Sample records for organic protomolecule assembly
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Self assembly of organic nanostructures and dielectrophoretic assembly of inorganic nanowires.
Dholakia, Geetha; Kuo, Steven; Allen, E. L.
2007-03-01
Self assembly techniques enable the organization of organic molecules into nanostructures. Currently engineering strategies for efficient assembly and routine integration of inorganic nanoscale objects into functional devices is very limited. AC Dielectrophoresis is an efficient technique to manipulate inorganic nanomaterials into higher dimensional structures. We used an alumina template based sol-gel synthesis method for the growth of various metal oxide nanowires with typical diameters of 100-150 nm, ranging in length from 3-10 μm. Here we report the dielectrophoretic assembly of TiO2 nanowires, an important material for photocatalysis and photovoltaics, onto interdigitated devices. Self assembly in organic nanostructures and its dependence on structure and stereochemistry of the molecule and dielectrophoretic field dependence in the assembly of inorganic nanowires will be compared and contrasted. Tunneling spectroscopy and DOS of these nanoscale systems will also be discussed.
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Properties of Molecular organized assemblies at interfaces
Indian Academy of Sciences (India)
Dr.AURNA
Organized molecular assemblies. An organized molecular assembly is a group of atoms or ..... Simulations of the growth of clusters on a .... dynamics and function. ➢Actively ... Study of amphiphilic derivatives of YIGSR, mutated at hyper active ...
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From self-organization to self-assembly: a new materialism?
Vincent, Bernadette Bensaude
2016-09-01
While self-organization has been an integral part of academic discussions about the distinctive features of living organisms, at least since Immanuel Kant's Critique of Judgement, the term 'self-assembly' has only been used for a few decades as it became a hot research topic with the emergence of nanotechnology. Could it be considered as an attempt at reducing vital organization to a sort of assembly line of molecules? Considering the context of research on self-assembly I argue that the shift of attention from self-organization to self-assembly does not really challenge the boundary between chemistry and biology. Self-assembly was first and foremost investigated in an engineering context as a strategy for manufacturing without human intervention and did not raise new perspectives on the emergence of vital organization itself. However self-assembly implies metaphysical assumptions that this paper tries to disentangle. It first describes the emergence of self-assembly as a research field in the context of materials science and nanotechnology. The second section outlines the metaphysical implications and will emphasize a sharp contrast between the ontology underlying two practices of self-assembly developed under the umbrella of synthetic biology. And unexpectedly, we shall see that chemists are less on the reductionist side than most synthetic biologists. Finally, the third section ventures some reflections on the kind of design involved in self-assembly practices.
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Assembly of cells and vesicles for organ engineering
International Nuclear Information System (INIS)
Taguchi, Tetsushi
2011-01-01
The development of materials and technologies for the assembly of cells and/or vesicles is a key for the next generation of tissue engineering. Since the introduction of the tissue engineering concept in 1993, various types of scaffolds have been developed for the regeneration of connective tissues in vitro and in vivo. Cartilage, bone and skin have been successfully regenerated in vitro, and these regenerated tissues have been applied clinically. However, organs such as the liver and pancreas constitute numerous cell types, contain small amounts of extracellular matrix, and are highly vascularized. Therefore, organ engineering will require the assembly of cells and/or vesicles. In particular, adhesion between cells/vesicles will be required for regeneration of organs in vitro. This review introduces and discusses the key technologies and materials for the assembly of cells/vesicles for organ regeneration. (topical review)
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Quantification of Stereochemical Communication in Metal–Organic Assemblies
Castilla, Ana M.; Miller, Mark A.; Nitschke, Jonathan R.; Smulders, Maarten M.J.
2016-01-01
The derivation and application of a statistical mechanical model to quantify stereochemical communication in metal–organic assemblies is reported. The factors affecting the stereochemical communication within and between the metal stereocenters of the assemblies were experimentally studied by
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Self-Organization and the Self-Assembling Process in Tissue Engineering
Eswaramoorthy, Rajalakshmanan; Hadidi, Pasha; Hu, Jerry C.
2015-01-01
In recent years, the tissue engineering paradigm has shifted to include a new and growing subfield of scaffoldless techniques which generate self-organizing and self-assembling tissues. This review aims to provide a cogent description of this relatively new research area, with special emphasis on applications toward clinical use and research models. Particular emphasis is placed on providing clear definitions of self-organization and the self-assembling process, as delineated from other scaffoldless techniques in tissue engineering and regenerative medicine. Significantly, during formation, self-organizing and self-assembling tissues display biological processes similar to those that occur in vivo. These help lead to the recapitulation of native tissue morphological structure and organization. Notably, functional properties of these tissues also approach native tissue values; some of these engineered tissues are already in clinical trials. This review aims to provide a cohesive summary of work in this field, and to highlight the potential of self-organization and the self-assembling process to provide cogent solutions to current intractable problems in tissue engineering. PMID:23701238
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Multifunctional Nanoparticles Self-Assembled from Small Organic Building Blocks for Biomedicine.
Xing, Pengyao; Zhao, Yanli
2016-09-01
Supramolecular self-assembly shows significant potential to construct responsive materials. By tailoring the structural parameters of organic building blocks, nanosystems can be fabricated, whose performance in catalysis, energy storage and conversion, and biomedicine has been explored. Since small organic building blocks are structurally simple, easily modified, and reproducible, they are frequently employed in supramolecular self-assembly and materials science. The dynamic and adaptive nature of self-assembled nanoarchitectures affords an enhanced sensitivity to the changes in environmental conditions, favoring their applications in controllable drug release and bioimaging. Here, recent significant research advancements of small-organic-molecule self-assembled nanoarchitectures toward biomedical applications are highlighted. Functionalized assemblies, mainly including vesicles, nanoparticles, and micelles are categorized according to their topological morphologies and functions. These nanoarchitectures with different topologies possess distinguishing advantages in biological applications, well incarnating the structure-property relationship. By presenting some important discoveries, three domains of these nanoarchitectures in biomedical research are covered, including biosensors, bioimaging, and controlled release/therapy. The strategies regarding how to design and characterize organic assemblies to exhibit biomedical applications are also discussed. Up-to-date research developments in the field are provided and research challenges to be overcome in future studies are revealed. © 2016 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.
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A simple method to prepare self-assembled organic-organic heterobilayers on metal substrates
Directory of Open Access Journals (Sweden)
L. D. Sun
2011-06-01
Full Text Available We demonstrate a self-assembly based simple method to prepare organic-organic heterobilayers on a metal substrate. By either sequential- or co-deposition of para-sexiphenyl (p-6P and pentacene molecules onto the Cu(110 surface in ultrahigh vacuum, p-6P/pentacene/Cu(110 heterobilayer is synthesized at room temperature. The layer sequence of the heterostructure is independent of the growth scenario indicating the p-6P/pentacene/Cu(110 is a self-assembled structure with lowest energy. Besides, the bilayer shows a very high orientational ordering and is thermally stable up to 430K.
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From metal-organic squares to porous zeolite-like supramolecular assemblies
Wang, Shuang
2010-12-29
We report the synthesis, structure, and characterization of two novel porous zeolite-like supramolecular assemblies, ZSA-1 and ZSA-2, having zeolite gis and rho topologies, respectively. The two compounds were assembled from functional metal-organic squares (MOSs) via directional hydrogen-bonding interactions and exhibited permanent microporosity and thermal stability up to 300 °C. © 2010 American Chemical Society.
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Improving Charge Injection in Organic Electronic Devices Using Self-Assembled Monolayers
Campbell, I. H.; Kress, J. D.; Martin, R. L.; Smith, D. L.; Barashkov, N. N.; Ferraris, J. P.
1997-03-01
Organic electronic devices consist of one or more insulating organic layers contacted by metallic conductors. The Schottky energy barrier between the metal and the organic material is determined by the work function of the metal contact as described in the ideal Schottky model. The magnitude of the metal/organic Schottky energy barrier controls charge injection from the metal into the organic layer. Previously, polar alkane-thiol based self-assembled monolayers (SAMs) were used to change the Schottky energy barrier between the metal and an organic film by more than 1 eV. In these SAMs, the large energy gap of the alkane molecules blocks charge injection into the organic layer despite the decrease of the Schottky energy barrier. Here, we demonstrate improved charge injection into the organic material by using conjugated self-assembled monolayers. The conjugated SAMs have modest energy gaps which allow improved charge injection into the organic layer. We present measurements of current-voltage characteristics and metal/organic Schottky energy barriers for device structures both with and without conjugated SAMs.
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Self-assembling bilayers of palladiumthiolates in organic media
Indian Academy of Sciences (India)
Unknown
applications in catalytic systems, solubalizing agents and drug delivery matrices. Following the pioneering efforts of ... In this context, self-assembly of amphipiles in nonpolar organic media assumes significance 8 since .... structures in clear contrast to lamellar phases formed by the higher members. We sought to image the ...
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Molecular self-assembly approaches for supramolecular electronic and organic electronic devices
Yip, Hin-Lap
Molecular self-assembly represents an efficient bottom-up strategy to generate structurally well-defined aggregates of semiconducting pi-conjugated materials. The capability of tuning the chemical structures, intermolecular interactions and nanostructures through molecular engineering and novel materials processing renders it possible to tailor a large number of unprecedented properties such as charge transport, energy transfer and light harvesting. This approach does not only benefit traditional electronic devices based on bulk materials, but also generate a new research area so called "supramolecular electronics" in which electronic devices are built up with individual supramolecular nanostructures with size in the sub-hundred nanometers range. My work combined molecular self-assembly together with several novel materials processing techniques to control the nucleation and growth of organic semiconducting nanostructures from different type of pi-conjugated materials. By tailoring the interactions between the molecules using hydrogen bonds and pi-pi stacking, semiconducting nanoplatelets and nanowires with tunable sizes can be fabricated in solution. These supramolecular nanostructures were further patterned and aligned on solid substrates through printing and chemical templating methods. The capability to control the different hierarchies of organization on surface provides an important platform to study their structural-induced electronic properties. In addition to using molecular self-assembly to create different organic nanostructures, functional self-assembled monolayer (SAM) formed by spontaneous chemisorption on surfaces was used to tune the interfacial property in organic solar cells. Devices showed dramatically improved performance when appropriate SAMs were applied to optimize the contact property for efficiency charge collection.
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Assembly of Nanoscale Organic Single-Crystal Cross-Wire Circuits
DEFF Research Database (Denmark)
Bjørnholm, Thomas
2009-01-01
Organic single-crystal transistors and circuits can be assembled by nanomechanical manipulation of nanowires of CuPc, F(16)CuPc, and SnO(2):Sb. The crossed bar devices have low operational voltage, high mobility and are stable in air. They can be combined into circuits, providing varied functions...... including inverters and NOR and NAND logic gates, opening new opportunities for organic nanoelectronics and highly sophisticated integrated logic devices....
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Tempas, Christopher D.
Self-assembled nanostructures at surfaces show promise for the development of next generation technologies including organic electronic devices and heterogeneous catalysis. In many cases, the functionality of these nanostructures is not well understood. This thesis presents strategies for the structural design of new on-surface metal-organic networks and probes their chemical reactivity. It is shown that creating uniform metal sites greatly increases selectivity when compared to ligand-free metal islands. When O2 reacts with single-site vanadium centers, in redox-active self-assembled coordination networks on the Au(100) surface, it forms one product. When O2 reacts with vanadium metal islands on the same surface, multiple products are formed. Other metal-organic networks described in this thesis include a mixed valence network containing Pt0 and PtII and a network where two Fe centers reside in close proximity. This structure is stable to temperatures >450 °C. These new on-surface assemblies may offer the ability to perform reactions of increasing complexity as future heterogeneous catalysts. The functionalization of organic semiconductor molecules is also shown. When a few molecular layers are grown on the surface, it is seen that the addition of functional groups changes both the film's structure and charge transport properties. This is due to changes in both first layer packing structure and the pi-electron distribution in the functionalized molecules compared to the original molecule. The systems described in this thesis were studied using high-resolution scanning tunneling microscopy, non-contact atomic force microscopy, and X-ray photoelectron spectroscopy. Overall, this work provides strategies for the creation of new, well-defined on-surface nanostructures and adds additional chemical insight into their properties.
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Organization and methods of radiation monitoring while working at nuclear critical assemblies
International Nuclear Information System (INIS)
Shishkin, G.V.; Komissarov, L.A.
1980-01-01
The organization and methods of environmental radiation monitoring while working at nuclear critical assemblies, are described. Necessary equipment for critical assemblies (signal and Ventilation systems, devices for recording accidental radiation levels of and for measuring radiation field distribution) and the personnel program of actions in case of nuclear accident. The dosimetric control at critical assemblies is usually ensured by telesystems. 8004-01 multi-channel dosimetric device is described as an example of such-system [ru
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Self-assembled fluorescent organic nanoparticles for live cell imaging
Fischer, I.; Petkau, K.; Dorland, Y.L.; Schenning, A.P.H.J.; Brunsveld, L.
2013-01-01
Fluorescent, cell-permeable, organic nanoparticles based on self-assembled p-conjugated oligomers with high absorption cross-sections and high quantum yields have been developed. The nanoparticles are generated with a tuneable density of amino groups for charge-mediated cellular uptake by a
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An introduction to ultrathin organic films from Langmuir-Blodgett to self-assembly
Ulman, Abraham
1991-01-01
The development of oriented organic monomolecular layers by the Langmuir-Blodgett (LB) and self-assembly (SA) techniques has led researchers toward their goal of assembling individual molecules into highly ordered architectures. Thus the continually growing contribution of LB and SA systems to the chemistry and physics of thin organic films is widely recognized. Equally well-known is the difficulty in keeping up to date with the burgeoning multidisciplinary research in this area. Dr. Ulman provides a massive survey of the available literature. The book begins with a section on analytical tools
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Controlling Schottky energy barriers in organic electronic devices using self-assembled monolayers
Campbell, I. H.; Rubin, S.; Zawodzinski, T. A.; Kress, J. D.; Martin, R. L.; Smith, D. L.; Barashkov, N. N.; Ferraris, J. P.
1996-11-01
We demonstrate tuning of Schottky energy barriers in organic electronic devices by utilizing chemically tailored electrodes. The Schottky energy barrier of Ag on poly[2-methoxy, 5-(2'-ethyl-hexyloxy)- 1,4-phenylene was tuned over a range of more than 1 eV by using self-assembled monolayers (SAM's) to attach oriented dipole layers to the Ag prior to device fabrication. Kelvin probe measurements were used to determine the effect of the SAM's on the Ag surface potential. Ab initio Hartree-Fock calculations of the molecular dipole moments successfully describe the surface potential changes. The chemically tailored electrodes were then incorporated in organic diode structures and changes in the metal/organic Schottky energy barriers were measured using an electroabsorption technique. These results demonstrate the use of self-assembled monolayers to control metal/organic interfacial electronic properties. They establish a physical principle for manipulating the relative energy levels between two materials and demonstrate an approach to improve metal/organic contacts in organic electronic devices.
