patterned materials. PMID:28946664

Revealing misassembled segments in the bovine reference genome by high resolution linkage disequilibrium scan

USDA-ARS?s Scientific Manuscript database

Misassembly signatures, created by shuffling the order of sequences while assembling a genome, can be easily seen by analyzing the unexpected behaviour of the linkage disequilibrium (LD) decay. A heuristic process was proposed to identify those misassembly signatures and presented the ones found in ...

High-resolution multi-code implementation of unsteady Navier-Stokes flow solver based on paralleled overset adaptive mesh refinement and high-order low-dissipation hybrid schemes

NASA Astrophysics Data System (ADS)

Li, Gaohua; Fu, Xiang; Wang, Fuxin

2017-10-01

The low-dissipation high-order accurate hybrid up-winding/central scheme based on fifth-order weighted essentially non-oscillatory (WENO) and sixth-order central schemes, along with the Spalart-Allmaras (SA)-based delayed detached eddy simulation (DDES) turbulence model, and the flow feature-based adaptive mesh refinement (AMR), are implemented into a dual-mesh overset grid infrastructure with parallel computing capabilities, for the purpose of simulating vortex-dominated unsteady detached wake flows with high spatial resolutions. The overset grid assembly (OGA) process based on collection detection theory and implicit hole-cutting algorithm achieves an automatic coupling for the near-body and off-body solvers, and the error-and-try method is used for obtaining a globally balanced load distribution among the composed multiple codes. The results of flows over high Reynolds cylinder and two-bladed helicopter rotor show that the combination of high-order hybrid scheme, advanced turbulence model, and overset adaptive mesh refinement can effectively enhance the spatial resolution for the simulation of turbulent wake eddies.

Organization of inorganic nanomaterials via programmable DNA self-assembly and peptide molecular recognition.

PubMed

Carter, Joshua D; LaBean, Thomas H

2011-03-22

An interesting alternative to top-down nanofabrication is to imitate biology, where nanoscale materials frequently integrate organic molecules for self-assembly and molecular recognition with ordered, inorganic minerals to achieve mechanical, sensory, or other advantageous functions. Using biological systems as inspiration, researchers have sought to mimic the nanoscale composite materials produced in nature. Here, we describe a combination of self-assembly, molecular recognition, and templating, relying on an oligonucleotide covalently conjugated to a high-affinity gold-binding peptide. After integration of the peptide-coupled DNA into a self-assembling superstructure, the templated peptides recognize and bind gold nanoparticles. In addition to providing new ways of building functional multinanoparticle systems, this work provides experimental proof that a single peptide molecule is sufficient for immobilization of a nanoparticle. This molecular construction strategy, combining DNA assembly and peptide recognition, can be thought of as programmable, granular, artificial biomineralization. We also describe the important observation that the addition of 1-2% Tween 20 surfactant to the solution during gold particle binding allows the gold nanoparticles to remain soluble within the magnesium-containing DNA assembly buffer under conditions that usually lead to the aggregation and precipitation of the nanoparticles.

Assembling of Steel Angle Headframe of Multifunctional Purpose

NASA Astrophysics Data System (ADS)

Kassikhina, E. G.; Pershin, V. V.; Volkov, V. M.

2017-10-01

The article reviews new technical solution on equipment provision of vertical shaft utilizing steel headframe of multifunctional purpose. Practice of construction of coal and ore mines provides application of various designs for steel angle headframes which are divided into separate large assembly blocks and constructive elements during assembling operations. Design of these blocks and elements, their weight and dimensions effect the chose of the method of assembling on which economic and technological indicators, as well as duration of down-time, depend on during performance of construction operations in shaft. The technical solution on equipment provision for mine vertical shaft using headframe of multifunctional purpose will allow changing the management construction of vertical shaft. The proposed headframe combines the functions of sinking and operation that eliminates costs for assembling/dissembling of temporary headgear. The constructive design of the headgear allows application of the effective method of assembly and thus to provide improvement of the technical and economic indexes, and high calendar time rate of the shaft construction due to reduction of duration of works on equipment provision for the shaft and to refurbishment of the shaft in order to carry out horizontal mining.

Pattern formation in binary colloidal assemblies: hidden symmetries in a kaleidoscope of structures.

PubMed

Lotito, Valeria; Zambelli, Tomaso

2018-06-10

In this study we present a detailed investigation of the morphology of binary colloidal structures formed by self-assembly at air/water interface of particles of two different sizes, with a size ratio such that the larger particles do not retain a hexagonal arrangement in the binary assembly. While the structure and symmetry of binary mixtures in which such hexagonal order is preserved has been thoroughly scrutinized, binary colloids in the regime of non-preservation of the hexagonal order have not been examined with the same level of detail due also to the difficulty in finding analysis tools suitable to recognize hidden symmetries in seemingly amorphous and disordered arrangements. For this purpose, we resorted to a combination of different analysis tools based on computational geometry and computational topology in order to get a comprehensive picture of the morphology of the assemblies. By carrying out an extensive investigation of binary assemblies in this regime with variable concentration of smaller particles with respect to larger particles, we identify the main patterns that coexist in the apparently disordered assemblies and detect transitions in the symmetries upon increase in the number of small particles. As the concentration of small particles increases, large particle arrangements become more dilute and a transition from hexagonal to rhombic and square symmetries occurs, accompanied also by an increase in clusters of small particles; the relative weight of each specific symmetry can be controlled by varying the composition of the assemblies. The demonstration of the possibility to control the morphology of apparently disordered binary colloidal assemblies by varying experimental conditions and the definition of a route for the investigation of disordered assemblies are precious for future studies of complex colloidal patterns to understand self-assembly mechanisms and to tailor physical properties of colloidal assemblies.

Scalable fabrication of nanostructured devices on flexible substrates using additive driven self-assembly and nanoimprint lithography

NASA Astrophysics Data System (ADS)

Watkins, James

2013-03-01

Roll-to-roll (R2R) technologies provide routes for continuous production of flexible, nanostructured materials and devices with high throughput and low cost. We employ additive-driven self-assembly to produce well-ordered polymer/nanoparticle hybrid materials that can serve as active device layers, we use highly filled nanoparticle/polymer hybrids for applications that require tailored dielectric constant or refractive index, and we employ R2R nanoimprint lithography for device scale patterning. Specific examples include the fabrication of flexible floating gate memory and large area films for optical/EM management. Our newly constructed R2R processing facility includes a custom designed, precision R2R UV-assisted nanoimprint lithography (NIL) system and hybrid nanostructured materials coaters.

Post-assembly magnetization of a 100 kW high speed permanent magnet rotor.

PubMed

Lv, Yiliang; Wang, Guobin; Li, Liang

2015-03-01

A post-assembly magnetizing fixture has been designed and successfully used to magnetize the rotor of a 100 kW high speed permanent magnet synchronous motor. The rotor is a solid cylinder with outer diameter of 80 mm and total length of 515 mm. The permanent magnet material is samarium-cobalt (Sm2Co17) with saturation magnetizing field of 6 T. The mechanical stability of the magnetizing fixture has been studied as well as the general design methodology. The magnetizing coil is subdivided in order to reduce the electromagnetic force, and the coils are separately reinforced in different ways. The electromagnetic and structural optimization is performed by finite element analysis and verified by experiments.

Cooperative light-induced molecular movements of highly ordered azobenzene self-assembled monolayers

PubMed Central

Pace, Giuseppina; Ferri, Violetta; Grave, Christian; Elbing, Mark; von Hänisch, Carsten; Zharnikov, Michael; Mayor, Marcel; Rampi, Maria Anita; Samorì, Paolo

2007-01-01

Photochromic systems can convert light energy into mechanical energy, thus they can be used as building blocks for the fabrication of prototypes of molecular devices that are based on the photomechanical effect. Hitherto a controlled photochromic switch on surfaces has been achieved either on isolated chromophores or within assemblies of randomly arranged molecules. Here we show by scanning tunneling microscopy imaging the photochemical switching of a new terminally thiolated azobiphenyl rigid rod molecule. Interestingly, the switching of entire molecular 2D crystalline domains is observed, which is ruled by the interactions between nearest neighbors. This observation of azobenzene-based systems displaying collective switching might be of interest for applications in high-density data storage. PMID:17535889

Hierarchical 3D ordered meso-/macroporous metal-organic framework produced through a facile template-free self-assembly

NASA Astrophysics Data System (ADS)

Yang, Xiaoli; Wu, Suilan; Wang, Panhao; Yang, Lin

2018-02-01

The synthesis of well-ordered hierarchical metal-organic frameworks (MOFs) in an efficient manner is a great challenge. Here, a 3D regular ordered meso-/macroporous MOF of Cu-TATAB (referred to as MM-MOF) was synthesized through a facile template-free self-assembly process with pore sizes of 31 nm and 119 nm.

Cellulose-pectin composite hydrogels: Intermolecular interactions and material properties depend on order of assembly.

PubMed

Lopez-Sanchez, Patricia; Martinez-Sanz, Marta; Bonilla, Mauricio R; Wang, Dongjie; Gilbert, Elliot P; Stokes, Jason R; Gidley, Michael J

2017-04-15

Plant cell walls have a unique combination of strength and flexibility however, further investigations are required to understand how those properties arise from the assembly of the relevant biopolymers. Recent studies indicate that Ca 2+ -pectates can act as load-bearing components in cell walls. To investigate this proposed role of pectins, bioinspired wall models were synthesised based on bacterial cellulose containing pectin-calcium gels by varying the order of assembly of cellulose/pectin networks, pectin degree of methylesterification and calcium concentration. Hydrogels in which pectin-calcium assembly occurred prior to cellulose synthesis showed evidence for direct cellulose/pectin interactions from small-angle scattering (SAXS and SANS), had the densest networks and the lowest normal stress. The strength of the pectin-calcium gel affected cellulose structure, crystallinity and material properties. The results highlight the importance of the order of assembly on the properties of cellulose composite networks and support the role of pectin in the mechanics of cell walls. Copyright © 2017 Elsevier Ltd. All rights reserved.

Complex collective dynamics of active torque-driven colloids at interfaces

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

Snezhko, Alexey

Modern self-assembly techniques aiming to produce complex structural order or functional diversity often rely on non-equilibrium conditions in the system. Light, electric, or magnetic fields are predominantly used to modify interaction profiles of colloidal particles during self-assembly or induce complex out-of-equilibrium dynamic ordering. The energy injection rate, properties of the environment are important control parameters that influence the outcome of active (dynamic) self-assembly. The current review is focused on a case of collective dynamics and self-assembly of particles with externally driven torques coupled to a liquid or solid interface. The complexity of interactions in such systems is further enriched bymore » strong hydrodynamic coupling between particles. Unconventionally ordered dynamic self-assembled patterns, spontaneous symmetry breaking phenomena, self-propulsion, and collective transport have been reported in torque-driven colloids. Some of the features of the complex collective behavior and dynamic pattern formation in those active systems have been successfully captured in simulations.« less

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

Self-assembled biomimetic antireflection coatings

NASA Astrophysics Data System (ADS)

Linn, Nicholas C.; Sun, Chih-Hung; Jiang, Peng; Jiang, Bin

2007-09-01

The authors report a simple self-assembly technique for fabricating antireflection coatings that mimic antireflective moth eyes. Wafer-scale, nonclose-packed colloidal crystals with remarkable large hexagonal domains are created by a spin-coating technology. The resulting polymer-embedded colloidal crystals exhibit highly ordered surface modulation and can be used directly as templates to cast poly(dimethylsiloxane) (PDMS) molds. Moth-eye antireflection coatings with adjustable reflectivity can then be molded against the PDMS master. The specular reflection of replicated nipple arrays matches the theoretical prediction using a thin-film multilayer model. These biomimetic films may find important technological application in optical coatings and solar cells.

Requirements for conformal coating and staking of printed wiring boards and electronic assemblies

NASA Technical Reports Server (NTRS)

1985-01-01

In order to maintain the high standards of the NASA conformal coating and staking program, this publication: prescribes NASA's requirements for assuring reliable conformal coating and staking for printed wiring boards and electronic assemblies; describes and incorporates basic considerations necessary to assure reliable conformal coating and staking; establishes the supplier's responsibility to train and certify personnel; provides for supplier documentation of the fabrication and inspection procedures to be used for NASA work, including supplier innovations and changes in technology; and provides visual workmanship standards to aid those responsible for determining quality conformance to the established requirements.

Structural Insights into the Coupling of Virion Assembly and Rotavirus Replication

PubMed Central

Trask, Shane D.; McDonald, Sarah M.; Patton, John T.

2013-01-01

Preface Viral replication is rapid and robust, but it is far from a chaotic process. Instead, successful production of infectious progeny requires that events occur in the correct place and at the correct time. Rotavirus, a segmented double-stranded RNA virus of the Reoviridae family, seems to govern its replication through ordered disassembly and assembly of a triple-layered icosahedral capsid. In recent years, high-resolution structural data have provided unprecedented insight into these events. In this Review, we explore the current understanding of rotavirus replication and how it compares to other Reoviridae family members. PMID:22266782

Task planning and control synthesis for robotic manipulation in space applications

NASA Technical Reports Server (NTRS)

Sanderson, A. C.; Peshkin, M. A.; Homem-De-mello, L. S.

1987-01-01

Space-based robotic systems for diagnosis, repair and assembly of systems will require new techniques of planning and manipulation to accomplish these complex tasks. Results of work in assembly task representation, discrete task planning, and control synthesis which provide a design environment for flexible assembly systems in manufacturing applications, and which extend to planning of manipulatiuon operations in unstructured environments are summarized. Assembly planning is carried out using the AND/OR graph representation which encompasses all possible partial orders of operations and may be used to plan assembly sequences. Discrete task planning uses the configuration map which facilitates search over a space of discrete operations parameters in sequential operations in order to achieve required goals in the space of bounded configuration sets.

Dynamic self-assembly of charged colloidal strings and walls in simple fluid flows.

PubMed

Abe, Yu; Zhang, Bo; Gordillo, Leonardo; Karim, Alireza Mohammad; Francis, Lorraine F; Cheng, Xiang

2017-02-22

Colloidal particles can self-assemble into various ordered structures in fluid flows that have potential applications in biomedicine, materials synthesis and encryption. These dynamic processes are also of fundamental interest for probing the general principles of self-assembly under non-equilibrium conditions. Here, we report a simple microfluidic experiment, where charged colloidal particles self-assemble into flow-aligned 1D strings with regular particle spacing near a solid boundary. Using high-speed confocal microscopy, we systematically investigate the influence of flow rates, electrostatics and particle polydispersity on the observed string structures. By studying the detailed dynamics of stable flow-driven particle pairs, we quantitatively characterize interparticle interactions. Based on the results, we construct a simple model that explains the intriguing non-equilibrium self-assembly process. Our study shows that the colloidal strings arise from a delicate balance between attractive hydrodynamic coupling and repulsive electrostatic interaction between particles. Finally, we demonstrate that, with the assistance of transverse electric fields, a similar mechanism also leads to the formation of 2D colloidal walls.

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

Majewski, Pawel W.; Yager, Kevin G.

Block-copolymers self-assemble into diverse morphologies, where nanoscale order can be finely tuned via block architecture and processing conditions. However, the ultimate usage of these materials in real-world applications may be hampered by the extremely long thermal annealing times—hours or days—required to achieve good order. Here, we provide an overview of the fundamentals of block-copolymer self-assembly kinetics, and review the techniques that have been demonstrated to influence, and enhance, these ordering kinetics. We discuss the inherent tradeoffs between oven annealing, solvent annealing, microwave annealing, zone annealing, and other directed self-assembly methods; including an assessment of spatial and temporal characteristics. Here, wemore » also review both real-space and reciprocal-space analysis techniques for quantifying order in these systems.« less

Influence of Geometries on the Assembly of Snowman-Shaped Janus Nanoparticles.

PubMed

Kang, Chengjun; Honciuc, Andrei

2018-04-24

The self-assembly of micro/nanoparticles into suprastructures is a promising way to develop reconfigurable materials and to gain insights into the fundamental question of how matter organizes itself. The geometry of particles, especially those deviating from perfectly spherical shapes, is of significant importance in colloidal assembly because it influences the particle "recognition", determines the particle packing, and ultimately dictates the formation of assembled suprastructures. In order to organize particles into desired structures, it is of vital importance to understand the relationship between the shape of the colloidal building blocks and the assembled suprastructures. This fundamental issue is an enduring topic in the assembly of molecular surfactants, but it remained elusive in colloidal assembly. To address this issue, we use snowman-shaped Janus nanoparticles (JNPs) as a model to systematically study the effect of colloidal geometries on their assembled suprastructures. Ten types of JNPs with identical chemical compositions but with different geometries were synthesized. Specifically, the synthesized JNPs differ in their lobe size ratios, phase separation degrees, and overall sizes. We show that by altering these parameters, both finite suprastructures, such as capsules with different curvatures, and nonfinite suprastructures, including free-standing single-layered or double-layered JNPs sheets, can be obtained via self-assembly. All these different types of suprastructures are constituted by highly oriented and hexagonally packed JNPs. These findings demonstrate the significance of geometries in colloidal assembly, such that slightly changing the building block geometries could result in a large variety of very different assembled structures, without altering the chemistry of the particles.

Thermodynamic and structural characterization of an antibody gel

PubMed Central

Esue, Osigwe; Xie, Anna X.; Kamerzell, Tim J.; Patapoff, Thomas W.

2013-01-01

Although extensively studied, protein–protein interactions remain highly elusive and are of increasing interest in drug development. We show the assembly of a monoclonal antibody, using multivalent carboxylate ions, into highly-ordered structures. While the presence and function of similar structures in vivo are not known, the results may present a possible unexplored area of antibody structure-function relationships. Using a variety of tools (e.g., mechanical rheology, electron microscopy, isothermal calorimetry, Fourier transform infrared spectroscopy), we characterized the physical, biochemical, and thermodynamic properties of these structures and found that citrate may interact directly with the amino acid residue histidine, after which the individual protein units assemble into a filamentous network gel exhibiting high elasticity and interfilament interactions. Citrate interacts exothermically with the monoclonal antibody with an association constant that is highly dependent on solution pH and temperature. Secondary structure analysis also reveals involvement of hydrophobic and aromatic residues. PMID:23425660

Controlling Molecular Ordering in Solution-State Conjugated Polymers

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

Zhu, Jiahua; Han, Youngkyu; Kumar, Rajeev

Rationally encoding molecular interactions that can control the assembly structure and functional expression in solution of conjugated polymers holds great potential for enabling optimal organic optoelectronic and sensory materials. In this work, we show that thermally-controlled and surfactant-guided assembly of water-soluble conjugated polymers in aqueous solution is a simple and effective strategy to generate optoelectronic materials with desired molecular ordering. We have studied a conjugated polymer consisting of a hydrophobic thiophene backbone and hydrophilic, thermo-responsive ethylene oxide side groups, which shows a step-wise, multi-dimensional assembly in water. By incorporating the polymer into phase-segregated domains of an amphiphilic surfactant in solution,more » we demonstrate that both chain conformation and degree of molecular ordering of the conjugated polymer can be tuned in hexagonal, micellar and lamellar phases of the surfactant solution. The controlled molecular ordering in conjugated polymer assembly is demonstrated as a key factor determining the electronic interaction and optical function.« less

Controlling Molecular Ordering in Solution-State Conjugated Polymers

DOE PAGES

Zhu, Jiahua; Han, Youngkyu; Kumar, Rajeev; ...

2015-07-17

Rationally encoding molecular interactions that can control the assembly structure and functional expression in solution of conjugated polymers holds great potential for enabling optimal organic optoelectronic and sensory materials. In this work, we show that thermally-controlled and surfactant-guided assembly of water-soluble conjugated polymers in aqueous solution is a simple and effective strategy to generate optoelectronic materials with desired molecular ordering. We have studied a conjugated polymer consisting of a hydrophobic thiophene backbone and hydrophilic, thermo-responsive ethylene oxide side groups, which shows a step-wise, multi-dimensional assembly in water. By incorporating the polymer into phase-segregated domains of an amphiphilic surfactant in solution,more » we demonstrate that both chain conformation and degree of molecular ordering of the conjugated polymer can be tuned in hexagonal, micellar and lamellar phases of the surfactant solution. The controlled molecular ordering in conjugated polymer assembly is demonstrated as a key factor determining the electronic interaction and optical function.« less

High content reduced graphene oxide reinforced copper with a bioinspired nano-laminated structure and large recoverable deformation ability

PubMed Central

Xiong, Ding-Bang; Cao, Mu; Guo, Qiang; Tan, Zhanqiu; Fan, Genlian; Li, Zhiqiang; Zhang, Di

2016-01-01

By using CuO/graphene-oxide/CuO sandwich-like nanosheets as the building blocks, bulk nacre-inspired copper matrix nano-laminated composite reinforced by molecular-level dispersed and ordered reduced graphene oxide (rGO) with content as high as ∼45 vol% was fabricated via a combined process of assembly, reduction and consolidation. Thanks to nanoconfinement effect, reinforcing effect, as well as architecture effect, the nanocomposite shows increased specific strength and at least one order of magnitude greater recoverable deformation ability as compared with monolithic Cu matrix. PMID:27647264

Biochemical and biophysical characterization of cell-free synthesized Rift Valley fever virus nucleoprotein capsids enables in vitro screening to identify novel antivirals.

PubMed

Broce, Sean; Hensley, Lisa; Sato, Tomoharu; Lehrer-Graiwer, Joshua; Essrich, Christian; Edwards, Katie J; Pajda, Jacqueline; Davis, Christopher J; Bhadresh, Rami; Hurt, Clarence R; Freeman, Beverly; Lingappa, Vishwanath R; Kelleher, Colm A; Karpuj, Marcela V

2016-05-14

Viral capsid assembly involves the oligomerization of the capsid nucleoprotein (NP), which is an essential step in viral replication and may represent a potential antiviral target. An in vitro transcription-translation reaction using a wheat germ (WG) extract in combination with a sandwich ELISA assay has recently been used to identify small molecules with antiviral activity against the rabies virus. Here, we examined the application of this system to viruses with capsids with a different structure, such as the Rift Valley fever virus (RVFV), the etiological agent of a severe emerging infectious disease. The biochemical and immunological characterization of the in vitro-generated RVFV NP assembly products enabled the distinction between intermediately and highly ordered capsid structures. This distinction was used to establish a screening method for the identification of potential antiviral drugs for RVFV countermeasures. These results indicated that this unique analytical system, which combines nucleoprotein oligomerization with the specific immune recognition of a highly ordered capsid structure, can be extended to various viral families and used both to study the early stages of NP assembly and to assist in the identification of potential antiviral drugs in a cost-efficient manner. Reviewed by Jeffry Skolnick and Noah Isakov. For the full reviews please go to the Reviewers' comments section.

Reference-guided de novo assembly approach improves genome reconstruction for related species.

PubMed

Lischer, Heidi E L; Shimizu, Kentaro K

2017-11-10

The development of next-generation sequencing has made it possible to sequence whole genomes at a relatively low cost. However, de novo genome assemblies remain challenging due to short read length, missing data, repetitive regions, polymorphisms and sequencing errors. As more and more genomes are sequenced, reference-guided assembly approaches can be used to assist the assembly process. However, previous methods mostly focused on the assembly of other genotypes within the same species. We adapted and extended a reference-guided de novo assembly approach, which enables the usage of a related reference sequence to guide the genome assembly. In order to compare and evaluate de novo and our reference-guided de novo assembly approaches, we used a simulated data set of a repetitive and heterozygotic plant genome. The extended reference-guided de novo assembly approach almost always outperforms the corresponding de novo assembly program even when a reference of a different species is used. Similar improvements can be observed in high and low coverage situations. In addition, we show that a single evaluation metric, like the widely used N50 length, is not enough to properly rate assemblies as it not always points to the best assembly evaluated with other criteria. Therefore, we used the summed z-scores of 36 different statistics to evaluate the assemblies. The combination of reference mapping and de novo assembly provides a powerful tool to improve genome reconstruction by integrating information of a related genome. Our extension of the reference-guided de novo assembly approach enables the application of this strategy not only within but also between related species. Finally, the evaluation of genome assemblies is often not straight forward, as the truth is not known. Thus one should always use a combination of evaluation metrics, which not only try to assess the continuity but also the accuracy of an assembly.

First-order approximation error analysis of Risley-prism-based beam directing system.

PubMed

Zhao, Yanyan; Yuan, Yan

2014-12-01

To improve the performance of a Risley-prism system for optical detection and measuring applications, it is necessary to be able to determine the direction of the outgoing beam with high accuracy. In previous works, error sources and their impact on the performance of the Risley-prism system have been analyzed, but their numerical approximation accuracy was not high. Besides, pointing error analysis of the Risley-prism system has provided results for the case when the component errors, prism orientation errors, and assembly errors are certain. In this work, the prototype of a Risley-prism system was designed. The first-order approximations of the error analysis were derived and compared with the exact results. The directing errors of a Risley-prism system associated with wedge-angle errors, prism mounting errors, and bearing assembly errors were analyzed based on the exact formula and the first-order approximation. The comparisons indicated that our first-order approximation is accurate. In addition, the combined errors produced by the wedge-angle errors and mounting errors of the two prisms together were derived and in both cases were proved to be the sum of errors caused by the first and the second prism separately. Based on these results, the system error of our prototype was estimated. The derived formulas can be implemented to evaluate beam directing errors of any Risley-prism beam directing system with a similar configuration.

Macroscopic and tunable nanoparticle superlattices

DOE PAGES

Zhang, Honghu; Wang, Wenjie; Mallapragada, Surya; ...

2016-10-24

In this paper, we describe a robust method to assemble nanoparticles into highly ordered superlattices by inducing aqueous phase separation of neutral capping polymers. Here we demonstrate the approach with thiolated polyethylene-glycol-functionalized gold nanoparticles (PEG-AuNPs) in the presence of salts (for example, K 2CO 3) in solutions that spontaneously migrate to the liquid–vapor interface to form a Gibbs monolayer. We show that by increasing salt concentration, PEG-AuNP monolayers transform from two-dimensional (2D) gas-like to liquid-like phase and eventually, beyond a threshold concentration, to a highly ordered hexagonal structure, as characterized by surface sensitive synchrotron X-ray reflectivity and grazing incidence X-raymore » diffraction. Furthermore, the method allows control of the inplane packing in the crystalline phase by varying the K 2CO 3 and PEG-AuNPs concentrations and the length of PEG. Using polymer-brush theory, we argue that the assembly and crystallization is driven by the need to reduce surface tension between PEG and the salt solution. Our approach of taking advantage of the phase separation of PEG in salt solutions is general (i.e., can be used with any nanoparticles) leads to high-quality macroscopic and tunable crystals. In conclusion, we discuss how the method can also be applied to the design of orderly 3D structures.« less

Effects of self-assembled monolayer structural order, surface homogeneity and surface energy on pentacene morphology and thin film transistor device performance.

PubMed

Hutchins, Daniel Orrin; Weidner, Tobias; Baio, Joe; Polishak, Brent; Acton, Orb; Cernetic, Nathan; Ma, Hong; Jen, Alex K-Y

2013-01-04

A systematic study of six phosphonic acid (PA) self-assembled monolayers (SAMs) with tailored molecular structures is performed to evaluate their effectiveness as dielectric modifying layers in organic field-effect transistors (OFETs) and determine the relationship between SAM structural order, surface homogeneity, and surface energy in dictating device performance. SAM structures and surface properties are examined by near edge X-ray absorption fine structure (NEXAFS) spectroscopy, contact angle goniometry, and atomic force microscopy (AFM). Top-contact pentacene OFET devices are fabricated on SAM modified Si with a thermally grown oxide layer as a dielectric. For less ordered methyl- and phenyl-terminated alkyl ~(CH 2 ) 12 PA SAMs of varying surface energies, pentacene OFETs show high charge carrier mobilities up to 4.1 cm 2 V -1 s -1 . It is hypothesized that for these SAMs, mitigation of molecular scale roughness and subsequent control of surface homogeneity allow for large pentacene grain growth leading to high performance pentacene OFET devices. PA SAMs that contain bulky terminal groups or are highly crystalline in nature do not allow for a homogenous surface at a molecular level and result in charge carrier mobilities of 1.3 cm 2 V -1 s -1 or less. For all molecules used in this study, no causal relationship between SAM surface energy and charge carrier mobility in pentacene FET devices is observed.

Effects of self-assembled monolayer structural order, surface homogeneity and surface energy on pentacene morphology and thin film transistor device performance

PubMed Central

Hutchins, Daniel Orrin; Weidner, Tobias; Baio, Joe; Polishak, Brent; Acton, Orb; Cernetic, Nathan; Ma, Hong; Jen, Alex K.-Y.

2013-01-01

A systematic study of six phosphonic acid (PA) self-assembled monolayers (SAMs) with tailored molecular structures is performed to evaluate their effectiveness as dielectric modifying layers in organic field-effect transistors (OFETs) and determine the relationship between SAM structural order, surface homogeneity, and surface energy in dictating device performance. SAM structures and surface properties are examined by near edge X-ray absorption fine structure (NEXAFS) spectroscopy, contact angle goniometry, and atomic force microscopy (AFM). Top-contact pentacene OFET devices are fabricated on SAM modified Si with a thermally grown oxide layer as a dielectric. For less ordered methyl- and phenyl-terminated alkyl ~(CH2)12 PA SAMs of varying surface energies, pentacene OFETs show high charge carrier mobilities up to 4.1 cm2 V−1 s−1. It is hypothesized that for these SAMs, mitigation of molecular scale roughness and subsequent control of surface homogeneity allow for large pentacene grain growth leading to high performance pentacene OFET devices. PA SAMs that contain bulky terminal groups or are highly crystalline in nature do not allow for a homogenous surface at a molecular level and result in charge carrier mobilities of 1.3 cm2 V−1 s−1 or less. For all molecules used in this study, no causal relationship between SAM surface energy and charge carrier mobility in pentacene FET devices is observed. PMID:24086795

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

Majetich, Sara

In the proposed research program we will investigate the time- and frequency-dependent behavior of ordered nanoparticle assemblies, or nanoparticle crystals. Magnetostatic interactions are long-range and anisotropic, and this leads to complex behavior in nanoparticle assemblies, particularly in the time- and frequency-dependent properties. We hypothesize that the high frequency performance of composite materials has been limited because of the range of relaxation times; if a composite is a dipolar ferromagnet at a particular frequency, it should have the advantages of a single phase material, but without significant eddy current power losses. Arrays of surfactant-coated monodomain magnetic nanoparticles can exhibit long-range magneticmore » order that is stable over time. The magnetic domain size and location of domain walls is governed not by structural grain boundaries but by the shape of the array, due to the local interaction field. Pores or gaps within an assembly pin domain walls and limit the domain size. Measurements of the magnetic order parameter as a function of temperature showed that domains can exist at high temoerature, and that there is a collective phase transition, just as in an exchange-coupled ferromagnet. Dipolar ferromagnets are not merely of fundamental interest; they provide an interesting alternative to exchange-based ferromagnets. Dipolar ferromagnets made with high moment metallic particles in an insulating matrix could have high permeability without large eddy current losses. Such nanocomposites could someday replace the ferrites now used in phase shifters, isolators, circulators, and filters in microwave communications and radar applications. We will investigate the time- and frequency-dependent behavior of nanoparticle crystals with different magnetic core sizes and different interparticle barrier resistances, and will measure the magnetic and electrical properties in the DC, low frequency (0.1 Hz - 1 kHz), moderate frequency (10 Hz - 500 MHz), and high frequency (up to 20 GHz) regimes. Our results will demonstrate whether a DC dipolar ferromagnet shows collective frequency-dependent reponse similar to that of an exchange-based ferromagnet, and will provide data for comparison of optimal nanocomposite properties with those of ferrites used in high frequency applications. Both the magnetic and electronic response of the composites will be examined in order to determine the frequency range where hopping conductivity leads to significant eddy current power losses. In the high frequency regime we will look for evidence of spin wave quantization and the resulting decrease in non-linear spin wave processes that could affect the performance of high frequency magnetic devices.« less

Self-assembly assisted polymerization (SAAP): approaching long multi-block copolymers with an ordered chain sequence and controllable block length.

PubMed

Wu, Chi; Xie, Zuowei; Zhang, Guangzhao; Zi, Guofu; Tu, Yingfeng; Yang, Yali; Cai, Ping; Nie, Ting

2002-12-07

A combination of polymer physics and synthetic chemistry has enabled us to develop self-assembly assisted polymerization (SAAP), leading to the preparation of long multi-block copolymers with an ordered chain sequence and controllable block lengths.

Self-assembly patterning of organic molecules on a surface

DOEpatents

Pan, Minghu; Fuentes-Cabrera, Miguel; Maksymovych, Petro; Sumpter, Bobby G.; Li, Qing

2017-04-04

The embodiments disclosed herein include all-electron control over a chemical attachment and the subsequent self-assembly of an organic molecule into a well-ordered three-dimensional monolayer on a metal surface. The ordering or assembly of the organic molecule may be through electron excitation. Hot-electron and hot-hole excitation enables tethering of the organic molecule to a metal substrate, such as an alkyne group to a gold surface. All-electron reactions may allow a direct control over the size and shape of the self-assembly, defect structures and the reverse process of molecular disassembly from single molecular level to mesoscopic scale.

SynTrack: DNA Assembly Workflow Management (SynTrack) v2.0.1

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

MENG, XIANWEI; SIMIRENKO, LISA

2016-12-01

SynTrack is a dynamic, workflow-driven data management system that tracks the DNA build process: Management of the hierarchical relationships of the DNA fragments; Monitoring of process tasks for the assembly of multiple DNA fragments into final constructs; Creations of vendor order forms with selectable building blocks. Organizing plate layouts barcodes for vendor/pcr/fusion/chewback/bioassay/glycerol/master plate maps (default/condensed); Creating or updating Pre-Assembly/Assembly process workflows with selected building blocks; Generating Echo pooling instructions based on plate maps; Tracking of building block orders, received and final assembled for delivering; Bulk updating of colony or PCR amplification information, fusion PCR and chewback results; Updating with QA/QCmore » outcome with .csv & .xlsx template files; Re-work assembly workflow enabled before and after sequencing validation; and Tracking of plate/well data changes and status updates and reporting of master plate status with QC outcomes.« less

Molecular Self-Assembly of Short Aromatic Peptides: From Biology to Nanotechnology and Material Science

NASA Astrophysics Data System (ADS)

Gazit, Ehud

2013-03-01

The formation of ordered amyloid fibrils is the hallmark of several diseases of unrelated origin. In spite of grave clinical consequence, the mechanism of amyloid formation is not fully understood. We have suggested, based on experimental and bioinformatic analysis, that aromatic interactions may provide energetic contribution as well as order and directionality in the molecular-recognition and self-association processes that lead to the formation of these assemblies. This is in line with the well-known central role of aromatic-stacking interactions in self-assembly processes. Our works on the mechanism of aromatic peptide self-assembly, lead to the discovery that the diphenylalanine recognition motif self-assembles into peptide nanotubes with a remarkable persistence length. Other aromatic homodipeptides could self-assemble in nano-spheres, nano-plates, nano-fibrils and hydrogels with nano-scale order. We demonstrated that the peptide nanostructures have unique chemical, physical and mechanical properties including ultra-rigidity as aramides, semi-conductive, piezoelectric and non-linear optic properties. We also demonstrated the ability to use these peptide nanostructures as casting mold for the fabrication of metallic nano-wires and coaxial nano-cables. The application of the nanostructures was demonstrated in various fields including electrochemical biosensors, tissue engineering, and molecular imaging. Finally, we had developed ways for depositing of the peptide nanostructures and their organization. We had use inkjet technology as well as vapour deposition methods to coat surface and from the peptide ``nano-forests''. We recently demonstrated that even a single phenylalanine amino-acid can form well-ordered fibrilar assemblies.

Planning and Control for Microassembly of Structures Composed of Stress-Engineered MEMS Microrobots

PubMed Central

Donald, Bruce R.; Levey, Christopher G.; Paprotny, Igor; Rus, Daniela

2013-01-01

We present control strategies that implement planar microassembly using groups of stress-engineered MEMS microrobots (MicroStressBots) controlled through a single global control signal. The global control signal couples the motion of the devices, causing the system to be highly underactuated. In order for the robots to assemble into arbitrary planar shapes despite the high degree of underactuation, it is desirable that each robot be independently maneuverable (independently controllable). To achieve independent control, we fabricated robots that behave (move) differently from one another in response to the same global control signal. We harnessed this differentiation to develop assembly control strategies, where the assembly goal is a desired geometric shape that can be obtained by connecting the chassis of individual robots. We derived and experimentally tested assembly plans that command some of the robots to make progress toward the goal, while other robots are constrained to remain in small circular trajectories (closed-loop orbits) until it is their turn to move into the goal shape. Our control strategies were tested on systems of fabricated MicroStressBots. The robots are 240–280 μm × 60 μm × 7–20 μm in size and move simultaneously within a single operating environment. We demonstrated the feasibility of our control scheme by accurately assembling five different types of planar microstructures. PMID:23580796

Hierarchical self-assembly of hexagonal single-crystal nanosheets into 3D layered superlattices with high conductivity.

PubMed

Tao, Yulun; Shen, Yuhua; Yang, Liangbao; Han, Bin; Huang, Fangzhi; Li, Shikuo; Chu, Zhuwang; Xie, Anjian

2012-06-21

While the number of man-made nano superstructures realized by self-assembly is growing in recent years, assemblies of conductive polymer nanocrystals, especially for superlattices, are still a significant challenge, not only because of the simplicity of the shape of the nanocrystal building blocks and their interactions, but also because of the poor control over these parameters in the fabrication of more elaborate nanocrystals. Here, we firstly report a facile and general route to a new generation of 3D layered superlattices of polyaniline doped with CSA (PANI-CSA) and show how PANI crystallize and self-assemble, in a suitable single solution environment. In cyclohexane, 1D amorphous nanofibers transformed to 1D nanorods as building blocks, and then to 2D single-crystal nanosheets with a hexagonal phase, and lastly to 3D ordered layered superlattices with the narrowest polydispersity value (M(w)/M(n) = 1.47). Remarkably, all the instructions for the hierarchical self-assembly are encoded in the layered shape in other non-polar solvents (hexane, octane) and their conductivity in the π-π stacking direction is improved to about 50 S cm(-1), which is even higher than that of the highest previously reported value (16 S cm(-1)). The method used in this study is greatly expected to be readily scalable to produce superlattices of conductive polymers with high quality and low cost.

Self-Assembly at the Colloidal Scale

NASA Astrophysics Data System (ADS)

Zhong, Xiao

The existence of self-assembly, the phenomenon of spontaneous structural formation from building blocks, transcends many orders of magnitude, ranging from molecular to cosmic. It is arguably the most common, important, and complex question in science. This thesis aims for understanding a spectrum of self-assembly-self assembly at the colloidal scale. Of the whole spectrum of self-assembly, the colloidal scale is of particular interest and importance to researchers, for not only comprehensive tools for colloidal scale studies have been well established, but also the various promising applications colloidal self-assembly can facilitate. In this thesis, a high throughput technique-Polymer Pen Lithography (PPL) is modified and its potential for creating corrals for colloidal assembly is evaluated. Then two different approaches of assembling colloids are explored in depth. One of them is by using a phenomenon called dielectrophoresis (DEP) as driving force to manipulate colloidal nucleation and crystal growth. And the other takes advantage of the Pt-catalyzed H2O 2 redox reaction to drive micrometer-scaled, rod-shaped colloids to swim and assemble. Lastly, an optical method called Holographic Video Microscopy (HVM) is used to monitor and characterize "bad" self-assembly of proteins, that is their aggregations. The four studies discussed in this thesis represent advancements in the colloidal scale from different aspects. The PPL technique enriched the toolbox for colloidal self-assembly. The DEP driven colloidal nucleation and crystal growth shed light on deeper understanding the mechanism of crystallization. And the swimming and assembly of micro-scale rods leads to kinetics reminiscent of bacterial run-and-tumble motion. Finally, the HVM technique for monitoring and understanding protein aggregation could potentially lead to better quality assurance for therapeutic proteins and could be a powerful tool for assessing their shelf lives.

Coherent assembly of heterostructures in ternary and quaternary carbonitrides

NASA Astrophysics Data System (ADS)

Caicedo, J. C.; Aperador, W.; Saldarriaga, W.

2018-05-01

In this study, ternary and quaternary carbonitride heterostructure systems were grown on silicon (100) substrates in order to investigate coherent assembly in TiCN/TiNbCN. The heterostructure films were grown using the reactive r. f. magnetron sputtering technique by systematically varying the bilayer period (Λ) and the bilayer number (n), while maintaining a constant total coating thickness (∼3 μm). The heterostructures were characterized by high angle X-ray diffraction (HA-XRD) and low angle X-ray diffraction, while the TiCN and TiNbCN layers were analyzed by X-ray photoelectron spectroscopy and transmission electron microscopy. The HA-XRD results indicated preferential growth in the face-centered cubic (111) crystal structure for the [TiCN/TiNbCN]n heterostructures. The maximum coherent assembly was observed with the presence of satellite peaks. Thus, ternary and quaternary carbonitride films were designed and deposited on Si (100) substrates with bilayer periods (Λ) in a broad range from nanometers to hundreds of nanometers in order to study the structural evolution and coherent assembly progress as the bilayer thickness decreased. We determined physical properties comprising the critical angle (θc) (0.362°), electronic density (ρe) (0.521 × 1033 el/m3), dispersion coefficient (δ) (0.554 el/m3), and refractive index (n) (0.999944) as functions of the number of bilayers (n).

Highly ordered nanocomposites via a monomer self-assembly in situ condensation approach

DOEpatents

Gin, D.L.; Fischer, W.M.; Gray, D.H.; Smith, R.C.

1998-12-15

A method for synthesizing composites with architectural control on the nanometer scale is described. A polymerizable lyotropic liquid-crystalline monomer is used to form an inverse hexagonal phase in the presence of a second polymer precursor solution. The monomer system acts as an organic template, providing the underlying matrix and order of the composite system. Polymerization of the template in the presence of an optional cross-linking agent with retention of the liquid-crystalline order is carried out followed by a second polymerization of the second polymer precursor within the channels of the polymer template to provide an ordered nanocomposite material. 13 figs.

Highly ordered nanocomposites via a monomer self-assembly in situ condensation approach

DOEpatents

Gin, Douglas L.; Fischer, Walter M.; Gray, David H.; Smith, Ryan C.

1998-01-01

A method for synthesizing composites with architectural control on the nanometer scale is described. A polymerizable lyotropic liquid-crystalline monomer is used to form an inverse hexagonal phase in the presence of a second polymer precursor solution. The monomer system acts as an organic template, providing the underlying matrix and order of the composite system. Polymerization of the template in the presence of an optional cross-linking agent with retention of the liquid-crystalline order is carried out followed by a second polymerization of the second polymer precursor within the channels of the polymer template to provide an ordered nanocomposite material.

Comparative genomic data of the Avian Phylogenomics Project.

PubMed

Zhang, Guojie; Li, Bo; Li, Cai; Gilbert, M Thomas P; Jarvis, Erich D; Wang, Jun

2014-01-01

The evolutionary relationships of modern birds are among the most challenging to understand in systematic biology and have been debated for centuries. To address this challenge, we assembled or collected the genomes of 48 avian species spanning most orders of birds, including all Neognathae and two of the five Palaeognathae orders, and used the genomes to construct a genome-scale avian phylogenetic tree and perform comparative genomics analyses (Jarvis et al. in press; Zhang et al. in press). Here we release assemblies and datasets associated with the comparative genome analyses, which include 38 newly sequenced avian genomes plus previously released or simultaneously released genomes of Chicken, Zebra finch, Turkey, Pigeon, Peregrine falcon, Duck, Budgerigar, Adelie penguin, Emperor penguin and the Medium Ground Finch. We hope that this resource will serve future efforts in phylogenomics and comparative genomics. The 38 bird genomes were sequenced using the Illumina HiSeq 2000 platform and assembled using a whole genome shotgun strategy. The 48 genomes were categorized into two groups according to the N50 scaffold size of the assemblies: a high depth group comprising 23 species sequenced at high coverage (>50X) with multiple insert size libraries resulting in N50 scaffold sizes greater than 1 Mb (except the White-throated Tinamou and Bald Eagle); and a low depth group comprising 25 species sequenced at a low coverage (~30X) with two insert size libraries resulting in an average N50 scaffold size of about 50 kb. Repetitive elements comprised 4%-22% of the bird genomes. The assembled scaffolds allowed the homology-based annotation of 13,000 ~ 17000 protein coding genes in each avian genome relative to chicken, zebra finch and human, as well as comparative and sequence conservation analyses. Here we release full genome assemblies of 38 newly sequenced avian species, link genome assembly downloads for the 7 of the remaining 10 species, and provide a guideline of genomic data that has been generated and used in our Avian Phylogenomics Project. To the best of our knowledge, the Avian Phylogenomics Project is the biggest vertebrate comparative genomics project to date. The genomic data presented here is expected to accelerate further analyses in many fields, including phylogenetics, comparative genomics, evolution, neurobiology, development biology, and other related areas.

Programmable DNA scaffolds for spatially-ordered protein assembly

NASA Astrophysics Data System (ADS)

Chandrasekaran, Arun Richard

2016-02-01

Ever since the notion of using DNA as a material was realized, it has been employed in the construction of complex structures that facilitate the assembly of nanoparticles or macromolecules with nanometer-scale precision. Specifically, tiles fashioned from DNA strands and DNA origami sheets have been shown to be suitable as scaffolds for immobilizing proteins with excellent control over their spatial positioning. Supramolecular assembly of proteins into periodic arrays in one or more dimensions is one of the most challenging aspects in the design of scaffolds for biomolecular investigations and macromolecular crystallization. This review provides a brief overview of how various biomolecular interactions with high degree of specificity such as streptavidin-biotin, antigen-antibody, and aptamer-protein interactions have been used to fabricate linear and multidimensional assemblies of structurally intact and functional proteins. The use of DNA-binding proteins as adaptors, polyamide recognition on DNA scaffolds and oligonucleotide linkers for protein assembly are also discussed.Ever since the notion of using DNA as a material was realized, it has been employed in the construction of complex structures that facilitate the assembly of nanoparticles or macromolecules with nanometer-scale precision. Specifically, tiles fashioned from DNA strands and DNA origami sheets have been shown to be suitable as scaffolds for immobilizing proteins with excellent control over their spatial positioning. Supramolecular assembly of proteins into periodic arrays in one or more dimensions is one of the most challenging aspects in the design of scaffolds for biomolecular investigations and macromolecular crystallization. This review provides a brief overview of how various biomolecular interactions with high degree of specificity such as streptavidin-biotin, antigen-antibody, and aptamer-protein interactions have been used to fabricate linear and multidimensional assemblies of structurally intact and functional proteins. The use of DNA-binding proteins as adaptors, polyamide recognition on DNA scaffolds and oligonucleotide linkers for protein assembly are also discussed. Dedicated to my advisor Ned Seeman on the occasion of his 70th birthday.

Hierarchical self-assembly of hexagonal single-crystal nanosheets into 3D layered superlattices with high conductivity

NASA Astrophysics Data System (ADS)

Tao, Yulun; Shen, Yuhua; Yang, Liangbao; Han, Bin; Huang, Fangzhi; Li, Shikuo; Chu, Zhuwang; Xie, Anjian

2012-05-01

While the number of man-made nano superstructures realized by self-assembly is growing in recent years, assemblies of conductive polymer nanocrystals, especially for superlattices, are still a significant challenge, not only because of the simplicity of the shape of the nanocrystal building blocks and their interactions, but also because of the poor control over these parameters in the fabrication of more elaborate nanocrystals. Here, we firstly report a facile and general route to a new generation of 3D layered superlattices of polyaniline doped with CSA (PANI-CSA) and show how PANI crystallize and self-assemble, in a suitable single solution environment. In cyclohexane, 1D amorphous nanofibers transformed to 1D nanorods as building blocks, and then to 2D single-crystal nanosheets with a hexagonal phase, and lastly to 3D ordered layered superlattices with the narrowest polydispersity value (Mw/Mn = 1.47). Remarkably, all the instructions for the hierarchical self-assembly are encoded in the layered shape in other non-polar solvents (hexane, octane) and their conductivity in the π-π stacking direction is improved to about 50 S cm-1, which is even higher than that of the highest previously reported value (16 S cm-1). The method used in this study is greatly expected to be readily scalable to produce superlattices of conductive polymers with high quality and low cost.While the number of man-made nano superstructures realized by self-assembly is growing in recent years, assemblies of conductive polymer nanocrystals, especially for superlattices, are still a significant challenge, not only because of the simplicity of the shape of the nanocrystal building blocks and their interactions, but also because of the poor control over these parameters in the fabrication of more elaborate nanocrystals. Here, we firstly report a facile and general route to a new generation of 3D layered superlattices of polyaniline doped with CSA (PANI-CSA) and show how PANI crystallize and self-assemble, in a suitable single solution environment. In cyclohexane, 1D amorphous nanofibers transformed to 1D nanorods as building blocks, and then to 2D single-crystal nanosheets with a hexagonal phase, and lastly to 3D ordered layered superlattices with the narrowest polydispersity value (Mw/Mn = 1.47). Remarkably, all the instructions for the hierarchical self-assembly are encoded in the layered shape in other non-polar solvents (hexane, octane) and their conductivity in the π-π stacking direction is improved to about 50 S cm-1, which is even higher than that of the highest previously reported value (16 S cm-1). The method used in this study is greatly expected to be readily scalable to produce superlattices of conductive polymers with high quality and low cost. Electronic supplementary information (ESI) available: SEM, and TEM images. See DOI: 10.1039/c2nr30743j

Quantitation of ten 30S ribosomal assembly intermediates using fluorescence triple correlation spectroscopy

PubMed Central

Ridgeway, William K.; Millar, David P.; Williamson, James R.

2012-01-01

The self-assembly of bacterial 30S ribosomes involves a large number of RNA folding and RNA-protein binding steps. The sequence of steps determines the overall assembly mechanism and the structure of the mechanism has ramifications for the robustness of biogenesis and resilience against kinetic traps. Thermodynamic interdependencies of protein binding inferred from omission-reconstitution experiments are thought to preclude certain assembly pathways and thus enforce ordered assembly, but this concept is at odds with kinetic data suggesting a more parallel assembly landscape. A major challenge is deconvolution of the statistical distribution of intermediates that are populated during assembly at high concentrations approaching in vivo assembly conditions. To specifically resolve the intermediates formed by binding of three ribosomal proteins to the full length 16S rRNA, we introduce Fluorescence Triple-Correlation Spectroscopy (F3CS). F3CS identifies specific ternary complexes by detecting coincident fluctuations in three-color fluorescence data. Triple correlation integrals quantify concentrations and diffusion kinetics of triply labeled species, and F3CS data can be fit alongside auto-correlation and cross-correlation data to quantify the populations of 10 specific ribosome assembly intermediates. The distribution of intermediates generated by binding three ribosomal proteins to the entire native 16S rRNA included significant populations of species that were not previously thought to be thermodynamically accessible, questioning the current interpretation of the classic omission-reconstitution experiments. F3CS is a general approach for analyzing assembly and function of macromolecular complexes, especially those too large for traditional biophysical methods. PMID:22869699

Self-assembly of water-soluble nanocrystals

DOEpatents

Fan, Hongyou [Albuquerque, NM; Brinker, C Jeffrey [Albuquerque, NM; Lopez, Gabriel P [Albuquerque, NM

2012-01-10

A method for forming an ordered array of nanocrystals where a hydrophobic precursor solution with a hydrophobic core material in an organic solvent is added to a solution of a surfactant in water, followed by removal of a least a portion of the organic solvent to form a micellar solution of nanocrystals. A precursor co-assembling material, generally water-soluble, that can co-assemble with individual micelles formed in the micellar solution of nanocrystals can be added to this micellar solution under specified reaction conditions (for example, pH conditions) to form an ordered-array mesophase material. For example, basic conditions are used to precipitate an ordered nanocrystal/silica array material in bulk form and acidic conditions are used to form an ordered nanocrystal/silica array material as a thin film.

Self-assembled nanoparticle aggregates: Organizing disorder for high performance surface-enhanced spectroscopy

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

Fasolato, C.; Center for Life Nanoscience@Sapienza, Istituto Italiano di Tecnologia, Rome; Domenici, F., E-mail: fabiodomenici@gmail.com

2015-06-23

The coherent oscillations of the surface electron gas, known as surface plasmons, in metal nanostructures can give rise to the localization of intense electromagnetic fields at the metal-dielectric interface. These strong fields are exploited in surface enhanced spectroscopies, such as Surface Enhanced Raman Scattering (SERS), for the detection and characterization of molecules at very low concentration. Still, the implementation of SERS-based biosensors requires a high level of reproducibility, combined with cheap and simple fabrication methods. For this purpose, SERS substrates based on self-assembled aggregates of commercial metallic nanoparticles (Nps) can meet all the above requests. Following this line, we reportmore » on a combined micro-Raman and Atomic Force Microscopy (AFM) analysis of the SERS efficiency of micrometric silver Np aggregates (enhancement factors up to 10{sup 9}) obtained by self-assembly. Despite the intrinsic disordered nature of these Np clusters, we were able to sort out some general rules relating the specific aggregate morphology to its plasmonic response. We found strong evidences of cooperative effects among the NPs within the cluster and namely a clear dependence of the SERS-efficiency on both the cluster area (basically linear) and the number of stacked NPs layers. A cooperative action among the superimposed layers has been proved also by electromagnetic simulations performed on simplified nanostructures consisting of stacking planes of ordered Nps. Being clear the potentialities of these disordered self-assembled clusters, in terms of both easy fabrication and signal enhancement, we developed a specific nanofabrication protocol, based on electron beam lithography and molecular functionalization, that allowed for a fine control of the Np assemblies into designed shapes fixing their area and height. In particular, we fabricated 2D ordered arrays of disordered clusters choosing gold Nps owing to their high stability. AFM measurements confirmed the regularity in spacing and size (i.e. area and layer number) of the aggregates. Preliminary SERS measurements confirm the high signal enhancement and demonstrate a quite good reproducibility over large number of aggregates within 100×100 μm{sup 2} 2D super-structure. The availability of such a multisensor could allow a careful statistical analysis of the SERS response, thus leading to a reliable quantitative estimate of the presence of relevant molecular species even at ultra-low concentration.« less

Highly Tunable Complementary Micro/Submicro-Nanopatterned Surfaces Combining Block Copolymer Self-Assembly and Colloidal Lithography.

PubMed

Chang, Tongxin; Du, Binyang; Huang, Haiying; He, Tianbai

2016-08-31

Two kinds of large-area ordered and highly tunable micro/submicro-nanopatterned surfaces in a complementary manner were successfully fabricated by elaborately combining block copolymer self-assembly and colloidal lithography. Employing a monolayer of polystyrene (PS) colloidal spheres assembled on top as etching mask, polystyrene-block-poly(2-vinylpyridine) (PS-b-P2VP) or polystyrene-block-poly(4-vinylpyridine) (PS-b-P4VP) micelle films were patterned into micro/submicro patches by plasma etching, which could be further transferred into micropatterned metal nanoarrays by subsequent metal precursor loading and a second plasma etching. On the other hand, micro/submicro-nanopatterns in a complementary manner were generated via preloading a metal precursor in initial micelle films before the assembly of PS colloidal spheres on top. Both kinds of micro/submicro-nanopatterns showed good fidelity at the micro/submicroscale and nanoscale; meanwhile, they could be flexibly tuned by the sample and processing parameters. Significantly, when the PS colloidal sphere size was reduced to 250 nm, a high-resolution submicro-nanostructured surface with 3-5 metal nanoparticles in each patch or a single-nanoparticle interconnected honeycomb network was achieved. Moreover, by applying gold (Au) nanoparticles as anchoring points, micronanopatterned Au arrays can serve as a flexible template to pattern bovine serum albumin (BSA) molecules. This facile and cost-effective approach may provide a novel platform for fabrication of micropatterned nanoarrays with high tunability and controllability, which are promising in the applications of biological and microelectronic fields.

Characterization of BaTiO3 nanocubes assembled into highly ordered monolayers using micro- and nano-Raman spectroscopy

NASA Astrophysics Data System (ADS)

Itasaka, Hiroki; Mimura, Ken-ichi; Nishi, Masayuki; Kato, Kazumi

2018-05-01

We investigated the influence of heat treatment on the crystallographic structure and ferroelectric phase transition behavior of barium titanate (BaTiO3, BT) nanocubes assembled into highly ordered monolayers, using tip-enhanced Raman spectroscopy (TERS), temperature-dependent micro-Raman spectroscopy, and scanning transmission electron microscopy (STEM). TER spectra from individual BT nanocubes with the size of about 20 nm were obtained with a side-illumination optical setup, and revealed that heat treatment enhances their tetragonality. The result of temperature-dependent micro-Raman spectroscopy showed that the ferroelectric phase transition behavior of the monolayers becomes similar to that of bulk BT through heat treatment in spite of their thickness. STEM observation for the cross-section of the heated BT nanocube monolayer showed that amorphous layers exist at the interface between BT nanocubes in face-to-face contact. These results indicate that the tetragonal crystal structure of BT nanocubes is stabilized by heat treatment and the formation of the interfacial amorphous layer during heat treatment may be a key to this phenomenon.

Self-Assembled Structures of Benzoic Acid on Au(111) Surface

NASA Astrophysics Data System (ADS)

Vu, Thu-Hien; Wandlowski, Thomas

2017-06-01

Electrochemical scanning tunneling microscopy combined with cyclic voltammetry were employed to explore the self-assembly of benzoic acid (BA) on a Au(111) substrate surface in a 0.1-M HClO4 solution. At the negatively charged surface, BA molecules form two highly ordered physisorbed adlayers with their phenyl rings parallel to the substrate surface. High-resolution scanning tunneling microscopy images reveal the packing arrangement and internal molecular structures. The striped pattern and zigzag structure of the BA adlayers are composed of parallel rows of dimers, in which two BA molecules are bound through a pair of O-H···O hydrogen bonds. Increasing the electrode potential further to positive charge densities of Au(111) leads to the desorption of the physisorbed hydrogen-bonded networks and the formation of a chemisorbed adlayer. BA molecules change their orientation from planar to upright fashion, which is accompanied by the deprotonation of the carboxyl group. Furthermore, potential-induced formation and dissolution of BA adlayers were also investigated. Structural transitions between the various types of ordered adlayers occur according to a nucleation and growth mechanism.

Coupling of carbon and peptide nanotubes.

PubMed

Montenegro, Javier; Vázquez-Vázquez, Carlos; Kalinin, Arseny; Geckeler, Kurt E; Granja, Juan R

2014-02-12

Two of the main types of nanotubular architectures are the single-walled carbon nanotubes (SWCNTs) and the self-assembling cyclic peptide nanotubes (SCPNs). We here report the preparation of the dual composite resulting from the ordered combination of both tubular motifs. In the resulting architecture, the SWCNTs can act as templates for the assembly of SCPNs that engage the carbon nanotubes noncovalently via pyrene "paddles", each member of the resulting hybrid stabilizing the other in aqueous solution. The particular hybrids obtained in the present study formed highly ordered oriented arrays and display complementary properties such as electrical conductivity. Furthermore, a self-sorting of the cyclic peptides toward semiconducting rather than metallic SWCNTs is also observed in the aqueous dispersions. It is envisaged that a broad range of exploitable properties may be achieved and/or controlled by varying the cyclic peptide components of similar SWCNT/SCPN hybrids.

Collagen peptide-based biomaterials for protein delivery and peptide-promoted self-assembly of gold nanoparticles

NASA Astrophysics Data System (ADS)

Ernenwein, Dawn M.