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Controlling Schottky energy barriers in organic electronic devices using self-assembled monolayers
Energy Technology Data Exchange (ETDEWEB)
Campbell, I.H.; Rubin, S.; Zawodzinski, T.A.; Kress, J.D.; Martin, R.L.; Smith, D.L. [Los Alamos National Laboratory, Los Alamos, New Mexico 87545 (United States); Barashkov, N.N.; Ferraris, J.P. [The University of Texas at Dallas, Richardson, Texas 75083 (United States)
1996-11-01
We demonstrate tuning of Schottky energy barriers in organic electronic devices by utilizing chemically tailored electrodes. The Schottky energy barrier of Ag on poly[2-methoxy], 5-(2{prime}-ethyl-hexyloxy)- 1,4-phenylene was tuned over a range of more than 1 eV by using self-assembled monolayers (SAM{close_quote}s) to attach oriented dipole layers to the Ag prior to device fabrication. Kelvin probe measurements were used to determine the effect of the SAM{close_quote}s on the Ag surface potential. {ital Ab} {ital initio} Hartree-Fock calculations of the molecular dipole moments successfully describe the surface potential changes. The chemically tailored electrodes were then incorporated in organic diode structures and changes in the metal/organic Schottky energy barriers were measured using an electroabsorption technique. These results demonstrate the use of self-assembled monolayers to control metal/organic interfacial electronic properties. They establish a physical principle for manipulating the relative energy levels between two materials and demonstrate an approach to improve metal/organic contacts in organic electronic devices. {copyright} {ital 1996 The American Physical Society.}
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Controlling Schottky energy barriers in organic electronic devices using self-assembled monolayers
International Nuclear Information System (INIS)
Campbell, I.H.; Rubin, S.; Zawodzinski, T.A.; Kress, J.D.; Martin, R.L.; Smith, D.L.; Barashkov, N.N.; Ferraris, J.P.
1996-01-01
We demonstrate tuning of Schottky energy barriers in organic electronic devices by utilizing chemically tailored electrodes. The Schottky energy barrier of Ag on poly[2-methoxy], 5-(2'-ethyl-hexyloxy)- 1,4-phenylene was tuned over a range of more than 1 eV by using self-assembled monolayers (SAM close-quote s) to attach oriented dipole layers to the Ag prior to device fabrication. Kelvin probe measurements were used to determine the effect of the SAM close-quote s on the Ag surface potential. Ab initio Hartree-Fock calculations of the molecular dipole moments successfully describe the surface potential changes. The chemically tailored electrodes were then incorporated in organic diode structures and changes in the metal/organic Schottky energy barriers were measured using an electroabsorption technique. These results demonstrate the use of self-assembled monolayers to control metal/organic interfacial electronic properties. They establish a physical principle for manipulating the relative energy levels between two materials and demonstrate an approach to improve metal/organic contacts in organic electronic devices. copyright 1996 The American Physical Society
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Nanopatched Graphene with Molecular Self-Assembly Toward Graphene-Organic Hybrid Soft Electronics.
Kang, Boseok; Lee, Seong Kyu; Jung, Jaehyuck; Joe, Minwoong; Lee, Seon Baek; Kim, Jinsung; Lee, Changgu; Cho, Kilwon
2018-04-30
Increasing the mechanical durability of large-area polycrystalline single-atom-thick materials is a necessary step toward the development of practical and reliable soft electronics based on these materials. Here, it is shown that the surface assembly of organosilane by weak epitaxy forms nanometer-thick organic patches on a monolayer graphene surface and dramatically increases the material's resistance to harsh postprocessing environments, thereby increasing the number of ways in which graphene can be processed. The nanopatched graphene with the improved mechanical durability enables stable operation when used as transparent electrodes of wearable strain sensors. Also, the nanopatched graphene applied as an electrode modulates the molecular orientation of deposited organic semiconductor layers, and yields favorable nominal charge injection for organic transistors. These results demonstrate the potential for use of self-assembled organic nanopatches in graphene-based soft electronics. © 2018 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.
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Improved organic thin-film transistor performance using novel self-assembled monolayers
McDowell, M.; Hill, I. G.; McDermott, J. E.; Bernasek, S. L.; Schwartz, J.
2006-02-01
Pentacene-based organic thin-film transistors have been fabricated using a phosphonate-linked anthracene self-assembled monolayer as a buffer between the silicon dioxide gate dielectric and the active pentacene channel region. Vast improvements in the subthreshold slope and threshold voltage are observed compared to control devices fabricated without the buffer. Both observations are consistent with a greatly reduced density of charge trapping states at the semiconductor-dielectric interface effected by introduction of the self-assembled monolayer.
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Exciplex formation and energy transfer in a self-assembled metal-organic hybrid system.
Haldar, Ritesh; Rao, K Venkata; George, Subi J; Maji, Tapas Kumar
2012-05-07
Exciting assemblies: A metal-organic self-assembly of pyrenebutyric acid (PBA), 1,10-phenanthroline (o-phen), and Mg(II) shows solid-state fluorescence originating from a 1:1 PBA-o-phen exciplex. This exciplex fluorescence is sensitized by another residual PBA chromophore through an excited-state energy-transfer process. The solvent polarity modulates the self-assembly and the corresponding exciplex as well as the energy transfer, resulting in tunable emission of the hybrid (see figure). Copyright © 2012 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.
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Assembly of Layered Monetite-Chitosan Nanocomposite and Its Transition to Organized Hydroxyapatite.
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.
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Controlling charge injection in organic electronic devices using self-assembled monolayers
Campbell, I. H.; Kress, J. D.; Martin, R. L.; Smith, D. L.; Barashkov, N. N.; Ferraris, J. P.
1997-12-01
We demonstrate control and improvement of charge injection in organic electronic devices by utilizing self-assembled monolayers (SAMs) to manipulate the Schottky energy barrier between a metal electrode and the organic electronic material. Hole injection from Cu electrodes into the electroluminescent conjugated polymer poly[2-methoxy,5-(2'-ethyl-hexyloxy)-1,4-phenylene vinylene] was varied by using two conjugated-thiol based SAMs. The chemically modified electrodes were incorporated in organic diode structures and changes in the metal/polymer Schottky energy barriers and current-voltage characteristics were measured. Decreasing (increasing) the Schottky energy barrier improves (degrades) charge injection into the polymer.
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Self-Assembly of Organic Ferroelectrics by Evaporative Dewetting: A Case of β-Glycine.
Seyedhosseini, Ensieh; Romanyuk, Konstantin; Vasileva, Daria; Vasilev, Semen; Nuraeva, Alla; Zelenovskiy, Pavel; Ivanov, Maxim; Morozovska, Anna N; Shur, Vladimir Ya; Lu, Haidong; Gruverman, Alexei; Kholkin, Andrei L
2017-06-14
Self-assembly of ferroelectric materials attracts significant interest because it offers a promising fabrication route to novel structures useful for microelectronic devices such as nonvolatile memories, integrated sensors/actuators, or energy harvesters. In this work, we demonstrate a novel approach for self-assembly of organic ferroelectrics (as exemplified by ferroelectric β-glycine) using evaporative dewetting, which allows forming quasi-regular arrays of nano- and microislands with preferred orientation of polarization axes. Surprisingly, self-assembled islands are crystallographically oriented in a radial direction from the center of organic "grains" formed during dewetting process. The kinetics of dewetting process follows the t -1/2 law, which is responsible for the observed polygon shape of the grain boundaries and island coverage as a function of radial position. The polarization in ferroelectric islands of β-glycine is parallel to the substrate and switchable under a relatively small dc voltage applied by the conducting tip of piezoresponse force microscope. Significant size effect on polarization is observed and explained within the Landau-Ginzburg-Devonshire phenomenological formalism.
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Supramolecular assembly of organic bicapped Keggin polyoxometalate
International Nuclear Information System (INIS)
Han Zhangang; Zhao Yulong; Peng Jun; Ma Huiyuan; Liu Qun; Wang Enbo; Hu Ninghai
2004-01-01
Two novel supramolecular assemblies of organic bicapped Keggin polyoxometalates (pbpy) 8 H 3 [PW 12 O 40 ]·2H 2 O (1) and (pbpy) 4 H[PMo 12 O 40 (VO)] (2) (pbpy=5-phenyl-2-(4-pyridinyl)pyridine) have been hydrothermally synthesized and structurally characterized by single-crystal X-ray diffraction. Crystallographic data for compound (1), C 128 H 103 N 16 O 42 PW 12 , triclinic, space group P1-bar: a=13.4759(8) A, b=14.6395(11) A, c=16.5743(10) A, α=95.764(2) deg., β=102.166(2) deg., γ=92.9870(10) deg., Z=1, V=3171.1(4) A 3 ; for compound (2), C 64 H 49 N 8 O 41 PMo 12 V, triclinic, space group P1-bar: a=11.5377(11) A, b=12.7552(8) A, c=14.9599(10) A, α=72.270(4) deg., β=88.916(2) deg., γ=67.865(4) deg., Z=1, V=1931.0(3) A 3 . X-ray analyses show that both 1 and 2 represent rare organic bicapped Keggin structures and are supported by supramolecular interactions to extend into a 3D framework. In particular, the unusual structure feature of compound 2 contains a simultaneously organic and inorganic capped structure
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Controlling charge injection in organic electronic devices using self-assembled monolayers
Energy Technology Data Exchange (ETDEWEB)
Campbell, I.H.; Kress, J.D.; Martin, R.L.; Smith, D.L. [Los Alamos National Laboratory, Los Alamos, New Mexico 87545 (United States); Barashkov, N.N.; Ferraris, J.P. [The University of Texas at Dallas, Richardson, Texas 75083 (United States)
1997-12-01
We demonstrate control and improvement of charge injection in organic electronic devices by utilizing self-assembled monolayers (SAMs) to manipulate the Schottky energy barrier between a metal electrode and the organic electronic material. Hole injection from Cu electrodes into the electroluminescent conjugated polymer poly[2-methoxy,5-(2{sup {prime}}-ethyl-hexyloxy)-1,4-phenylene vinylene] was varied by using two conjugated-thiol based SAMs. The chemically modified electrodes were incorporated in organic diode structures and changes in the metal/polymer Schottky energy barriers and current{endash}voltage characteristics were measured. Decreasing (increasing) the Schottky energy barrier improves (degrades) charge injection into the polymer. {copyright} {ital 1997 American Institute of Physics.}
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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.
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Polyelectrolyte Layer-by-Layer Assembly on Organic Electrochemical Transistors
Pappa, Anna-Maria
2017-03-06
Oppositely charged polyelectrolyte multilayers (PEMs) were built up in a layer-by-layer (LbL) assembly on top of the conducting polymer channel of an organic electrochemical transistor (OECT), aiming to combine the advantages of well-established PEMs with a high performance electronic transducer. The multilayered film is a model system to investigate the impact of biofunctionalization on the operation of OECTs comprising a poly(3,4-ethylenedioxythiophene) polystyrenesulfonate (PEDOT:PSS) film as the electrically active layer. Understanding the mechanism of ion injection into the channel that is in direct contact with charged polymer films provides useful insights for novel biosensing applications such as nucleic acid sensing. Moreover, LbL is demonstrated to be a versatile electrode modification tool enabling tailored surface features in terms of thickness, softness, roughness, and charge. LbL assemblies built up on top of conducting polymers will aid the design of new bioelectronic platforms for drug delivery, tissue engineering, and medical diagnostics.
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Polyelectrolyte Layer-by-Layer Assembly on Organic Electrochemical Transistors
Pappa, Anna-Maria; Inal, Sahika; Roy, Kirsty; Zhang, Yi; Pitsalidis, Charalampos; Hama, Adel; Pas, Jolien; Malliaras, George G.; Owens, Roisin M.
2017-01-01
Oppositely charged polyelectrolyte multilayers (PEMs) were built up in a layer-by-layer (LbL) assembly on top of the conducting polymer channel of an organic electrochemical transistor (OECT), aiming to combine the advantages of well-established PEMs with a high performance electronic transducer. The multilayered film is a model system to investigate the impact of biofunctionalization on the operation of OECTs comprising a poly(3,4-ethylenedioxythiophene) polystyrenesulfonate (PEDOT:PSS) film as the electrically active layer. Understanding the mechanism of ion injection into the channel that is in direct contact with charged polymer films provides useful insights for novel biosensing applications such as nucleic acid sensing. Moreover, LbL is demonstrated to be a versatile electrode modification tool enabling tailored surface features in terms of thickness, softness, roughness, and charge. LbL assemblies built up on top of conducting polymers will aid the design of new bioelectronic platforms for drug delivery, tissue engineering, and medical diagnostics.
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"Artificial micro organs"--a microfluidic device for dielectrophoretic assembly of liver sinusoids.
Schütte, Julia; Hagmeyer, Britta; Holzner, Felix; Kubon, Massimo; Werner, Simon; Freudigmann, Christian; Benz, Karin; Böttger, Jan; Gebhardt, Rolf; Becker, Holger; Stelzle, Martin
2011-06-01
In order to study possible toxic side effects of potential drug compounds in vitro a reliable test system is needed. Predicting liver toxicity presents a major challenge of particular importance as liver cells grown in a cell culture suffer from a rapid loss of their liver specific functions. Therefore we are developing a new microfluidic test system for liver toxicity. This test system is based on an organ-like liver 3D co-culture of hepatocytes and endothelial cells. We devised a microfluidic chip featuring cell culture chambers with integrated electrodes for the assembly of liver sinusoids by dielectrophoresis. Fluid channels enable an organ-like perfusion with culture media and test compounds. Different chamber designs were studied and optimized with regard to dielectrophoretic force distribution, hydrodynamic flow profile, and cell trapping rate using numeric simulations. Based on simulation results a microchip was injection-moulded from COP. This chip allowed the assembly of viable hepatocytes and endothelial cells in a sinusoid-like fashion.
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Kim, Aryeon; Jang, Kwang-Suk; Kim, Jinsoo; Won, Jong Chan; Yi, Mi Hye; Kim, Hanim; Yoon, Dong Ki; Shin, Tae Joo; Lee, Myong-Hoon; Ka, Jae-Won; Kim, Yun Ho
2013-11-20
Highly ordered organic semiconductor micropatterns of the liquid-crystalline small molecule 2,7-didecylbenzothienobenzothiophene (C10 -BTBT) are fabricated using a simple method based on template-assisted self-assembly (TASA). The liquid crystallinity of C10 -BTBT allows solvent-free fabrication of high-performance printed organic field-effect transistors (OFETs). © 2013 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.