2011-12-01

Bottom-up self-assembly of peptides has driven the research progress for the following two projects: protein delivery vehicles of collagen microflorettes and the assembly of gold nanoparticles with coiled-coil peptides. Collagen is the most abundant protein in the mammals yet due to immunogenic responses, batch-to-batch variability and lack of sequence modifications, synthetic collagen has been designed to self-assemble into native collagen-like structures. In particular with this research, metal binding ligands were incorporated on the termini of collagen-like peptides to generate micron-sized particles, microflorettes. The over-arching goal of the first research project is to engineer MRI-active microflorettes, loaded with His-tagged growth factors with differential release rates while bound to stem cells that can be implemented toward regenerative cell-based therapies. His-tagged proteins, such as green fluorescent protein, have successfully been incorporated on the surface and throughout the microflorettes. Protein release was monitored under physiological conditions and was related to particle degradation. In human plasma full release was obtained within six days. Stability of the microflorettes under physiological conditions was also examined for the development of a therapeutically relevant delivery agent. Additionally, MRI active microflorettes have been generated through the incorporation of a gadolinium binding ligand, DOTA within the collagen-based peptide sequence. To probe peptide-promoted self-assemblies of gold nanoparticles (GNPs) by non-covalent, charge complementary interactions, a highly anionic coiled-coil peptide was designed and synthesized. Upon formation of peptide-GNP interactions, the hydrophobic domain of the coiled-coil were shown to promote the self-assembly of peptide-GNPs clustering. Hydrophobic forces were found to play an important role in the assembly process, as a peptide with an equally overall negative charge, but lacking an ordered hydrophobic face had no effect on GNP assembly. The self-assembly system herein is advantageous due to its reversible nature upon addition of high salt concentrations which masks the surface charge. There is great potential for using this uniquely designed self-assembled peptide-gold nanoparticle system for exploring the interplay between peptide ligation and GNP self-assembly.

Parallel robot for micro assembly with integrated innovative optical 3D-sensor

NASA Astrophysics Data System (ADS)

Hesselbach, Juergen; Ispas, Diana; Pokar, Gero; Soetebier, Sven; Tutsch, Rainer

2002-10-01

Recent advances in the fields of MEMS and MOEMS often require precise assembly of very small parts with an accuracy of a few microns. In order to meet this demand, a new approach using a robot based on parallel mechanisms in combination with a novel 3D-vision system has been chosen. The planar parallel robot structure with 2 DOF provides a high resolution in the XY-plane. It carries two additional serial axes for linear and rotational movement in/about z direction. In order to achieve high precision as well as good dynamic capabilities, the drive concept for the parallel (main) axes incorporates air bearings in combination with a linear electric servo motors. High accuracy position feedback is provided by optical encoders with a resolution of 0.1 μm. To allow for visualization and visual control of assembly processes, a camera module fits into the hollow tool head. It consists of a miniature CCD camera and a light source. In addition a modular gripper support is integrated into the tool head. To increase the accuracy a control loop based on an optoelectronic sensor will be implemented. As a result of an in-depth analysis of different approaches a photogrammetric system using one single camera and special beam-splitting optics was chosen. A pattern of elliptical marks is applied to the surfaces of workpiece and gripper. Using a model-based recognition algorithm the image processing software identifies the gripper and the workpiece and determines their relative position. A deviation vector is calculated and fed into the robot control to guide the gripper.

z~2: An Epoch of Disk Assembly

NASA Astrophysics Data System (ADS)

Simons, Raymond C.; Kassin, Susan A.; Weiner, Benjamin; Heckman, Timothy M.; Trump, Jonathan; SIGMA, DEEP2

2018-01-01

At z = 0, the majority of massive star-forming galaxies contain thin, rotationally supported gas disks. It was once accepted that galaxies form thin disks early: collisional gas with high velocity dispersion should dissipate energy, conserve angular momentum, and develop strong rotational support in only a few galaxy crossing times (~few hundred Myr). However, this picture is complicated at high redshift, where the processes governing galaxy assembly tend to be violent and inhospitable to disk formation. We present results from our SIGMA survey of star-forming galaxy kinematics at z = 2. These results challenge the simple picture described above: galaxies at z = 2 are unlike local well-ordered disks. Their kinematics tend to be much more disordered, as quantified by their low ratios of rotational velocity to gas velocity dispersion (Vrot/σg): less than 35% of galaxies have Vrot/σg > 3. For comparison, nearly 100% of local star-forming galaxies meet this same threshold. We combine our high redshift sample with a similar low redshift sample from the DEEP2 survey. This combined sample covers a continuous redshift baseline over 0.1 < z < 2.5, spanning 10 Gyrs of cosmic time. Over this period, galaxies exhibit remarkably smooth kinematic evolution on average. All galaxies tend towards rotational support with time, and it is reached earlier in higher mass systems. This is due to both a significant decline in gas velocity dispersion and a mild rise in ordered rotational motions. These results indicate that z = 2 is a period of disk assembly, during which the strong rotational support present in today’s massive disk galaxies is only just beginning to emerge.

EUNIS; Extreme-Ultraviolet Normal-Incidence Spectrometer

NASA Technical Reports Server (NTRS)

Thomas, Roger J.; Davila, Joseph M.; Fisher, Richard R. (Technical Monitor)

2001-01-01

GSFC is in the process of assembling an Extreme-Ultraviolet Normal Incidence Spectrometer called EUNIS, to be flown as a sounding rocket payload. The instrument builds on the many technical innovations pioneered by our highly successful SERTS experiment, which has now flown a total of ten times, most recently last summer. The new design will have somewhat improved spatial and spectral resolutions, as well as two orders of magnitude greater sensitivity, permitting high signal/noise EUV spectroscopy with a temporal resolution near 1 second for the first time ever. In order to achieve such high time cadence, a novel detector system is being developed, based on Active-Pixel-Sensor electronics, a key component of our design.

Self-Assembled Materials Made from Functional Recombinant Proteins.

PubMed

Jang, Yeongseon; Champion, Julie A

2016-10-18

Proteins are potent molecules that can be used as therapeutics, sensors, and biocatalysts with many advantages over small-molecule counterparts due to the specificity of their activity based on their amino acid sequence and folded three-dimensional structure. However, they also have significant limitations in their stability, localization, and recovery when used in soluble form. These opportunities and challenges have motivated the creation of materials from such functional proteins in order to protect and present them in a way that enhances their function. We have designed functional recombinant fusion proteins capable of self-assembling into materials with unique structures that maintain or improve the functionality of the protein. Fusion of either a functional protein or an assembly domain to a leucine zipper domain makes the materials design strategy modular, based on the high affinity between leucine zippers. The self-assembly domains, including elastin-like polypeptides (ELPs) and defined-sequence random coil polypeptides, can be fused with a leucine zipper motif in order to promote assembly of the fusion proteins into larger structures upon specific stimuli such as temperature and ionic strength. Fusion of other functional domains with the counterpart leucine zipper motif endows the self-assembled materials with protein-specific functions such as fluorescence or catalytic activity. In this Account, we describe several examples of materials assembled from functional fusion proteins as well as the structural characterization, functionality, and understanding of the assembly mechanism. The first example is zipper fusion proteins containing ELPs that assemble into particles when introduced to a model extracellular matrix and subsequently disassemble over time to release the functional protein for drug delivery applications. Under different conditions, the same fusion proteins can self-assemble into hollow vesicles. The vesicles display a functional protein on the surface and can also carry protein, small-molecule, or nanoparticle cargo in the vesicle lumen. To create a material with a more complex hierarchical structure, we combined calcium phosphate with zipper fusion proteins containing random coil polypeptides to produce hybrid protein-inorganic supraparticles with high surface area and porous structure. The use of a functional enzyme created supraparticles with the ability to degrade inflammatory cytokines. Our characterization of these protein materials revealed that the molecular interactions are complex because of the large size of the protein building blocks, their folded structures, and the number of potential interactions including hydrophobic interactions, electrostatic interactions, van der Waals forces, and specific affinity-based interactions. It is difficult or even impossible to predict the structures a priori. However, once the basic assembly principles are understood, there is opportunity to tune the material properties, such as size, through control of the self-assembly conditions. Our future efforts on the fundamental side will focus on identifying the phase space of self-assembly of these fusion proteins and additional experimental levers with which to control and tune the resulting materials. On the application side, we are investigating an array of different functional proteins to expand the use of these structures in both therapeutic protein delivery and biocatalysis.

Supramolecular metal-organic frameworks that display high homogeneous and heterogeneous photocatalytic activity for H2 production

NASA Astrophysics Data System (ADS)

Tian, Jia; Xu, Zi-Yue; Zhang, Dan-Wei; Wang, Hui; Xie, Song-Hai; Xu, Da-Wen; Ren, Yuan-Hang; Wang, Hao; Liu, Yi; Li, Zhan-Ting

2016-05-01

Self-assembly has a unique presence when it comes to creating complicated, ordered supramolecular architectures from simple components under mild conditions. Here, we describe a self-assembly strategy for the generation of the first homogeneous supramolecular metal-organic framework (SMOF-1) in water at room temperature from a hexaarmed [Ru(bpy)3]2+-based precursor and cucurbit[8]uril (CB[8]). The solution-phase periodicity of this cubic transition metal-cored supramolecular organic framework (MSOF) is confirmed by small-angle X-ray scattering and diffraction experiments, which, as supported by TEM imaging, is commensurate with the periodicity in the solid state. We further demonstrate that SMOF-1 adsorbs anionic Wells-Dawson-type polyoxometalates (WD-POMs) in a one-cage-one-guest manner to give WD-POM@SMOF-1 hybrid assemblies. Upon visible-light (500 nm) irradiation, such hybrids enable fast multi-electron injection from photosensitive [Ru(bpy)3]2+ units to redox-active WD-POM units, leading to efficient hydrogen production in aqueous media and in organic media. The demonstrated strategy opens the door for the development of new classes of liquid-phase and solid-phase ordered porous materials.

Supramolecular metal-organic frameworks that display high homogeneous and heterogeneous photocatalytic activity for H 2 production

DOE PAGES

Tian, Jia; Xu, Zi-Yue; Zhang, Dan-Wei; ...

2016-05-10

Self-assembly has a unique presence when it comes to creating complicated, ordered supramolecular architectures from simple components under mild conditions. Here, we describe a self-assembly strategy for the generation of the first homogeneous supramolecular metal-organic framework (SMOF-1) in water at room temperature from a hexaarmed [Ru(bpy) 3 ] 2+ -based precursor and cucurbit[8] uril (CB[8]). The solution-phase periodicity of this cubic transition metal-cored supramolecular organic framework (MSOF) is confirmed by small-angle X-ray scattering and diffraction experiments, which, as supported by TEM imaging, is commensurate with the periodicity in the solid state. We further demonstrate that SMOF-1 adsorbs anionic Wells-'Dawson-type polyoxometalatesmore » (WD-POMs) in a one-cage-one-guest manner to give WD-POM@SMOF-1 hybrid assemblies. Upon visible-light (500 nm) irradiation, such hybrids enable fast multi-electron injection from photosensitive [Ru(bpy) 3 ] 2+ units to redox-active WD-POM units, leading to efficient hydrogen production in aqueous media and in organic media. The demonstrated strategy opens the door for the development of new classes of liquid-phase and solid-phase ordered porous materials.« less

Ultrathin self-assembled anionic polymer membranes for superfast size-selective separation

NASA Astrophysics Data System (ADS)

Deng, Chao; Zhang, Qiu Gen; Han, Guang Lu; Gong, Yi; Zhu, Ai Mei; Liu, Qing Lin

2013-10-01

Nanoporous membranes with superior separation performance have become more crucial with increasing concerns in functional nanomaterials. Here novel ultrahigh permeable nanoporous membranes have been fabricated on macroporous supports by self-assembly of anionic polymer on copper hydroxide nanostrand templates in organic solution. This facile approach has a great potential for the fabrication of ultrathin anionic polymer membranes as a general method. The as-fabricated self-assembled membranes have a mean pore size of 5-12 nm and an adjustable thickness as low as 85 nm. They allow superfast permeation of water, and exhibit excellent size-selective separation properties and good fouling resistance for negatively-charged solutes during filtration. The 85 nm thick membrane has an ultrahigh water flux (3306 l m-2 h-1 bar-1) that is an order of magnitude larger than commercial membranes, and can highly efficiently separate 5 and 15 nm gold nanoparticles from their mixtures. The newly developed nanoporous membranes have a wide application in separation and purification of biomacromolecules and nanoparticles.Nanoporous membranes with superior separation performance have become more crucial with increasing concerns in functional nanomaterials. Here novel ultrahigh permeable nanoporous membranes have been fabricated on macroporous supports by self-assembly of anionic polymer on copper hydroxide nanostrand templates in organic solution. This facile approach has a great potential for the fabrication of ultrathin anionic polymer membranes as a general method. The as-fabricated self-assembled membranes have a mean pore size of 5-12 nm and an adjustable thickness as low as 85 nm. They allow superfast permeation of water, and exhibit excellent size-selective separation properties and good fouling resistance for negatively-charged solutes during filtration. The 85 nm thick membrane has an ultrahigh water flux (3306 l m-2 h-1 bar-1) that is an order of magnitude larger than commercial membranes, and can highly efficiently separate 5 and 15 nm gold nanoparticles from their mixtures. The newly developed nanoporous membranes have a wide application in separation and purification of biomacromolecules and nanoparticles. Electronic supplementary information (ESI) available: Synthesis and characterization of SPEK-C; effect of the sulfonation degree on membrane formation; structure and properties of the self-assembled membranes; separation of cyt.c by the self-assembled membranes; size-selective separation of gold nanoparticles by the self-assembled membranes; comparison with commercial flat sheet ultrafiltration membranes. See DOI: 10.1039/c3nr03362g

Peptide π-Electron Conjugates: Organic Electronics for Biology?

PubMed

Ardoña, Herdeline Ann M; Tovar, John D

2015-12-16

Highly ordered arrays of π-conjugated molecules are often viewed as a prerequisite for effective charge-transporting materials. Studies involving these materials have traditionally focused on organic electronic devices, with more recent emphasis on biological systems. In order to facilitate the transition to biological environments, biomolecules that can promote hierarchical ordering and water solubility are often covalently appended to the π-electron unit. This review highlights recent work on π-conjugated systems bound to peptide moieties that exhibit self-assembly and aims to provide an overview on the development and emerging applications of peptide-based supramolecular π-electron systems.

Peptide-based biosensors: From self-assembled interfaces to molecular probes in electrochemical assays.

PubMed

Puiu, Mihaela; Bala, Camelia

2018-04-01

Redox-tagged peptides have emerged as functional materials with multiple applications in the area of sensing and biosensing applications due to their high stability, excellent redox properties and versatility of biomolecular interactions. They allow direct observation of molecular interactions in a wide range of affinity and enzymatic assays and act as electron mediators. Short helical peptides possess the ability to self-assemble in specific configurations with the possibility to develop in highly-ordered, stable 1D, 2D and 3D architectures in a hierarchical controlled manner. We provide here a brief overview of the electrochemical techniques available to study the electron transfer in peptide films with particular interest in developing biosensors with immobilized peptide motifs, for biological and clinical applications. Copyright © 2017 Elsevier B.V. All rights reserved.

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

Samant, Saumil P.; Grabowski, Christopher A.; Kisslinger, Kim

Emerging needs for fast charge/discharge yet high-power, lightweight, and flexible electronics requires the use of polymer-film-based solid-state capacitors with high energy densities. Fast charge/discharge rates of film capacitors on the order of microseconds are not achievable with slower charging conventional batteries, supercapacitors and related hybrid technologies. However, the current energy densities of polymer film capacitors fall short of rising demand, and could be significantly enhanced by increasing the breakdown strength (E BD) and dielectric permittivity (ε r) of the polymer films. Co-extruded two-homopolymer component multilayered films have demonstrated much promise in this regard showing higher E BD over that ofmore » component polymers. Multilayered films can also help incorporate functional features besides energy storage, such as enhanced optical, mechanical, thermal and barrier properties. In this work, we report accomplishing multilayer, multicomponent block copolymer dielectric films (BCDF) with soft-shear driven highly oriented self-assembled lamellar diblock copolymers (BCP) as a novel application of this important class of self-assembling materials. Results of a model PS-b-PMMA system show ~50% enhancement in E BD of self-assembled multilayer lamellar BCP films compared to unordered as-cast films, indicating that the breakdown is highly sensitive to the nanostructure of the BCP. The enhancement in E BD is attributed to the “barrier effect”, where the multiple interfaces between the lamellae block components act as barriers to the dielectric breakdown through the film. The increase in E BD corresponds to more than doubling the energy storage capacity using a straightforward directed self-assembly strategy. This approach opens a new nanomaterial paradigm for designing high energy density dielectric materials.« less

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

Samant, Saumil P.; Grabowski, Christopher A.; Kisslinger, Kim

Emerging needs for fast charge/discharge yet high-power, lightweight, and flexible electronics requires the use of polymer-film-based solid-state capacitors with high energy densities. Fast charge/discharge rates of film capacitors on the order of microseconds are not achievable with slower charging conventional batteries, supercapacitors and related hybrid technologies. However, the current energy densities of polymer film capacitors fall short of rising demand, and could be significantly enhanced by increasing the breakdown strength (E BD) and dielectric permittivity (ε r) of the polymer films. Co-extruded two-homopolymer component multilayered films have demonstrated much promise in this regard showing higher E BD over that ofmore » component polymers. Multilayered films can also help incorporate functional features besides energy storage, such as enhanced optical, mechanical, thermal and barrier properties. In this work, we report accomplishing multilayer, multicomponent block copolymer dielectric films (BCDF) with soft-shear driven highly oriented self-assembled lamellar diblock copolymers (BCP) as a novel application of this important class of self-assembling materials. Results of a model PS- b-PMMA system show ~50% enhancement in E BD of self-assembled multilayer lamellar BCP films compared to unordered as-cast films, indicating that the breakdown is highly sensitive to the nanostructure of the BCP. The enhancement in E BD is attributed to the “barrier effect”, where the multiple interfaces between the lamellae block components act as barriers to the dielectric breakdown through the film. The increase in E BD corresponds to more than doubling the energy storage capacity using a straightforward directed self-assembly strategy. Lastly, this approach opens a new nanomaterial paradigm for designing high energy density dielectric materials.« less

Nonlinear Dynamic Analysis of Disordered Bladed-Disk Assemblies

NASA Technical Reports Server (NTRS)

McGee, Oliver G., III

1997-01-01

In a effort to address current needs for efficient, air propulsion systems, we have developed some new analytical predictive tools for understanding and alleviating aircraft engine instabilities which have led to accelerated high cycle fatigue and catastrophic failures of these machines during flight. A frequent cause of failure in Jets engines is excessive resonant vibrations and stall flutter instabilities. The likelihood of these phenomena is reduced when designers employ the analytical models we have developed. These prediction models will ultimately increase the nation's competitiveness in producing high performance Jets engines with enhanced operability, energy economy, and safety. The objectives of our current threads of research in the final year are directed along two lines. First, we want to improve the current state of blade stress and aeromechanical reduced-ordered modeling of high bypass engine fans, Specifically, a new reduced-order iterative redesign tool for passively controlling the mechanical authority of shroudless, wide chord, laminated composite transonic bypass engine fans has been developed. Second, we aim to advance current understanding of aeromechanical feedback control of dynamic flow instabilities in axial flow compressors. A systematic theoretical evaluation of several approaches to aeromechanical feedback control of rotating stall in axial compressors has been conducted. Attached are abstracts of two .papers under preparation for the 1998 ASME Turbo Expo in Stockholm, Sweden sponsored under Grant No. NAG3-1571. Our goals during the final year under Grant No. NAG3-1571 is to enhance NASA's capabilities of forced response of turbomachines (such as NASA FREPS). We with continue our development of the reduced-ordered, three-dimensional component synthesis models for aeromechanical evaluation of integrated bladeddisk assemblies (i.e., the disk, non-identical bladeing etc.). We will complete our development of component systems design optimization strategies for specified vibratory stresses and increased fatigue life prediction of assembly components, and for specified frequency margins on the Campbell diagrams of turbomachines. Finally, we will integrate the developed codes with NASA's turbomachinery aeromechanics prediction capability (such as NASA FREPS).

A physical map of the bovine genome

PubMed Central

Snelling, Warren M; Chiu, Readman; Schein, Jacqueline E; Hobbs, Matthew; Abbey, Colette A; Adelson, David L; Aerts, Jan; Bennett, Gary L; Bosdet, Ian E; Boussaha, Mekki; Brauning, Rudiger; Caetano, Alexandre R; Costa, Marcos M; Crawford, Allan M; Dalrymple, Brian P; Eggen, André; Everts-van der Wind, Annelie; Floriot, Sandrine; Gautier, Mathieu; Gill, Clare A; Green, Ronnie D; Holt, Robert; Jann, Oliver; Jones, Steven JM; Kappes, Steven M; Keele, John W; de Jong, Pieter J; Larkin, Denis M; Lewin, Harris A; McEwan, John C; McKay, Stephanie; Marra, Marco A; Mathewson, Carrie A; Matukumalli, Lakshmi K; Moore, Stephen S; Murdoch, Brenda; Nicholas, Frank W; Osoegawa, Kazutoyo; Roy, Alice; Salih, Hanni; Schibler, Laurent; Schnabel, Robert D; Silveri, Licia; Skow, Loren C; Smith, Timothy PL; Sonstegard, Tad S; Taylor, Jeremy F; Tellam, Ross; Van Tassell, Curtis P; Williams, John L; Womack, James E; Wye, Natasja H; Yang, George; Zhao, Shaying

2007-01-01

Background Cattle are important agriculturally and relevant as a model organism. Previously described genetic and radiation hybrid (RH) maps of the bovine genome have been used to identify genomic regions and genes affecting specific traits. Application of these maps to identify influential genetic polymorphisms will be enhanced by integration with each other and with bacterial artificial chromosome (BAC) libraries. The BAC libraries and clone maps are essential for the hybrid clone-by-clone/whole-genome shotgun sequencing approach taken by the bovine genome sequencing project. Results A bovine BAC map was constructed with HindIII restriction digest fragments of 290,797 BAC clones from animals of three different breeds. Comparative mapping of 422,522 BAC end sequences assisted with BAC map ordering and assembly. Genotypes and pedigree from two genetic maps and marker scores from three whole-genome RH panels were consolidated on a 17,254-marker composite map. Sequence similarity allowed integrating the BAC and composite maps with the bovine draft assembly (Btau3.1), establishing a comprehensive resource describing the bovine genome. Agreement between the marker and BAC maps and the draft assembly is high, although discrepancies exist. The composite and BAC maps are more similar than either is to the draft assembly. Conclusion Further refinement of the maps and greater integration into the genome assembly process may contribute to a high quality assembly. The maps provide resources to associate phenotypic variation with underlying genomic variation, and are crucial resources for understanding the biology underpinning this important ruminant species so closely associated with humans. PMID:17697342

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.

Shape-specific nanostructured protein mimics from de novo designed chimeric peptides.

PubMed

Jiang, Linhai; Yang, Su; Lund, Reidar; Dong, He

2018-01-30

Natural proteins self-assemble into highly-ordered nanoscaled architectures to perform specific functions. The intricate functions of proteins have provided great impetus for researchers to develop strategies for designing and engineering synthetic nanostructures as protein mimics. Compared to the success in engineering fibrous protein mimetics, the design of discrete globular protein-like nanostructures has been challenging mainly due to the lack of precise control over geometric packing and intermolecular interactions among synthetic building blocks. In this contribution, we report an effective strategy to construct shape-specific nanostructures based on the self-assembly of chimeric peptides consisting of a coiled coil dimer and a collagen triple helix folding motif. Under salt-free conditions, we showed spontaneous self-assembly of the chimeric peptides into monodisperse, trigonal bipyramidal-like nanoparticles with precise control over the stoichiometry of two folding motifs and the geometrical arrangements relative to one another. Three coiled coil dimers are interdigitated on the equatorial plane while the two collagen triple helices are located in the axial position, perpendicular to the coiled coil plane. A detailed molecular model was proposed and further validated by small angle X-ray scattering experiments and molecular dynamics (MD) simulation. The results from this study indicated that the molecular folding of each motif within the chimeric peptides and their geometric packing played important roles in the formation of discrete protein-like nanoparticles. The peptide design and self-assembly mechanism may open up new routes for the construction of highly organized, discrete self-assembling protein-like nanostructures with greater levels of control over assembly accuracy.

Preparation and enhanced infrared response properties of ordered W-doped VO2 nanowire array

NASA Astrophysics Data System (ADS)

Xie, Bing He; Fu, Wen Biao; Fei, Guang Tao; Xu, Shao Hui; Gao, Xu Dong; Zhang, Li De

2018-04-01

In this article, pure and tungsten-doped (W-doped) highly ordered two-dimensional (2D) vanadium dioxide (VO2) nanowire arrays were successfully prepared by a hydrothermal treatment, followed by a self-assembly progress and the in-situ high temperature treatment. The infrared photodetector devices based on monoclinic VO2 (VO2(M)) and W-doped VO2(M) nanowires were comparatively studied . It was found that the device based on W-doped VO2(M) nanowires exhibits a rapid infrared response and an enhanced photoelectric responsivity of 21.4 mA/W under the incident infrared light intensity of 280 mW/cm2, which is nearly two orders of magnitude superior to pure VO2(M) nanowire array. Our experimental results provided a direct and convenient path for design of future high-performance photodetector devices.

Self-assembly of proteins into a three-dimensional multilayer system: investigation of the surface of the human fungal pathogen Aspergillus fumigatus.

PubMed

Zykwinska, Agata; Pihet, Marc; Radji, Sadia; Bouchara, Jean-Philippe; Cuenot, Stéphane

2014-06-01

Hydrophobins are small surface active proteins that fulfil a wide spectrum of functions in fungal growth and development. The human fungal pathogen Aspergillus fumigatus expresses RodA hydrophobins that self-assemble on the outer conidial surface into tightly organized nanorods known as rodlets. AFM investigation of the conidial surface allows us to evidence that RodA hydrophobins self-assemble into rodlets through bilayers. Within bilayers, hydrophilic domains of hydrophobins point inward, thus making a hydrophilic core, while hydrophobic domains point outward. AFM measurements reveal that several rodlet bilayers are present on the conidial surface thus showing that proteins self-assemble into a complex three-dimensional multilayer system. The self-assembly of RodA hydrophobins into rodlets results from attractive interactions between stacked β-sheets, which conduct to a final linear cross-β spine structure. A Monte Carlo simulation shows that anisotropic interactions are the main driving forces leading the hydrophobins to self-assemble into parallel rodlets, which are further structured in nanodomains. Taken together, these findings allow us to propose a mechanism, which conducts RodA hydrophobins to a highly ordered rodlet structure. The mechanism of hydrophobin assembly into rodlets offers new prospects for the development of more efficient strategies leading to disruption of rodlet formation allowing a rapid detection of the fungus by the immune system. Copyright © 2014 Elsevier B.V. All rights reserved.

Investigate the Effect of Thawing Process on the Self-Assembly of Silk Protein for Tissue Applications.

PubMed

Nguyen, Hiep Thi; Luong, Hien Thu; Nguyen, Hai Dai; Tran, Hien Anh; Huynh, Khon Chan; Vo, Toi Van

2017-01-01

Biological self-assembly is a process in which building blocks autonomously organize to form stable supermolecules of higher order and complexity through domination of weak, noncovalent interactions. For silk protein, the effect of high incubating temperature on the induction of secondary structure and self-assembly was well investigated. However, the effect of freezing and thawing on silk solution has not been studied. The present work aimed to investigate a new all-aqueous process to form 3D porous silk fibroin matrices using a freezing-assisted self-assembly method. This study proposes an experimental investigation and optimization of environmental parameters for the self-assembly process such as freezing temperature, thawing process, and concentration of silk solution. The optical images demonstrated the possibility and potential of -80ST48 treatment to initialize the self-assembly of silk fibroin as well as controllably fabricate a porous scaffold. Moreover, the micrograph images illustrate the assembly of silk protein chain in 7 days under the treatment of -80ST48 process. The surface morphology characterization proved that this method could control the pore size of porous scaffolds by control of the concentration of silk solution. The animal test showed the support of silk scaffold for cell adhesion and proliferation, as well as the cell migration process in the 3D implantable scaffold.

Investigate the Effect of Thawing Process on the Self-Assembly of Silk Protein for Tissue Applications

PubMed Central

Tran, Hien Anh; Huynh, Khon Chan; Vo, Toi Van

2017-01-01

Biological self-assembly is a process in which building blocks autonomously organize to form stable supermolecules of higher order and complexity through domination of weak, noncovalent interactions. For silk protein, the effect of high incubating temperature on the induction of secondary structure and self-assembly was well investigated. However, the effect of freezing and thawing on silk solution has not been studied. The present work aimed to investigate a new all-aqueous process to form 3D porous silk fibroin matrices using a freezing-assisted self-assembly method. This study proposes an experimental investigation and optimization of environmental parameters for the self-assembly process such as freezing temperature, thawing process, and concentration of silk solution. The optical images demonstrated the possibility and potential of −80ST48 treatment to initialize the self-assembly of silk fibroin as well as controllably fabricate a porous scaffold. Moreover, the micrograph images illustrate the assembly of silk protein chain in 7 days under the treatment of −80ST48 process. The surface morphology characterization proved that this method could control the pore size of porous scaffolds by control of the concentration of silk solution. The animal test showed the support of silk scaffold for cell adhesion and proliferation, as well as the cell migration process in the 3D implantable scaffold. PMID:28367442

Experimental study of an adaptive CFRC reflector for high order wave-front error correction

NASA Astrophysics Data System (ADS)

Lan, Lan; Fang, Houfei; Wu, Ke; Jiang, Shuidong; Zhou, Yang

2018-03-01

The recent radio frequency communication system developments are generating the need for creating space antennas with lightweight and high precision. The carbon fiber reinforced composite (CFRC) materials have been used to manufacture the high precision reflector. The wave-front errors caused by fabrication and on-orbit distortion are inevitable. The adaptive CFRC reflector has received much attention to do the wave-front error correction. Due to uneven stress distribution that is introduced by actuation force and fabrication, the high order wave-front errors such as print-through error is found on the reflector surface. However, the adaptive CFRC reflector with PZT actuators basically has no control authority over the high order wave-front errors. A new design architecture assembled secondary ribs at the weak triangular surfaces is presented in this paper. The virtual experimental study of the new adaptive CFRC reflector has conducted. The controllability of the original adaptive CFRC reflector and the new adaptive CFRC reflector with secondary ribs are investigated. The virtual experimental investigation shows that the new adaptive CFRC reflector is feasible and efficient to diminish the high order wave-front error.

Helical self-organization and hierarchical self-assembly of an oligoheterocyclic pyridine-pyridazine strand into extended supramolecular fibers.

PubMed

Cuccia, Louis A; Ruiz, Eliseo; Lehn, Jean-Marie; Homo, Jean-Claude; Schmutz, Marc

2002-08-02

The synthesis and characterization of an alternating pyridine-pyridazine strand comprising thirteen heterocycles are described. Spontaneous folding into a helical secondary structure is based on a general molecular self-organization process enforced by the conformational information encoded within the primary structure of the molecular strand itself. Conformational control based on heterocyclic "helicity codons" illustrates a strategy for designing folding properties into synthetic oligomers (foldamers). Strong intermolecular interactions of the highly ordered lock-washer subunits of compound 3 results in hierarchical supramolecular self-assembly into protofibrils and fibrils. Compound 3 also forms mechanically stable two-dimensional Langmuir-Blodgett and cast thin films.

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.

Non-equilibrium magnetic colloidal dispersions at liquid-air interfaces: dynamic patterns, magnetic order and self-assembled swimmers.

PubMed

Snezhko, Alexey

2011-04-20

Colloidal dispersions of interacting particles subjected to an external periodic forcing often develop nontrivial self-assembled patterns and complex collective behavior. A fundamental issue is how collective ordering in such non-equilibrium systems arises from the dynamics of discrete interacting components. In addition, from a practical viewpoint, by working in regimes far from equilibrium new self-organized structures which are generally not available through equilibrium thermodynamics can be created. In this review spontaneous self-assembly phenomena in magnetic colloidal dispersions suspended at liquid-air interfaces and driven out of equilibrium by an alternating magnetic field are presented. Experiments reveal a new type of nontrivially ordered self-assembled structures emerging in such systems in a certain range of excitation parameters. These dynamic structures emerge as a result of the competition between magnetic and hydrodynamic forces and have complex unconventional magnetic ordering. Nontrivial self-induced hydrodynamic fields accompany each out-of-equilibrium pattern. Spontaneous symmetry breaking of the self-induced surface flows leading to a formation of self-propelled microstructures has been discovered. Some features of the self-localized structures can be understood in the framework of the amplitude equation (Ginzburg-Landau type equation) for parametric waves coupled to the conservation law equation describing the evolution of the magnetic particle density and the Navier-Stokes equation for hydrodynamic flows. To understand the fundamental microscopic mechanisms governing self-assembly processes in magnetic colloidal dispersions at liquid-air interfaces a first-principle model for a non-equilibrium self-assembly is presented. The latter model allows us to capture in detail the entire process of out-of-equilibrium self-assembly in the system and reproduces most of the observed phenomenology.

GAAP: Genome-organization-framework-Assisted Assembly Pipeline for prokaryotic genomes.

PubMed

Yuan, Lina; Yu, Yang; Zhu, Yanmin; Li, Yulai; Li, Changqing; Li, Rujiao; Ma, Qin; Siu, Gilman Kit-Hang; Yu, Jun; Jiang, Taijiao; Xiao, Jingfa; Kang, Yu

2017-01-25

Next-generation sequencing (NGS) technologies have greatly promoted the genomic study of prokaryotes. However, highly fragmented assemblies due to short reads from NGS are still a limiting factor in gaining insights into the genome biology. Reference-assisted tools are promising in genome assembly, but tend to result in false assembly when the assigned reference has extensive rearrangements. Herein, we present GAAP, a genome assembly pipeline for scaffolding based on core-gene-defined Genome Organizational Framework (cGOF) described in our previous study. Instead of assigning references, we use the multiple-reference-derived cGOFs as indexes to assist in order and orientation of the scaffolds and build a skeleton structure, and then use read pairs to extend scaffolds, called local scaffolding, and distinguish between true and chimeric adjacencies in the scaffolds. In our performance tests using both empirical and simulated data of 15 genomes in six species with diverse genome size, complexity, and all three categories of cGOFs, GAAP outcompetes or achieves comparable results when compared to three other reference-assisted programs, AlignGraph, Ragout and MeDuSa. GAAP uses both cGOF and pair-end reads to create assemblies in genomic scale, and performs better than the currently available reference-assisted assembly tools as it recovers more assemblies and makes fewer false locations, especially for species with extensive rearranged genomes. Our method is a promising solution for reconstruction of genome sequence from short reads of NGS.

Patterning at the 10 nanometer length scale using a strongly segregating block copolymer thin film and vapor phase infiltration of inorganic precursors

NASA Astrophysics Data System (ADS)

Choi, Jonathan W.; Li, Zhaodong; Black, Charles T.; Sweat, Daniel P.; Wang, Xudong; Gopalan, Padma

2016-06-01

In this work, we demonstrate the use of self-assembled thin films of the cylinder-forming block copolymer poly(4-tert-butylstyrene-block-2-vinylpyridine) to pattern high density features at the 10 nm length scale. This material's large interaction parameter facilitates pattern formation in single-digit nanometer dimensions. This block copolymer's accessible order-disorder transition temperature allows thermal annealing to drive the assembly of ordered 2-vinylpyridine cylinders that can be selectively complexed with the organometallic precursor trimethylaluminum. This unique chemistry converts organic 2-vinylpyridine cylinders into alumina nanowires with diameters ranging from 8 to 11 nm, depending on the copolymer molecular weight. Graphoepitaxy of this block copolymer aligns and registers sub-12 nm diameter nanowires to larger-scale rectangular, curved, and circular features patterned by optical lithography. The alumina nanowires function as a robust hard mask to withstand the conditions required for patterning the underlying silicon by plasma etching. We conclude with a discussion of some of the challenges that arise with using block copolymers for patterning at sub-10 nm feature sizes.In this work, we demonstrate the use of self-assembled thin films of the cylinder-forming block copolymer poly(4-tert-butylstyrene-block-2-vinylpyridine) to pattern high density features at the 10 nm length scale. This material's large interaction parameter facilitates pattern formation in single-digit nanometer dimensions. This block copolymer's accessible order-disorder transition temperature allows thermal annealing to drive the assembly of ordered 2-vinylpyridine cylinders that can be selectively complexed with the organometallic precursor trimethylaluminum. This unique chemistry converts organic 2-vinylpyridine cylinders into alumina nanowires with diameters ranging from 8 to 11 nm, depending on the copolymer molecular weight. Graphoepitaxy of this block copolymer aligns and registers sub-12 nm diameter nanowires to larger-scale rectangular, curved, and circular features patterned by optical lithography. The alumina nanowires function as a robust hard mask to withstand the conditions required for patterning the underlying silicon by plasma etching. We conclude with a discussion of some of the challenges that arise with using block copolymers for patterning at sub-10 nm feature sizes. Electronic supplementary information (ESI) available. See DOI: 10.1039/c6nr01409g

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

Michael Viola, J. Edwards, T. Brown, L. Dudek, R. Ellis, P. Heitzenroeder, R. Strykowsky and Michael Cole

The National Compact Stellarator Experiment (NCSX) was a collaborative effort between ORNL and PPPL. PPPL provided the assembly techniques with guidance from ORNL to meet design criteria. The individual vacuum vessel segments, modular coils, trim coils, and toroidal field coils components were delivered to the Field Period Assembly (FPA) crew who then would complete the component assemblies and then assemble the final three field period assemblies, each consisting of two sets of three modular coils assembled over a 120o vacuum vessel segment with the trim coils and toroidal field coils providing the outer layer. The requirements for positioning the modularmore » coils were found to be most demanding. The assembly tolerances required for accurate positioning of the field coil windings in order to generate sufficiently accurate magnetic fields strained state of the art techniques in metrology and alignment and required constant monitoring of assembly steps with laser trackers, measurement arms, and photogrammetry. The FPA activities were being performed concurrently while engineering challenges were being resolved. For example, it was determined that high friction electrically isolated shims were needed between the modular coil interface joints and low distortion welding was required in the nose region of those joints. This took months of analysis and development yet the assembly was not significantly impacted because other assembly tasks could be performed in parallel with ongoing assembly tasks as well as tasks such as advance tooling setup preparation for the eventual welding tasks. The crew technicians developed unique, accurate time saving techniques and tooling which provided significant cost and schedule savings. Project management displayed extraordinary foresight and every opportunity to gain advanced knowledge and develop techniques was taken advantage of. Despite many risk concerns, the cost and schedule performance index was maintained nearly 1.0 during the assembly phase until project cancellation. In this paper, the assembly logic, the engineering challenges, solutions to those challenges and some of the unique and clever assembly techniques, will be presented.« less

Light-emitting self-assembled peptide nucleic acids exhibit both stacking interactions and Watson-Crick base pairing.

PubMed

Berger, Or; Adler-Abramovich, Lihi; Levy-Sakin, Michal; Grunwald, Assaf; Liebes-Peer, Yael; Bachar, Mor; Buzhansky, Ludmila; Mossou, Estelle; Forsyth, V Trevor; Schwartz, Tal; Ebenstein, Yuval; Frolow, Felix; Shimon, Linda J W; Patolsky, Fernando; Gazit, Ehud

2015-04-01

The two main branches of bionanotechnology involve the self-assembly of either peptides or DNA. Peptide scaffolds offer chemical versatility, architectural flexibility and structural complexity, but they lack the precise base pairing and molecular recognition available with nucleic acid assemblies. Here, inspired by the ability of aromatic dipeptides to form ordered nanostructures with unique physical properties, we explore the assembly of peptide nucleic acids (PNAs), which are short DNA mimics that have an amide backbone. All 16 combinations of the very short di-PNA building blocks were synthesized and assayed for their ability to self-associate. Only three guanine-containing di-PNAs-CG, GC and GG-could form ordered assemblies, as observed by electron microscopy, and these di-PNAs efficiently assembled into discrete architectures within a few minutes. The X-ray crystal structure of the GC di-PNA showed the occurrence of both stacking interactions and Watson-Crick base pairing. The assemblies were also found to exhibit optical properties including voltage-dependent electroluminescence and wide-range excitation-dependent fluorescence in the visible region.

Metal-Folded Single-Chain Nanoparticle: Nanoclusters and Self-Assembled Reduction-Responsive Sub-5-nm Discrete Subdomains.

PubMed

Cao, Hui; Cui, Zhigang; Gao, Pan; Ding, Yi; Zhu, Xuechao; Lu, Xinhua; Cai, Yuanli

2017-09-01

Easy access to discrete nanoclusters in metal-folded single-chain nanoparticles (metal-SCNPs) and independent ultrafine sudomains in the assemblies via coordination-driven self-assembly of hydrophilic copolymer containing 9% imidazole groups is reported herein. 1 H NMR, dynamic light scattering, and NMR diffusion-ordered spectroscopy results demonstrate self-assembly into metal-SCNPs (>70% imidazole-units folded) by neutralization in the presence of Cu(II) in water to pH 4.6. Further neutralization induces self-assembly of metal-SCNPs (pH 4.6-5.0) and shrinkage (pH 5.0-5.6), with concurrent restraining residual imidazole motifs and hydrophilic segment, which organized into constant nanoparticles over pH 5.6-7.5. Atomic force microscopy results evidence discrete 1.2 nm nanoclusters and sub-5-nm subdomains in metal-SCNP and assembled nanoparticle. Reduction of metal center using sodium ascorbate induces structural rearrangement to one order lower than the precursor. Enzyme mimic catalysis required media-tunable discrete ultrafine interiors in metal-SCNPs and assemblies have hence been achieved. © 2017 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Vapor deposition and characterization of supramolecular assemblies for integrated nonlinear optics

NASA Astrophysics Data System (ADS)

Esembeson, Bweh

Very recently, some organic molecules have been developed that are very compact and have exceptionally high molecular polarizabilities which approach the fundamental quantum limit. Supramolecular assemblies created from such highly nonlinear molecules could find applications in integrated nonlinear optics such as all-optical signal processing, electro-optic modulators and frequency conversion. In this work, we have constructed a versatile vacuum deposition system for the creation of organic thin films from these molecules that can be sublimated without decomposition. We have used deposition temperatures of the order of 100--200°C in a high vacuum of 10-6--10 -7 Torrs. While some molecules showed a tendency to form polycrystalline films, others led to very high optical quality films, with a roughness of less than 10 nm over tens of micrometers and no grains detected down to a size of 2 nm, as seen in Atomic Force and Scanning Electron Microscopy studies. The best material we developed has a linear refractive index of 1.8 +/- 0.1 at 1.5 mum and an off-resonant third order susceptibility, chi (3), measured through Degenerate Four Wave Mixing, of 2 +/- 1 x 10-19 m2V-2 at 1.5 mum, a value three orders of magnitude larger than fused silica. This vapor deposited thin film may represent one of the best materials demonstrated to date whereby a large third order susceptibility, high optical quality, and simplicity of fabrication and integration are in perfect harmony for integrated nonlinear optical applications. We have used this novel organic material to create a hybrid organic/silicon-on-insulator waveguide that showed a record high nonlinearity coefficient of 10 5 W-1m-1 and has been used as an all-optical switch for demultiplexing a 120 Gbit/s data stream to 10 Gbit/s on a 6 mm long device.

Ordered Self-Assembled Monolayers of Peptide Nucleic Acids with DNA Recognition Capability

NASA Astrophysics Data System (ADS)

Briones, C.; Mateo-Marti, E.; Gómez-Navarro, C.; Parro, V.; Román, E.; Martín-Gago, J. A.

2004-11-01

We report on the formation of ordered self-assembled monolayers (SAMs) of single-stranded peptide nucleic acids (ssPNA). In spite of their remarkable length (7nm) thiolated PNAs assemble standing up on gold surfaces similarly to the SAMs of short alkanethiols. SAMs of ssPNA recognize complementary nucleic acids, acting as specific biosensors that discriminate even a point mutation in target ssDNA. These results are obtained by surface characterization techniques that avoid labeling of the target molecule: x-ray photoemission, x-ray absorption and atomic force microscopy.

Structure and dynamics of optically directed self-assembly of nanoparticles

PubMed Central

Roy, Debjit; Mondal, Dipankar; Goswami, Debabrata

2016-01-01

Self-assembly of nanoparticles leading to the formation of colloidal clusters often serves as the representative analogue for understanding molecular assembly. Unravelling the in situ structure and dynamics of such clusters in liquid suspensions is highly challenging. Presently colloidal clusters are first isolated from their generating environment and then their structures are probed by light scattering methods. In order to measure the in situ structure and dynamics of colloidal clusters, we have generated them using the high-repetition-rate femtosecond laser pulse optical tweezer. Since the constituent of our dimer, trimer or tetramer clusters are 250 nm radius two-photon resonant fluorophore coated nanospheres under the optical trap, they inherently produce Two-Photon Fluorescence, which undergo intra-nanosphere Fluorescence Energy Transfer. This unique energy transfer signature, in turn, enables us to visualize structures and orientations of these colloidal clusters during the process of their formation and subsequent dynamics in a liquid suspension. We also show that due to shape-birefringence, orientation and structural control of these colloidal clusters are possible as the polarization of the trapping laser is changed from linear to circular. We thus report important progress in sampling the smallest possible aggregates of nanoparticles, dimers, trimers or tetramers, formed early in the self-assembly process. PMID:27006305

Layer-by-layer self-assembled graphene oxide/silica microsphere composites as stationary phase for high performance liquid chromatography.

PubMed

Liang, Xiaojing; Liu, Shujuan; Song, Xinwang; Zhu, Yangwen; Jiang, Shengxiang

2012-11-21

Graphene oxide (GO) has been layer-by-layer assembled onto silica microspheres to form a GO/SiO(2) composite stationary phase. All the characterizations of GO/SiO(2) by elemental analysis, Raman spectroscopy and Fourier transformed infrared spectrometry confirmed that with the increase of the assembled layer, GO gradually increases on the silica surface. The chromatographic properties of bare SiO(2) and GO/SiO(2) with different GO assembled layers show that the amount of GO plays an important role in the separation of analytes. Only the appropriate amount of GO on SiO(2) can perform a good chromatographic separation. The comparison between chromatographic performances of bare SiO(2) column, GO/SiO(2)-2 column and C18 commercial column clearly show that GO/SiO(2)-2 and C18 columns obtained a better separation; GO/SiO(2)-2 exhibits a large π-electron system and C18 exhibits hydrophobicity. The eluting order, peak width and resolution of analyte on GO/SiO(2)-2 column was highly dependent on the size of its π-electron system, while on the C18 column the decisive factor is its hydrophobic property.

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.

Ordered patterns and structures via interfacial self-assembly: superlattices, honeycomb structures and coffee rings.

PubMed

Ma, Hongmin; Hao, Jingcheng

2011-11-01

Self-assembly is now being intensively studied in chemistry, physics, biology, and materials engineering and has become an important "bottom-up" approach to create intriguing structures for different applications. Self-assembly is not only a practical approach for creating a variety of nanostructures, but also shows great superiority in building hierarchical structures with orders on different length scales. The early work in self-assembly focused on molecular self-assembly in bulk solution, including the resultant dye aggregates, liposomes, vesicles, liquid crystals, gels and so on. Interfacial self-assembly has been a great concern over the last two decades, largely because of the unique and ingenious roles of this method for constructing materials at interfaces, such as self-assembled monolayers, Langmuir-Blodgett films, and capsules. Nanocrystal superlattices, honeycomb films and coffee rings are intriguing structural materials with more complex features and can be prepared by interfacial self-assembly on different length scales. In this critical review, we outline the recent development in the preparation and application of colloidal nanocrystal superlattices, honeycomb-patterned macroporous structures by the breath figure method, and coffee-ring-like patterns (247 references). This journal is © The Royal Society of Chemistry 2011

Synthesis, characterization, and catalytic application of ordered mesoporous carbon–niobium oxide composites

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

Gao, Juan-Li; Gao, Shuang; Liu, Chun-Ling

2014-11-15

Graphical abstract: The ordered mesoporous carbon–niobium oxide composites have been synthesized by a multi-component co-assembly method associated with a carbonization process. - Highlights: • Ordered mesoporous carbon–niobium oxide composites were synthesized. • The content of Nb{sub 2}O{sub 5} in the composites could be tuned from 38 to 75%. • Niobium species were highly dispersed in amorphous carbon framework walls. • The composites exhibited good catalytic performance in the dehydration of fructose. - Abstract: Ordered mesoporous carbon–niobium oxide composites have been synthesized by a multi-component co-assembly method associated with a carbonization process using phenolic resol as carbon source, niobium chloride asmore » precursor and amphiphilic triblock copolymer Pluronic F127 as template. The resulting materials were characterized using a combination of techniques including differential scanning calorimetry–thermogravimetric analysis, N{sub 2} physical adsorption, X-ray diffraction, transmission electron microscopy, and X-ray photoelectron spectroscopy. The results show that with increasing the content of Nb{sub 2}O{sub 5} from 38 to 75% the specific surface area decreases from 306.4 to 124.5 m{sup 2} g{sup −1}, while the ordered mesoporous structure is remained. Niobium species is well dispersed in the amorphous carbon framework. The mesoporous carbon–niobium oxide composites exhibit high catalytic activity in the dehydration of fructose to 5-hydroxymethylfurfural. A 100% conversion of fructose and a 76.5% selectivity of 5-hydroxymethylfurfural were obtained over the carbon–niobium oxide composite containing 75% Nb{sub 2}O{sub 5} under the investigated reaction conditions.« less

Assembly-history dynamics of a pitcher-plant protozoan community in experimental microcosms.

PubMed

Kadowaki, Kohmei; Inouye, Brian D; Miller, Thomas E

2012-01-01

History drives community assembly through differences both in density (density effects) and in the sequence in which species arrive (sequence effects). Density effects arise from predictable population dynamics, which are free of history, but sequence effects are due to a density-free mechanism, arising solely from the order and timing of immigration events. Few studies have determined how components of immigration history (timing, number of individuals, frequency) alter local dynamics to determine community assembly, beyond addressing when immigration history produces historically contingent assembly. We varied density and sequence effects independently in a two-way factorial design to follow community assembly in a three-species aquatic protozoan community. A superior competitor, Colpoda steinii, mediated alternative community states; early arrival or high introduction density allowed this species to outcompete or suppress the other competitors (Poterioochromonas malhamensis and Eimeriidae gen. sp.). Multivariate analysis showed that density effects caused greater variation in community states, whereas sequence effects altered the mean community composition. A significant interaction between density and sequence effects suggests that we should refine our understanding of priority effects. These results highlight a practical need to understand not only the "ingredients" (species) in ecological communities but their "recipes" as well.

Exploring SMBH assembly with semi-analytic modelling

NASA Astrophysics Data System (ADS)

Ricarte, Angelo; Natarajan, Priyamvada

2018-02-01

We develop a semi-analytic model to explore different prescriptions of supermassive black hole (SMBH) fuelling. This model utilizes a merger-triggered burst mode in concert with two possible implementations of a long-lived steady mode for assembling the mass of the black hole in a galactic nucleus. We improve modelling of the galaxy-halo connection in order to more realistically determine the evolution of a halo's velocity dispersion. We use four model variants to explore a suite of observables: the M•-σ relation, mass functions of both the overall and broad-line quasar population, and luminosity functions as a function of redshift. We find that `downsizing' is a natural consequence of our improved velocity dispersion mappings, and that high-mass SMBHs assemble earlier than low-mass SMBHs. The burst mode of fuelling is sufficient to explain the assembly of SMBHs to z = 2, but an additional steady mode is required to both assemble low-mass SMBHs and reproduce the low-redshift luminosity function. We discuss in detail the trade-offs in matching various observables and the interconnected modelling components that govern them. As a result, we demonstrate the utility as well as the limitations of these semi-analytic techniques.

Algorithms and Application of Sparse Matrix Assembly and Equation Solvers for Aeroacoustics

NASA Technical Reports Server (NTRS)

Watson, W. R.; Nguyen, D. T.; Reddy, C. J.; Vatsa, V. N.; Tang, W. H.

2001-01-01

An algorithm for symmetric sparse equation solutions on an unstructured grid is described. Efficient, sequential sparse algorithms for degree-of-freedom reordering, supernodes, symbolic/numerical factorization, and forward backward solution phases are reviewed. Three sparse algorithms for the generation and assembly of symmetric systems of matrix equations are presented. The accuracy and numerical performance of the sequential version of the sparse algorithms are evaluated over the frequency range of interest in a three-dimensional aeroacoustics application. Results show that the solver solutions are accurate using a discretization of 12 points per wavelength. Results also show that the first assembly algorithm is impractical for high-frequency noise calculations. The second and third assembly algorithms have nearly equal performance at low values of source frequencies, but at higher values of source frequencies the third algorithm saves CPU time and RAM. The CPU time and the RAM required by the second and third assembly algorithms are two orders of magnitude smaller than that required by the sparse equation solver. A sequential version of these sparse algorithms can, therefore, be conveniently incorporated into a substructuring for domain decomposition formulation to achieve parallel computation, where different substructures are handles by different parallel processors.

Patterning layer-by-layer self-assembled multilayer by lithography and its applications to thin film devices

NASA Astrophysics Data System (ADS)

Hua, Feng

Nanoparticles are exciting materials because they exhibit unique electronic, catalytic, and optical properties. As a novel and promising nanobuilding block, it attracts considerable research efforts in its integration into a wide variety of thin film devices. Nanoparticles were adsorbed onto the substrate with layer-by-layer self-assembly which becomes of great interest due to its suitability in colloid particle assembly. Without extremely high temperatures and sophisticated equipment, molecularly organized films in an exactly pre-designed order can grow on almost all the substrates in nature. Two approaches generating spatially separated patterns comprised of nanoparticles are demonstrated, as well as two approaches patterning more than one type of nonoparticle on a silicon wafer. The structure of the thin film patterned by these approaches are analyzed and considered suitable to the thin film device. Finally, the combination of lithography and layer-by-layer (lbl) self-assembly is utilized to realize the microelectronic device with functional nonoparticles. The lbl self-assembly is the way to coat the nonoparticles and the lighography to pattern them. Based on the coating and patterning technique, a MOS-capacitor, a MOS field-effect-transistor and magnetic thin film cantilever are fabricated.

Assembling Transgender Moments

ERIC Educational Resources Information Center

Greteman, Adam J.

2017-01-01

In this article, the author seeks to assemble moments--scholarly, popular, and aesthetic--in order to explore the possibilities that emerge as moments collect in education's encounters with the needs, struggles, and possibilities of transgender lives and practices. Assembling moments, the author argues, illustrates the value of "moments"…

Protein cage assembly across multiple length scales.

PubMed

Aumiller, William M; Uchida, Masaki; Douglas, Trevor

2018-05-21

Within the materials science community, proteins with cage-like architectures are being developed as versatile nanoscale platforms for use in protein nanotechnology. Much effort has been focused on the functionalization of protein cages with biological and non-biological moieties to bring about new properties of not only individual protein cages, but collective bulk-scale assemblies of protein cages. In this review, we report on the current understanding of protein cage assembly, both of the cages themselves from individual subunits, and the assembly of the individual protein cages into higher order structures. We start by discussing the key properties of natural protein cages (for example: size, shape and structure) followed by a review of some of the mechanisms of protein cage assembly and the factors that influence it. We then explore the current approaches for functionalizing protein cages, on the interior or exterior surfaces of the capsids. Lastly, we explore the emerging area of higher order assemblies created from individual protein cages and their potential for new and exciting collective properties.

Subtle balance of tropoelastin molecular shape and flexibility regulates dynamics and hierarchical assembly.

PubMed

Yeo, Giselle C; Tarakanova, Anna; Baldock, Clair; Wise, Steven G; Buehler, Markus J; Weiss, Anthony S

2016-02-01

The assembly of the tropoelastin monomer into elastin is vital for conferring elasticity on blood vessels, skin, and lungs. Tropoelastin has dual needs for flexibility and structure in self-assembly. We explore the structure-dynamics-function interplay, consider the duality of molecular order and disorder, and identify equally significant functional contributions by local and global structures. To study these organizational stratifications, we perturb a key hinge region by expressing an exon that is universally spliced out in human tropoelastins. We find a herniated nanostructure with a displaced C terminus and explain by molecular modeling that flexible helices are replaced with substantial β sheets. We see atypical higher-order cross-linking and inefficient assembly into discontinuous, thick elastic fibers. We explain this dysfunction by correlating local and global structural effects with changes in the molecule's assembly dynamics. This work has general implications for our understanding of elastomeric proteins, which balance disordered regions with defined structural modules at multiple scales for functional assembly.

Electrical Switching in Semiconductor-Metal Self-Assembled VO2 Disordered Metamaterial Coatings

PubMed Central

Kumar, Sunil; Maury, Francis; Bahlawane, Naoufal

2016-01-01

As a strongly correlated metal oxide, VO2 inspires several highly technological applications. The challenging reliable wafer-scale synthesis of high quality polycrystalline VO2 coatings is demonstrated on 4” Si taking advantage of the oxidative sintering of chemically vapor deposited VO2 films. This approach results in films with a semiconductor-metal transition (SMT) quality approaching that of the epitaxial counterpart. SMT occurs with an abrupt electrical resistivity change exceeding three orders of magnitude with a narrow hysteresis width. Spatially resolved infrared and Raman analyses evidence the self-assembly of VO2 disordered metamaterial, compresing monoclinic (M1 and M2) and rutile (R) domains, at the transition temperature region. The M2 mediation of the M1-R transition is spatially confined and related to the localized strain-stabilization of the M2 phase. The presence of the M2 phase is supposed to play a role as a minor semiconducting phase far above the SMT temperature. In terms of application, we show that the VO2 disordered self-assembly of M and R phases is highly stable and can be thermally triggered with high precision using short heating or cooling pulses with adjusted strengths. Such a control enables an accurate and tunable thermal control of the electrical switching. PMID:27883052

78 FR 11154 - Large Residential Washers From the Republic of Korea: Countervailing Duty Order

Federal Register 2010, 2011, 2012, 2013, 2014

2013-02-15

... externally mounted steel frame at least six inches high that is designed to house a coin/token operated... ``stacked washer-dryers'' denotes distinct washing and drying machines that are built on a unitary frame and... of steel and is assembled with security fasteners;\\8\\ or \\7\\ ``Payment system electronics'' denotes a...

The novel support structure design of high stability for space borne primary reflector

NASA Astrophysics Data System (ADS)

Yu, Fei; Ding, Lin; Tan, Ting; Pei, Jing-yang.; Zhao, Xue-min; Bai, Shao-jun

2018-01-01

The novel support structure design of high stability for space borne primary mirror is presented. The structure is supported by a ball head support rod, for statically determinate support of reflector. The ball head assembly includes the supporting rod, nesting, bushing and other important parts. The liner bushing of the resistant material is used to fit for ball head approximated with the reflector material, and then the bad impact of thermal mismatch could be minimized to minimum. In order to ensure that the structure of the support will not be damaged, the glue spots for limitation is added around the reflector, for position stability of reflector. Through analysis and calculation, it can be seen that the novel support structure would not transfer the external stresses to the reflector, and the external stresses usually result from thermal mismatch and assembly misalignment. The novel method is useful for solving the problem of the bad influence form thermal stress and assembly force. In this paper, the supporting structure is introduced and analyzed in detail. The simulation results show that the ball head support reflector works more stably.

Patterns in the English language: phonological networks, percolation and assembly models

NASA Astrophysics Data System (ADS)

Stella, Massimo; Brede, Markus

2015-05-01

In this paper we provide a quantitative framework for the study of phonological networks (PNs) for the English language by carrying out principled comparisons to null models, either based on site percolation, randomization techniques, or network growth models. In contrast to previous work, we mainly focus on null models that reproduce lower order characteristics of the empirical data. We find that artificial networks matching connectivity properties of the English PN are exceedingly rare: this leads to the hypothesis that the word repertoire might have been assembled over time by preferentially introducing new words which are small modifications of old words. Our null models are able to explain the ‘power-law-like’ part of the degree distributions and generally retrieve qualitative features of the PN such as high clustering, high assortativity coefficient and small-world characteristics. However, the detailed comparison to expectations from null models also points out significant differences, suggesting the presence of additional constraints in word assembly. Key constraints we identify are the avoidance of large degrees, the avoidance of triadic closure and the avoidance of large non-percolating clusters.

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.

The self-assembled behavior of DNA bases on the interface.