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Cerveau, Nicolas; Jackson, Daniel J
2016-12-09
Next-generation sequencing (NGS) technologies are arguably the most revolutionary technical development to join the list of tools available to molecular biologists since PCR. For researchers working with nonconventional model organisms one major problem with the currently dominant NGS platform (Illumina) stems from the obligatory fragmentation of nucleic acid material that occurs prior to sequencing during library preparation. This step creates a significant bioinformatic challenge for accurate de novo assembly of novel transcriptome data. This challenge becomes apparent when a variety of modern assembly tools (of which there is no shortage) are applied to the same raw NGS dataset. With the same assembly parameters these tools can generate markedly different assembly outputs. In this study we present an approach that generates an optimized consensus de novo assembly of eukaryotic coding transcriptomes. This approach does not represent a new assembler, rather it combines the outputs of a variety of established assembly packages, and removes redundancy via a series of clustering steps. We test and validate our approach using Illumina datasets from six phylogenetically diverse eukaryotes (three metazoans, two plants and a yeast) and two simulated datasets derived from metazoan reference genome annotations. All of these datasets were assembled using three currently popular assembly packages (CLC, Trinity and IDBA-tran). In addition, we experimentally demonstrate that transcripts unique to one particular assembly package are likely to be bioinformatic artefacts. For all eight datasets our pipeline generates more concise transcriptomes that in fact possess more unique annotatable protein domains than any of the three individual assemblers we employed. Another measure of assembly completeness (using the purpose built BUSCO databases) also confirmed that our approach yields more information. Our approach yields coding transcriptome assemblies that are more likely to be
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Metal complexation and monolayer self-assembly of the bio-organic semiconductor Alizarin
Energy Technology Data Exchange (ETDEWEB)
Uppal, Neeti [Dept. Earth and Environmental Sciences, Ludwig-Maximilians-Universitaet Muenchen (LMU) and Center for NanoSciences (CeNS), Muenchen (Germany); Institut fuer Physik, Universitaet Augsburg (Germany); Gast, Norbert [Dept. Earth and Environmental Sciences, Ludwig-Maximilians-Universitaet Muenchen (LMU) and Center for NanoSciences (CeNS), Muenchen (Germany); Zentrum Neue Technologien, Deutsches Museum, Muenchen (Germany); Bueno, Martin [Fakultaet Feinwerk- und Mikrotechnik, Physikalische Technik, Hochschule Muenchen (Germany); Heckl, Wolfgang M. [Dept. of Physics, Technische Universitaet Muenchen (TUM), Garching (Germany); Zentrum Neue Technologien, Deutsches Museum, Muenchen (Germany); Trixler, Frank [Dept. Earth and Environmental Sciences, Ludwig-Maximilians-Universitaet Muenchen (LMU) and Center for NanoSciences (CeNS), Muenchen (Germany); Dept. of Physics, Technische Universitaet Muenchen (TUM), Garching (Germany); Zentrum Neue Technologien, Deutsches Museum, Muenchen (Germany)
2010-07-01
Organic Solid/Solid Wetting Deposition (OSWD) (Trixler et al.: Chem.Eur.J. 13 (2007), 7785) enables to deposit insoluble molecules such as organic pigments and semiconductors on substrate surfaces under ambient conditions. We explore the potential of OSWD to grow and manipulate monolayers of biomolecules and their chelates on graphite and use Alizarin as a model system - a natural organic compound which occurs mainly as an anthraquinone glycoside in plants. Our investigations via Scanning Tunneling Microscopy (STM), Tunneling Spectroscopy (TS) and Molecular Modelling reveal that OSWD works also with bio-organic molecules and chelate complexes and show that the advantages of OSWD (self-assembly under ambient conditions in a non-solvent environment, nanomanipulation via molecular extraction) can all be tapped.
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Hou, Xiang; Cheng, Xue-Feng; Zhou, Jin; He, Jing-Hui; Xu, Qing-Feng; Li, Hua; Li, Na-Jun; Chen, Dong-Yun; Lu, Jian-Mei
2017-11-16
Recently, surface engineering of the indium tin oxide (ITO) electrode of sandwich-like organic electric memory devices was found to effectively improve their memory performances. However, there are few methods to modify the ITO substrates. In this paper, we have successfully prepared alkyltrichlorosilane self-assembled monolayers (SAMs) on ITO substrates, and resistive random access memory devices are fabricated on these surfaces. Compared to the unmodified ITO substrates, organic molecules (i.e., 2-((4-butylphenyl)amino)-4-((4-butylphenyl)iminio)-3-oxocyclobut-1-en-1-olate, SA-Bu) grown on these SAM-modified ITO substrates have rougher surface morphologies but a smaller mosaicity. The organic layer on the SAM-modified ITO further aged to eliminate the crystalline phase diversity. In consequence, the ternary memory yields are effectively improved to approximately 40-47 %. Our results suggest that the insertion of alkyltrichlorosilane self-assembled monolayers could be an efficient method to improve the performance of organic memory devices. © 2017 Wiley-VCH Verlag GmbH & Co. KGaA, Weinheim.
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Photosensitive self-assembling materials as functional dopants for organic photovoltaic cells
Czech Academy of Sciences Publication Activity Database
Bubnov, Alexej; Iwan, A.; Cigl, Martin; Boharewicz, B.; Tazbir, I.; Wójcik, K.; Sikora, A.; Hamplová, Věra
2016-01-01
Roč. 6, č. 14 (2016), s. 11577-11590 ISSN 2046-2069 R&D Projects: GA MŠk 7AMB13PL041; GA MŠk(CZ) LD14007; GA ČR GA15-02843S Grant - others:EU - ICT(XE) COST Action IC1208 Institutional support: RVO:68378271 Keywords : self-assembling materials * functional dopants * organic photovoltaic cells * azo group * liquid crystal Subject RIV: JI - Composite Materials Impact factor: 3.108, year: 2016
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Nanobump assembly for plasmonic organic solar cells
Song, Hyung-Jun; Jung, Kinam; Lee, Gunhee; Ko, Youngjun; Lee, Jong-Kwon; Choi, Mansoo; Lee, Changhee
2014-10-01
We demonstrate novel plasmonic organic solar cells (OSCs) by embedding an easy processible nanobump assembly (NBA) for harnessing more light. The NBA is consisted of precisely size-controlled Ag nanoparticles (NPs) generated by an aerosol process at atmospheric pressure and thermally deposited molybdenum oxide (MoO3) layer which follows the underlying nano structure of NPs. The active layer, spin-casted polymer blend solution, has an undulated structure conformably covering the NBA structure. To find the optimal condition of the NBA structure for enhancing light harvest as well as carrier transfer, we systematically investigate the effect of the size of Ag NPs and the MoO3 coverage on the device performance. It is observed that the photocurrent of device increases as the size of Ag NP increases owing to enhanced plasmonic and scattering effect. In addition, the increased light absorption is effectively transferred to the photocurrent with small carrier losses, when the Ag NPs are fully covered by the MoO3 layer. As a result, the NBA structure consisted of 40 nm Ag NPs enclosed by 20 nm MoO3 layer leads to 18% improvement in the power conversion efficiency compared to the device without the NBA structure. Therefore, the NBA plasmonic structure provides a reliable and efficient light harvesting in a broad range of wavelength, which consequently enhances the performance of organic solar cells.
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Multivalent protein assembly using monovalent self-assembling building blocks
Petkau - Milroy, K.; Sonntag, M.H.; Colditz, A.; Brunsveld, L.
2013-01-01
Discotic molecules, which self-assemble in water into columnar supramolecular polymers, emerged as an alternative platform for the organization of proteins. Here, a monovalent discotic decorated with one single biotin was synthesized to study the self-assembling multivalency of this system in regard
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Kotzsch, Alexander; Pawolski, Damian; Milentyev, Alexander; Shevchenko, Anna; Scheffel, André; Poulsen, Nicole; Shevchenko, Andrej; Kröger, Nils
2016-03-04
The nano- and micropatterned biosilica cell walls of diatoms are remarkable examples of biological morphogenesis and possess highly interesting material properties. Only recently has it been demonstrated that biosilica-associated organic structures with specific nanopatterns (termed insoluble organic matrices) are general components of diatom biosilica. The model diatom Thalassiosira pseudonana contains three types of insoluble organic matrices: chitin meshworks, organic microrings, and organic microplates, the latter being described in the present study for the first time. To date, little is known about the molecular composition, intracellular assembly, and biological functions of organic matrices. Here we have performed structural and functional analyses of the organic microrings and organic microplates from T. pseudonana. Proteomics analysis yielded seven proteins of unknown function (termed SiMat proteins) together with five known silica biomineralization proteins (four cingulins and one silaffin). The location of SiMat1-GFP in the insoluble organic microrings and the similarity of tyrosine- and lysine-rich functional domains identifies this protein as a new member of the cingulin protein family. Mass spectrometric analysis indicates that most of the lysine residues of cingulins and the other insoluble organic matrix proteins are post-translationally modified by short polyamine groups, which are known to enhance the silica formation activity of proteins. Studies with recombinant cingulins (rCinY2 and rCinW2) demonstrate that acidic conditions (pH 5.5) trigger the assembly of mixed cingulin aggregates that have silica formation activity. Our results suggest an important role for cingulins in the biogenesis of organic microrings and support the hypothesis that this type of insoluble organic matrix functions in biosilica morphogenesis. © 2016 by The American Society for Biochemistry and Molecular Biology, Inc.
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Organization of Mitochondrial Gene Expression in Two Distinct Ribosome-Containing Assemblies
Directory of Open Access Journals (Sweden)
Kirsten Kehrein
2015-02-01
Full Text Available Mitochondria contain their own genetic system that provides subunits of the complexes driving oxidative phosphorylation. A quarter of the mitochondrial proteome participates in gene expression, but how all these factors are orchestrated and spatially organized is currently unknown. Here, we established a method to purify and analyze native and intact complexes of mitochondrial ribosomes. Quantitative mass spectrometry revealed extensive interactions of ribosomes with factors involved in all the steps of posttranscriptional gene expression. These interactions result in large expressosome-like assemblies that we termed mitochondrial organization of gene expression (MIOREX complexes. Superresolution microscopy revealed that most MIOREX complexes are evenly distributed throughout the mitochondrial network, whereas a subset is present as nucleoid-MIOREX complexes that unite the whole spectrum of organellar gene expression. Our work therefore provides a conceptual framework for the spatial organization of mitochondrial protein synthesis that likely developed to facilitate gene expression in the organelle.
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Peptide assembly-driven metal-organic framework (MOF) motors for micro electric generators.
Ikezoe, Yasuhiro; Fang, Justin; Wasik, Tomasz L; Uemura, Takashi; Zheng, Yongtai; Kitagawa, Susumu; Matsui, Hiroshi
2015-01-14
Peptide-metal-organic framework (Pep-MOF) motors, whose motions are driven by anisotropic surface tension gradients created via peptide self-assembly around frameworks, can rotate microscopic rotors and magnets fast enough to generate an electric power of 0.1 μW. A new rigid Pep-MOF motor can be recycled by refilling the peptide fuel into the nanopores of the MOF. © 2014 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.
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Energy Technology Data Exchange (ETDEWEB)
Vijaya Prakash, G; Pradeesh, K [Nanophotonics Lab, Department of Physics, Indian Institute of Technology Delhi, New Delhi (India); Ratnani, R; Saraswat, K [Department of Pure and Applied Chemistry, MDS University, Ajmer (India); Light, M E [School of Chemistry, University of Southampton, Southampton (United Kingdom); Baumberg, J J, E-mail: prakash@physics.iitd.ac.i [Nanophotonic Centre, Cavendish Laboratory, University Cambridge, Cambridge CB3 OHE (United Kingdom)
2009-09-21
The structural and optical spectra of two related lead iodide (PbI) based self-assembled hybrid organic-inorganic semiconductors are compared. During the synthesis, depending on the bridging of organic moiety intercalated between the PbI two-dimensional planes, different crystal structures are produced. These entirely different networks show different structural and optical features, including excitonic bandgaps. In particular, the modified organic environment of the excitons is sensitive to the local disorder both in single crystal and thin film forms. Such information is vital for incorporating these semiconductors into photonic device architectures.
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Directory of Open Access Journals (Sweden)
Santiago Montero-Mendieta
2017-09-01
Full Text Available Whole genome sequencing (WGS is a very valuable resource to understand the evolutionary history of poorly known species. However, in organisms with large genomes, as most amphibians, WGS is still excessively challenging and transcriptome sequencing (RNA-seq represents a cost-effective tool to explore genome-wide variability. Non-model organisms do not usually have a reference genome and the transcriptome must be assembled de-novo. We used RNA-seq to obtain the transcriptomic profile for Oreobates cruralis, a poorly known South American direct-developing frog. In total, 550,871 transcripts were assembled, corresponding to 422,999 putative genes. Of those, we identified 23,500, 37,349, 38,120 and 45,885 genes present in the Pfam, EggNOG, KEGG and GO databases, respectively. Interestingly, our results suggested that genes related to immune system and defense mechanisms are abundant in the transcriptome of O. cruralis. We also present a pipeline to assist with pre-processing, assembling, evaluating and functionally annotating a de-novo transcriptome from RNA-seq data of non-model organisms. Our pipeline guides the inexperienced user in an intuitive way through all the necessary steps to build de-novo transcriptome assemblies using readily available software and is freely available at: https://github.com/biomendi/TRANSCRIPTOME-ASSEMBLY-PIPELINE/wiki.
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Probe based manipulation and assembly of nanowires into organized mesostructures
Reynolds, K.; Komulainen, J.; Kivijakola, J.; Lovera, P.; Iacopino, D.; Pudas, M.; Vähäkangas, J.; Röning, J.; Redmond, G.
2008-12-01
A convenient approach to patterning inorganic and organic nanowires using a novel probe manipulator is presented. The system utilizes an electrochemically etched tungsten wire probe mounted onto a 3D actuator that is directed by a 3D controller. When it is engaged by the user, the movement of the probe and the forces experienced by the tip are simultaneously reported in real time. Platinum nanowires are manipulated into organized mesostructures on silicon chip substrates. In particular, individual nanowires are systematically removed from aggregates, transferred to a chosen location, and manipulated into complex structures in which selected wires occupy specific positions with defined orientations. Rapid prototyping of complex mesostructures, by pushing, rotating and bending conjugated polymer, i.e., polyfluorene, nanowires into various configurations, is also achieved. By exploiting the strong internal axial alignment of polymer chains within the polyfluorene nanowires, mesostructures tailored to exhibit distinctly anisotropic optical properties, such as birefringence and photoluminescence dichroism, are successfully assembled on fused silica substrates.