PubMed

Liu, Lei; Xia, Dan; Klausen, Lasse H; Dong, Mingdong

2014-01-27

A successful example of self-assembly in a biological system is that DNA can be an excellent agent to self-assemble into desirable two and three-dimensional nanostructures in a well-ordered manner by specific hydrogen bonding interactions between the DNA bases. The self-assembly of DNA bases have played a significant role in constructing the hierarchical nanostructures. In this review article we will introduce the study of nucleic acid base self-assembly by scanning tunneling microscopy (STM) at vacuum and ambient condition (the liquid/solid interface), respectively. From the ideal condition to a more realistic environment, the self-assembled behaviors of DNA bases are introduced. In a vacuum system, the energetic advantages will dominate the assembly formation of DNA bases, while at ambient condition, more factors such as conformational freedom and the biochemical environment will be considered. Therefore, the assemblies of DNA bases at ambient condition are different from the ones obtained under vacuum. We present the ordered nanostructures formed by DNA bases at both vacuum and ambient condition. To construct and tailor the nanostructure through the interaction between DNA bases, it is important to understand the assembly behavior and features of DNA bases and their derivatives at ambient condition. The utilization of STM offers the advantage of investigating DNA base self-assembly with sub-molecular level resolution at the surface.

The Self-Assembled Behavior of DNA Bases on the Interface

PubMed Central

Liu, Lei; Xia, Dan; Klausen, Lasse H.; Dong, Mingdong

2014-01-01

A successful example of self-assembly in a biological system is that DNA can be an excellent agent to self-assemble into desirable two and three-dimensional nanostructures in a well-ordered manner by specific hydrogen bonding interactions between the DNA bases. The self-assembly of DNA bases have played a significant role in constructing the hierarchical nanostructures. In this review article we will introduce the study of nucleic acid base self-assembly by scanning tunneling microscopy (STM) at vacuum and ambient condition (the liquid/solid interface), respectively. From the ideal condition to a more realistic environment, the self-assembled behaviors of DNA bases are introduced. In a vacuum system, the energetic advantages will dominate the assembly formation of DNA bases, while at ambient condition, more factors such as conformational freedom and the biochemical environment will be considered. Therefore, the assemblies of DNA bases at ambient condition are different from the ones obtained under vacuum. We present the ordered nanostructures formed by DNA bases at both vacuum and ambient condition. To construct and tailor the nanostructure through the interaction between DNA bases, it is important to understand the assembly behavior and features of DNA bases and their derivatives at ambient condition. The utilization of STM offers the advantage of investigating DNA base self-assembly with sub-molecular level resolution at the surface. PMID:24473140

Ordered mesoporous MFe(2)O(4) (M = Co, Cu, Mg, Ni, Zn) thin films with nanocrystalline walls, uniform 16 nm diameter pores and high thermal stability: template-directed synthesis and characterization of redox active trevorite.

PubMed

Haetge, Jan; Suchomski, Christian; Brezesinski, Torsten

2010-12-20

In this paper, we report on ordered mesoporous NiFe(2)O(4) thin films synthesized via co-assembly of hydrated ferric nitrate and nickel chloride with an amphiphilic diblock copolymer, referred to as KLE. We establish that the NiFe(2)O(4) samples are highly crystalline after calcination at 600 °C, and that the conversion of the amorphous inorganic framework comes at little cost to the ordering of the high quality cubic network of pores averaging 16 nm in diameter. We further show that the synthesis method employed in this work can be readily extended to other ferrites, such as CoFe(2)O(4), CuFe(2)O(4), MgFe(2)O(4), and ZnFe(2)O(4), which could pave the way for innovative device design. While this article focuses on the self-assembly and characterization of these materials using various state-of-the-art techniques, including electron microscopy, grazing incidence small-angle X-ray scattering (GISAXS), time-of-flight secondary ion mass spectrometry (TOF-SIMS), X-ray photoelectron spectroscopy (XPS), as well as UV-vis and Raman spectroscopy, we also examine the electrochemical properties and show the benefits of combining a continuous mesoporosity with nanocrystalline films. KLE-templated NiFe(2)O(4) electrodes exhibit reasonable levels of lithium ion storage at short charging times which stem from facile pseudocapacitance.

Virus templated plasmonic nanoclusters with icosahedral symmetry via directed assembly

NASA Astrophysics Data System (ADS)

Ratna, Banahalli; Fontana, Jake; Dressick, Walter; Phelps, Jamie; Johnson, John; Sampson, Travian; Rendell, Ronald; Soto, Carissa

2015-03-01

Controlling the spatial and orientational order of plasmonic nanoparticles may lead to structures with novel electromagnetic properties and applications such as sub-wavelength imaging and ultra-sensitive chemical sensors. Here we report the directed assembly of three-dimensional, icosahedral plasmonic nanoclusters with resonances at visible wavelengths. We show using transmission electron microcopy and in situ dynamic light scattering the nanoclusters consist of twelve gold nanospheres attached to thiol groups at predefined locations on the surface of a genetically engineered cowpea mosaic virus with icosahedral symmetry. We measured the bulk absorbance from aqueous suspensions of nanoclusters and reproduced the major features of the spectrum using finite-element simulations. Furthermore, because the viruses are easily produced in gram quantities the directed assembly approach is capable of high-throughput, providing a strategy to realize large quantities for applications. NRL summer intern under the HBCU/MI Summer Research Program.

Improving Fire Resistance of Cotton Fabric through Layer-by-Layer Assembled Graphene Multilayer Nanocoating

NASA Astrophysics Data System (ADS)

Jang, Wonjun; Chung, Il Jun; Kim, Junwoo; Seo, Seongmin; Park, Yong Tae; Choi, Kyungwho

2018-05-01

In this study, thin films containing poly(vinyl alcohol) (PVA) and graphene nanoplatelets (GNPs), stabilized with poly(4-styrene-sulfonic acid) (PSS), were assembled by a simple and cost-effective layer-by-layer (LbL) technique in order to introduce the anti-flammability to cotton. These antiflammable layers were characterized by using UV-vis spectrometry and quartz crystal microbalance as a function of the number of bilayers deposited. Scanning electron microscopy was used to visualize the morphology of the thin film coatings on the cotton fabric. The graphene-polymer thin films introduced anti-flammable properties through thermally stable carbonaceous layers at a high temperature. The thermal stability and flame retardant property of graphene-coated cotton was demonstrated by thermogravimetric analysis, cone calorimetry, and vertical flame test. The results indicate that LbL-assembled graphene-polymer thin films can be applied largely in the field of flame retardant.

Integrating DNA strand displacement circuitry to the nonlinear hybridization chain reaction.

PubMed

Zhang, Zhuo; Fan, Tsz Wing; Hsing, I-Ming

2017-02-23

Programmable and modular attributes of DNA molecules allow one to develop versatile sensing platforms that can be operated isothermally and enzyme-free. In this work, we present an approach to integrate upstream DNA strand displacement circuits that can be turned on by a sequence-specific microRNA analyte with a downstream nonlinear hybridization chain reaction for a cascading hyperbranched nucleic acid assembly. This system provides a two-step amplification strategy for highly sensitive detection of the miRNA analyte, conducive for multiplexed detection. Multiple miRNA analytes were tested with our integrated circuitry using the same downstream signal amplification setting, showing the decoupling of nonlinear self-assembly with the analyte sequence. Compared with the reported methods, our signal amplification approach provides an additional control module for higher-order DNA self-assembly and could be developed into a promising platform for the detection of critical nucleic-acid based biomarkers.

Directed block copolymer self-assembly implemented via surface-embedded electrets

NASA Astrophysics Data System (ADS)

Wu, Mei-Ling; Wang, Dong; Wan, Li-Jun

2016-02-01

Block copolymer (BCP) nanolithography is widely recognized as a promising complementary approach to circumvent the feature size limits of conventional photolithography. The directed self-assembly of BCP thin film to form ordered nanostructures with controlled orientation and localized pattern has been the key challenge for practical nanolithography applications. Here we show that BCP nanopatterns can be directed on localized surface electrets defined by electron-beam irradiation to realize diverse features in a simple, effective and non-destructive manner. Charged electrets can generate a built-in electric field in BCP thin film and induce the formation of perpendicularly oriented microdomain of BCP film. The electret-directed orientation control of BCP film can be either integrated with mask-based patterning technique or realized by electron-beam direct-writing method to fabricate microscale arbitrary lateral patterns down to single BCP cylinder nanopattern. The electret-directed BCP self-assembly could provide an alternative means for BCP-based nanolithography, with high resolution.

Graphene chiral liquid crystals and macroscopic assembled fibres

PubMed Central

Xu, Zhen; Gao, Chao

2011-01-01

Chirality and liquid crystals are both widely expressed in nature and biology. Helical assembly of mesophasic molecules and colloids may produce intriguing chiral liquid crystals. To date, chiral liquid crystals of 2D colloids have not been explored. As a typical 2D colloid, graphene is now receiving unprecedented attention. However, making macroscopic graphene fibres is hindered by the poor dispersibility of graphene and by the lack of an assembly method. Here we report that soluble, chemically oxidized graphene or graphene oxide sheets can form chiral liquid crystals in a twist-grain-boundary phase-like model with simultaneous lamellar ordering and long-range helical frustrations. Aqueous graphene oxide liquid crystals were continuously spun into metres of macroscopic graphene oxide fibres; subsequent chemical reduction gave the first macroscopic neat graphene fibres with high conductivity and good mechanical performance. The flexible, strong graphene fibres were knitted into designed patterns and into directionally conductive textiles. PMID:22146390

Engineering the entropy-driven free-energy landscape of a dynamic nanoporous protein assembly.

PubMed

Alberstein, Robert; Suzuki, Yuta; Paesani, Francesco; Tezcan, F Akif

2018-04-30

De novo design and construction of stimuli-responsive protein assemblies that predictably switch between discrete conformational states remains an essential but highly challenging goal in biomolecular design. We previously reported synthetic, two-dimensional protein lattices self-assembled via disulfide bonding interactions, which endows them with a unique capacity to undergo coherent conformational changes without losing crystalline order. Here, we carried out all-atom molecular dynamics simulations to map the free-energy landscape of these lattices, validated this landscape through extensive structural characterization by electron microscopy and established that it is predominantly governed by solvent reorganization entropy. Subsequent redesign of the protein surface with conditionally repulsive electrostatic interactions enabled us to predictably perturb the free-energy landscape and obtain a new protein lattice whose conformational dynamics can be chemically and mechanically toggled between three different states with varying porosities and molecular densities.

Insights into cellulosome assembly and dynamics: from dissection to reconstruction of the supramolecular enzyme complex.

PubMed

Smith, Steven P; Bayer, Edward A

2013-10-01

Cellulosomes are multi-enzyme complexes produced by anaerobic bacteria for the efficient deconstruction of plant cell wall polysaccharides. The assembly of enzymatic subunits onto a central non-catalytic scaffoldin subunit is mediated by a highly specific interaction between the enzyme-bearing dockerin modules and the resident cohesin modules of the scaffoldin, which affords their catalytic activities to work synergistically. The scaffoldin also imparts substrate-binding and bacterial-anchoring properties, the latter of which involves a second cohesin-dockerin interaction. Recent structure-function studies reveal an ever-growing array of unique and increasingly complex cohesin-dockerin complexes and cellulosomal enzymes with novel activities. A 'build' approach involving multimodular cellulosomal segments has provided a structural model of an organized yet conformationally dynamic supramolecular assembly with the potential to form higher order structures. Copyright © 2013. Published by Elsevier Ltd.

Assembly of the Human Signal Recognition Particle

NASA Astrophysics Data System (ADS)

Menichelli, Elena; Nagai, Kiyoshi

Large RNA-protein complexes (ribonucleoprotein particles or RNPs) control fundamental biological processes. Their correct assembly is essential for function and occurs by the ordered addition of proteins to the RNA. A good model system for studying RNP assembly is provided by the Signal Recognition Particle (SRP), an RNP conserved from bacteria to humans, with different degrees of complexity. Human SRP, composed of a single RNA molecule and six pro teins, is responsible for the co-translational targeting of secretory and membrane proteins to the endoplasmic reticulum membrane. In vitro studies reveal that the SRP proteins need to be added to the RNA sequentially. If the order of addition is altered, non-native particles are formed. The sequential association of proteins causes conformational changes in the RNA, allowing binding of other proteins. The in vivo assembly is regulated by the translocation of precursors between different cellular compartments. In this chapter we review the current understanding of the human SRP assembly mechanism.

High-definition polymeric membranes: construction of 3D lithographed channel arrays through control of natural building blocks dynamics.

PubMed

Speranza, Valentina; Trotta, Francesco; Drioli, Enrico; Gugliuzza, Annarosa

2010-02-01

The fabrication of well-defined interfaces is in high demand in many fields of biotechnologies. Here, high-definition membrane-like arrays are developed through the self-assembly of water droplets, which work as natural building blocks for the construction of ordered channels. Solution viscosity together with the dynamics of the water droplets can decide the final formation of three-dimensional well-ordered patterns resembling anodic structures, especially because solvents denser than water are used. Particularly, the polymer solution viscosity is demonstrated to be a powerful tool for control of the mobility of submerged droplets during the microfabrication process. The polymeric patterns are structured at very high levels of organization and exhibit well-established transport-surface property relationships, considered basics for any types of advanced biotechnologies.

Hybrid reduced order modeling for assembly calculations

DOE PAGES

Bang, Youngsuk; Abdel-Khalik, Hany S.; Jessee, Matthew A.; ...

2015-08-14

While the accuracy of assembly calculations has greatly improved due to the increase in computer power enabling more refined description of the phase space and use of more sophisticated numerical algorithms, the computational cost continues to increase which limits the full utilization of their effectiveness for routine engineering analysis. Reduced order modeling is a mathematical vehicle that scales down the dimensionality of large-scale numerical problems to enable their repeated executions on small computing environment, often available to end users. This is done by capturing the most dominant underlying relationships between the model's inputs and outputs. Previous works demonstrated the usemore » of the reduced order modeling for a single physics code, such as a radiation transport calculation. This paper extends those works to coupled code systems as currently employed in assembly calculations. Finally, numerical tests are conducted using realistic SCALE assembly models with resonance self-shielding, neutron transport, and nuclides transmutation/depletion models representing the components of the coupled code system.« less

Pre-transition effects mediate forces of assembly between transmembrane proteins

DOE PAGES

Katira, Shachi; Mandadapu, Kranthi K.; Vaikuntanathan, Suriyanarayanan; ...

2016-02-24

We present a mechanism for a generic, powerful force of assembly and mobility for transmembrane proteins in lipid bilayers. This force is a pre-transition (or pre-melting) effect for the first-order transition between ordered and disordered phases in the membrane. Using large-scale molecular simulation, we show that a protein with hydrophobic thickness equal to that of the disordered phase embedded in an ordered bilayer stabilizes a microscopic order–disorder interface. The stiffness of that interface is finite. When two such proteins approach each other, they assemble because assembly reduces the net interfacial energy. Analogous to the hydrophobic effect, we refer to thismore » phenomenon as the 'orderphobic effect'. The effect is mediated by proximity to the order–disorder phase transition and the size and hydrophobic mismatch of the protein. The strength and range of forces arising from this effect are significantly larger than those that could arise from membrane elasticity for the membranes considered.« less

Pre-transition effects mediate forces of assembly between transmembrane proteins

PubMed Central

Katira, Shachi; Mandadapu, Kranthi K; Vaikuntanathan, Suriyanarayanan; Smit, Berend; Chandler, David

2016-01-01

We present a mechanism for a generic, powerful force of assembly and mobility for transmembrane proteins in lipid bilayers. This force is a pre-transition (or pre-melting) effect for the first-order transition between ordered and disordered phases in the membrane. Using large-scale molecular simulation, we show that a protein with hydrophobic thickness equal to that of the disordered phase embedded in an ordered bilayer stabilizes a microscopic order–disorder interface. The stiffness of that interface is finite. When two such proteins approach each other, they assemble because assembly reduces the net interfacial energy. Analogous to the hydrophobic effect, we refer to this phenomenon as the 'orderphobic effect'. The effect is mediated by proximity to the order–disorder phase transition and the size and hydrophobic mismatch of the protein. The strength and range of forces arising from this effect are significantly larger than those that could arise from membrane elasticity for the membranes considered. DOI: http://dx.doi.org/10.7554/eLife.13150.001 PMID:26910009

Self-assembly of polyhedral metal-organic framework particles into three-dimensional ordered superstructures

NASA Astrophysics Data System (ADS)

Avci, Civan; Imaz, Inhar; Carné-Sánchez, Arnau; Pariente, Jose Angel; Tasios, Nikos; Pérez-Carvajal, Javier; Alonso, Maria Isabel; Blanco, Alvaro; Dijkstra, Marjolein; López, Cefe; Maspoch, Daniel

2018-01-01

Self-assembly of particles into long-range, three-dimensional, ordered superstructures is crucial for the design of a variety of materials, including plasmonic sensing materials, energy or gas storage systems, catalysts and photonic crystals. Here, we have combined experimental and simulation data to show that truncated rhombic dodecahedral particles of the metal-organic framework (MOF) ZIF-8 can self-assemble into millimetre-sized superstructures with an underlying three-dimensional rhombohedral lattice that behave as photonic crystals. Those superstructures feature a photonic bandgap that can be tuned by controlling the size of the ZIF-8 particles and is also responsive to the adsorption of guest substances in the micropores of the ZIF-8 particles. In addition, superstructures with different lattices can also be assembled by tuning the truncation of ZIF-8 particles, or by using octahedral UiO-66 MOF particles instead. These well-ordered, sub-micrometre-sized superstructures might ultimately facilitate the design of three-dimensional photonic materials for applications in sensing.

Pre-transition effects mediate forces of assembly between transmembrane proteins

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

Katira, Shachi; Mandadapu, Kranthi K.; Vaikuntanathan, Suriyanarayanan

We present a mechanism for a generic, powerful force of assembly and mobility for transmembrane proteins in lipid bilayers. This force is a pre-transition (or pre-melting) effect for the first-order transition between ordered and disordered phases in the membrane. Using large-scale molecular simulation, we show that a protein with hydrophobic thickness equal to that of the disordered phase embedded in an ordered bilayer stabilizes a microscopic order–disorder interface. The stiffness of that interface is finite. When two such proteins approach each other, they assemble because assembly reduces the net interfacial energy. Analogous to the hydrophobic effect, we refer to thismore » phenomenon as the 'orderphobic effect'. The effect is mediated by proximity to the order–disorder phase transition and the size and hydrophobic mismatch of the protein. The strength and range of forces arising from this effect are significantly larger than those that could arise from membrane elasticity for the membranes considered.« less

Integrated starting and running amalgam assembly for an electrodeless fluorescent lamp

DOEpatents

Borowiec, Joseph Christopher; Cocoma, John Paul; Roberts, Victor David

1998-01-01

An integrated starting and running amalgam assembly for an electrodeless SEF fluorescent lamp includes a wire mesh amalgam support constructed to jointly optimize positions of a starting amalgam and a running amalgam in the lamp, thereby optimizing mercury vapor pressure in the lamp during both starting and steady-state operation in order to rapidly achieve and maintain high light output. The wire mesh amalgam support is constructed to support the starting amalgam toward one end thereof and the running amalgam toward the other end thereof, and the wire mesh is rolled for friction-fitting within the exhaust tube of the lamp. The positions of the starting and running amalgams on the wire mesh are jointly optimized such that high light output is achieved quickly and maintained, while avoiding any significant reduction in light output between starting and running operation.

19 CFR 351.225 - Scope rulings.

Code of Federal Regulations, 2011 CFR

2011-04-01

... order or suspended investigation. (b) Self-initiation. If the Secretary determines from available... to merchandise completed or assembled in the United States (other than minor completion or assembly... components referred to in section 781(a)(1)(B) of the Act that are used in the completion or assembly of the...

"Assembling" the Ideal Learner: The School Assembly as Regulatory Ritual

ERIC Educational Resources Information Center

Silbert, Patti; Jacklin, Heather

2015-01-01

"School assemblies" are rituals that celebrate and mark the school community. They carry messages of allegiance and belonging that are disseminated both verbally and nonverbally. Although verbal messages are explicitly stated, nonverbal messages are conveyed through subjection to habits, rules, and orders (Foucault 1977) and are…

Student Learning about Biomolecular Self-Assembly Using Two Different External Representations

ERIC Educational Resources Information Center

Host, Gunnar E.; Larsson, Caroline; Olson, Arthur; Tibell, Lena A. E.

2013-01-01

Self-assembly is the fundamental but counterintuitive principle that explains how ordered biomolecular complexes form spontaneously in the cell. This study investigated the impact of using two external representations of virus self-assembly, an interactive tangible three-dimensional model and a static two-dimensional image, on student learning…

Hierarchical TiN nanoparticles-assembled nanopillars for flexible supercapacitors with high volumetric capacitance.

PubMed

Qin, Ping; Li, Xingxing; Gao, Biao; Fu, Jijiang; Xia, Lu; Zhang, Xuming; Huo, Kaifu; Shen, Wenli; Chu, Paul K

2018-05-10

Titanium nitride (TiN) is an attractive electrode material in fast charging/discharging supercapacitors because of its excellent conductivity. However, the low capacitance and mechanical brittleness of TiN restricts its further application in flexible supercapacitors with high energy density. Thus, it is still a challenge to rationally design TiN electrodes with both high electrochemical and mechanical properties. Herein, the hierarchical TiN nanoparticles-assembled nanopillars (H-TiN NPs) array as binder free electrodes were obtained by nitriding of hierarchical titanium dioxide (TiO2) nanopillars, which was produced by a simple hydrothermal treatment of anodic TiO2 nanotubes (NTs) array in water. The porous TiN nanoparticles connected to each other to form ordered nanopillar arrays, effectively providing larger specific surface area and more active sites for charge storage. The H-TiN NPs delivered a high volumetric capacitance of 120 F cm-3 at 0.83 A cm-3, which is better than that of TiN NTs arrays (69 F cm-3 at 0.83 A cm-3). After assembling into all-solid-state devices, the H-TiN NPs based supercapacitors exhibited outstanding volumetric capacitance of 5.9 F cm-3 at 0.02 A cm-3 and a high energy density of 0.53 mW h cm-3. Our results reveal a new strategy to optimize the supercapacitive performance of metal nitrides.

SXI prototype mirror mount

NASA Technical Reports Server (NTRS)

1995-01-01

The purpose of this contract was to provide optomechanical engineering and fabrication support to the Solar X-ray Imager (SXI) program in the areas of mirror, optical bench and camera assemblies of the telescope. The Center for Applied Optics (CAO) worked closely with the Optics and S&E technical staff of MSFC to develop and investigate the most viable and economical options for the design and fabrication of a number of parts for the various telescope assemblies. All the tasks under this delivery order have been successfully completed within budget and schedule. A number of development hardware parts have been designed and fabricated jointly by MSFC and UAH for the engineering model of SXI. The major parts include a nickel electroformed mirror and a mirror mount, plating and coating of the ceramic spacers, and gold plating of the contact rings and fingers for the camera assembly. An aluminum model of the high accuracy sun sensor (HASS) was also designed and fabricated. A number of fiber optic tapers for the camera assembly were also coated with indium tin oxide and phosphor for testing and evaluation by MSFC. A large number of the SXI optical bench parts were also redesigned and simplified for a prototype telescope. These parts include the forward and rear support flanges, front aperture plate, the graphite epoxy optical bench and a test fixture for the prototype telescope. More than fifty (50) drawings were generated for various components of the prototype telescope. Some of these parts were subsequently fabricated at UAH machine shop or at MSFC or by the outside contractors. UAH also provide technical support to MSFC staff for a number of preliminary and critical design reviews. These design reviews included PDR and CDR for the mirror assembly by United Technologies Optical Systems (UTOS), and the program quarterly reviews, and SXI PDR and CDR. UAH staff also regularly attended the monthly status reviews, and made a significant number of suggestions to improve the design, assembly and alignment of the telescope. Finally, a high level assembly and alignment plan for the entire telescope was prepared by UAH. This plan addresses the sequence of assembly, the required assembly and alignment tolerances, and the methods to verify the alignment at each step during the assembly process. This assembly and alignment plan will be used to assemble and integrate the engineering model (EM) of the telescope. Later on, based on this plan more detailed assembly and alignment procedures will be developed for the lower-level assemblies of SXI.

Automated assembly of fast-axis collimation (FAC) lenses for diode laser bar modules

NASA Astrophysics Data System (ADS)

Miesner, Jörn; Timmermann, Andre; Meinschien, Jens; Neumann, Bernhard; Wright, Steve; Tekin, Tolga; Schröder, Henning; Westphalen, Thomas; Frischkorn, Felix

2009-02-01

Laser diodes and diode laser bars are key components in high power semiconductor lasers and solid state laser systems. During manufacture, the assembly of the fast axis collimation (FAC) lens is a crucial step. The goal of our activities is to design an automated assembly system for high volume production. In this paper the results of an intermediate milestone will be reported: a demonstration system was designed, realized and tested to prove the feasibility of all of the system components and process features. The demonstration system consists of a high precision handling system, metrology for process feedback, a powerful digital image processing system and tooling for glue dispensing, UV curing and laser operation. The system components as well as their interaction with each other were tested in an experimental system in order to glean design knowledge for the fully automated assembly system. The adjustment of the FAC lens is performed by a series of predefined steps monitored by two cameras concurrently imaging the far field and the near field intensity distributions. Feedback from these cameras processed by a powerful and efficient image processing algorithm control a five axis precision motion system to optimize the fast axis collimation of the laser beam. Automated cementing of the FAC to the diode bar completes the process. The presentation will show the system concept, the algorithm of the adjustment as well as experimental results. A critical discussion of the results will close the talk.

Indirect Measurement of Rotor Dynamic Imbalance for Control Moment Gyroscopes via Gimbal Disturbance Observer.

PubMed

Huang, Liya; Wu, Zhong; Wang, Kan

2018-06-07

The high-precision speed control of gimbal servo systems is the key to generating high-precision torque for control moment gyroscopes (CMGs) in spacecrafts. However, the control performance of gimbal servo systems may be degraded significantly by disturbances, especially a dynamic imbalance disturbance with the same frequency as the high-speed rotor. For assembled CMGs, it is very difficult to measure the rotor imbalance directly by using a dynamic balancing machine. In this paper, a gimbal disturbance observer is proposed to estimate the dynamic imbalance of the rotor assembled in the CMG. First, a third-order dynamical system is established to describe the disturbance dynamics of the gimbal servo system, in which the rotor dynamic imbalance torque along the gimbal axis and the other disturbances are modeled to be periodic and bounded, respectively. Then, the gimbal disturbance observer is designed for the third-order dynamical system by using the total disturbance as a virtual measurement. Since the virtual measurement is derived from the inverse dynamics of the gimbal servo system, the information of the rotor dynamic imbalance can be obtained indirectly only using the measurements of gimbal speed and three-phase currents. Semi-physical experimental results demonstrate the effectiveness of the observer by using a CMG simulator.

Microintaglio Printing for Soft Lithography-Based in Situ Microarrays

PubMed Central

Biyani, Manish; Ichiki, Takanori

2015-01-01

Advances in lithographic approaches to fabricating bio-microarrays have been extensively explored over the last two decades. However, the need for pattern flexibility, a high density, a high resolution, affordability and on-demand fabrication is promoting the development of unconventional routes for microarray fabrication. This review highlights the development and uses of a new molecular lithography approach, called “microintaglio printing technology”, for large-scale bio-microarray fabrication using a microreactor array (µRA)-based chip consisting of uniformly-arranged, femtoliter-size µRA molds. In this method, a single-molecule-amplified DNA microarray pattern is self-assembled onto a µRA mold and subsequently converted into a messenger RNA or protein microarray pattern by simultaneously producing and transferring (immobilizing) a messenger RNA or a protein from a µRA mold to a glass surface. Microintaglio printing allows the self-assembly and patterning of in situ-synthesized biomolecules into high-density (kilo-giga-density), ordered arrays on a chip surface with µm-order precision. This holistic aim, which is difficult to achieve using conventional printing and microarray approaches, is expected to revolutionize and reshape proteomics. This review is not written comprehensively, but rather substantively, highlighting the versatility of microintaglio printing for developing a prerequisite platform for microarray technology for the postgenomic era. PMID:27600226

Self-assembled ordered carbon-nanotube arrays and membranes.

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

Overmyer, Donald L.; Siegal, Michael P.; Yelton, William Graham

2004-11-01

Imagine free-standing flexible membranes with highly-aligned arrays of carbon nanotubes (CNTs) running through their thickness. Perhaps with both ends of the CNTs open for highly controlled nanofiltration? Or CNTs at heights uniformly above a polymer membrane for a flexible array of nanoelectrodes or field-emitters? How about CNT films with incredible amounts of accessible surface area for analyte adsorption? These self-assembled crystalline nanotubes consist of multiple layers of graphene sheets rolled into concentric cylinders. Tube diameters (3-300 nm), inner-bore diameters (2-15 nm), and lengths (nanometers - microns) are controlled to tailor physical, mechanical, and chemical properties. We proposed to explore growthmore » and characterize nanotube arrays to help determine their exciting functionality for Sandia applications. Thermal chemical vapor deposition growth in a furnace nucleates from a metal catalyst. Ordered arrays grow using templates from self-assembled hexagonal arrays of nanopores in anodized-aluminum oxide. Polymeric-binders can mechanically hold the CNTs in place for polishing, lift-off, and membrane formation. The stiffness, electrical and thermal conductivities of CNTs make them ideally suited for a wide-variety of possible applications. Large-area, highly-accessible gas-adsorbing carbon surfaces, superb cold-cathode field-emission, and unique nanoscale geometries can lead to advanced microsensors using analyte adsorption, arrays of functionalized nanoelectrodes for enhanced electrochemical detection of biological/explosive compounds, or mass-ionizers for gas-phase detection. Materials studies involving membrane formation may lead to exciting breakthroughs in nanofiltration/nanochromatography for the separation of chemical and biological agents. With controlled nanofilter sizes, ultrafiltration will be viable to separate and preconcentrate viruses and many strains of bacteria for 'down-stream' analysis.« less

Self-ordering of InAs nanostructures on (631)A/B GaAs substrates

NASA Astrophysics Data System (ADS)

Eugenio-López, Eric; Alejandro Mercado-Ornelas, Christian; Kisan Patil, Pallavi; Cortes-Mestizo, Irving Eduardo; Ángel Espinoza-Figueroa, José; Gorbatchev, Andrei Yu; Shimomura, Satoshi; Ithsmel Espinosa-Vega, Leticia; Méndez-García, Víctor Hugo

2018-02-01

The high order self-organization of quantum dots is demonstrated in the growth of InAs on a GaAs(631)-oriented crystallographic plane. The unidimensional ordering of the quantum dots (QDs) strongly depends on the As flux beam equivalent pressure (P As) and the cation/anion terminated surface, i.e., A- or B-type GaAs(631). The self-organization of QDs occurs for both surface types along [\\bar{1}13], while the QD shape and size distribution were found to be different for the self-assembly on the A- and B-type surfaces. In addition, the experiments showed that any misorientation from the (631) plane, which results from the buffer layer waviness, does not allow a high order of unidimensional arrangements of QDs. The optical properties were studied by photoluminescence spectroscopy, where good correspondence was obtained between the energy transitions and the size of the QDs.

Master dye laser oscillator including a specific grating assembly for use therein

DOEpatents

Davin, James M.

1992-01-01

A dye laser oscillator for producing a tuned dye beam is disclosed herein and includes, among other components, a beam output coupling assembly, a dye cell assembly, a beam expander assembly, an etalon assembly, and a grating assembly. Each of three assemblies is vertically supported from a horizontal base so as to be readily removable from the base without interference from or interfering with the other assemblies. The particular grating assembly disclosed is specifically designed for proper optical alignment with the intended path of the dye beam to be produced and for accurate pivotal movement relative to the beam path in order to function as a coarse tuning mechanism in the production of the ultimately tuned beam.

Master dye laser oscillator including a specific grating assembly for use therein

DOEpatents

Davin, J.M.

1992-09-01

A dye laser oscillator for producing a tuned dye beam is disclosed herein and includes, among other components, a beam output coupling assembly, a dye cell assembly, a beam expander assembly, an etalon assembly, and a grating assembly. Each of three assemblies is vertically supported from a horizontal base so as to be readily removable from the base without interference from or interfering with the other assemblies. The particular grating assembly disclosed is specifically designed for proper optical alignment with the intended path of the dye beam to be produced and for accurate pivotal movement relative to the beam path in order to function as a coarse tuning mechanism in the production of the ultimately tuned beam. 5 figs.

Hierarchical assembly strategy and multiscale structural origin of exceptional mechanical performance in nacre

NASA Astrophysics Data System (ADS)

Huang, Zaiwang

Nacre (mother of pearl) is a self-assembled hierarchical nanocomposite in possession of exquisite multiscale architecture and exceptional mechanical properties. Previous work has shown that the highly-ordered brick-mortar-like structure in nacre is assembled via epitaxial growth and the aragonite platelets are pure single-crystals. Our results challenge this conclusion and propose that nacre's individual aragonite platelets are constructed with highly-aligned aragonite nanoparticles mediated by screw dislocation and amorphous aggregation. The underlying physics mechanism why the aragonite nanoparticles choose highly-oriented attachment as its crystallization pathway is rationalized in terms of thermodynamics. The aragonite nanoparticle order-disorder transformation can be triggered by high temperature and mechanical deformation, which in turn confirms that the aragonite nanoparticles are basic building blocks for aragonite platelets. Particularly fascinating is the fracture toughness enhancement of nacre through exquisitely collecting mechanically inferior calcium carbonate (CaCO3) and biomolecules. The sandwich-like microarchitecture with a geometrically staggered arrangement can induce crack deflection along its biopolymer interface, thus significantly enhancing nacre's fracture toughness. Our new findings ambiguously demonstrate that, aside from crack deflection, the advancing crack can invade aragonite platelet, leaving a zigzag crack propagation pathway. These unexpected experimental observations disclose, for the first time, the inevitable structural role of aragonite platelets in enhancing nacre's fracture toughness. Simultaneously, the findings that the crack propagates in a zigzag manner within individual aragonite platelets overturn the previously well-established wisdom that considers aragonite platelets as brittle single-crystals. Moreover, we investigated the dynamical mechanical response of nacre under unixial compression. Our results show that the high strain rate sensitivity reaching ˜0.1 can be directly related to the localized plastic activation volume. Nacre's hierarchical energy-dissipation mechanism under dynamic compression loading comes from a mechanical optimization derived from its inherently multiscale functional structure design.

System Design and Implementation of the Detector Assembly of the Astro-H Soft X-Ray Spectrometer

NASA Technical Reports Server (NTRS)

Chiao, M. P.; Adams, J.; Goodwin, P.; Hobson, C.W.; Kelley, R. L.; Kilbourne, C. A.; McCammom, D.; McGuinness, D. S.; Moseley, S. J.; Porter, F. S.;

Periodically microstructured composite films made by electric- and magnetic-directed colloidal assembly

PubMed Central

Demirörs, Ahmet Faik; Courty, Diana; Libanori, Rafael; Studart, André R.

2016-01-01

Living organisms often combine soft and hard anisotropic building blocks to fabricate composite materials with complex microstructures and outstanding mechanical properties. An optimum design and assembly of the anisotropic components reinforces the material in specific directions and sites to best accommodate multidirectional external loads. Here, we fabricate composite films with periodic modulation of the soft–hard microstructure by simultaneously using electric and magnetic fields. We exploit forefront directed-assembly approaches to realize highly demanded material microstructural designs and showcase a unique example of how one can bridge colloidal sciences and composite technology to fabricate next-generation advanced structural materials. In the proof-of-concept experiments, electric fields are used to dictate the position of the anisotropic particles through dielectrophoresis, whereas a rotating magnetic field is used to control the orientation of the particles. By using such unprecedented control over the colloidal assembly process, we managed to fabricate ordered composite microstructures with up to 2.3-fold enhancement in wear resistance and unusual site-specific hardness that can be locally modulated by a factor of up to 2.5. PMID:27071113

New Technical Solution for Vertical Shaft Equipping Using Steel Headframe of Multifunction Purpose

NASA Astrophysics Data System (ADS)

Kassikhina, Elena; Pershin, Vladimir; Glazkov, Yurij

2017-11-01

The article reviews a novel approach to the design of steel angle headframe for vertical shafts of coal and ore mines on the basis of rational design solutions. Practice of construction of coal and ore mines provides application of various designs for steel angle headframes which are divided into separate large assembly blocks and constructive elements during assembling operations. Design of these blocks and elements, their weight and dimensions effect the chose of the method of assembling on which economic and technological indicators, as well as duration of down-time, depend on during performance of construction operations in shaft. The technical solution on equipment provision for mine vertical shaft using headframe of multifunctional purpose will allow changing the management construction of vertical shaft. The constructive design of the headgear allows application of the effective method of assembly and thus to provide improvement of the technical and economic indexes, and high calendar time rate of the shaft construction due to reduction of duration of works on equipment provision for the shaft and to refurbishment of the shaft in order to carry out horizontal mining.

Formation of charge-nanopatterned templates with flexible geometry via layer by layer deposition of polyelectrolytes for directed self-assembly of gold nanoparticles

NASA Astrophysics Data System (ADS)

Sayin, Mustafa; Dahint, Reiner

2017-03-01

Nanostructure formation via self-assembly processes offers a fast and cost-effective approach to generate surface patterns on large lateral scale. In particular, if the high precision of lithographic techniques is not required, a situation typical of many biotechnological and biomedical applications, it may be considered as the method of choice as it does not require any sophisticated instrumentation. However, in many cases the variety and complexity of the surface structures accessible with a single self-assembly based technique is limited. Here, we report on a new approach which combines two different self-assembly strategies, colloidal lithography and layer-by-layer deposition of polyelectrolytes, in order to significantly expand the spectrum of accessible patterns. In particular, flat and donut-like charge-patterned templates have been generated, which facilitate subsequent deposition of gold nanoparticles in dot, grid, ring, out-of-ring and circular patch structures. Potential applications are e.g. in the fields of biofunctional interfaces with well-defined lateral dimensions, optical devices with tuned properties, and controlled three-dimensional material growth.

Controlling the Surface Chemistry of Graphite by Engineered Self-Assembled Peptides

PubMed Central

Khatayevich, Dmitriy; So, Christopher R.; Hayamizu, Yuhei; Gresswell, Carolyn; Sarikaya, Mehmet

2012-01-01

The systematic control over surface chemistry is a long-standing challenge in biomedical and nanotechnological applications for graphitic materials. As a novel approach, we utilize graphite-binding dodecapeptides that self-assemble into dense domains to form monolayer thick long-range ordered films on graphite. Specifically, the peptides are rationally designed through their amino acid sequences to predictably display hydrophilic and hydrophobic characteristics while maintaining their self-assembly capabilities on the solid substrate. The peptides are observed to maintain a high tolerance for sequence modification, allowing the control over surface chemistry via their amino acid sequence. Furthermore, through a single step co-assembly of two different designed peptides, we predictably and precisely tune the wettability of the resulting functionalized graphite surfaces from 44 to 83 degrees. The modular molecular structures and predictable behavior of short peptides demonstrated here give rise to a novel platform for functionalizing graphitic materials that offers numerous advantages, including non-invasive modification of the substrate, bio-compatible processing in an aqueous environment, and simple fusion with other functional biological molecules. PMID:22428620

Minifactory: a precision assembly system adaptable to the product life cycle

NASA Astrophysics Data System (ADS)

Muir, Patrick F.; Rizzi, Alfred A.; Gowdy, Jay W.

1997-12-01

Automated product assembly systems are traditionally designed with the intent that they will be operated with few significant changes for as long as the product is being manufactured. This approach to factory design and programming has may undesirable qualities which have motivated the development of more 'flexible' systems. In an effort to improve agility, different types of flexibility have been integrated into factory designs. Specifically, automated assembly systems have been endowed with the ability to assemble differing products by means of computer-controlled robots, and to accommodate variations in parts locations and dimensions by means of sensing. The product life cycle (PLC) is a standard four-stage model of the performance of a product from the time that it is first introduced in the marketplace until the time that it is discontinued. Manufacturers can improve their return on investment by adapting the production process to the PLC. We are developing two concepts to enable manufacturers to more readily achieve this goal: the agile assembly architecture (AAA), an abstract framework for distributed modular automation; and minifactory, our physical instantation of this architecture for the assembly of precision electro-mechanical devices. By examining the requirements which each PLC stage places upon the production system, we identify characteristics of factory design and programming which are appropriate for that stage. As the product transitions from one stage to the next, the factory design and programing should also transition from one embodiment to the next in order to achieve the best return on investment. Modularity of the factory components, highly flexible product transport mechanisms, and a high level of distributed intelligence are key characteristics of minifactory that enable this adaptation.

DHS Internship Summary-Crystal Assembly at Different Length Scales

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

Mishchenko, L

2009-08-06

I was part of a project in which in situ atomic force microscopy (AFM) was used to monitor growth and dissolution of atomic and colloidal crystals. At both length scales, the chemical environment of the system greatly altered crystal growth and dissolution. Calcium phosphate was used as a model system for atomic crystals. A dissolution-reprecipitation reaction was observed in this first system, involving the conversion of brushite (DCPD) to octacalcium phosphate (OCP). In the second system, polymeric colloidal crystals were dissolved in an ionic solvent, revealing the underlying structure of the crystal. The dissolved crystal was then regrown through anmore » evaporative step method. Recently, we have also found that colloids can be reversibly deposited in situ onto an ITO (indium tin oxide) substrate via an electrochemistry setup. The overall goal of this project was to develop an understanding of the mechanisms that control crystallization and order, so that these might be controlled during material synthesis. Controlled assembly of materials over a range of length scales from molecules to nanoparticles to colloids is critical for designing new materials. In particular, developing materials for sensor applications with tailorable properties and long range order is important. In this work, we examine two of these length scales: small molecule crystallization of calcium phosphate (whose crystal phases include DCPD, OCP, and HAP) and colloidal crystallization of Poly(methyl methacrylate) beads. Atomic Force Microscopy is ideal for this line of work because it allows for the possibility of observing non-conducting samples in fluid during growth with high resolution ({approx} 10 nm). In fact, during atomic crystal growth one can observe changes in atomic steps, and with colloidal crystals, one can monitor the individual building blocks of the crystal. Colloids and atoms crystallize under the influence of different forces acting at different length scales as seen in Table 1. In particular, molecular crystals, which are typically dominated by ionic and covalent bonding, are an order of magnitude more strongly bonded than colloidal crystals. In molecular crystals, ordering is driven by the interaction potentials between molecules. By contrast, colloidal assembly is a competition between the repulsive electrostatic forces that prevent aggregation in solution (due to surface charge), and short-range van der Waals and entropic forces that leads to ordering. Understanding atomic crystallization is fundamentally important for fabrication of tailorable crystalline materials, for example for biological or chemical sensors. The transformation of brushite to OCP not only serves as a model system for atomic crystal growth (applicable to many other crystal growth processes), but is also important in bone cements. Colloidal crystals have unique optical properties which respond to chemical and mechanical stimuli, making them very important for sensing applications. The mechanism of colloidal crystal assembly is thus fundamentally important. Our in situ dissolution and regrowth experiments are one good method of analyzing how these crystals pack under different conditions and how defect sites are formed and filled. In these experiments, a silica additive was used to strengthen the colloidal crystal during initial assembly (ex situ) and to increase domain size and long range order. Reversible electrodeposition of colloids onto a conductive substrate (ITO in our case) is another system which can further our knowledge of colloidal assembly. This experiment holds promise of allowing in situ observation of colloidal crystal growth and the influence of certain additives on crystal order. The ultimate goal would be to achieve long range order in these crystals by changing the surface charge or the growth environment.« less

Ionic self-assembly of surface functionalized metal-organic polyhedra nanocages and their ordered honeycomb architecture at the air/water interface.

PubMed

Li, Yantao; Zhang, Daojun; Gai, Fangyuan; Zhu, Xingqi; Guo, Ya-nan; Ma, Tianliang; Liu, Yunling; Huo, Qisheng

2012-08-18

Metal-organic polyhedra (MOP) nanocages were successfully surface functionalized via ionic self-assembly and the ordered honeycomb architecture of the encapsulated MOP nanocages was also fabricated at the air/water surface. The results provide a novel synthetic method and membrane processing technique of amphiphilic MOP nanocages for various applications.

Elliptical vortex and oblique vortex lattice in the FeSe superconductor based on the nematicity and mixed superconducting orders

NASA Astrophysics Data System (ADS)

Lu, Da-Chuan; Lv, Yang-Yang; Li, Jun; Zhu, Bei-Yi; Wang, Qiang-Hua; Wang, Hua-Bing; Wu, Pei-Heng

2018-03-01

The electronic nematic phase is characterized as an ordered state of matter with rotational symmetry breaking, and has been well studied in the quantum Hall system and the high-Tc superconductors, regardless of cuprate or pnictide family. The nematic state in high-Tc systems often relates to the structural transition or electronic instability in the normal phase. Nevertheless, the electronic states below the superconducting transition temperature is still an open question. With high-resolution scanning tunneling microscope measurements, direct observation of vortex core in FeSe thin films revealed the nematic superconducting state by Song et al. Here, motivated by the experiment, we construct the extended Ginzburg-Landau free energy to describe the elliptical vortex, where a mixed s-wave and d-wave superconducting order is coupled to the nematic order. The nematic order induces the mixture of two superconducting orders and enhances the anisotropic interaction between the two superconducting orders, resulting in a symmetry breaking from C4 to C2. Consequently, the vortex cores are stretched into an elliptical shape. In the equilibrium state, the elliptical vortices assemble a lozenge-like vortex lattice, being well consistent with experimental results.

Direct Visualization of Planar Assembly of Plasmonic Nanoparticles Adjacent to Electrodes in Oscillatory Electric Fields.

PubMed

Ferrick, Adam; Wang, Mei; Woehl, Taylor J

2018-05-29

Electric field-directed assembly of colloidal nanoparticles (NPs) has been widely adopted for fabricating functional thin films and nanostructured surfaces. While first-order electrokinetic effects on NPs are well-understood in terms of classical models, effects of second-order electrokinetics that involve induced surface charge are still poorly understood. Induced charge electroosmotic phenomena, such as electrohydrodynamic (EHD) flow, have long been implicated in electric field-directed NP assembly with little experimental basis. Here, we use in situ dark-field optical microscopy and plasmonic NPs to directly observe the dynamics of planar assembly of colloidal NPs adjacent to a planar electrode in low-frequency (<1 kHz) oscillatory electric fields. We exploit the change in plasmonic NP color resulting from interparticle plasmonic coupling to visualize the assembly dynamics and assembly structure of silver NPs. Planar assembly of NPs is unexpected because of strong electrostatic repulsion between NPs and indicates that there are strong attractive interparticle forces oriented perpendicular to the electric field direction. A parametric investigation of the voltage- and frequency-dependent phase behavior reveals that planar NP assembly occurs over a narrow frequency range below which irreversible ballistic deposition occurs. Two key experimental observations are consistent with EHD flow-induced NP assembly: (1) NPs remain mobile during assembly and (2) electron microscopy observations reveal randomly close-packed planar assemblies, consistent with strong interparticle attraction. We interpret planar assembly in terms of EHD fluid flow and develop a scaling model that qualitatively agrees with the measured phase regions. Our results are the first direct in situ observations of EHD flow-induced NP assembly and shed light on long-standing unresolved questions concerning the formation of NP superlattices during electric field-induced NP deposition.

Challenging Students' Intuitions--The Influence of a Tangible Model of Virus Assembly on Students' Conceptual Reasoning about the Process of Self-Assembly

ERIC Educational Resources Information Center

Larsson, Caroline; Tibell, Lena A.

2015-01-01

A well-ordered biological complex can be formed by the random motion of its components, i.e. self-assemble. This is a concept that incorporates issues that may contradict students' everyday experiences and intuitions. In previous studies, we have shown that a tangible model of virus self-assembly, used in a group exercise, helps students to grasp…

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

Evaluation of Cleanliness Test Methods for Spacecraft PCB Assemblies

NASA Astrophysics Data System (ADS)

Tegehall, P.-E.; Dunn, B. D.

2006-10-01

Ionic contamination on printed-circuit-board assemblies may cause current leakage and short-circuits. The present cleanliness requirement in ECSS-Q-70-08, "The manual soldering of high-reliability electrical connections", is that the ionic contamination shall be less than 1.56 fl-glcm2 NaCI equivalents. The relevance of the method used for measurement of the ionic contamination level, resistivity of solvent extract, has been questioned. Alternative methods are ion chromatography and measurement of surface insulation resistance, but these methods also have their drawbacks. These methods are first described and their advantages and drawbacks are discussed. This is followed by an experimental evaluation of the three methods. This was done by soldering test vehicles at four manufacturers of space electronics using their ordinary processes for soldering and cleaning printed board assemblies. The experimental evaluation showed that the ionic contamination added by the four assemblers was very small and well below the acceptance criterion in ECSS-Q-70-80. Ion-chromatography analysis showed that most of the ionic contamination on the cleaned assembled boards originated from the hot-oil fusing of the printed circuit boards. Also, the surface insulation resistance was higher on the assembled boards compared to the bare printed circuit boards. Since strongly activated fluxes are normally used when printed circuit boards are hot-oil fused, it is essential that they are thoroughly cleaned in order to achieve low contamination levels on the final printed-board assemblies.

Liquid crystal-type assembly of native cellulose-glucuronoxylans extracted from plant cell wall.

PubMed

Reis, D; Vian, B; Chanzy, H; Roland, J C

1991-01-01

In numerous plant cell walls, the cellulose microfibrils are arranged in a helicoidal pattern which has been considered as an analog to a cholesteric order. Here, we report on the spontaneous helicoidal organization which occurs in acellular conditions from aqueous suspensions of cellulose. The cellulosic mucilage of mature seeds of quince (Cydonia oblonga L) was studied both in situ (pre-release mucilage) and after water extraction and in in vitro re-assembly (prolonged high speed ultracentrifugation, further progressive dehydration and embedding in LR White methacrylate or hydrosoluble melamine resin). The cellulosic component was characterized by the use of cellobiohydrolase (CBH1) bound to colloidal gold, and the glucuronic acid residues of the xylan matrix were characterized by the use of cationised gold. Inside the seeds, the pre-release mucilage is mostly helicoidal, with the occurrence of more or less ordered domains, which indicate a fluid organization relevant to an actual liquid crystal state. Cytochemical tests revealed the tight association between cellulose and glucuronoxylans, the latter constituting a charged coat around each microfibril. Following the hydration of the seed, a cellulosic suspension was extracted in which microfibrils were totally dispersed. The progressive dehydration of the suspension gave rise to concentrated viscous drops. Ultrastructural observations revealed the occurrence of multidomain organization, from non-ordered to cholesteric-like regions, revealing that the mucilage is at the same time crystalline and liquid. This constitutes the first demonstration that liquid crystal type assemblies can arise from crystalline and biological cellulose in aqueous suspension. It strengthens the hypothesis that a transient liquid crystal state must occur during the cellulose ordering. The possible morphogenetic role of the glucuronoxylans in the cholesteric organization of the cellulose is discussed.

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

Light-induced Self-Assembly and Diffusion of Nanoclusters

NASA Astrophysics Data System (ADS)

Lian, Wenxuan

Novel methods to build multiple types of three-dimensional structures from various nanoscale components are the most exciting and challenging questions in nano-science. The properties of the assembled structures can be potentially and designed, but the development of such approaches is challenging. In order to realize such rational assembly, a tunable interaction medium is often introduced into the system. Soft matter, such as polymers, surfactants and biomolecules are used to modify the surfaces of the nanoscale building blocks. Deoxyribonucleic acid (DNA) strands are known as polynucleotides since they are composed of simpler units called nucleotides. There are unique base pairing rules that are predictable and programmable, which can be used to regulate self-assembly process with high degree of control. Besides controlling static structure, it is important to develop methods for controlling systems in dynamic matter, with chemical stimuli or external fields. For example, here we study the use of azobezene-trimethylammonium bromide (AzoTAB) as a molecular agent that can control self-assembly via light excitation. In this thesis, DNA assisted self-assembly was conducted. The ability of AzoTAB as a light induced surfactant to control DNA assisted self-assembly was confirmed. The mechanism of AzoTAB as a light controlled self-assembly promoter was studied. In the second project, diffusion of nanoclusters was studied. The presence of polymers brings strong entanglement with nanoclusters. This entanglement is more obvious when the nanocluster is a framed structure like the octahedron in the study. The diffusion coefficient of the octahedron becomes larger during traveling. The following up studies are required to elucidate the origin of the observed effect.

Towards Self-Assembled Hybrid Artificial Cells: Novel Bottom-Up Approaches to Functional Synthetic Membranes

PubMed Central

Brea, Roberto J.; Hardy, Michael D.; Devaraj, Neal K.

2015-01-01

There has been increasing interest in utilizing bottom-up approaches to develop synthetic cells. A popular methodology is the integration of functionalized synthetic membranes with biological systems, producing “hybrid” artificial cells. This Concept article covers recent advances and the current state-of-the-art of such hybrid systems. Specifically, we describe minimal supramolecular constructs that faithfully mimic the structure and/or function of living cells, often by controlling the assembly of highly ordered membrane architectures with defined functionality. These studies give us a deeper understanding of the nature of living systems, bring new insights into the origin of cellular life, and provide novel synthetic chassis for advancing synthetic biology. PMID:26149747

Research on automated disassembly technology for waste LCD

NASA Astrophysics Data System (ADS)

Qin, Qin; Zhu, Dongdong; Wang, Jingwei; Dou, Jianfang; Wang, Sujuan; Tu, Zimei

2017-11-01

In the field of Waste LCD disassembling and recycling, there are existing two major problems: 1) disassembling waste LCD mainly depends on manually mechanical crushing; 2) the resource level is not high. In order to deal with the above problems, in this paper, we develop an efficient, safe and automated waste LCD disassembling assembly line technology. This technology can disassembly and classify mainstream LCD into four components, which are liquid crystal display panels, housings and metal shield, PCB assembly. It can also disassembly many kinds of waste LCD. Compared with the traditional cooperation of manual labor and electric tools method, our proposed technology can significantly improve disassembling efficiency and demonstrate good prospects and promotional value.

Modeling the self-assembly of functionalized fullerenes on solid surfaces using Monte Carlo simulations

NASA Astrophysics Data System (ADS)

Bubnis, Gregory J.

Since their discovery 25 years ago, carbon fullerenes have been widely studied for their unique physicochemical properties and for applications including organic electronics and photovoltaics. For these applications it is highly desirable for crystalline fullerene thin films to spontaneously self-assemble on surfaces. Accordingly, many studies have functionalized fullerenes with the aim of tailoring their intermolecular interactions and controlling interactions with the solid substrate. The success of these rational design approaches hinges on the subtle interplay of intermolecular forces and molecule-substrate interactions. Molecular modeling is well-suited to studying these interactions by directly simulating self-assembly. In this work, we consider three different fullerene functionalization approaches and for each approach we carry out Monte Carlo simulations of the self-assembly process. In all cases, we use a "coarse-grained" molecular representation that preserves the dominant physical interactions between molecules and maximizes computational efficiency. The first approach we consider is the traditional gold-thiolate SAM (self-assembled monolayer) strategy which tethers molecules to a gold substrate via covalent sulfur-gold bonds. For this we study an asymmetric fullerene thiolate bridged by a phenyl group. Clusters of 40 molecules are simulated on the Au(111) substrate at different temperatures and surface coverage densities. Fullerenes and S atoms are found to compete for Au(111) surface sites, and this competition prevents self-assembly of highly ordered monolayers. Next, we investigate self-assembled monolayers formed by fullerenes with hydrogen-bonding carboxylic acid substituents. We consider five molecules with different dimensions and symmetries. Monte Carlo cooling simulations are used to find the most stable solid structures of clusters adsorbed to Au(111). The results show cases where fullerene-Au(111) attraction, fullerene close-packing, and hydrogen-bonding interactions can cooperate to guide self-assembly or compete to hinder it. Finally, we consider three bis-fullerene molecules, each with a different "bridging group" covalently joining two fullerenes. To effectively study the competing "standing-up" and "lying-down" morphologies, we use Monte Carlo simulations in conjunction with replica exchange and force field biasing methods. For clusters adsorbed to smooth model surfaces, we determine free energy landscapes and demonstrate their utility for rationalizing and predicting self-assembly.

Role of strongly interacting additives in tuning the structure and properties of polymer systems

NASA Astrophysics Data System (ADS)

Daga, Vikram Kumar

Block copolymer (BCP) nanocomposites are an important class of hybrid materials in which the BCP guides the spatial location and the periodic assembly of the additives. High loadings of well-dispersed nanofillers are generally important for many applications including mechanical reinforcing of polymers. In particular the composites shown in this work might find use as etch masks in nanolithography, or for enabling various phase selective reactions for new materials development. This work explores the use of hydrogen bonding interactions between various additives (such as homopolymers and non-polymeric additives) and small, disordered BCPs to cause the formation of well-ordered morphologies with small domains. A detailed study of the organization of homopolymer chains and the evolution of structure during the process of ordering is performed. The results demonstrate that by tuning the selective interaction of the additive with the incorporating phase of the BCP, composites with significantly high loadings of additives can be formed while maintaining order in the BCP morphology. The possibility of high and selective loading of additives in one of the phases of the ordered BCP composite opens new avenues due to high degree of functionalization and the proximity of the additives within the incorporating phase. This aspect is utilized in one case for the formation of a network structure between adjoining additive cores to derive mesoporous inorganic materials with their structures templated by the BCP. The concept of additive-driven assembly is extended to formulate BCPadditive blends with an ability to undergo photo-induced ordering. Underlying this strategy is the ability to transition a weakly interacting additive to its strongly interacting form. This strategy provides an on-demand, non-intrusive route for formation of well-ordered nanostructures in arbitrarily defined regions of an otherwise disordered material. The second area explored in this dissertation deals with the incorporation of additives into photoresists for next generation extreme ultra violet (EUV) photolithography applications. The concept of hydrogen bonding between the additives and the polymeric photoresist was utilized to cause formation of a physical network that is expected to slow down the diffusion of photoacid leading to better photolithographic performance (25-30 nm resolution obtained).

Development of Highly Ordered Heterostructured Semiconductor Nanowire Arrays for Sub-Wavelength Optical Devices

DTIC Science & Technology

2007-06-01

properties of nanowires" J. Appl. Phys 98, 094306 (2005) 9. Harry E. Ruda and Alexander Shik, "Polarization-sensitive optical properties of metallic and...34Biexcitons in parabolic quantum dots", Phys. Rev. B. 73, 125321 (2006). 11. M. Blumin, H.E. Ruda, I. Savelyev , A Shik and H. Wang, "Self-assembled InAs

The emergence of superstructural order in insulin amyloid fibrils upon multiple rounds of self-seeding

NASA Astrophysics Data System (ADS)

Surmacz-Chwedoruk, Weronika; Babenko, Viktoria; Dec, Robert; Szymczak, Piotr; Dzwolak, Wojciech

2016-08-01

Typically, elongation of an amyloid fibril entails passing conformational details of the mother seed to daughter generations of fibrils with high fidelity. There are, however, several factors that can potentially prevent such transgenerational structural imprinting from perpetuating, for example heterogeneity of mother seeds or so-called conformational switching. Here, we examine phenotypic persistence of bovine insulin amyloid ([BI]) upon multiple rounds of self-seeding under quiescent conditions. According to infrared spectroscopy, with the following passages of homologous seeding, daughter fibrils gradually depart from the mother seed’s spectral characteristics. We note that this transgenerational structural drift in [BI] amyloid leads toward fibrils with infrared, chiroptical, and morphological traits similar to those of the superstructural variant of fibrils which normally forms upon strong agitation of insulin solutions. However, in contrast to agitation-induced insulin amyloid, the superstructural assemblies of daughter fibrils isolated through self-seeding are sonication-resistant. Our results suggest that formation of single amyloid fibrils is not a dead-end of the amyloidogenic self-assembly. Instead, the process appears to continue toward the self-assembly of higher-order structures although on longer time-scales. From this perspective, the fast agitation-induced aggregation of insulin appears to be a shortcut to amyloid superstructures whose formation under quiescent conditions is slow.