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Probe based manipulation and assembly of nanowires into organized mesostructures
International Nuclear Information System (INIS)
Reynolds, K; Lovera, P; Iacopino, D; Redmond, G; Komulainen, J; Pudas, M; Vaehaekangas, J; Kivijakola, J; Roening, J
2008-01-01
A convenient approach to patterning inorganic and organic nanowires using a novel probe manipulator is presented. The system utilizes an electrochemically etched tungsten wire probe mounted onto a 3D actuator that is directed by a 3D controller. When it is engaged by the user, the movement of the probe and the forces experienced by the tip are simultaneously reported in real time. Platinum nanowires are manipulated into organized mesostructures on silicon chip substrates. In particular, individual nanowires are systematically removed from aggregates, transferred to a chosen location, and manipulated into complex structures in which selected wires occupy specific positions with defined orientations. Rapid prototyping of complex mesostructures, by pushing, rotating and bending conjugated polymer, i.e., polyfluorene, nanowires into various configurations, is also achieved. By exploiting the strong internal axial alignment of polymer chains within the polyfluorene nanowires, mesostructures tailored to exhibit distinctly anisotropic optical properties, such as birefringence and photoluminescence dichroism, are successfully assembled on fused silica substrates.
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Energy Technology Data Exchange (ETDEWEB)
Yang, Xia [Southwest University, Key Laboratory of Luminescent and Real-Time Analytical Chemistry, Ministry of Education, College of Chemistry and Chemical Engineering (China); Liu, Linlin [City University of Hong Kong, Department of Physics and Materials Science, Center of Super-Diamond and Advanced Films (COSDAF) (Hong Kong); Yuan, Ruo, E-mail: yuanruo@swu.edu.cn [Southwest University, Key Laboratory of Luminescent and Real-Time Analytical Chemistry, Ministry of Education, College of Chemistry and Chemical Engineering (China); Lee, Chun-Sing, E-mail: apcslee@cityu.edu.hk [City University of Hong Kong, Department of Physics and Materials Science, Center of Super-Diamond and Advanced Films (COSDAF) (Hong Kong)
2016-10-15
We fabricated composites of Fe{sub 2}O{sub 3}/reduced graphene oxide as lithium-ion batteries anode material with controlled structures by employing self-assembly of metal–organic frameworks (MOFs) and polymer-functionalized graphene oxide as precursors. By electrostatic interaction, the negatively charged MOFs, Prussian Blue (PB), are assembled on poly(diallyldimethylammonium chloride) (PDDA)-functionalized graphene oxide (positive charge). Then the PB cubes become FeOOH nanosheets when treated with sodium hydroxide. Upon further annealing, the FeOOH nanosheets transform to Fe{sub 2}O{sub 3} nanoparticles while the graphene oxide become reduced graphene oxide simultaneously. It was found that the composites have good performance as anode of lithium-ion battery. This work shows a new way for self-assembling MOFs and 2D materials.
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International Nuclear Information System (INIS)
Dague, E; Jauvert, E; Laplatine, L; Thibault, C; Viallet, B; Ressier, L
2011-01-01
Immobilization of live micro-organisms on solid substrates is an important prerequisite for atomic force microscopy (AFM) bio-experiments. The method employed must immobilize the cells firmly enough to enable them to withstand the lateral friction forces exerted by the tip during scanning but without denaturing the cell interface. In this work, a generic method for the assembly of living cells on specific areas of substrates is proposed. It consists in assembling the living cells within the patterns of microstructured, functionalized poly-dimethylsiloxane (PDMS) stamps using convective/capillary deposition. This versatile approach is validated by applying it to two systems of foremost importance in biotechnology and medicine: Saccharomyces cerevisiae yeasts and Aspergillus fumigatus fungal spores. We show that this method allows multiplexing AFM nanomechanical measurements by force spectroscopy on S. cerevisiae yeasts and high-resolution AFM imaging of germinated Aspergillus conidia in buffer medium. These two examples clearly demonstrate the immense potential of micro-organism assembly on functionalized, microstructured PDMS stamps by convective/capillary deposition for performing rigorous AFM bio-experiments on living cells.
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2014-01-24
Interfacial Tuning via Electron-Blocking/Hole-Transport Layers and Indium Tin Oxide Surface Treatment in Bulk- Heterojunction Organic Photovoltaic Cells...devices Figure 3 shows the compounds we prepared to assemble on gold (Au) surfaces. Results of TPA-C60 dyads (1 and 2) self-assembled on Au electrodes...surface hydroxyl groups, respectively, we decided to prepare compounds 5-7 to attach as SAMs, see Figure 5. Difficulties and unexpected problems
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Lv, Wenping; Wu, Ren'an
2013-03-01
A computational investigation was carried out to understand the aggregation of nanoscale graphene with two typical pathways of stacking assembly and sliding assembly in water. The interfacial-organized monolayer water film (MWF) induced ``two-step'' aggregation of nanographene in both stacking and sliding assembly pathways was reported for the first time. By means of potential mean forces (PMFs) calculation, no energy barrier was observed during the sliding assembly of two graphene nanosheets, while the PMF profiles could be impacted by the contact forms of nanographene and the MWF within the interplate of two graphene nanosheets. To explore the potential physical basis of the ``hindering role'' of self-organized interfacial water, the dynamical and structural properties as well as the status of hydrogen bonds (H-bonds) for interfacial water were investigated. We found that the compact, ordered structure and abundant H-bonds of the MWF could be taken as the fundamental aspects of the ``hindering role'' of interfacial water for the hydrophobic assembly of nanographene. These findings are displaying a potential to further understand the hydrophobic assembly which mostly dominate the behaviors of nanomaterials, proteins etc. in aqueous solutions.A computational investigation was carried out to understand the aggregation of nanoscale graphene with two typical pathways of stacking assembly and sliding assembly in water. The interfacial-organized monolayer water film (MWF) induced ``two-step'' aggregation of nanographene in both stacking and sliding assembly pathways was reported for the first time. By means of potential mean forces (PMFs) calculation, no energy barrier was observed during the sliding assembly of two graphene nanosheets, while the PMF profiles could be impacted by the contact forms of nanographene and the MWF within the interplate of two graphene nanosheets. To explore the potential physical basis of the ``hindering role'' of self-organized interfacial
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Laporte, Daphné; Huot, Jonathan L; Bader, Gaétan; Enkler, Ludovic; Senger, Bruno; Becker, Hubert Dominique
2014-11-28
Aminoacyl-tRNA synthetases (aaRSs) are ubiquitous and ancient enzymes, mostly known for their essential role in generating aminoacylated tRNAs. During the last two decades, many aaRSs have been found to perform additional and equally crucial tasks outside translation. In metazoans, aaRSs have been shown to assemble, together with non-enzymatic assembly proteins called aaRSs-interacting multifunctional proteins (AIMPs), into so-called multi-synthetase complexes (MSCs). Metazoan MSCs are dynamic particles able to specifically release some of their constituents in response to a given stimulus. Upon their release from MSCs, aaRSs can reach other subcellular compartments, where they often participate to cellular processes that do not exploit their primary function of synthesizing aminoacyl-tRNAs. The dynamics of MSCs and the expansion of the aaRSs functional repertoire are features that are so far thought to be restricted to higher and multicellular eukaryotes. However, much can be learnt about how MSCs are assembled and function from apparently 'simple' organisms. Here we provide an overview on the diversity of these MSCs, their composition, mode of assembly and the functions that their constituents, namely aaRSs and AIMPs, exert in unicellular organisms. Copyright © 2014 Federation of European Biochemical Societies. Published by Elsevier B.V. All rights reserved.
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Directory of Open Access Journals (Sweden)
Janina Baumbach
2015-05-01
Full Text Available Acentriolar microtubule organizing centers (aMTOCs are formed during meiosis and mitosis in several cell types, but their function and assembly mechanism is unclear. Importantly, aMTOCs can be overactive in cancer cells, enhancing multipolar spindle formation, merotelic kinetochore attachment and aneuploidy. Here we show that aMTOCs can form in acentriolar Drosophila somatic cells in vivo via an assembly pathway that depends on Asl, Cnn and, to a lesser extent, Spd-2--the same proteins that appear to drive mitotic centrosome assembly in flies. This finding enabled us to ablate aMTOC formation in acentriolar cells, and so perform a detailed genetic analysis of the contribution of aMTOCs to acentriolar mitotic spindle formation. Here we show that although aMTOCs can nucleate microtubules, they do not detectably increase the efficiency of acentriolar spindle assembly in somatic fly cells. We find that they are required, however, for robust microtubule array assembly in cells without centrioles that also lack microtubule nucleation from around the chromatin. Importantly, aMTOCs are also essential for dynein-dependent acentriolar spindle pole focusing and for robust cell proliferation in the absence of centrioles and HSET/Ncd (a kinesin essential for acentriolar spindle pole focusing in many systems. We propose an updated model for acentriolar spindle pole coalescence by the molecular motors Ncd/HSET and dynein in conjunction with aMTOCs.
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Dohn, Michael R; Mundell, Nathan A; Sawyer, Leah M; Dunlap, Julie A; Jessen, Jason R
2013-11-01
Zebrafish gastrulation cell movements occur in the context of dynamic changes in extracellular matrix (ECM) organization and require the concerted action of planar cell polarity (PCP) proteins that regulate cell elongation and mediolateral alignment. Data obtained using Xenopus laevis gastrulae have shown that integrin-fibronectin interactions underlie the formation of polarized cell protrusions necessary for PCP and have implicated PCP proteins themselves as regulators of ECM. By contrast, the relationship between establishment of PCP and ECM assembly/remodeling during zebrafish gastrulation is unclear. We previously showed that zebrafish embryos carrying a null mutation in the four-pass transmembrane PCP protein vang-like 2 (vangl2) exhibit increased matrix metalloproteinase activity and decreased immunolabeling of fibronectin. These data implicated for the first time a core PCP protein in the regulation of pericellular proteolysis of ECM substrates and raised the question of whether other zebrafish PCP proteins also impact ECM organization. In Drosophila melanogaster, the cytoplasmic PCP protein Prickle binds Van Gogh and regulates its function. Here we report that similar to vangl2, loss of zebrafish prickle1a decreases fibronectin protein levels in gastrula embryos. We further show that Prickle1a physically binds Vangl2 and regulates both the subcellular distribution and total protein level of Vangl2. These data suggest that the ability of Prickle1a to impact fibronectin organization is at least partly due to effects on Vangl2. In contrast to loss of either Vangl2 or Prickle1a function, we find that glypican4 (a Wnt co-receptor) and frizzled7 mutant gastrula embryos with disrupted non-canonical Wnt signaling exhibit the opposite phenotype, namely increased fibronectin assembly. Our data show that glypican4 mutants do not have decreased proteolysis of ECM substrates, but instead have increased cell surface cadherin protein expression and increased intercellular
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International Nuclear Information System (INIS)
Yuan, Yi; Liu, Zheming; Liu, Zhenyang; Peng, Lan; Li, Yongjie; Tang, Aiwei
2017-01-01
Highlights: • CsPbBr_3 perovskite nanocrystals have been synthesized in the presence of organic amines with different hydrocarbon length. • The photoluminescence of the CsPbBr_3 nanocrystals is affected by the varying the carbon length of the organic amines. • The lower reaction temperature and hydrocarbon chain length of the organic ligands play a significant role in the self-assembly of CsPbBr_3 nanocrystals. - Abstract: All-inorganic halide perovskites have become one of the most prospective materials for lightening and display technology due to their color-tunable and narrow-band emission. Herein, we have systematically studied the effects of organic amines with different hydrocarbon chain length on the optical properties and morphology as well as the crystal structure of colloidal CsPbBr_3 nanocrystals (NCs), which were synthesized in the presence of oleic acid (OA) and organic amines by using a simple hot-injection approach. The hydrocarbon chain length has shown an independent correlation to the morphology and crystal structure of the as-obtained CsPbBr_3 NCs at 160 °C, but their optical properties can be affected to some extent. The photoluminescence quantum yields (PLQYs) of the CsPbBr_3 NCs synthesized in the presence of organic amines with long carbon chain length are generally in the range of 55–80% for different reaction time, but the PLQYs of less than 20% are obtained for the products synthesized in the presence of octylamine (OTAm) with short carbon chain length. The effects of the reaction temperature on the optical properties, size and crystal structure of the CsPbBr_3 NCs synthesized in the presence of cetylamine (CTAm) are studied. Interestingly, some nanoplates also appear in these CsPbBr_3 NCs obtained at relatively low temperatures (120 and 140 °C), which have a strong tendency to self-assemble into face-to-face nanostructures. Such a similar self-assembly behavior is also observed in the product synthesized in the presence of
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Energy Technology Data Exchange (ETDEWEB)
Yuan, Yi; Liu, Zheming; Liu, Zhenyang; Peng, Lan; Li, Yongjie; Tang, Aiwei, E-mail: awtang@bjtu.edu.cn
2017-05-31
Highlights: • CsPbBr{sub 3} perovskite nanocrystals have been synthesized in the presence of organic amines with different hydrocarbon length. • The photoluminescence of the CsPbBr{sub 3} nanocrystals is affected by the varying the carbon length of the organic amines. • The lower reaction temperature and hydrocarbon chain length of the organic ligands play a significant role in the self-assembly of CsPbBr{sub 3} nanocrystals. - Abstract: All-inorganic halide perovskites have become one of the most prospective materials for lightening and display technology due to their color-tunable and narrow-band emission. Herein, we have systematically studied the effects of organic amines with different hydrocarbon chain length on the optical properties and morphology as well as the crystal structure of colloidal CsPbBr{sub 3} nanocrystals (NCs), which were synthesized in the presence of oleic acid (OA) and organic amines by using a simple hot-injection approach. The hydrocarbon chain length has shown an independent correlation to the morphology and crystal structure of the as-obtained CsPbBr{sub 3} NCs at 160 °C, but their optical properties can be affected to some extent. The photoluminescence quantum yields (PLQYs) of the CsPbBr{sub 3} NCs synthesized in the presence of organic amines with long carbon chain length are generally in the range of 55–80% for different reaction time, but the PLQYs of less than 20% are obtained for the products synthesized in the presence of octylamine (OTAm) with short carbon chain length. The effects of the reaction temperature on the optical properties, size and crystal structure of the CsPbBr{sub 3} NCs synthesized in the presence of cetylamine (CTAm) are studied. Interestingly, some nanoplates also appear in these CsPbBr{sub 3} NCs obtained at relatively low temperatures (120 and 140 °C), which have a strong tendency to self-assemble into face-to-face nanostructures. Such a similar self-assembly behavior is also observed in the
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Kind, Martin; Wöll, Christof
2009-07-01
Organic surfaces play a major role in materials science. Most surfaces that we touch in our daily lives are made from organic materials, e.g., vegetables, fruit, skin, wood, and textiles made from natural fibers. In the context of biology, organic surfaces play a prominent role too, proteins docking onto cell surfaces are a good example. To better understand the characteristics of organic surfaces, including physico-chemical properties like wettability or chemical reactivities and physical properties like friction and lubrication, a structurally well-defined model system that can be investigated with numerous analytical techniques is desirable. In the last two decades, one particular system, self-assembled monolayers or SAMs, have demonstrated their suitability for this purpose. In particular, organothiols consisting of an organic molecule with an attached SH-group are well suited to fabricating structurally well-defined adlayers of monolayer thickness on gold substrates using a simple preparation procedure. These ultrathin monolayers expose an organic surface with properties that can be tailored by varying the type of organothiol employed. After a short introduction into the preparation of SAMs, this article provides an overview of the possibilities and limitations of organic surfaces exposed by Au-thiolate SAMs. Applications are as diverse as the metallization of organic surfaces, a fundamental problem in materials science, and the fabrication of surfaces that resist the adsorption of proteins. In addition to a number of different case studies, we will also discuss the most powerful analytical techniques needed to characterize these important model systems.