See evil, hear evil

NASA Astrophysics Data System (ADS)

Pressel, Phil

2014-12-01

The purpose of this project was to design a "telescope" whose mirrors and support structures were all made of aluminum in order for it to remain in focus for all environmental temperatures. The telescope was mounted on a gimbal structure that was an elevation over azimuth assembly. The purpose of the telescope was to track in all directions in order to detect "enemy" activities such as visual or sound detection at the site of the telescope. The final assembly was eventually purchased by the Secession Activists of Quebec to scan all around for non-French speaking dissidents seeking to spy on them. It was also shipped to South Korea to detect activities by North Korea and shipped to Northern Ireland to spy on the British and finally it also was sent to a high altitude location in Israel. The peculiar thing about the one in Israel was that similar to reading and writing Hebrew from right to left, the telescope was only allowed to scan from right to left. Two unique mechanical designs involved in this telescope are discussed here. The first one is the design of a stop at each end of the azimuth travel that was greater than 360 degrees, and the second was the design of a gearing system that drove both elevation and azimuth assemblies with no backlash

Architectonics: Design of Molecular Architecture for Functional Applications.

PubMed

Avinash, M B; Govindaraju, Thimmaiah

2018-02-20

The term architectonics has its roots in the architectural and philosophical (as early as 1600s) literature that refers to "the theory of structure" and "the structure of theory", respectively. The concept of architectonics has been adapted to advance the field of molecular self-assembly and termed as molecular architectonics. In essence, the methodology of organizing molecular units in the required and controlled configurations to develop advanced functional systems for materials and biological applications comprises the field of molecular architectonics. This concept of designing noncovalent systems enables to focus on different functional aspects of designer molecules for biological and nonbiological applications and also strengthens our efforts toward the mastery over the art of controlled molecular self-assemblies. Programming complex molecular interactions and assemblies for specific functions has been one of the most challenging tasks in the modern era. Meticulously ordered molecular assemblies can impart remarkable developments in several areas spanning energy, health, and environment. For example, the well-defined nano-, micro-, and macroarchitectures of functional molecules with specific molecular ordering possess potential applications in flexible electronics, photovoltaics, photonic crystals, microreactors, sensors, drug delivery, biomedicine, and superhydrophobic coatings, among others. The functional molecular architectures having unparalleled properties are widely evident in various designs of Nature. By drawing inspirations from Nature, intended molecular architectures can be designed and developed to harvest various functions, as there is an inexhaustible resource and scope. In this Account, we present exquisite designer molecules developed by our group and others with an objective to master the art of molecular recognition and self-assembly for functional applications. We demonstrate the tailor-ability of molecular self-assemblies by employing biomolecules like amino acids and nucleobases as auxiliaries. Naphthalenediimide (NDI), perylenediimide (PDI), and few other molecular systems serve as functional modules. The effects of stereochemistry and minute structural modifications in the molecular designs on the supramolecular interactions, and construction of self-assembled zero-dimensional (OD), one-dimensional (1D), and two-dimensional (2D) nano- and microarchitectures like particles, spheres, cups, bowls, fibers, belts, helical belts, supercoiled helices, sheets, fractals, and honeycomb-like arrays are discussed in extensive detail. Additionally, we present molecular systems that showcase the elegant designs of coassembly, templated assembly, hierarchical assembly, transient self-assembly, chiral denaturation, retentive helical memory, self-replication, supramolecular regulation, supramolecular speciation, supernon linearity, dynamic pathway complexity, supramolecular heterojunction, living supramolecular polymerization, and molecular machines. Finally, we describe the molecular engineering principles learnt over the years that have led to several applications, namely, organic electronics, self-cleaning, high-mechanical strength, and tissue engineering.

Development of self-assembled molecular structures on polymeric surfaces and their applications as ultrasonically responsive barrier coatings for on-demand, pulsatile drug delivery

NASA Astrophysics Data System (ADS)

Kwok, Connie Sau-Kuen

Nature in the form of DNA, proteins, and cells has the remarkable ability to interact with its environment by processing biological information through specific molecular recognition at the interface. As such, materials that are capable of triggering an appropriate biological response need to be engineered at the biomaterial surface. Chemically and structurally well-defined self-assembled monolayers (SAMs), biomimetics of the lipid bilayer in cell membranes, have been created and studied mostly on rigid metallic surfaces. This dissertation is motivated by the lack of methods to generate a molecularly designed surface for biomedical polymers and thus provides an enabling technology to engineer a polymeric surface precisely at a molecular and cellular level. To take this innovation one step further, we demonstrated that such self-assembled molecular structure coated on drug-containing polymeric devices could act as a stimulus-responsive barrier for controlled drug delivery. A simple, one-step procedure for generating ordered, crystalline methylene chains on polymeric surfaces via urethane linkages was successfully developed. The self-assemblies and molecular structures of these crystalline methylene chains are comparable to the SAM model surfaces, as evidenced by various surface characterization techniques (XPS, TOF-SIMS, and FTIR-ATR). For the first time, these self-assembled molecular structures are shown to function collectively as an ultrasound-responsive barrier membrane for pulsatile drug delivery, including delivery of low-molecular-weight ciprofloxacin and high-molecular-weight insulin. Encouraging results, based on the insulin-activated deoxyglucose uptakes in adipocytes, indicate that the released insulin remained biologically active. Both chemical and acoustic analyses suggest that the ultrasound-assisted release mechanism is primarily induced by transient cavitation, which causes temporary disruption of the self-assembled overlayer, and thus allows temporal release of the encapsulated drugs. In addition to acoustic energy, self-assembled surfaces experience order-disorder transition and have a transition temperature higher than body temperature if longer alkyl chains (C18) are used. The C18-assembled surface barrier membrane exhibits a relatively superior impermeable coating than the shorter C12 chains. The versatility of derivatizing the terminal groups of the self-assembled molecular structures is illustrated by attaching poly (ethyleneoxide) oligomers to the alkyl chains to minimize nonspecific protein adsorption. This study lays an important foundation for future work in conjugating other biomolecules to develop surface-based diagnostics and biomaterials. With much success, this original research work of forming self-assembled crystalline structures on synthetic materials still allows for numerous opportunities for new applications and possibly even more new discoveries.

Nacre-nanomimetics: Strong, Stiff, and Plastic.

PubMed

De Luca, Francois; Menzel, Robert; Blaker, Jonny J; Birkbeck, John; Bismarck, Alexander; Shaffer, Milo S P

2015-12-09

The bricks and mortar in the classic structure of nacre have characteristic geometry, aspect ratios and relative proportions; these key parameters can be retained while scaling down the absolute length scale by more than 1 order of magnitude. The results shed light on fundamental scaling behavior and provide new opportunities for high performance, yet ductile, lightweight nanocomposites. Reproducing the toughening mechanisms of nacre at smaller length scales allows a greater volume of interface per unit volume while simultaneously increasing the intrinsic properties of the inorganic constituents. Layer-by-layer (LbL) assembly of poly(sodium 4-styrenesulfonate) (PSS) polyelectrolyte and well-defined [Mg2Al(OH)6]CO3.nH2O layered double hydroxide (LDH) platelets produces a dense, oriented, high inorganic content (∼90 wt %) nanostructure resembling natural nacre, but at a shorter length scale. The smaller building blocks enable the (self-) assembly of a higher quality nanostructure than conventional mimics, leading to improved mechanical properties, matching those of natural nacre, while allowing for substantial plastic deformation. Both strain hardening and crack deflection mechanisms were observed in situ by scanning electron microscopy (SEM) during nanoindentation. The best properties emerge from an ordered nanostructure, generated using regular platelets, with narrow size dispersion.

Enhanced Thermoelectric Properties of Polyaniline Nanofilms Induced by Self-Assembled Supramolecules.

PubMed

Wang, Liming; Yao, Qin; Xiao, Juanxiu; Zeng, Kaiyang; Shi, Wei; Qu, Sanyin; Chen, Lidong

2016-07-05

Polyaniline (PANI) is one of the most promising candidates for flexible organic thermoelectric (TE) applications owing to its relatively low cost and high stability. Herein, the self-assembled supramolecule (SAS) (3,6-dioctyldecyloxy-1,4-benzenedicarboxylic acid) was used as an additive and was introduced into PANI films as a template. Raman spectroscopy, X-ray diffraction, and conductive atomic force microscopy analyses demonstrated that the highly ordered chain structure of PANI was achieved by chemical interactions between PANI and the SAS. Moreover, the ordered regions in the PANI-SAS film increased with a decrease in the film thickness. Consequently, the TE properties of PANI-SAS films were not only much higher than those of PANI films, but they also increased with a decrease in film thickness. The maximum TE power factor of the PANI-SAS film reached 31 μW m(-1)  K(-2) , which is approximately six times higher than the power factor of a PANI film with a similar thickness. This work offers a promising way to prepare PANI thin films with enhanced TE properties. © 2016 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

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.

Synthesis and Self-Assembly of fcc Phase FePt Nanorods

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

Chen, Min; Pica, Timothy; Jiang, Ying-Bing

2007-05-01

In this paper, we report a synthesis of FePt nanorods by confining decomposition of Fe(CO) 5 and reduction of Pt(caca) 2 in surfactant reverse cylindrical micelles. The controlled nucleation and growth kinetics in confined environment allows easy control over Fe/Pt composition, nanorod uniformity, and nanorod aspect ratio. The FePt nanorods tend to self-assemble into ordered arrays along three-dimensions. Directed assembly under external magnetic field leads to two-dimensional ordered arrays, parallel to the substrate magnetic field. We expect that with optimized external magnetic fields, we should be able to assemble these nanorods into orientated one or two-dimensional arrays, providing a uniformmore » anisotropic magnetic platform for varied applications in enhanced data storage, magneto-electron transport, etc.« less

Directed Self-Assembly of Diblock Copolymer Thin Films on Prepatterned Metal Nanoarrays.

PubMed

Chang, Tongxin; Huang, Haiying; He, Tianbai

2016-01-01

The sequential layer by layer self-assembly of block copolymer (BCP) nanopatterns is an effective approach to construct 3D nanostructures. Here large-scale highly ordered metal nano-arrays prepared from solvent annealed thin films of polystyrene-block-poly(2-vinylpyridine) (PS-b-P2VP) diblock copolymer are used to direct the assembly of the same BCP. The influence of initial loading concentration of metal precursor, the type of metal nanoparticle (gold, platinum, and silver), and the nanoparticle-substrate interaction on the directed assembly behavior of the upper BCP layer have been focused. It is found that the upper BCP film can be completely directed by the gold nanoarray with P2VP domain exclusively located between two adjacent gold nanowires or nanodots, which behaves the same way as on the platinum nanoarray. While the silver nanoarray can be destroyed during the upper BCP self-assembly with the silver nanoparticles assembled into the P2VP domain. Based on the discussions of the surface energy of nanoparticles and the interplay between nanoparticle-substrate interaction and nanoparticle-polymer interaction, it is concluded that the effect of immobilization of nanoparticles on the substrate, together with entropy effect to minimize the energetically unfavorable chain stretching contributes to the most effective alignment between each layer. © 2015 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Time-resolved viscoelastic properties of self-assembling iron oxide nanocube superlattices probed by quartz crystal microbalance with dissipation monitoring.

PubMed

Kapuscinski, Martin; Agthe, Michael; Bergström, Lennart

2018-07-15

Self-assembly of nanoparticles into superlattices can be used to create hierarchically structured materials with tailored functions. We have used the surface sensitive quartz crystal microbalance with dissipation monitoring (QCM-D) technique in combination with video microscopy (VM) to obtain time-resolved information on the mass increase and rheological properties of evaporation-induced self-assembly of nanocubes. We have recorded the frequency and dissipation shifts during growth and densification of superlattices formed by self-assembly of oleic acid capped, truncated iron oxide nanocubes and analyzed the time-resolved QCM-D data using a Kelvin-Voigt viscoelastic model. We show that the nanoparticles first assemble into solvent-containing arrays dominated by a viscous response followed by a solvent-releasing step that results in the formation of rigid and well-ordered superlattices. Our findings demonstrate that QCM-D can be successfully used to follow self-assembly and assist in the design of optimized routes to produce well-ordered superlattices. Copyright © 2018 The Authors. Published by Elsevier Inc. All rights reserved.

Directed self-assembly of nanogold using a chemically modified nanopatterned surface

NASA Astrophysics Data System (ADS)

Nidetz, Robert; Kim, Jinsang

2012-02-01

Electron-beam lithography (EBL) was used to define an aminosilane nanopatterned surface in order to electrostatically self-assemble gold nanoparticles (Au NPs). The chemically modified nanopatterned surfaces were immersed into a Au NP solution to allow the Au NPs to self-assemble. Equilibrium self-assembly was achieved in only 20 min. The number of Au NPs that self-assembled on an aminosilane dot was controlled by manipulating the diameters of both the Au NPs and the dots. Adding salt to the Au NP solution enabled the Au NPs to self-assemble in greater numbers on the same sized dot. However, the preparation of the Au NP solution containing salt was sensitive to spikes in the salt concentration. These spikes led to aggregation of the Au NPs and non-specific deposition of Au NPs on the substrate. The Au NP patterned surfaces were immersed in a sodium hydroxide solution in order to lift-off the patterned Au NPs, but no lift-off was observed without adequate physical agitation. The van der Waals forces are too strong to allow for lift-off despite the absence of electrostatic forces.

De novo assembly of the pepper transcriptome (Capsicum annuum): a benchmark for in silico discovery of SNPs, SSRs and candidate genes.

PubMed

Ashrafi, Hamid; Hill, Theresa; Stoffel, Kevin; Kozik, Alexander; Yao, Jiqiang; Chin-Wo, Sebastian Reyes; Van Deynze, Allen

2012-10-30

Molecular breeding of pepper (Capsicum spp.) can be accelerated by developing DNA markers associated with transcriptomes in breeding germplasm. Before the advent of next generation sequencing (NGS) technologies, the majority of sequencing data were generated by the Sanger sequencing method. By leveraging Sanger EST data, we have generated a wealth of genetic information for pepper including thousands of SNPs and Single Position Polymorphic (SPP) markers. To complement and enhance these resources, we applied NGS to three pepper genotypes: Maor, Early Jalapeño and Criollo de Morelos-334 (CM334) to identify SNPs and SSRs in the assembly of these three genotypes. Two pepper transcriptome assemblies were developed with different purposes. The first reference sequence, assembled by CAP3 software, comprises 31,196 contigs from >125,000 Sanger-EST sequences that were mainly derived from a Korean F1-hybrid line, Bukang. Overlapping probes were designed for 30,815 unigenes to construct a pepper Affymetrix GeneChip® microarray for whole genome analyses. In addition, custom Python scripts were used to identify 4,236 SNPs in contigs of the assembly. A total of 2,489 simple sequence repeats (SSRs) were identified from the assembly, and primers were designed for the SSRs. Annotation of contigs using Blast2GO software resulted in information for 60% of the unigenes in the assembly. The second transcriptome assembly was constructed from more than 200 million Illumina Genome Analyzer II reads (80-120 nt) using a combination of Velvet, CLC workbench and CAP3 software packages. BWA, SAMtools and in-house Perl scripts were used to identify SNPs among three pepper genotypes. The SNPs were filtered to be at least 50 bp from any intron-exon junctions as well as flanking SNPs. More than 22,000 high-quality putative SNPs were identified. Using the MISA software, 10,398 SSR markers were also identified within the Illumina transcriptome assembly and primers were designed for the identified markers. The assembly was annotated by Blast2GO and 14,740 (12%) of annotated contigs were associated with functional proteins. Before availability of pepper genome sequence, assembling transcriptomes of this economically important crop was required to generate thousands of high-quality molecular markers that could be used in breeding programs. In order to have a better understanding of the assembled sequences and to identify candidate genes underlying QTLs, we annotated the contigs of Sanger-EST and Illumina transcriptome assemblies. These and other information have been curated in a database that we have dedicated for pepper project.

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.

Shape-dependent dispersion and alignment of nonaggregating plasmonic gold nanoparticles in lyotropic and thermotropic liquid crystals.

PubMed

Liu, Qingkun; Tang, Jianwei; Zhang, Yuan; Martinez, Angel; Wang, Shaowei; He, Sailing; White, Timothy J; Smalyukh, Ivan I

2014-05-01

We use both lyotropic liquid crystals composed of prolate micelles and thermotropic liquid crystals made of rod-like molecules to uniformly disperse and unidirectionally align relatively large gold nanorods and other complex-shaped nanoparticles at high concentrations. We show that some of these ensuing self-assembled orientationally ordered soft matter systems exhibit polarization-dependent plasmonic properties with strongly pronounced molar extinction exceeding that previously achieved in self-assembled composites. The long-range unidirectional alignment of gold nanorods is mediated mainly by anisotropic surface anchoring interactions at the surfaces of gold nanoparticles. Polarization-sensitive absorption, scattering, and extinction are used to characterize orientations of nanorods and other nanoparticles. The experimentally measured unique optical properties of these composites, which stem from the collective plasmonic effect of the gold nanorods with long-range order in a liquid crystal matrix, are reproduced in computer simulations. A simple phenomenological model based on anisotropic surface interaction explains the alignment of gold nanorods dispersed in liquid crystals and the physical underpinnings behind our observations.

Platypus chain reaction: directional and ordered meiotic pairing of the multiple sex chromosome chain in Ornithorhynchus anatinus.

PubMed

Daish, Tasman; Casey, Aaron; Grützner, Frank

2009-01-01

Monotremes are phylogenetically and phenotypically unique animals with an unusually complex sex chromosome system that is composed of ten chromosomes in platypus and nine in echidna. These chromosomes are alternately linked (X1Y1, X2Y2, ...) at meiosis via pseudoautosomal regions and segregate to form spermatozoa containing either X or Y chromosomes. The physical and epigenetic mechanisms involved in pairing and assembly of the complex sex chromosome chain in early meiotic prophase I are completely unknown. We have analysed the pairing dynamics of specific sex chromosome pseudoautosomal regions in platypus spermatocytes during prophase of meiosis I. Our data show a highly coordinated pairing process that begins at the terminal Y5 chromosome and completes with the union of sex chromosomes X1Y1. The consistency of this ordered assembly of the chain is remarkable and raises questions about the mechanisms and factors that regulate the differential pairing of sex chromosomes and how this relates to potential meiotic silencing mechanisms and alternate segregation.

Design of hybrid two-dimensional and three-dimensional nanostructured arrays for electronic and sensing applications

NASA Astrophysics Data System (ADS)

Ko, Hyunhyub

This dissertation presents the design of organic/inorganic hybrid 2D and 3D nanostructured arrays via controlled assembly of nanoscale building blocks. Two representative nanoscale building blocks such as carbon nanotubes (one-dimension) and metal nanoparticles (zero-dimension) are the core materials for the study of solution-based assembly of nanostructured arrays. The electrical, mechanical, and optical properties of the assembled nanostructure arrays have been investigated for future device applications. We successfully demonstrated the prospective use of assembled nanostructure arrays for electronic and sensing applications by designing flexible carbon nanotube nanomembranes as mechanical sensors, highly-oriented carbon nanotubes arrays for thin-film transistors, and gold nanoparticle arrays for SERS chemical sensors. In first section, we fabricated highly ordered carbon nanotube (CNT) arrays by tilted drop-casting or dip-coating of CNT solution on silicon substrates functionalized with micropatterned self-assembled monolayers. We further exploited the electronic performance of thin-film transistors based on highly-oriented, densely packed CNT micropatterns and showed that the carrier mobility is largely improved compared to randomly oriented CNTs. The prospective use of Raman-active CNTs for potential mechanical sensors has been investigated by studying the mechano-optical properties of flexible carbon nanotube nanomembranes, which contain freely-suspended carbon nanotube array encapsulated into ultrathin (<50 nm) layer-by-layer (LbL) polymer multilayers. In second section, we fabricated 3D nano-canal arrays of porous alumina membranes decorated with gold nanoparticles for prospective SERS sensors. We showed extraordinary SERS enhancement and suggested that the high performance is associated with the combined effects of Raman-active hot spots of nanoparticle aggregates and the optical waveguide properties of nano-canals. We demonstrated the ability of this SERS substrate for trace level sensing of nitroaromatic explosives by detecting down to 100 zeptogram (˜330 molecules) of DNT.

Triple acting radial seal

DOEpatents

Ebert, Todd A [West Palm Beach, FL; Carella, John A [Jupiter, FL

2012-03-13

A triple acting radial seal used as an interstage seal assembly in a gas turbine engine, where the seal assembly includes an interstage seal support extending from a stationary inner shroud of a vane ring, the interstage seal support includes a larger annular radial inward facing groove in which an outer annular floating seal assembly is secured for radial displacement, and the outer annular floating seal assembly includes a smaller annular radial inward facing groove in which an inner annular floating seal assembly is secured also for radial displacement. A compliant seal is secured to the inner annular floating seal assembly. The outer annular floating seal assembly encapsulates the inner annular floating seal assembly which is made from a very low alpha material in order to reduce thermal stress.

Hydrolysis of Surfactants Containing Ester Bonds: Modulation of Reaction Kinetics and Important Aspects of Surfactant Self-Assembly

ERIC Educational Resources Information Center

Lundberg, Dan; Stjerndahl, Maria

2011-01-01

The effects of self-assembly on the hydrolysis kinetics of surfactants that contain ester bonds are discussed. A number of examples on how reaction rates and apparent reaction orders can be modulated by changes in the conditions, including an instance of apparent zero-order kinetics, are presented. Furthermore, it is shown that the examples on…

Data acquisition system for chemical kinetic studies

PubMed Central

Zhu, Yu-zhen; Zhou, Xin; Zang, Xiang-sheng

1989-01-01

A microcomputer-interfaced data acquisition system for chemical kinetics (interfacing with laboratory analogue instruments) has been developed. Analogue signals from instruments used in kinetics experiments are amplifed by a wide-range adjustable high-gain operational amplifier and smoothed by an op-based filter, and then digitized at rates of up to 104 samples per channel by an ADC 0816 digitizer. The ADC data transfer and manipulation routine was written in Assembler code and in high-level language; the graphics package and data treatment package is in Basic. For the various sampling speeds, all of the program can be written using Basic-Assembler or completely in Assembler if a high sampling rate is needed. Several numerical treatment methods for chemical kinetics have been utilized to smooth the data from experiments. The computer-interfaced system for second-order chemical kinetic studies was applied to the determination of the rate constant of the saponification of ethyl acetate at 35°C. For this specific problem, an averaging treatment was used which can be called an interval method. The use of this method avoids the diffcully of measuring the starting time of the reaction. Two groups of experimental data and results were used to evaluate the systems performance. All of the results obtained are in agreement with the reference value. PMID:18925219

Highly Ordered Block Copolymer Templates for the Generation of Nanostructured Materials

NASA Astrophysics Data System (ADS)

Bhoje Gowd, E.; Nandan, Bhanu; Bigall, Nadja C.; Eychmuller, Alexander; Stamm, Manfred

2009-03-01

Among many different types of self-assembled materials, block copolymers have attracted immense interest for applications in nanotechnology. Block copolymer thin film can be used as a template for patterning of hard inorganic materials such as metal nanoparticles. In the present work, we demonstrate a new approach to fabricate highly ordered arrays of nanoscopic inorganic dots and wires using switchable block copolymer thin films. Various inorganic nanoparticles from a simple aqueous solution were directly deposited on the surface reconstructed block copolymer templates. The preferential interaction of the nanoparticles with one of the blocks is mainly responsible for the lateral distribution of the nanoparticles in addition to the capillary forces. Subsequent stabilization by UV-irradiation followed by pyrolysis in air at 450 ^oC removes the polymer to produce highly ordered metallic nanostructures. This method is highly versatile as the procedure used here is simple, eco-friendly and provides a facile approach to fabricate a broad range of nanoscaled architectures with tunable lateral spacing.

Self assembled linear polymeric chains with tuneable semiflexibility using isotropic interactions.

PubMed

Abraham, Alex; Chatterji, Apratim

2018-04-21

We propose a two-body spherically symmetric (isotropic) potential such that particles interacting by the potential self-assemble into linear semiflexible polymeric chains without branching. By suitable control of the potential parameters, we can control the persistence length of the polymer and can even introduce a controlled number of branches. Thus we show how to achieve effective directional interactions starting from spherically symmetric potentials. The self-assembled polymers have an exponential distribution of chain lengths akin to what is observed for worm-like micellar systems. On increasing particle density, the polymeric chains self-organize to an ordered line-hexagonal phase where every chain is surrounded by six parallel chains, the transition is first order. On further increase in monomer density, the order is destroyed and we get a branched gel-like phase. This potential can be used to model semi-flexible equilibrium polymers with tunable semiflexibility and excluded volume. The use of the potential is computationally cheap and hence can be used to simulate and probe equilibrium polymer dynamics with long chains. The potential also gives a plausible method of tuning colloidal interactions in experiments such that one can obtain self-assembling polymeric chains made up of colloids and probe polymer dynamics using an optical microscope. Furthermore, we show how a modified potential leads to the observation of an intermediate nematic phase of self-assembled chains in between the low density disordered phase and the line-ordered hexagonal phase.

Self assembled linear polymeric chains with tuneable semiflexibility using isotropic interactions

NASA Astrophysics Data System (ADS)

Abraham, Alex; Chatterji, Apratim

2018-04-01

We propose a two-body spherically symmetric (isotropic) potential such that particles interacting by the potential self-assemble into linear semiflexible polymeric chains without branching. By suitable control of the potential parameters, we can control the persistence length of the polymer and can even introduce a controlled number of branches. Thus we show how to achieve effective directional interactions starting from spherically symmetric potentials. The self-assembled polymers have an exponential distribution of chain lengths akin to what is observed for worm-like micellar systems. On increasing particle density, the polymeric chains self-organize to an ordered line-hexagonal phase where every chain is surrounded by six parallel chains, the transition is first order. On further increase in monomer density, the order is destroyed and we get a branched gel-like phase. This potential can be used to model semi-flexible equilibrium polymers with tunable semiflexibility and excluded volume. The use of the potential is computationally cheap and hence can be used to simulate and probe equilibrium polymer dynamics with long chains. The potential also gives a plausible method of tuning colloidal interactions in experiments such that one can obtain self-assembling polymeric chains made up of colloids and probe polymer dynamics using an optical microscope. Furthermore, we show how a modified potential leads to the observation of an intermediate nematic phase of self-assembled chains in between the low density disordered phase and the line-ordered hexagonal phase.

Roles of Gag-RNA interactions in HIV-1 virus assembly deciphered by single-molecule localization microscopy.

PubMed

Yang, Yantao; Qu, Na; Tan, Jie; Rushdi, Muaz N; Krueger, Christopher J; Chen, Antony K

2018-06-11

During HIV-1 assembly, the retroviral structural protein Gag forms an immature capsid, containing thousands of Gag molecules, at the plasma membrane (PM). Interactions between Gag nucleocapsid (NC) and viral RNA (vRNA) are thought to drive assembly, but the exact roles of these interactions have remained poorly understood. Since previous studies have shown that Gag dimer- or trimer-forming mutants (Gag ZiL ) lacking an NC domain can form immature capsids independent of RNA binding, it is often hypothesized that vRNA drives Gag assembly by inducing Gag to form low-ordered multimers, but is dispensable for subsequent assembly. In this study, we examined the role of vRNA in HIV-1 assembly by characterizing the distribution and mobility of Gag and Gag NC mutants at the PM using photoactivated localization microscopy (PALM) and single-particle tracking PALM (spt-PALM). We showed that both Gag and Gag ZiL assembly involve a similar basic assembly unit, as expected. Unexpectedly, the two proteins underwent different subsequent assembly pathways, with Gag cluster density increasing asymptotically, while Gag ZiL cluster density increased linearly. Additionally, the directed movement of Gag, but not Gag ZiL , was maintained at a constant speed, suggesting that the two proteins experience different external driving forces. Assembly was abolished when Gag was rendered monomeric by NC deletion. Collectively, these results suggest that, beyond inducing Gag to form low-ordered multimer basic assembly units, vRNA is essential in scaffolding and maintaining the stability of the subsequent assembly process. This finding should advance the current understanding of HIV-1 and, potentially, other retroviruses. Copyright © 2018 the Author(s). Published by PNAS.

Low profile, high load vertical rolling positioning stage

DOEpatents

Shu, Deming; Barraza, Juan

1996-01-01

A stage or support platform assembly for use in a synchrotron accurately positions equipment to be used in the beam line of the synchrotron. The support platform assembly includes an outer housing in which is disposed a lifting mechanism having a lifting platform or stage at its upper extremity on which the equipment is mounted. A worm gear assembly is located in the housing and is adapted to raise and lower a lifting shaft that is fixed to the lifting platform by an anti-binding connection. The lifting platform is moved vertically as the lifting shaft is moved vertically. The anti-binding connection prevents the shaft from rotating with respect to the platform, but does permit slight canting of the shaft with respect to the lifting platform so as to eliminate binding and wear due to possible tolerance mismatches. In order to ensure that the lifting mechanism does not move in a horizontal direction as it is moved vertically, at least three linear roller bearing assemblies are arranged around the outer-periphery of the lifting mechanism. One of the linear roller bearing assemblies can be adjusted so that the roller bearings apply a loading force against the lifting mechanism. Alternatively, a cam mechanism can be used to provide such a loading force.

Hygrothermal Performance of West Coast Wood Deck Roofing System

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

Pallin, Simon B.; Kehrer, Manfred; Desjarlais, Andre Omer

2014-02-01

Simulations of roofing assemblies are necessary in order to understand and adequately predict actual the hygrothermal performance. At the request of GAF, simulations have been setup to verify the difference in performance between white and black roofing membrane colors in relation to critical moisture accumulation for traditional low slope wood deck roofing systems typically deployed in various western U.S. Climate Zones. The performance of these roof assemblies has been simulated in the hygrothermal calculation tool of WUFI, from which the result was evaluated based on a defined criterion for moisture safety. The criterion was defined as the maximum accepted watermore » content for wood materials and the highest acceptable moisture accumulation rate in relation to the risk of rot. Based on the criterion, the roof assemblies were certified as being either safe, risky or assumed to fail. The roof assemblies were simulated in different western climates, with varying insulation thicknesses, two different types of wooden decking, applied with varying interior moisture load and with either a high or low solar absorptivity at the roof surface (black or white surface color). The results show that the performance of the studied roof assemblies differs with regard to all of the varying parameters, especially the climate and the indoor moisture load.« less

Order from the disorder: hierarchical nanostructures self-assembled from the gas phase (Conference Presentation)

NASA Astrophysics Data System (ADS)

Di Fonzo, Fabio

2017-02-01

The assembly of nanoscale building blocks in engineered mesostructures is one of the fundamental goals of nanotechnology. Among the various processes developed to date, self-assembly emerges as one of the most promising, since it relays solely on basic physico-chemical forces. Our research is focused on a new type of self-assembly strategy from the gas-phase: Scattered Ballistic Deposition (SBD). SBD arises from the interaction of a supersonic molecular beam with a static gas and enables the growth of quasi-1D hierarchical mesostructures. Overall, they resemble a forest composed of individual, high aspect-ratio, tree-like structures, assembled from amorphous or crystalline nanoparticles. SBD is a general occurring phenomenon and can be obtained with different vapour or cluster sources. In particular, SBD by Pulsed Laser Deposition is a convenient physical vapor technique that allows the generation of supersonic plasma jets from any inorganic material irrespective of melting temperature, preserving even the most complex stoichiometries. One of the advantages of PLD over other vapour deposition techniques is extremely wide operational pressure range, from UHV to ambient pressure. These characteristics allowed us to develop quasi-1D hierarchical nanostructures from different transition metal oxides, semiconductors and metals. The precise control offered by the SBD-PLD technique over material properties at the nanoscale allowed us to fabricate ultra-thin, high efficiency hierarchical porous photonic crystals with Bragg reflectivity up to 85%. In this communication we will discuss the application of these materials to solar energy harvesting and storage, stimuli responsive photonic crystals and smart surfaces with digital control of their wettability behaviour.

Unraveling the Driving Forces in the Self-Assembly of Monodisperse Naphthalenediimide-Oligodimethylsiloxane Block Molecules

PubMed Central

2017-01-01

Block molecules belong to a rapidly growing research field in materials chemistry in which discrete macromolecular architectures bridge the gap between block copolymers (BCP) and liquid crystals (LCs). The merging of characteristics from both BCP and LCs is expected to result in exciting breakthroughs, such as the discovery of unexpected morphologies or significant shrinking of domain spacings in materials that possess the high definition of organic molecules and the processability of polymers. Here we report the bulk self-assembly of two families of monodisperse block molecules comprised of naphthalenediimides (NDIs) and oligodimethylsiloxanes (ODMS). These materials are characterized by waxy texture, strong long-range order, and very low mobility, typical properties of conformationally disordered crystals. Our investigation unambiguously reveals that thermodynamic immiscibility and crystallization direct the self-assembly of ODMS-based block molecules. We show that a synergy of high incompatibility between the blocks and crystallization of the NDIs causes nanophase separation, giving access to hexagonally packed columnar (Colh) and lamellar (LAM) morphologies with sub-10 nm periodicities. The domain spacings can be tuned by mixing molecules with different ODMS lengths and the same number of NDIs, introducing an additional layer of control. X-ray scattering experiments reveal macrophase separation whenever this constitutional bias is not observed. Finally, we highlight our “ingredient approach” to obtain perfect order in sub-10 nm structured materials with a simple strategy built on a crystalline “hard” moiety and an incompatible “soft” ODMS partner. Following this simple rule, our recipe can be extended to a number of systems. PMID:28380290

Surface confined metallosupramolecular architectures: formation and scanning tunneling microscopy characterization.

PubMed

Li, Shan-Shan; Northrop, Brian H; Yuan, Qun-Hui; Wan, Li-Jun; Stang, Peter J

2009-02-17

Metallosupramolecular compounds have attracted a great deal of attention over the past two decades largely because of their unique, highly complex structural characteristics and their potential electronic, magnetic, optical, and catalytic properties. These molecules can be prepared with relative ease using coordination-driven self-assembly techniques. In particular, the use of electron-poor square-planar Pt(II) transition metals in conjunction with rigid, electron-rich pyridyl donors has enabled the spontaneous self-assembly of a rich library of 2D metallacyclic and 3D metallacage assemblies via the directional-bonding approach. With this progress in the preparation and characterization of metallosupramolecules, researchers have now turned their attention toward fully exploring and developing their materials properties. Assembling metallosupramolecular compounds on solid supports represents a vitally important step toward developing their materials properties. Surfaces provide a means of uniformly aligning and orienting these highly symmetric metallacycles and metallacages. This uniformity increases the level of coherence between molecules above that which can be achieved in the solution phase and provides a way to integrate adsorbed layers, or adlayers, into a solid-state materials setting. The dynamic nature of kinetically labile Pt(II)-N coordination bonds requires us to adjust deposition and imaging conditions to retain the assemblies' stability. Toward these aims, we have used scanning tunneling microscopy (STM) to image these adlayers and to understand the factors that govern surface self-assembly and the interactions that influence their structure and stability. This Account describes our efforts to deposit 2D rectangular and square metallacycles and 3D trigonal bipyramidal and chiral trigonal prism metallacages on highly oriented pyrolytic graphite (HOPG) and Au(111) substrates to give intact assemblies and ordered adlayers. We have investigated the effects of varying the size, symmetry, and dimensionality of supramolecular adsorbates, the choice of substrate, the use of a molecular template, and the effects of chirality. Our systematic investigations provide insights into the various adsorbate-adsorbate and substrate-adsorbate interactions that largely determine the architecture of each assembly and affect their performance in a materials setting. Rational control over adlayer formation and structure will greatly enhance the potential of these supramolecules to be used in a variety of applications such as host-guest sensing/diagnostic systems, molecular electronic devices, and heterogeneous stereoselective synthesis and catalysis.

Controlling Self-Assembly of Engineered Peptides on Graphite by Rational Mutation

PubMed Central

So, Christopher R.; Hayamizu, Yuhei; Yazici, Hilal; Gresswell, Carolyn; Khatayevich, Dmitriy; Tamerler, Candan; Sarikaya, Mehmet

2012-01-01

Self-assembly of proteins on surfaces is utilized in many fields to integrate intricate biological structures and diverse functions with engineered materials. Controlling proteins at bio-solid interfaces relies on establishing key correlations between their primary sequences and resulting spatial organizations on substrates. Protein self-assembly, however, remains an engineering challenge. As a novel approach, we demonstrate here that short dodecapeptides selected by phage display are capable of self-assembly on graphite and form long-range ordered biomolecular nanostructures. Using atomic force microscopy and contact angle studies, we identify three amino-acid domains along the primary sequence that steer peptide ordering and lead to nanostructures with uniformly displayed residues. The peptides are further engineered via simple mutations to control fundamental interfacial processes, including initial binding, surface aggregation and growth kinetics, and intermolecular interactions. Tailoring short peptides via their primary sequence offers versatile control over molecular self-assembly, resulting in well-defined surface properties essential in building engineered, chemically rich, bio-solid interfaces. PMID:22233341

Facile Control of the Porous Structure of Larch-Derived Mesoporous Carbons via Self-Assembly for Supercapacitors

PubMed Central

Zhao, Xin; Li, Wei; Chen, Honglei; Wang, Shoujuan; Kong, Fangong; Liu, Shouxin

2017-01-01

Mesoporous carbons have been successfully synthesized via self-assembly using larch-based resins as precursors and triblock copolymers as soft templates. The porous structure of mesoporous carbons can be tailored by adjusting the ratio of hydrophilic/hydrophobic (EO/PO) units owing to interfacial curvature. Interestingly, the porous structures show a distinct change from vortex-like to worm-like pores, to stripe-like pores, and to ordered two-dimensional hexagonal pores as the ratio of hydrophilic/hydrophobic units increases, indicating the significant effect of EO/PO ratio on the porous structure. The mesoporous carbons as supercapacitor electrodes exhibit superior electrochemical capacitive performance and a high degree of reversibility after 2000 cycles for supercapacitors due to the well-defined mesoporosity of the carbon materials. Meanwhile, the superior carbon has a high specific capacitance of 107 F·g−1 in 6 M KOH at a current density of 10 A·g−1. PMID:29156641

Facile Control of the Porous Structure of Larch-Derived Mesoporous Carbons via Self-Assembly for Supercapacitors.

PubMed

Zhao, Xin; Li, Wei; Chen, Honglei; Wang, Shoujuan; Kong, Fangong; Liu, Shouxin

2017-11-20

Mesoporous carbons have been successfully synthesized via self-assembly using larch-based resins as precursors and triblock copolymers as soft templates. The porous structure of mesoporous carbons can be tailored by adjusting the ratio of hydrophilic/hydrophobic (EO/PO) units owing to interfacial curvature. Interestingly, the porous structures show a distinct change from vortex-like to worm-like pores, to stripe-like pores, and to ordered two-dimensional hexagonal pores as the ratio of hydrophilic/hydrophobic units increases, indicating the significant effect of EO/PO ratio on the porous structure. The mesoporous carbons as supercapacitor electrodes exhibit superior electrochemical capacitive performance and a high degree of reversibility after 2000 cycles for supercapacitors due to the well-defined mesoporosity of the carbon materials. Meanwhile, the superior carbon has a high specific capacitance of 107 F·g -1 in 6 M KOH at a current density of 10 A·g -1 .

Self-Assembled Array of Tethered Manganese Oxide Nanoparticles for the Next Generation of Energy Storage

PubMed Central

Stevens, Tyler E.; Pearce, Charles J.; Whitten, Caleah N.; Grant, Richard P.; Monson, Todd C.

2017-01-01

Many challenges must be overcome in order to create reliable electrochemical energy storage devices with not only high energy but also high power densities. Gaps exist in both battery and supercapacitor technologies, with neither one satisfying the need for both large power and energy densities in a single device. To begin addressing these challenges (and others), we report a process to create a self-assembled array of electrochemically active nanoparticles bound directly to a current collector using extremely short (2 nm or less) conductive tethers. The tethered array of nanoparticles, MnO in this case, bound directly to a gold current collector via short conducting linkages eliminates the need for fillers, resulting in a material which achieves 99.9% active material by mass (excluding the current collector). This strategy is expected to be both scalable as well as effective for alternative tethers and metal oxide nanoparticles. PMID:28287183

Smart substrates: Making multi-chip modules smarter

NASA Astrophysics Data System (ADS)

Wunsch, T. F.; Treece, R. K.

1995-05-01

A novel multi-chip module (MCM) design and manufacturing methodology which utilizes active CMOS circuits in what is normally a passive substrate realizes the 'smart substrate' for use in highly testable, high reliability MCMS. The active devices are used to test the bare substrate, diagnose assembly errors or integrated circuit (IC) failures that require rework, and improve the testability of the final MCM assembly. A static random access memory (SRAM) MCM has been designed and fabricated in Sandia Microelectronics Development Laboratory in order to demonstrate the technical feasibility of this concept and to examine design and manufacturing issues which will ultimately determine the economic viability of this approach. The smart substrate memory MCM represents a first in MCM packaging. At the time the first modules were fabricated, no other company or MCM vendor had incorporated active devices in the substrate to improve manufacturability and testability, and thereby improve MCM reliability and reduce cost.

A translator writing system for microcomputer high-level languages and assemblers

NASA Technical Reports Server (NTRS)

Collins, W. R.; Knight, J. C.; Noonan, R. E.

1980-01-01

In order to implement high level languages whenever possible, a translator writing system of advanced design was developed. It is intended for routine production use by many programmers working on different projects. As well as a fairly conventional parser generator, it includes a system for the rapid generation of table driven code generators. The parser generator was developed from a prototype version. The translator writing system includes various tools for the management of the source text of a compiler under construction. In addition, it supplies various default source code sections so that its output is always compilable and executable. The system thereby encourages iterative enhancement as a development methodology by ensuring an executable program from the earliest stages of a compiler development project. The translator writing system includes PASCAL/48 compiler, three assemblers, and two compilers for a subset of HAL/S.

Rapid Ordering in "Wet Brush" Block Copolymer/Homopolymer Ternary Blends.

PubMed

Doerk, Gregory S; Yager, Kevin G

2017-12-26

The ubiquitous presence of thermodynamically unfavored but kinetically trapped topological defects in nanopatterns formed via self-assembly of block copolymer thin films may prevent their use for many envisioned applications. Here, we demonstrate that lamellae patterns formed by symmetric polystyrene-block-poly(methyl methacrylate) diblock copolymers self-assemble and order extremely rapidly when the diblock copolymers are blended with low molecular weight homopolymers of the constituent blocks. Being in the "wet brush" regime, the homopolymers uniformly distribute within their respective self-assembled microdomains, preventing increases in domain widths. An order-of-magnitude increase in topological grain size in blends over the neat (unblended) diblock copolymer is achieved within minutes of thermal annealing as a result of the significantly higher power law exponent for ordering kinetics in the blends. Moreover, the blends are demonstrated to be capable of rapid and robust domain alignment within micrometer-scale trenches, in contrast to the corresponding neat diblock copolymer. These results can be attributed to the lowering of energy barriers associated with domain boundaries by bringing the system closer to an order-disorder transition through low molecular weight homopolymer blending.

77 FR 52682 - Tapered Roller Bearings and Parts Thereof, Finished and Unfinished, From the People's Republic of...

Federal Register 2010, 2011, 2012, 2013, 2014

2012-08-30

... OTR Wheel Engineering, Inc.'s Wheel Hub Assemblies and TRBs,'' dated February 7, 2011 (finding Blackstone OTR LLC and OTR Wheel Engineering, Inc.'s wheel hub assemblies are within the scope of the order... Trend Engineering Ltd.'s Wheel Hub Assemblies,'' dated April 18, 2011 (finding New Trend Engineering...

Driving Forces of the Self-Assembly of Supramolecular Systems: Partially Ordered Mesophases

NASA Astrophysics Data System (ADS)

Shcherbina, M. A.; Chvalun, S. N.

2018-06-01

The main aspects are considered of the self-organization of a new class of liquid crystalline compounds, rigid sector-shaped and cone-shaped dendrons. Theoretical approaches to the self-assembly of different amphiphilic compounds (lipids, bolaamphiphiles, block copolymers, and polyelectrolytes) are described. Particular attention is given to the mesophase structures that emerge during the self-organization of mesophases characterized by intermediate degrees of ordering, e.g., plastic crystals, the rotation-crystalline phase in polymers, ordered and disordered two-dimensional columnar phases, and bicontinuous cubic phases of different symmetry.

Self-Assembly and Crystallization of Hairy (f-Star) and DNA-Grafted Nanocubes

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

Knorowski, Christopher; Travesset, Alex

Nanoparticle superlattices are key to realizing many of the materials that will solve current technological challenges. Particularly important for their optical, mechanical or catalytic properties are superlattices of anisotropic (nonspherical) nanoparticles. The key challenge is how to program anisotropic nanoparticles to self-assemble into the relevant structures. In this Article, using numerical simulations, we show that “hairy” (f-star) or DNA grafted on nanocubes provides a general framework to direct the self-assembly into phases with crystalline, liquid crystalline, rotator, or noncrystalline phases with both long-range positional and orientational order. We discuss the relevance of these phases for engineering nanomaterials or micromaterials displayingmore » precise orientational order, realization of dry superlattices as well as for the field of programmed self-assembly of anisotropic nanoparticles in general.« less

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

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

Block Copolymers and Ionic Liquids: A New Class of Functional Nanocomposites

NASA Astrophysics Data System (ADS)

Lodge, Timothy

2009-03-01

Block copolymers provide a remarkably versatile platform for achieving desired nanostructures by self-assembly, with lengthscales varying from a few nanometers up to several hundred nanometers. Ionic liquids are an emerging class of solvents, with an appealing set of physical attributes. These include negligible vapor pressure, high chemical and thermal stability, tunable solvation properties, high ionic conductivity, and wide electrochemical windows. For various applications it will be necessary to solidify the ionic liquid into particular spatial arrangements, such as membranes or gels, or to partition the ionic liquid in coexisting phases, such as microemulsions and micelles. One example includes formation of spherical, cylindrical, and vesicular micelles by poly(butadiene-b-ethylene oxide) and poly(styrene-b-methylmethacrylate) in the common hydrophobic ionic liquids [BMI][PF6] and [EMI][TFSI]. This work has been extended to the formation of reversible micelle shuttles between ionic liquids and water, whereby entire micelles transfer from one phase to the other, reversibly, depending on temperature and solvent quality. Formation of ion gels has been achieved by self-assembly of poly(styrene-b-ethylene oxide-b-styrene) triblocks in ionic liquids, and by the thermoreversible system poly(N-isopropylacrylamide-b-ethylene oxide-b-N-isopropylacrylamide), using as little as 4% copolymer. Further, these gels have been shown to be remarkably effective as gate dielectrics in organic thin film transistors. The remarkably high capacitance of the ion gels (> 10 μF/cm^2) supports a very high carrier density in an organic semiconductor such as poly(3-hexylthiophene), leading to milliamp currents for low applied voltages. Furthermore, the rapid mobility of the ions enables switching speeds approaching 10 kHz, orders of magnitude higher than achievable with other polymer-based dielectrics such as PEO/LiClO4. Finally, we have shown that ordered nanostructures of block copolymers plus ionic liquids show the characteristic self-assembly properties of strongly-segregated systems. Prospects for anisotropic ionic conductivity are also being explored.

Molecular Motor-Induced Instabilities and Cross Linkers Determine Biopolymer Organization

PubMed Central

Smith, D.; Ziebert, F.; Humphrey, D.; Duggan, C.; Steinbeck, M.; Zimmermann, W.; Käs, J.

2007-01-01

All eukaryotic cells rely on the active self-organization of protein filaments to form a responsive intracellular cytoskeleton. The necessity of motility and reaction to stimuli additionally requires pathways that quickly and reversibly change cytoskeletal organization. While thermally driven order-disorder transitions are, from the viewpoint of physics, the most obvious method for controlling states of organization, the timescales necessary for effective cellular dynamics would require temperatures exceeding the physiologically viable temperature range. We report a mechanism whereby the molecular motor myosin II can cause near-instantaneous order-disorder transitions in reconstituted cytoskeletal actin solutions. When motor-induced filament sliding diminishes, the actin network structure rapidly and reversibly self-organizes into various assemblies. Addition of stable cross linkers was found to alter the architectures of ordered assemblies. These isothermal transitions between dynamic disorder and self-assembled ordered states illustrate that the interplay between passive crosslinking and molecular motor activity plays a substantial role in dynamic cellular organization. PMID:17604319

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.

X-Ray Optics at NASA Marshall Space Flight Center

NASA Technical Reports Server (NTRS)

O'Dell, Stephen L.; Atkins, Carolyn; Broadway, David M.; Elsner, Ronald F.; Gaskin, Jessica A.; Gubarev, Mikhail V.; Kilaru, Kiranmayee; Kolodziejczak, Jeffery J.; Ramsey, Brian D.; Roche, Jacqueline M.;

Large three-dimensional photonic crystals based on monocrystalline liquid crystal blue phases.

PubMed

Chen, Chun-Wei; Hou, Chien-Tsung; Li, Cheng-Chang; Jau, Hung-Chang; Wang, Chun-Ta; Hong, Ching-Lang; Guo, Duan-Yi; Wang, Cheng-Yu; Chiang, Sheng-Ping; Bunning, Timothy J; Khoo, Iam-Choon; Lin, Tsung-Hsien

2017-09-28

Although there have been intense efforts to fabricate large three-dimensional photonic crystals in order to realize their full potential, the technologies developed so far are still beset with various material processing and cost issues. Conventional top-down fabrications are costly and time-consuming, whereas natural self-assembly and bottom-up fabrications often result in high defect density and limited dimensions. Here we report the fabrication of extraordinarily large monocrystalline photonic crystals by controlling the self-assembly processes which occur in unique phases of liquid crystals that exhibit three-dimensional photonic-crystalline properties called liquid-crystal blue phases. In particular, we have developed a gradient-temperature technique that enables three-dimensional photonic crystals to grow to lateral dimensions of ~1 cm (~30,000 of unit cells) and thickness of ~100 μm (~ 300 unit cells). These giant single crystals exhibit extraordinarily sharp photonic bandgaps with high reflectivity, long-range periodicity in all dimensions and well-defined lattice orientation.Conventional fabrication approaches for large-size three-dimensional photonic crystals are problematic. By properly controlling the self-assembly processes, the authors report the fabrication of monocrystalline blue phase liquid crystals that exhibit three-dimensional photonic-crystalline properties.

Real-Time Probing of Nanowire Assembly Kinetics at the Air-Water Interface by In Situ Synchrotron X-Ray Scattering.

PubMed

He, Zhen; Jiang, Hui-Jun; Wu, Long-Long; Liu, Jian-Wei; Wang, Geng; Wang, Xiao; Wang, Jin-Long; Hou, Zhong-Huai; Chen, Gang; Yu, Shu-Hong

2018-07-02

Although many assembly strategies have been used to successfully construct well-aligned nanowire (NW) assemblies, the understanding of their assembly kinetics has remained elusive, which restricts the development of NW-based device and circuit fabrication. Now a versatile strategy that combines interfacial assembly and synchrotron-based grazing-incidence small-angle X-ray scattering (GISAXS) is presented to track the assembly evolution of the NWs in real time. During the interface assembly process, the randomly dispersed NWs gradually aggregate to form small ordered NW-blocks and finally are constructed into well-defined NW monolayer driven by the conformation entropy. The NW assembly mechanism can be well revealed by the thermodynamic analysis and large-scale molecular dynamics theoretical evaluation. These findings point to new opportunities for understanding NW assembly kinetics and manipulating NW assembled structures by bottom-up strategy. © 2018 Wiley-VCH Verlag GmbH & Co. KGaA, Weinheim.

Symmetry based assembly of a 2 dimensional protein lattice

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

Poulos, Sandra; Agah, Sayeh; Jallah, Nikardi

2017-04-18

The design of proteins that self-assemble into higher order architectures is of great interest due to their potential application in nanotechnology. Specifically, the self-assembly of proteins into ordered lattices is of special interest to the field of structural biology. Here we designed a 2 dimensional (2D) protein lattice using a fusion of a tandem repeat of three TelSAM domains (TTT) to the Ferric uptake regulator (FUR) domain. We determined the structure of the designed (TTT-FUR) fusion protein to 2.3 Å by X-ray crystallographic methods. In agreement with the design, a 2D lattice composed of TelSAM fibers interdigitated by the FURmore » domain was observed. As expected, the fusion of a tandem repeat of three TelSAM domains formed 21 screw axis, and the self-assembly of the ordered oligomer was under pH control. We demonstrated that the fusion of TTT to a domain having a 2-fold symmetry, such as the FUR domain, can produce an ordered 2D lattice. The TTT-FUR system combines features from the rotational symmetry matching approach with the oligomer driven crystallization method. This TTT-FUR fusion was amenable to X-ray crystallographic methods, and is a promising crystallization chaperone.« less

Applied metrology in the production of superconducting model magnets for particle accelerators

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

Ferradas Troitino, Jose; Bestmann, Patrick; Bourcey, Nicolas

2017-12-22

The production of superconducting magnets for particle accelerators involves high precision assemblies and tight tolerances, in order to achieve the requirements for their appropriate performance. It is therefore essential to have a strict control and traceability over the geometry of each component of the system, and also to be able to compensate possible inherent deviations coming from the production process.

Development of IS2100: An Information Systems Laboratory.

DTIC Science & Technology

1985-03-01

systems for digital logic; hardware architecture; machine, assembly, and high order language programming; and application packages such as database... applications and limitations. They should be able to define, demonstrate and/or discuss how computers are used, how they do their work, how to use them, and...limitations. Hands on operation of the hardware and software provides experience that aids in future selection of hardware systems and applications

Origin of the Reflectin Gene and Hierarchical Assembly of Its Protein.

PubMed

Guan, Zhe; Cai, Tiantian; Liu, Zhongmin; Dou, Yunfeng; Hu, Xuesong; Zhang, Peng; Sun, Xin; Li, Hongwei; Kuang, Yao; Zhai, Qiran; Ruan, Hao; Li, Xuanxuan; Li, Zeyang; Zhu, Qihui; Mai, Jingeng; Wang, Qining; Lai, Luhua; Ji, Jianguo; Liu, Haiguang; Xia, Bin; Jiang, Taijiao; Luo, Shu-Jin; Wang, Hong-Wei; Xie, Can

2017-09-25

Cephalopods, the group of animals including octopus, squid, and cuttlefish, have remarkable ability to instantly modulate body coloration and patterns so as to blend into surrounding environments [1, 2] or send warning signals to other animals [3]. Reflectin is expressed exclusively in cephalopods, filling the lamellae of intracellular Bragg reflectors that exhibit dynamic iridescence and structural color change [4]. Here, we trace the possible origin of the reflectin gene back to a transposon from the symbiotic bioluminescent bacterium Vibrio fischeri and report the hierarchical structural architecture of reflectin protein. Intrinsic self-assembly, and higher-order assembly tightly modulated by aromatic compounds, provide insights into the formation of multilayer reflectors in iridophores and spherical microparticles in leucophores and may form the basis of structural color change in cephalopods. Self-assembly and higher-order assembly in reflectin originated from a core repeating octapeptide (here named protopeptide), which may be from the same symbiotic bacteria. The origin of the reflectin gene and assembly features of reflectin protein are of considerable biological interest. The hierarchical structural architecture of reflectin and its domain and protopeptide not only provide insights for bioinspired photonic materials but also serve as unique "assembly tags" and feasible molecular platforms in biotechnology. Copyright © 2017 Elsevier Ltd. All rights reserved.

Backward assembly planning with DFA analysis

NASA Technical Reports Server (NTRS)

Lee, Sukhan (Inventor)

1995-01-01

An assembly planning system that operates based on a recursive decomposition of assembly into subassemblies, and analyzes assembly cost in terms of stability, directionality, and manipulability to guide the generation of preferred assembly plans is presented. The planning in this system incorporates the special processes, such as cleaning, testing, labeling, etc. that must occur during the assembly, and handles nonreversible as well as reversible assembly tasks through backward assembly planning. In order to increase the planning efficiency, the system avoids the analysis of decompositions that do not correspond to feasible assembly tasks. This is achieved by grouping and merging those parts that can not be decomposable at the current stage of backward assembly planning due to the requirement of special processes and the constraint of interconnection feasibility. The invention includes methods of evaluating assembly cost in terms of the number of fixtures (or holding devices) and reorientations required for assembly, through the analysis of stability, directionality, and manipulability. All these factors are used in defining cost and heuristic functions for an AO* search for an optimal plan.

Surface Confined Metallosupramolecular Architectures: Formation and STM Characterization

PubMed Central

Li, Shan-Shan; Northrop, Brian H.; Yuan, Qun-Hui; Wan, Li-Jun; Stang, Peter J.

2009-01-01

CONSPECTUS Metallosupramolecular compounds have attracted a great deal of attention over the past two decades largely because of their unique, highly-complex structural characteristics, the fact that they can be prepared with relative ease using coordination-driven self-assembly techniques, and their potential electronic, magnetic, optical, and catalytic properties. In particular, the use of electron-poor square planar Pt(II) transition metals in conjunction with rigid, electron-rich pyridyl donors had enabled the spontaneous self-assembly of a rich library of 2D metallacyclic and 3D metallacage assemblies via the directional-bonding approach. With the tremendous progress that has been made in the preparation and characterization of metallosupramolecules, much attention is now being turned toward fully exploring and developing their materials properties. Assembling metallosupramolecular compounds on solid supports represents a vitally important step toward developing their materials properties. Surfaces provide a means of uniformly aligning and orienting these highly symmetric metallacycles and metallacages, which increases the level of coherence between molecules above that which can be achieved in the solution phase and affords a means of integrating adlayers into a solid-state materials setting. The dynamic nature of kinetically labile Pt(II)-N coordination bonds, however, requires that deposition and imaging conditions be appropriate to retain the assemblies' stability. Toward these aims it is imperative to understand the factors that govern surface self-assembly and the interactions that influence the structure and stability of the resulting adlayer. Such insight can be obtained from Scanning Tunneling Microscopy (STM), which has emerged as a powerful technique for the imaging and characterization of self-assembled adlayers. This account describes the means by which 2D rectangular and square metallacycles and 3D trigonal bipyrimidal and chiral trigonal prism metallacages can be deposited on Highly Oriented Pyrolytic Graphite (HOPG) and Au(111) substrates such that the assemblies remain intact and result in ordered adlayers. The effects of varying the size, symmetry, and dimensionality of supramolecular adsorbates, the choice of substrate, the use of a molecular template, and the effects of chirality have been investigated. These systematic investigations provide much insight into the various adsorbate-adsorbate and substrate-adsorbate interactions that largely determine the architecture of each assembly and affect their performance in a materials setting. Exhibiting the ability to rationally control adlayer formation and structure will greatly enhance the potential of these supramolecules to be used in a variety of applications such as in host-guest sensing/diagnostic systems, molecular electronic devices, and in heterogeneous stereoselective synthesis and catalysis. PMID:19072706

Regulation of Corneal Stroma Extracellular Matrix Assembly

PubMed Central

Chen, Shoujun; Mienaltowski, Michael J.; Birk, David E.

2014-01-01

The transparent cornea is the major refractive element of the eye. A finely controlled assembly of the stromal extracellular matrix is critical to corneal function, as well as in establishing the appropriate mechanical stability required to maintain corneal shape and curvature. In the stroma, homogeneous, small diameter collagen fibrils, regularly packed with a highly ordered hierarchical organization, are essential for function. This review focuses on corneal stroma assembly and the regulation of collagen fibrillogenesis. Corneal collagen fibrillogenesis involves multiple molecules interacting in sequential steps, as well as interactions between keratocytes and stroma matrix components. The stroma has the highest collagen V:I ratio in the body. Collagen V regulates the nucleation of protofibril assembly, thus controlling the number of fibrils and assembly of smaller diameter fibrils in the stroma. The corneal stroma is also enriched in small leucine-rich proteoglycans (SLRPs) that cooperate in a temporal and spatial manner to regulate linear and lateral collagen fibril growth. In addition, the fibril-associated collagens (FACITs) such as collagen XII and collagen XIV have roles in the regulation of fibril packing and inter-lamellar interactions. A communicating keratocyte network contributes to the overall and long-range regulation of stromal extracellular matrix assembly, by creating micro-domains where the sequential steps in stromal matrix assembly are controlled. Keratocytes control the synthesis of extracellular matrix components, which interact with the keratocytes dynamically to coordinate the regulatory steps into a cohesive process. Mutations or deficiencies in stromal regulatory molecules result in altered interactions and deficiencies in both transparency and refraction, leading to corneal stroma pathobiology such as stromal dystrophies, cornea plana and keratoconus. PMID:25819456