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Preliminary High-Throughput Metagenome Assembly
Energy Technology Data Exchange (ETDEWEB)
Dusheyko, Serge; Furman, Craig; Pangilinan, Jasmyn; Shapiro, Harris; Tu, Hank
2007-03-26
Metagenome data sets present a qualitatively different assembly problem than traditional single-organism whole-genome shotgun (WGS) assembly. The unique aspects of such projects include the presence of a potentially large number of distinct organisms and their representation in the data set at widely different fractions. In addition, multiple closely related strains could be present, which would be difficult to assemble separately. Failure to take these issues into account can result in poor assemblies that either jumble together different strains or which fail to yield useful results. The DOE Joint Genome Institute has sequenced a number of metagenomic projects and plans to considerably increase this number in the coming year. As a result, the JGI has a need for high-throughput tools and techniques for handling metagenome projects. We present the techniques developed to handle metagenome assemblies in a high-throughput environment. This includes a streamlined assembly wrapper, based on the JGI?s in-house WGS assembler, Jazz. It also includes the selection of sensible defaults targeted for metagenome data sets, as well as quality control automation for cleaning up the raw results. While analysis is ongoing, we will discuss preliminary assessments of the quality of the assembly results (http://fames.jgi-psf.org).
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Lee, Wi Hyoung; Park, Jaesung; Sim, Sung Hyun; Lim, Soojin; Kim, Kwang S; Hong, Byung Hee; Cho, Kilwon
2011-03-30
Organic electronic devices that use graphene electrodes have received considerable attention because graphene is regarded as an ideal candidate electrode material. Transfer and lithographic processes during fabrication of patterned graphene electrodes typically leave polymer residues on the graphene surfaces. However, the impact of these residues on the organic semiconductor growth mechanism on graphene surface has not been reported yet. Here, we demonstrate that polymer residues remaining on graphene surfaces induce a stand-up orientation of pentacene, thereby controlling pentacene growth such that the molecular assembly is optimal for charge transport. Thus, pentacene field-effect transistors (FETs) using source/drain monolayer graphene electrodes with polymer residues show a high field-effect mobility of 1.2 cm(2)/V s. In contrast, epitaxial growth of pentacene having molecular assembly of lying-down structure is facilitated by π-π interaction between pentacene and the clean graphene electrode without polymer residues, which adversely affects lateral charge transport at the interface between electrode and channel. Our studies provide that the obtained high field-effect mobility in pentacene FETs using monolayer graphene electrodes arises from the extrinsic effects of polymer residues as well as the intrinsic characteristics of the highly conductive, ultrathin two-dimensional monolayer graphene electrodes.
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Molecular self-assembly advances and applications
Dequan, Alex Li
2012-01-01
In the past several decades, molecular self-assembly has emerged as one of the main themes in chemistry, biology, and materials science. This book compiles and details cutting-edge research in molecular assemblies ranging from self-organized peptide nanostructures and DNA-chromophore foldamers to supramolecular systems and metal-directed assemblies, even to nanocrystal superparticles and self-assembled microdevices
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GAAP: Genome-organization-framework-Assisted Assembly Pipeline for prokaryotic genomes.
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.
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Majima, Yutaka; Hackenberger, Guillaume; Azuma, Yasuo; Kano, Shinya; Matsuzaki, Kosuke; Susaki, Tomofumi; Sakamoto, Masanori; Teranishi, Toshiharu
2017-01-01
Single-electron transistors (SETs) are sub-10-nm scale electronic devices based on conductive Coulomb islands sandwiched between double-barrier tunneling barriers. Chemically assembled SETs with alkanethiol-protected Au nanoparticles show highly stable Coulomb diamonds and two-input logic operations. The combination of bottom-up and top-down processes used to form the passivation layer is vital for realizing multi-gate chemically assembled SET circuits, as this combination enables us to connect conventional complementary metal oxide semiconductor (CMOS) technologies via planar processes. Here, three-input gate exclusive-OR (XOR) logic operations are demonstrated in passivated chemically assembled SETs. The passivation layer is a hybrid bilayer of self-assembled monolayers (SAMs) and pulsed laser deposited (PLD) aluminum oxide (AlO[Formula: see text]), and top-gate electrodes were prepared on the hybrid passivation layers. Top and two-side-gated SETs showed clear Coulomb oscillation and diamonds for each of the three available gates, and three-input gate XOR logic operation was clearly demonstrated. These results show the potential of chemically assembled SETs to work as logic devices with multi-gate inputs using organic and inorganic hybrid passivation layers.
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Schmaltz, Thomas; Gothe, Bastian; Krause, Andreas; Leitherer, Susanne; Steinrück, Hans-Georg; Thoss, Michael; Clark, Timothy; Halik, Marcus
2017-09-26
Self-assembled monolayer field-effect transistors (SAMFETs) are not only a promising type of organic electronic device but also allow detailed analyses of structure-property correlations. The influence of the morphology on the charge transport is particularly pronounced, due to the confined monolayer of 2D-π-stacked organic semiconductor molecules. The morphology, in turn, is governed by relatively weak van-der-Waals interactions and is thus prone to dynamic structural fluctuations. Accordingly, combining electronic and physical characterization and time-averaged X-ray analyses with the dynamic information available at atomic resolution from simulations allows us to characterize self-assembled monolayer (SAM) based devices in great detail. For this purpose, we have constructed transistors based on SAMs of two molecules that consist of the organic p-type semiconductor benzothieno[3,2-b][1]benzothiophene (BTBT), linked to a C 11 or C 12 alkylphosphonic acid. Both molecules form ordered SAMs; however, our experiments show that the size of the crystalline domains and the charge-transport properties vary considerably in the two systems. These findings were confirmed by molecular dynamics (MD) simulations and semiempirical molecular-orbital electronic-structure calculations, performed on snapshots from the MD simulations at different times, revealing, in atomistic detail, how the charge transport in organic semiconductors is influenced and limited by dynamic disorder.
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Adaptive self-assembly and induced-fit transformations of anion-binding metal-organic macrocycles
Zhang, Ting; Zhou, Li-Peng; Guo, Xiao-Qing; Cai, Li-Xuan; Sun, Qing-Fu
2017-06-01
Container-molecules are attractive to chemists due to their unique structural characteristics comparable to enzymes and receptors in nature. We report here a family of artificial self-assembled macrocyclic containers that feature induced-fit transformations in response to different anionic guests. Five metal-organic macrocycles with empirical formula of MnL2n (M=Metal L=Ligand n=3, 4, 5, 6, 7) are selectively obtained starting from one simple benzimidazole-based ligand and square-planar palladium(II) ions, either by direct anion-adaptive self-assembly or induced-fit transformations. Hydrogen-bonding interactions between the inner surface of the macrocycles and the anionic guests dictate the shape and size of the product. A comprehensive induced-fit transformation map across all the MnL2n species is drawn, with a representative reconstitution process from Pd7L14 to Pd3L6 traced in detail, revealing a gradual ring-shrinking mechanism. We envisage that these macrocyclic molecules with adjustable well-defined hydrogen-bonding pockets will find wide applications in molecular sensing or catalysis.
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DEFF Research Database (Denmark)
Milovanov, A.V.; Juul Rasmussen, J.
2002-01-01
Self-assembling organic polymers and copper-oxide compounds are two classes of unconventional superconductors, whose challenging behavior does not comply with the traditional picture of Bardeen-Cooper-Schrieffer (BCS) superconductivity in regular crystals. In this paper, we propose a theoretical...... or holes) exchange fracton excitations, quantum oscillations of fractal lattices that mimic the complex microscopic organization of the unconventional superconductors. For the copper oxides, the superconducting transition temperature T-c as predicted by the fracton mechanism is of the order of similar to......150 K. We suggest that the marginal ingredient of the high-temperature superconducting phase is provided by fracton coupled holes that condensate in the conducting copper-oxygen planes owing to the intrinsic field-effect-transistor configuration of the cuprate compounds. For the gate...
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Denadai, Angelo M L; De Sousa, Frederico B; Passos, Joel J; Guatimosim, Fernando C; Barbosa, Kirla D; Burgos, Ana E; de Oliveira, Fernando Castro; da Silva, Jeann C; Neves, Bernardo R A; Mohallem, Nelcy D S; Sinisterra, Rubén D
2012-01-01
Organic-inorganic magnetic hybrid materials (MHMs) combine a nonmagnetic and a magnetic component by means of electrostatic interactions or covalent bonds, and notable features can be achieved. Herein, we describe an application of a self-assembled material based on ferrite associated with β-cyclodextrin (Fe-Ni/Zn/βCD) at the nanoscale level. This MHM and pure ferrite (Fe-Ni/Zn) were used as an adsorbent system for Cr(3+) and Cr(2)O(7) (2-) ions in aqueous solutions. Prior to the adsorption studies, both ferrites were characterized in order to determine the particle size distribution, morphology and available binding sites on the surface of the materials. Microscopy analysis demonstrated that both ferrites present two different size domains, at the micro- and nanoscale level, with the latter being able to self-assemble into larger particles. Fe-Ni/Zn/βCD presented smaller particles and a more homogeneous particle size distribution. Higher porosity for this MHM compared to Fe-Ni/Zn was observed by Brunauer-Emmett-Teller isotherms and positron-annihilation-lifetime spectroscopy. Based on the pKa values, potentiometric titrations demonstrated the presence of βCD in the inorganic matrix, indicating that the lamellar structures verified by transmission electronic microscopy can be associated with βCD assembled structures. Colloidal stability was inferred as a function of time at different pH values, indicating the sedimentation rate as a function of pH. Zeta potential measurements identified an amphoteric behavior for the Fe-Ni/Zn/βCD, suggesting its better capability to remove ions (cations and anions) from aqueous solutions compared to that of Fe-Ni/Zn.
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From metal-organic squares to porous zeolite-like supramolecular assemblies
Wang, Shuang; Zhao, Tingting; Li, Guanghua; Wojtas, Łukasz; Huo, Qisheng; Eddaoudi, Mohamed; Liu, Yunling
2010-01-01
We report the synthesis, structure, and characterization of two novel porous zeolite-like supramolecular assemblies, ZSA-1 and ZSA-2, having zeolite gis and rho topologies, respectively. The two compounds were assembled from functional metal
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Wang, Shuang; Belmabkhout, Youssef; Cairns, Amy; Li, Guanghua; Huo, Qisheng; Liu, Yunling; Eddaoudi, Mohamed
2017-01-01
A strategy based on metal-ligand directed assembly of metal-organic squares (MOSs), built-up from four-membered ring (4MR) secondary building units (SBUs), has been employed for the design and construction of isoreticular zeolite-like supramolecular
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Centrioles: Some Self-Assembly Required
Song, Mi Hye; Miliaras, Nicholas B.; Peel, Nina; O'Connell, Kevin F.
2008-01-01
Centrioles play an important role in organizing microtubules and are precisely duplicated once per cell cycle. New (daughter) centrioles typically arise in association with existing (mother) centrioles (canonical assembly), suggesting that mother centrioles direct the formation of daughter centrioles. However, under certain circumstances, centrioles can also self-assemble free of an existing centriole (de novo assembly). Recent work indicates that the canonical and de novo pathways utilize a ...
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Hapsembler: An Assembler for Highly Polymorphic Genomes
Donmez, Nilgun; Brudno, Michael
As whole genome sequencing has become a routine biological experiment, algorithms for assembly of whole genome shotgun data has become a topic of extensive research, with a plethora of off-the-shelf methods that can reconstruct the genomes of many organisms. Simultaneously, several recently sequenced genomes exhibit very high polymorphism rates. For these organisms genome assembly remains a challenge as most assemblers are unable to handle highly divergent haplotypes in a single individual. In this paper we describe Hapsembler, an assembler for highly polymorphic genomes, which makes use of paired reads. Our experiments show that Hapsembler produces accurate and contiguous assemblies of highly polymorphic genomes, while performing on par with the leading tools on haploid genomes. Hapsembler is available for download at http://compbio.cs.toronto.edu/hapsembler.
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Centrioles: some self-assembly required.
Song, Mi Hye; Miliaras, Nicholas B; Peel, Nina; O'Connell, Kevin F
2008-12-01
Centrioles play an important role in organizing microtubules and are precisely duplicated once per cell cycle. New (daughter) centrioles typically arise in association with existing (mother) centrioles (canonical assembly), suggesting that mother centrioles direct the formation of daughter centrioles. However, under certain circumstances, centrioles can also selfassemble free of an existing centriole (de novo assembly). Recent work indicates that the canonical and de novo pathways utilize a common mechanism and that a mother centriole spatially constrains the self-assembly process to occur within its immediate vicinity. Other recently identified mechanisms further regulate canonical assembly so that during each cell cycle, one and only one daughter centriole is assembled per mother centriole.
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Operon Gene Order Is Optimized for Ordered Protein Complex Assembly
Wells, Jonathan N.; Bergendahl, L. Therese; Marsh, Joseph A.
2016-01-01
Summary The assembly of heteromeric protein complexes is an inherently stochastic process in which multiple genes are expressed separately into proteins, which must then somehow find each other within the cell. Here, we considered one of the ways by which prokaryotic organisms have attempted to maximize the efficiency of protein complex assembly: the organization of subunit-encoding genes into operons. Using structure-based assembly predictions, we show that operon gene order has been optimized to match the order in which protein subunits assemble. Exceptions to this are almost entirely highly expressed proteins for which assembly is less stochastic and for which precisely ordered translation offers less benefit. Overall, these results show that ordered protein complex assembly pathways are of significant biological importance and represent a major evolutionary constraint on operon gene organization. PMID:26804901
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Yuan, Yi; Liu, Zheming; Liu, Zhenyang; Peng, Lan; Li, Yongjie; Tang, Aiwei
2017-05-01
All-inorganic halide perovskites have become one of the most prospective materials for lightening and display technology due to their color-tunable and narrow-band emission. Herein, we have systematically studied the effects of organic amines with different hydrocarbon chain length on the optical properties and morphology as well as the crystal structure of colloidal CsPbBr3 nanocrystals (NCs), which were synthesized in the presence of oleic acid (OA) and organic amines by using a simple hot-injection approach. The hydrocarbon chain length has shown an independent correlation to the morphology and crystal structure of the as-obtained CsPbBr3 NCs at 160 °C, but their optical properties can be affected to some extent. The photoluminescence quantum yields (PLQYs) of the CsPbBr3 NCs synthesized in the presence of organic amines with long carbon chain length are generally in the range of 55-80% for different reaction time, but the PLQYs of less than 20% are obtained for the products synthesized in the presence of octylamine (OTAm) with short carbon chain length. The effects of the reaction temperature on the optical properties, size and crystal structure of the CsPbBr3 NCs synthesized in the presence of cetylamine (CTAm) are studied. Interestingly, some nanoplates also appear in these CsPbBr3 NCs obtained at relatively low temperatures (120 and 140 °C), which have a strong tendency to self-assemble into face-to-face nanostructures. Such a similar self-assembly behavior is also observed in the product synthesized in the presence of oleylamine (OLAm), but only flat nanoplates are observed in the products in the presence of OTAm at 120 °C. The results indicate that the lower reaction temperature and hydrocarbon chain length of the organic ligands play a significant role in the self-assembly of CsPbBr3 NCs. This work opens up an alternative approach to controllable-synthesis of perovskite NCs through varying the carbon chain length of organic surfactants, and enlightens
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V-GAP: Viral genome assembly pipeline
Nakamura, Yoji
2015-10-22
Next-generation sequencing technologies have allowed the rapid determination of the complete genomes of many organisms. Although shotgun sequences from large genome organisms are still difficult to reconstruct perfect contigs each of which represents a full chromosome, those from small genomes have been assembled successfully into a very small number of contigs. In this study, we show that shotgun reads from phage genomes can be reconstructed into a single contig by controlling the number of read sequences used in de novo assembly. We have developed a pipeline to assemble small viral genomes with good reliability using a resampling method from shotgun data. This pipeline, named V-GAP (Viral Genome Assembly Pipeline), will contribute to the rapid genome typing of viruses, which are highly divergent, and thus will meet the increasing need for viral genome comparisons in metagenomic studies.
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V-GAP: Viral genome assembly pipeline
Nakamura, Yoji; Yasuike, Motoshige; Nishiki, Issei; Iwasaki, Yuki; Fujiwara, Atushi; Kawato, Yasuhiko; Nakai, Toshihiro; Nagai, Satoshi; Kobayashi, Takanori; Gojobori, Takashi; Ototake, Mitsuru
2015-01-01
Next-generation sequencing technologies have allowed the rapid determination of the complete genomes of many organisms. Although shotgun sequences from large genome organisms are still difficult to reconstruct perfect contigs each of which represents a full chromosome, those from small genomes have been assembled successfully into a very small number of contigs. In this study, we show that shotgun reads from phage genomes can be reconstructed into a single contig by controlling the number of read sequences used in de novo assembly. We have developed a pipeline to assemble small viral genomes with good reliability using a resampling method from shotgun data. This pipeline, named V-GAP (Viral Genome Assembly Pipeline), will contribute to the rapid genome typing of viruses, which are highly divergent, and thus will meet the increasing need for viral genome comparisons in metagenomic studies.
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δ-Protocadherins: Organizers of neural circuit assembly.
Light, Sarah E W; Jontes, James D
2017-09-01
The δ-protocadherins comprise a small family of homophilic cell adhesion molecules within the larger cadherin superfamily. They are essential for neural development as mutations in these molecules give rise to human neurodevelopmental disorders, such as schizophrenia and epilepsy, and result in behavioral defects in animal models. Despite their importance to neural development, a detailed understanding of their mechanisms and the ways in which their loss leads to changes in neural function is lacking. However, recent results have begun to reveal roles for the δ-protocadherins in both regulation of neurogenesis and lineage-dependent circuit assembly, as well as in contact-dependent motility and selective axon fasciculation. These evolutionarily conserved mechanisms could have a profound impact on the robust assembly of the vertebrate nervous system. Future work should be focused on unraveling the molecular mechanisms of the δ-protocadherins and understanding how this family functions broadly to regulate neural development. Copyright © 2017 Elsevier Ltd. All rights reserved.
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Silicon based near infrared photodetector using self-assembled organic crystalline nano-pillars
Energy Technology Data Exchange (ETDEWEB)
Ajiki, Yoshiharu, E-mail: yoshiharu-ajiki@ot.olympus.co.jp, E-mail: isao@i.u-tokyo.ac.jp [Micromachine Center, 67 Kanda Sakumagashi, Chiyoda-ku, Tokyo 100-0026 (Japan); Kan, Tetsuo [Department of Mechano-Informatics, Graduate School of Information Science and Technology, The University of Tokyo, 7-3-1 Hongo, Bunkyo, Tokyo 113-8656 (Japan); Yahiro, Masayuki; Hamada, Akiko; Adachi, Chihaya [Center for Organic Photonics and Electronics Research (OPERA), Kyushu University, 744 Motooka, Nishi, Fukuoka 819-0395 (Japan); Adachi, Junji [Office for Strategic Research Planning, Kyushu University, 6-10-1 Hakozaki, Higashi, Fukuoka 812-8581 (Japan); Matsumoto, Kiyoshi [IRT Research Initiative, The University of Tokyo, 7-3-1 Hongo, Bunkyo, Tokyo 113-8656 (Japan); Shimoyama, Isao, E-mail: yoshiharu-ajiki@ot.olympus.co.jp, E-mail: isao@i.u-tokyo.ac.jp [Department of Mechano-Informatics, Graduate School of Information Science and Technology, The University of Tokyo, 7-3-1 Hongo, Bunkyo, Tokyo 113-8656 (Japan); IRT Research Initiative, The University of Tokyo, 7-3-1 Hongo, Bunkyo, Tokyo 113-8656 (Japan)
2016-04-11
We propose a silicon (Si) based near-infrared photodetector using self-assembled organic crystalline nano-pillars, which were formed on an n-type Si substrate and were covered with an Au thin-film. These structures act as antennas for near-infrared light, resulting in an enhancement of the light absorption on the Au film. Because the Schottky junction is formed between the Au/n-type Si, the electron excited by the absorbed light can be detected as photocurrent. The optical measurement revealed that the nano-pillar structures enhanced the responsivity for the near-infrared light by 89 (14.5 mA/W) and 16 (0.433 mA/W) times compared with those of the photodetector without nano-pillars at the wavelengths of 1.2 and 1.3 μm, respectively. Moreover, no polarization dependency of the responsivity was observed, and the acceptable incident angle ranged from 0° to 30°. These broad responses were likely to be due to the organic nano-pillar structures' having variation in their orientation, which is advantageous for near-infrared detector uses.
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Energy Technology Data Exchange (ETDEWEB)
Matsui, Hiroshi
2014-09-09
Work is reported in these areas: Large-scale & reconfigurable 3D structures of precise nanoparticle assemblies in self-assembled collagen peptide grids; Binary QD-Au NP 3D superlattices assembled with collagen-like peptides and energy transfer between QD and Au NP in 3D peptide frameworks; Catalytic peptides discovered by new hydrogel-based combinatorial phage display approach and their enzyme-mimicking 2D assembly; New autonomous motors of metal-organic frameworks (MOFs) powered by reorganization of self-assembled peptides at interfaces; Biomimetic assembly of proteins into microcapsules on oil-in-water droplets with structural reinforcement via biomolecular recognition-based cross-linking of surface peptides; and Biomimetic fabrication of strong freestanding genetically-engineered collagen peptide films reinforced by quantum dot joints. We gained the broad knowledge about biomimetic material assembly from nanoscale to microscale ranges by coassembling peptides and NPs via biomolecular recognition. We discovered: Genetically-engineered collagen-like peptides can be self-assembled with Au NPs to generate 3D superlattices in large volumes (> μm{sup 3}); The assembly of the 3D peptide-Au NP superstructures is dynamic and the interparticle distance changes with assembly time as the reconfiguration of structure is triggered by pH change; QDs/NPs can be assembled with the peptide frameworks to generate 3D superlattices and these QDs/NPs can be electronically coupled for the efficient energy transfer; The controlled assembly of catalytic peptides mimicking the catalytic pocket of enzymes can catalyze chemical reactions with high selectivity; and, For the bacteria-mimicking swimmer fabrication, peptide-MOF superlattices can power translational and propellant motions by the reconfiguration of peptide assembly at the MOF-liquid interface.
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SolidWorks 2011 Assemblies Bible
Lombard, Matt
2011-01-01
A fan of the SolidWorks Bible, but want more detail on assemblies? Here you go. SolidWorks fans have long sought more detail on SolidWorks topics, and now you have it. We took our popular SolidWorks Bible, divided it into two books (SolidWorks 2011 Assemblies Bible and SolidWorks 2011 Parts Bible) and packed each new book with a host of items from your wish lists, such as more extensive coverage of the basics, additional tutorials, and expanded coverage of topics largely ignored by other books. This SolidWorks 2011 Assemblies Bible shows you how to organize parts data to create assemblies or s
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Self-assembled biomimetic nanoreactors I: Polymeric template
McTaggart, Matt; Malardier-Jugroot, Cecile; Jugroot, Manish
2015-09-01
The variety of nanoarchitectures made feasible by the self-assembly of alternating copolymers opens new avenues for biomimicry. Indeed, self-assembled structures allow the development of nanoreactors which combine the efficiency of high surface area metal active centres to the effect of confinement due to the very small cavities generated by the self-assembly process. A novel self-assembly of high molecular weight alternating copolymers is characterized in the present study. The self-assembly is shown to organize into nanosheets, providing a 2 nm hydrophobic cavity with a 1D confinement.
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Staff Association
2011-01-01
Tuesday 12 April at 14.00 Council Chamber, Bldg 503 In conformity with the Statutes of the Staff Association, an ordinary General Assembly is organized once a year (article IV.2.1). Agenda Adoption of the Agenda Approval of the Draft Minutes of the Ordinary General Assembly of 20 April 2010 Presentation and approval of the Activity Report 2010 Presentation and approval of the Financial Report 2010 Presentation and approval of the Auditors Report 2010 Programme for 2011 Presentation et and approval of the draft budget and subscription rate 2012 Election of the Election Committee Election of the Board of Auditors Miscellaneous We remind members of article IV.3.4 in the Statutes of the Association which reads: “After having dealt with all the items on the agenda, the members may, with the consent of the Assembly, have other matters discussed, but decisions may be taken only on the items listed on the agenda. Nevertheless, the Assembly ma...
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Staff Association
2011-01-01
Tuesday 12 April at 14.00 Council Chamber, Bldg 503 In conformity with the Statutes of the Staff Association, an ordinary General Assembly is organized once a year (article IV.2.1). Agenda Adoption of the Agenda Approval of the Draft Minutes of the Ordinary General Assembly of 20 April 2010 Presentation and approval of the Activity Report 2010 Presentation and approval of the Financial Report 2010 Presentation and approval of the Auditors Report 2010 Programme for 2011 Presentation and approval of the draft budget and subscription rate 2012 Election of the Election Committee Election of the Board of Auditors Miscellaneous We remind members of article IV.3.4 in the Statutes of the Association which reads: “After having dealt with all the items on the agenda, the members may, with the consent of the Assembly, have other matters discussed, but decisions may be taken only on the items listed on the agenda. Nevertheless, the Assembly may r...
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Staff Association
2010-01-01
Tuesday 20 April at 10.00 Council Chamber, Bldg 503 In conformity with the Statutes of the Staff Association, an ordinary General Assembly is organized once a year (article IV.2.1). Agenda Adoption of the Agenda Approval of the Draft Minutes of the Ordinary General Assembly of 12 May 2009 Presentation and approval of the Activity Report 2009 Presentation and approval of the Financial Report 2009 Presentation and approval of the Auditors Report 2009 Programme for 2010 Presentation et and approval of the draft budget and subscription rate 2010 Election of the Election Committee Election of the Board of Auditors Miscellaneous We remind members of article IV.3.4 in the Statutes of the Association which reads: “After having dealt with all the items on the agenda, the members may, with the consent of the Assembly, have other matters discussed, but decisions may be taken only on the items listed on the agenda. Nevertheless, the Assembly may require t...
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The Electrochemical Assembly of Semiconducting Organic-Inorganic Lamellar Domains for Photovoltaics
Herman, David John
This dissertation investigates the one-step electrodeposition of alternating nanoscale domains of n-type ZnO and p-type organic molecules for photovoltaics. In such hybrid photovoltaic systems, a nanoscale lamellar periodicity of 5-10 nm between electron donor and electron acceptor materials is ideal for efficient exciton separation. In addition, achieving uniform density and substrate-wide alignment of the hybrid lamellar structures with orientation perpendicular to substrate surfaces is important in providing direct pathways for charge carriers to the electrodes. To this end, it is first reported how to control the assembly of the pyrene-based surfactant 1-pyrenebutyric acid (PyBA) with zinc hydroxide (a precursor to the semiconductor ZnO), resulting in a nanoscale lamellar structure with a periodicity of 3.2 nm. By exploring solution chemistry parameters, the surfactant concentration and solvent composition are shown to have the greatest effect on the morphology of lamellar growth. By studying the early nucleation and growth on indium tin oxide (ITO) substrates with 2D grazing incidence small angle X-ray scattering, it is revealed that the lamellae preferentially nucleate parallel to the hydrophilic ITO surface. It is hypothesized that the conductive and more hydrophobic poly(3,4-ethylenedioxythiophene):poly(styrenesulfonate) (PEDOT:PSS) surface increases the affinity for the pyrene functions to the surface, and therefore the oriented growth of the lamellae changes from parallel to perpendicular with respect to the substrate surface. The second part of this thesis investigates the effects of conjugated surfactant design in directing the growth of hybrid lamellar structures by incorporating either a pyrene or terthiophene moiety and varying overall molecular design. It is found that high aspect ratio and amphiphilic surfactants possessing a flexible alkyl spacer between the carboxylic acid and conjugated moiety consistently allow for the controlled and directed
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Directory of Open Access Journals (Sweden)
Haznedaroglu Berat Z
2012-07-01
Full Text Available Abstract Background The k-mer hash length is a key factor affecting the output of de novo transcriptome assembly packages using de Bruijn graph algorithms. Assemblies constructed with varying single k-mer choices might result in the loss of unique contiguous sequences (contigs and relevant biological information. A common solution to this problem is the clustering of single k-mer assemblies. Even though annotation is one of the primary goals of a transcriptome assembly, the success of assembly strategies does not consider the impact of k-mer selection on the annotation output. This study provides an in-depth k-mer selection analysis that is focused on the degree of functional annotation achieved for a non-model organism where no reference genome information is available. Individual k-mers and clustered assemblies (CA were considered using three representative software packages. Pair-wise comparison analyses (between individual k-mers and CAs were produced to reveal missing Kyoto Encyclopedia of Genes and Genomes (KEGG ortholog identifiers (KOIs, and to determine a strategy that maximizes the recovery of biological information in a de novo transcriptome assembly. Results Analyses of single k-mer assemblies resulted in the generation of various quantities of contigs and functional annotations within the selection window of k-mers (k-19 to k-63. For each k-mer in this window, generated assemblies contained certain unique contigs and KOIs that were not present in the other k-mer assemblies. Producing a non-redundant CA of k-mers 19 to 63 resulted in a more complete functional annotation than any single k-mer assembly. However, a fraction of unique annotations remained (~0.19 to 0.27% of total KOIs in the assemblies of individual k-mers (k-19 to k-63 that were not present in the non-redundant CA. A workflow to recover these unique annotations is presented. Conclusions This study demonstrated that different k-mer choices result in various quantities
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Kim, Sung-Kon; Jung, Euiyeon; Goodman, Matthew D; Schweizer, Kenneth S; Tatsuda, Narihito; Yano, Kazuhisa; Braun, Paul V
2015-05-06
We report a three-dimensional (3D) porous carbon electrode containing both nanoscale and microscale porosity, which has been hierarchically organized to provide efficient ion and electron transport. The electrode organization is provided via the colloidal self-assembly of monodisperse starburst carbon spheres (MSCSs). The periodic close-packing of the MSCSs provides continuous pores inside the 3D structure that facilitate ion and electron transport (electrode electrical conductivity ∼0.35 S m(-1)), and the internal meso- and micropores of the MSCS provide a good specific capacitance. The capacitance of the 3D-ordered porous MSCS electrode is ∼58 F g(-1) at 0.58 A g(-1), 48% larger than that of disordered MSCS electrode at the same rate. At 1 A g(-1) the capacitance of the ordered electrode is 57 F g(-1) (95% of the 0.24 A g(-1) value), which is 64% greater than the capacitance of the disordered electrode at the same rate. The ordered electrode preserves 95% of its initial capacitance after 4000 charging/discharging cycles.
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Multi-protein assemblies underlie the mesoscale organization of the plasma membrane
Saka, Sinem K.; Honigmann, Alf; Eggeling, Christian; Hell, Stefan W.; Lang, Thorsten; Rizzoli, Silvio O.
2014-01-01
Most proteins have uneven distributions in the plasma membrane. Broadly speaking, this may be caused by mechanisms specific to each protein, or may be a consequence of a general pattern that affects the distribution of all membrane proteins. The latter hypothesis has been difficult to test in the past. Here, we introduce several approaches based on click chemistry, through which we study the distribution of membrane proteins in living cells, as well as in membrane sheets. We found that the plasma membrane proteins form multi-protein assemblies that are long lived (minutes), and in which protein diffusion is restricted. The formation of the assemblies is dependent on cholesterol. They are separated and anchored by the actin cytoskeleton. Specific proteins are preferentially located in different regions of the assemblies, from their cores to their edges. We conclude that the assemblies constitute a basic mesoscale feature of the membrane, which affects the patterning of most membrane proteins, and possibly also their activity. PMID:25060237
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Conjugated material self-assembly : towards supramolecular electronics
Leclère, P.E.L.G.; Surin, M.; Cavallini, M.; Jonkheijm, P.; Henze, O.; Schenning, A.P.H.J.; Biscarini, F.; Grimsdale, A.C.; Feast, W.J.; Meijer, E.W.; Müllen, K.; Brédas, J.L.; Lazzaroni, R.
2004-01-01
Properties of organic electronic materials in solid-state are determined as individual molecules and molecular assembly. It is essential to optimize conjugated materials to control performance of molecular assembly that constitute electronic devices such as light-emitting diodes and solar cells, and
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Ikeda, Masato; Nobori, Tadahito; Schmutz, Marc; Lehn, Jean-Marie
2005-01-07
The bow-shaped molecule 1 bearing a self-complementary DAAD-ADDA (D=donor A=acceptor) hydrogen-bonding array generates, in hydrocarbon solvents, highly ordered supramolecular sheet aggregates that subsequently give rise to gels by formation of an entangled network. The process of hierarchical self-assembly of compound 1 was investigated by the concentration and temperature dependence of UV-visible and (1)H NMR spectra, fluorescence spectra, and electron microscopy data. The temperature dependence of the UV-visible spectra indicates a highly cooperative process for the self-assembly of compound 1 in decaline. The electron micrograph of the decaline solution of compound 1 (1.0 mM) revealed supramolecular sheet aggregates forming an entangled network. The selected area electronic diffraction patterns of the supramolecular sheet aggregates were typical for single crystals, indicative of a highly ordered assembly. The results exemplify the generation, by hierarchical self-assembly, of highly organized supramolecular materials presenting novel collective properties at each level of organization.
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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.
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Czarnecki, Sebastian; Bertin, Annabelle
2018-03-07
Hybrid silicon-based organic/inorganic (multi)block copolymers are promising polymeric precursors to create robust nano-objects and nanomaterials due to their sol-gel active moieties via self-assembly in solution or in bulk. Such nano-objects and nanomaterials have great potential in biomedicine as nanocarriers or scaffolds for bone regeneration as well as in materials science as Pickering emulsifiers, photonic crystals or coatings/films with antibiofouling, antibacterial or water- and oil-repellent properties. Thus, this Review outlines recent synthetic efforts in the preparation of these hybrid inorganic/organic block copolymers, gives an overview of their self-assembled structures and finally presents recent examples of their use in the biomedical field and material science. © 2018 Wiley-VCH Verlag GmbH & Co. KGaA, Weinheim.
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Bogdanov, Mikhail; Mileykovskaya, Eugenia; Dowhan, William
2008-01-01
Lipids play important roles in cellular dysfunction leading to disease. Although a major role for phospholipids is in defining the membrane permeability barrier, phospholipids play a central role in a diverse range of cellular processes and therefore are important factors in cellular dysfunction and disease. This review is focused on the role of phospholipids in normal assembly and organization of the membrane proteins, multimeric protein complexes, and higher order supercomplexes. Since lipi...
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International Nuclear Information System (INIS)
Weber, A.P.
1978-01-01
A description is given of the plan for assembly, instrumentation, emplacement, and operational checkout of the soil temperature test assembly and dry well liner. The activities described cover all operations necessary to accomplish the receiving inspection, instrumentation and pre-construction handling of the dry well liner, plus all operations performed with the test article. Actual details of construction work are not covered by this procedure. Each part and/or section of this procedure is a separate function to be accomplished as required by the nature of the operation. The organization of the procedure is not intended to imply a special operational sequence or schedular requirement. Specific procedure operational sections include: receiving inspection; liner assembly operations; construction operations (by others); prepare shield plug; test article assembly and installation; and operational checkout
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International Nuclear Information System (INIS)
Hunter, C.N.; Pennoyer, J.D.; Niederman, R.A.
1982-01-01
The B875 and B800-850 light-harvesting pigment-protein complexes of Rhodopseudomonas sphaeroides are characterized further by lithium dodecyl sulfate/polyacrylamide gel electrophoresis at 4 degrees C. Bacteriochlorophyll a was shown in reconstruction studies to remain complexed with its respective binding proteins during this procedure. From distributions in these gels, a quantitative description for the arrangement of the complexes is proposed. Assembly of the complexes was examined in delta-aminolevulinate-requiring mutant H-5 after a shift from high- to low-light intensity. After 10 h of delta-[ 3 H]aminolevulinate labeling, the specific radioactivity of bacteriochlorophyll in a fraction containing putative membrane invaginations reached the maximal level, while that of the mature photosynthetic membrane was at only one-third this level. This suggests that membrane invaginations are sites of preferential bacteriochlorophyll synthesis in which completed pigment-proteins exist transiently. Analysis of the 3 H distribution after electrophoretic separation further suggests that photosynthetic membranes grow mainly by addition of B800-850 to preformed membrane consisting largely of B875 and photochemical reaction centers. These results corroborate the above model for the structural organization of the light-harvesting system and indicate that the structurally and functionally discrete B800-850 pool is not completely assembled until all B875 sites for B800-850 interactions are occupied
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Liquid-liquid interfacial nanoparticle assemblies
Emrick, Todd S [South Deerfield, MA; Russell, Thomas P [Amherst, MA; Dinsmore, Anthony [Amherst, MA; Skaff, Habib [Amherst, MA; Lin, Yao [Amherst, MA
2008-12-30
Self-assembly of nanoparticles at the interface between two fluids, and methods to control such self-assembly process, e.g., the surface density of particles assembling at the interface; to utilize the assembled nanoparticles and their ligands in fabrication of capsules, where the elastic properties of the capsules can be varied from soft to tough; to develop capsules with well-defined porosities for ultimate use as delivery systems; and to develop chemistries whereby multiple ligands or ligands with multiple functionalities can be attached to the nanoparticles to promote the interfacial segregation and assembly of the nanoparticles. Certain embodiments use cadmium selenide (CdSe) nanoparticles, since the photoluminescence of the particles provides a convenient means by which the spatial location and organization of the particles can be probed. However, the systems and methodologies presented here are general and can, with suitable modification of the chemistries, be adapted to any type of nanoparticle.
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Research advances in theories and methods of community assembly and succession
Directory of Open Access Journals (Sweden)
WenJun Zhang
2014-09-01
Full Text Available Community succession refers to the regular and predictable process of species replacement in the environment that all species had been eliminated or that had been disturbed. Community assembly is the process that species growth and interact to establish a community. Community assembly stresses the change of community over a single phase. So far a lot of theories and methods have been proposed for community assembly and succession. In present article I introduced research advances in theories and methods of community assembly and succession. Finally, continuing my past propositions, I further proposed the unified theory and methodology on community assembly and succession. I suggested that community assembly and succession is a process of self-organization. It follows the major principles and mechanisms of self-organization. Agentbased modeling was suggested being used to describe the dynamics of community assembly and succession.
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Miyamura, Hiroyuki; Sonoyama, Arisa; Hayrapetyan, Davit; Kobayashi, Shū
2015-09-01
While water-compatible Lewis acids have great potential as accessible and environmentally benign catalysts for various organic transformations, efficient immobilization of such Lewis acids while keeping high activity and without leaching of metals even under aqueous conditions is a challenging task. Self-assembled nanocomposite catalysts of organic polymers, carbon black, aluminum reductants, and scandium salts as heterogeneous water-compatible Lewis acid catalysts are described. These catalysts could be successfully applied to various C-C bond-forming reactions without leaching of metals. Scanning transmission electron microscopy analyses revealed that the nanocomposite structure of Al and Sc was fabricated in these heterogeneous catalysts. It is noted that Al species, which are usually decomposed rapidly in the presence of water, are stabilized under aqueous conditions. © 2015 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.
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Self-assembly of inorganic nanoparticles: Ab ovo
Kotov, Nicholas A.
2017-09-01
There are numerous remarkable studies related to the self-organization of polymers, coordination compounds, microscale particles, biomolecules, macroscale particles, surfactants, and reactive molecules on surfaces. The focus of this paper is on the self-organization of nanoscale inorganic particles or simply nanoparticles (NPs). Although there are fascinating and profound discoveries made with other self-assembling structures, the ones involving NPs deserve particular attention because they (a) are omnipresent in Nature; (b) have relevance to numerous disciplines (physics, chemistry, biology, astronomy, Earth sciences, and others); (c) embrace most of the features, geometries, and intricacies observed for the self-organization of other chemical species; (d) offer new tools for studies of self-organization phenomena; and (e) have a large economic impact, extending from energy and construction industries, to optoelectronics, biomedical technologies, and food safety. Despite the overall success of the field it is necessary to step back from its multiple ongoing research venues and consider two questions: What is self-assembly of nanoparticles? and Why do we need to study it? The reason to bring them up is to achieve greater scientific depth in the understanding of these omnipresent phenomena and, perhaps, deepen their multifaceted impact. Contribution to the Focus Issue Self-assemblies of Inorganic and Organic Nanomaterials edited by Marie-Paule Pileni.
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DNA-nanoparticle assemblies go organic: Macroscopic polymeric materials with nanosized features
Directory of Open Access Journals (Sweden)
Mentovich Elad D
2012-05-01
Full Text Available Abstract Background One of the goals in the field of structural DNA nanotechnology is the use of DNA to build up 2- and 3-D nanostructures. The research in this field is motivated by the remarkable structural features of DNA as well as by its unique and reversible recognition properties. Nucleic acids can be used alone as the skeleton of a broad range of periodic nanopatterns and nanoobjects and in addition, DNA can serve as a linker or template to form DNA-hybrid structures with other materials. This approach can be used for the development of new detection strategies as well as nanoelectronic structures and devices. Method Here we present a new method for the generation of unprecedented all-organic conjugated-polymer nanoparticle networks guided by DNA, based on a hierarchical self-assembly process. First, microphase separation of amphiphilic block copolymers induced the formation of spherical nanoobjects. As a second ordering concept, DNA base pairing has been employed for the controlled spatial definition of the conjugated-polymer particles within the bulk material. These networks offer the flexibility and the diversity of soft polymeric materials. Thus, simple chemical methodologies could be applied in order to tune the network's electrical, optical and mechanical properties. Results and conclusions One- two- and three-dimensional networks have been successfully formed. Common to all morphologies is the integrity of the micelles consisting of DNA block copolymer (DBC, which creates an all-organic engineered network.
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DNA-nanoparticle assemblies go organic: macroscopic polymeric materials with nanosized features.
Mentovich, Elad D; Livanov, Konstantin; Prusty, Deepak K; Sowwan, Mukules; Richter, Shachar
2012-05-30
One of the goals in the field of structural DNA nanotechnology is the use of DNA to build up 2- and 3-D nanostructures. The research in this field is motivated by the remarkable structural features of DNA as well as by its unique and reversible recognition properties. Nucleic acids can be used alone as the skeleton of a broad range of periodic nanopatterns and nanoobjects and in addition, DNA can serve as a linker or template to form DNA-hybrid structures with other materials. This approach can be used for the development of new detection strategies as well as nanoelectronic structures and devices. Here we present a new method for the generation of unprecedented all-organic conjugated-polymer nanoparticle networks guided by DNA, based on a hierarchical self-assembly process. First, microphase separation of amphiphilic block copolymers induced the formation of spherical nanoobjects. As a second ordering concept, DNA base pairing has been employed for the controlled spatial definition of the conjugated-polymer particles within the bulk material. These networks offer the flexibility and the diversity of soft polymeric materials. Thus, simple chemical methodologies could be applied in order to tune the network's electrical, optical and mechanical properties. One- two- and three-dimensional networks have been successfully formed. Common to all morphologies is the integrity of the micelles consisting of DNA block copolymer (DBC), which creates an all-organic engineered network.
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Payne, Abby-Jo; Li, Shi; Dayneko, Sergey V; Risko, Chad; Welch, Gregory C
2017-09-21
Correction for 'An unsymmetrical non-fullerene acceptor: synthesis via direct heteroarylation, self-assembly, and utility as a low energy absorber in organic photovoltaic cells' by Abby-Jo Payne et al., Chem. Commun., 2017, 53, 10168-10171.
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Stereochemistry in subcomponent self-assembly.
Castilla, Ana M; Ramsay, William J; Nitschke, Jonathan R
2014-07-15
CONSPECTUS: As Pasteur noted more than 150 years ago, asymmetry exists in matter at all organization levels. Biopolymers such as proteins or DNA adopt one-handed conformations, as a result of the chirality of their constituent building blocks. Even at the level of elementary particles, asymmetry exists due to parity violation in the weak nuclear force. While the origin of homochirality in living systems remains obscure, as does the possibility of its connection with broken symmetries at larger or smaller length scales, its centrality to biomolecular structure is clear: the single-handed forms of bio(macro)molecules interlock in ways that depend upon their handednesses. Dynamic artificial systems, such as helical polymers and other supramolecular structures, have provided a means to study the mechanisms of transmission and amplification of stereochemical information, which are key processes to understand in the context of the origins and functions of biological homochirality. Control over stereochemical information transfer in self-assembled systems will also be crucial for the development of new applications in chiral recognition and separation, asymmetric catalysis, and molecular devices. In this Account, we explore different aspects of stereochemistry encountered during the use of subcomponent self-assembly, whereby complex structures are prepared through the simultaneous formation of dynamic coordinative (N → metal) and covalent (N═C) bonds. This technique provides a useful method to study stereochemical information transfer processes within metal-organic assemblies, which may contain different combinations of fixed (carbon) and labile (metal) stereocenters. We start by discussing how simple subcomponents with fixed stereogenic centers can be incorporated in the organic ligands of mononuclear coordination complexes and communicate stereochemical information to the metal center, resulting in diastereomeric enrichment. Enantiopure subcomponents were then
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Brennan, James R; Hocking, Denise C
2016-03-01
The cell-dependent polymerization of intercellular fibronectin fibrils can stimulate cells to self-assemble into multicellular structures. The local physical cues that support fibronectin-mediated cellular self-assembly are largely unknown. Here, fibronectin matrix analogs were used as synthetic adhesive substrates to model cell-matrix fibronectin fibrils having different integrin-binding specificity, affinity, and/or density. We utilized this model to quantitatively assess the relationship between adhesive forces derived from cell-substrate interactions and the ability of fibronectin fibril assembly to induce cellular self-assembly. Results indicate that the strength of initial, rather than mature, cell-substrate attachments correlates with the ability of substrates to support fibronectin-mediated cellular self-assembly. The cellular response to soluble fibronectin was bimodal and independent of the integrin-binding specificity of the substrate; increasing soluble fibronectin levels above a critical threshold increased aggregate cohesion on permissive substrates. Once aggregates formed, continuous fibronectin polymerization was necessary to maintain cohesion. During self-assembly, soluble fibronectin decreased cell-substrate adhesion strength and induced aggregate cohesion via a Rho-dependent mechanism, suggesting that the balance of contractile forces derived from fibronectin fibrils within cell-cell versus cell-substrate adhesions controls self-assembly and aggregate cohesion. Thus, initial cell-substrate attachment strength may provide a quantitative basis with which to build predictive models of fibronectin-mediated microtissue fabrication on a variety of substrates. Cellular self-assembly is a process by which cells and extracellular matrix (ECM) proteins spontaneously organize into three-dimensional (3D) tissues in the absence of external forces. Cellular self-assembly can be initiated in vitro, and represents a potential tool for tissue engineers to
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Nanotechnology: A molecular assembler
Kelly, T. Ross; Snapper, Marc L.
2017-09-01
The idea of nanometre-scale machines that can assemble molecules has long been thought of as the stuff of science fiction. Such a machine has now been built -- and might herald a new model for organic synthesis. See Letter p.374
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Association du personnel
2010-01-01
Tuesday 20 April at 10.00 Council Chamber, Bldg 503 In conformity with the Statutes of the Staff Association, an ordinary General Assembly is organized once a year (article IV.2.1). Agenda Adoption of the Agenda Approval of the Draft Minutes of the Ordinary General Assembly of 12 May 2009 Presentation and approval of the Activity Report 2009 Presentation and approval of the Financial Report 2009 Presentation and approval of the Auditors Report 2009 Programme for 2010 Presentation et and approval of the draft budget and subscription rate 2010 Modifications to the statutes of the association Election of the Election Committee Election of the Board of Auditors Miscellaneous We remind members of article IV.3.4 in the Statutes of the Association which reads: “After having dealt with all the items on the agenda, the members may, with the consent of the Assembly, have other matters discussed, but decisions may be taken only on the items listed on the agenda...
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Maity, Kuntal; Mandal, Dipankar
2018-05-30
Rapid development of wearable electronics, piezoelectric nanogenerator (PNG), has been paid a special attention because of its sustainable and accessible energy generation. In this context, we present a simple yet highly efficient design strategy to enhance the output performance of an all-organic PNG (OPNG) based on multilayer assembled electrospun poly(vinylidene fluoride) (PVDF) nanofiber (NF) mats where vapor-phase polymerized poly(3,4-ethylenedioxythiophene)-coated PVDF NFs are assembled as electrodes and neat PVDF NFs are utilized as an active component. In addition to the multilayer assembly, electrode compatibility and durability remain a challenging task to mitigate the primary requirements of wearable electronics. A multilayer networked three-dimensional structure integrated with a compatible electrode thereby provides enhanced output voltage and current (e.g., open-circuit voltage, V oc ≈ 48 V, and short-circuit current, I sc ≈ 6 μA, upon 8.3 kPa of the applied stress amplitude) with superior piezoelectric energy conversion efficiency of 66% compared to the single-mat device. Besides, OPNG also shows ultrasensitivity toward human movements such as foot strikes and walking. The weight measurement mapping is critically explored by principal component analysis that may have enormous applications in medical diagnosis to smart packaging industries. More importantly, fatigue test under continuous mechanical impact (over 6 months) shows great promise as a robust wearable mechanical energy harvester.
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Anisotropic Self-Assembly of Organic–Inorganic Hybrid Microtoroids
Al-Rehili, Safa’a
2016-10-24
Toroidal structures based on self-assembly of predesigned building blocks are well-established in the literature, but spontaneous self-organization to prepare such structures has not been reported to date. Here, organic–inorganic hybrid microtoroids synthesized by simultaneous coordination-driven assembly of amphiphilic molecules and hydrophilic polymers are reported. Mixing amphiphilic molecules with iron(III) chloride and hydrophilic polymers in water leads, within minutes, to the formation of starlike nanostructures. A spontaneous self-organization of these nanostructures is then triggered to form stable hybrid microtoroids. Interestingly, the toroids exhibit anisotropic hierarchical growth, giving rise to a layered toroidal framework. These microstructures are mechanically robust and can act as templates to host metallic nanoparticles such as gold and silver. Understanding the nature of spontaneous assembly driven by coordination multiple non-covalent interactions can help explain the well-ordered complexity of many biological organisms in addition to expanding the available tools to mimic such structures at a molecular level.
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Radical probing of spliceosome assembly.
Grewal, Charnpal S; Kent, Oliver A; MacMillan, Andrew M
2017-08-01
Here we describe the synthesis and use of a directed hydroxyl radical probe, tethered to a pre-mRNA substrate, to map the structure of this substrate during the spliceosome assembly process. These studies indicate an early organization and proximation of conserved pre-mRNA sequences during spliceosome assembly. This methodology may be adapted to the synthesis of a wide variety of modified RNAs for use as probes of RNA structure and RNA-protein interaction. Copyright © 2017 Elsevier Inc. All rights reserved.
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Assembly of Repeat Content Using Next Generation Sequencing Data
Energy Technology Data Exchange (ETDEWEB)
labutti, Kurt; Kuo, Alan; Grigoriev, Igor; Copeland, Alex
2014-03-17
Repetitive organisms pose a challenge for short read assembly, and typically only unique regions and repeat regions shorter than the read length, can be accurately assembled. Recently, we have been investigating the use of Pacific Biosciences reads for de novo fungal assembly. We will present an assessment of the quality and degree of repeat reconstruction possible in a fungal genome using long read technology. We will also compare differences in assembly of repeat content using short read and long read technology.
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Probing Interactions in Complex Molecular Systems through Ordered Assembly
International Nuclear Information System (INIS)
De Yoreo, J.J.; Bartelt, M.C.; Orme, C.A.; Villacampa, A.; Weeks, B.L.; Miller, A.E.
2002-01-01
Emerging from the machinery of epitaxial science and chemical synthesis, is a growing emphasis on development of self-organized systems of complex molecular species. The nature of self-organization in these systems spans the continuum from simple crystallization of large molecules such as dendrimers and proteins, to assembly into large organized networks of nanometer-scale structures such as quantum dots or nanoparticles. In truth, self-organization in complex molecular systems has always been a central feature of many scientific disciplines including fields as diverse as structural biology, polymer science and geochemistry. But over the past decade, changes in those fields have often been marked by the degree to which researchers are using molecular-scale approaches to understand the hierarchy of structures and processes driven by this ordered assembly. At the same time, physical scientists have begun to use their knowledge of simple atomic and molecular systems to fabricate synthetic self-organized systems. This increasing activity in the field of self-organization is testament to the success of the physical and chemical sciences in building a detailed understanding of crystallization and epitaxy in simple atomic and molecular systems, one that is soundly rooted in thermodynamics and chemical kinetics. One of the fundamental challenges of chemistry and materials science in the coming decades is to develop a similarly well-founded physical understanding of assembly processes in complex molecular systems. Over the past five years, we have successfully used in situ atomic force microscopy (AFM) to investigate the physical controls on single crystal epitaxy from solutions for a wide range of molecular species. More recently, we have combined this method with grazing incidence X-ray diffraction and kinetic Monte Carlo modeling in order to relate morphology to surface atomic structure and processes. The purpose of this proposal was to extend this approach to assemblies
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Optimizing de novo common wheat transcriptome assembly using short-read RNA-Seq data
Directory of Open Access Journals (Sweden)
Duan Jialei
2012-08-01
Full Text Available Abstract Background Rapid advances in next-generation sequencing methods have provided new opportunities for transcriptome sequencing (RNA-Seq. The unprecedented sequencing depth provided by RNA-Seq makes it a powerful and cost-efficient method for transcriptome study, and it has been widely used in model organisms and non-model organisms to identify and quantify RNA. For non-model organisms lacking well-defined genomes, de novo assembly is typically required for downstream RNA-Seq analyses, including SNP discovery and identification of genes differentially expressed by phenotypes. Although RNA-Seq has been successfully used to sequence many non-model organisms, the results of de novo assembly from short reads can still be improved by using recent bioinformatic developments. Results In this study, we used 212.6 million pair-end reads, which accounted for 16.2 Gb, to assemble the hexaploid wheat transcriptome. Two state-of-the-art assemblers, Trinity and Trans-ABySS, which use the single and multiple k-mer methods, respectively, were used, and the whole de novo assembly process was divided into the following four steps: pre-assembly, merging different samples, removal of redundancy and scaffolding. We documented every detail of these steps and how these steps influenced assembly performance to gain insight into transcriptome assembly from short reads. After optimization, the assembled transcripts were comparable to Sanger-derived ESTs in terms of both continuity and accuracy. We also provided considerable new wheat transcript data to the community. Conclusions It is feasible to assemble the hexaploid wheat transcriptome from short reads. Special attention should be paid to dealing with multiple samples to balance the spectrum of expression levels and redundancy. To obtain an accurate overview of RNA profiling, removal of redundancy may be crucial in de novo assembly.
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Spontaneous Assembly of Exopolymers from Phytoplankton
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Yong-Xue Ding
2009-01-01
Full Text Available Phytoplankton exopolymeric substances (EPS contribute significantly to the dissolved organic car bon (DOC pool in the ocean, playing crucial roles in the surface ocean car bon cycle. Recent studies have demonstrated that ~10% of marine DOC can self-assemble as microgels through electro static Ca bonds providing hotspots of enriched microbial substrate. How ever, the question whether EPS can self-assemble and the formation mechanisms for EPS microgels have not been examined. Here were port that EPS from three representative phytoplankton species, Synechococcus, Emiliania huxleyi, and Skeletonema costatum can spontaneously self assemble in artificial sea water (ASW, forming microscopic gels of ~ 3 - 4 __m in diameter. Different from the marine DOC polymers assembly, these EPS samples can self-assemble in Ca2+-free ASW. Further experiments from fluorescence enhancement and chemical composition analysis confirmed the existence of fair amounts of hydrophobic domains in these EPS samples. These results suggest that hydrophobic interactions play a key role in the assembly of EPS from these three species of marine phytoplankton.
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Equilibrium polymerization models of re-entrant self-assembly
Dudowicz, Jacek; Douglas, Jack F.; Freed, Karl F.
2009-04-01
As is well known, liquid-liquid phase separation can occur either upon heating or cooling, corresponding to lower and upper critical solution phase boundaries, respectively. Likewise, self-assembly transitions from a monomeric state to an organized polymeric state can proceed either upon increasing or decreasing temperature, and the concentration dependent ordering temperature is correspondingly called the "floor" or "ceiling" temperature. Motivated by the fact that some phase separating systems exhibit closed loop phase boundaries with two critical points, the present paper analyzes self-assembly analogs of re-entrant phase separation, i.e., re-entrant self-assembly. In particular, re-entrant self-assembly transitions are demonstrated to arise in thermally activated equilibrium self-assembling systems, when thermal activation is more favorable than chain propagation, and in equilibrium self-assembly near an adsorbing boundary where strong competition exists between adsorption and self-assembly. Apparently, the competition between interactions or equilibria generally underlies re-entrant behavior in both liquid-liquid phase separation and self-assembly transitions.
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Models of natural computation : gene assembly and membrane systems
Brijder, Robert
2008-01-01
This thesis is concerned with two research areas in natural computing: the computational nature of gene assembly and membrane computing. Gene assembly is a process occurring in unicellular organisms called ciliates. During this process genes are transformed through cut-and-paste operations. We
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Polymorphism of lipid self-assembly systems
International Nuclear Information System (INIS)
Takahashi, Hiroshi
2002-01-01
When lipid molecules are dispersed into an aqueous medium, various self-organized structures are formed, depending on conditions (temperature, concentration, etc), in consequence of the amphipathic nature of the molecules. In addition, lipid self-assembly systems exhibit polymorphic phase transition behavior. Since lipids are one of main components of biomembranes, studies on the structure and thermodynamic properties of lipid self-assembly systems are fundamentally important for the consideration of the stability of biomembranes. (author)
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Sze, Sing-Hoi; Parrott, Jonathan J; Tarone, Aaron M
2017-12-06
While the continued development of high-throughput sequencing has facilitated studies of entire transcriptomes in non-model organisms, the incorporation of an increasing amount of RNA-Seq libraries has made de novo transcriptome assembly difficult. Although algorithms that can assemble a large amount of RNA-Seq data are available, they are generally very memory-intensive and can only be used to construct small assemblies. We develop a divide-and-conquer strategy that allows these algorithms to be utilized, by subdividing a large RNA-Seq data set into small libraries. Each individual library is assembled independently by an existing algorithm, and a merging algorithm is developed to combine these assemblies by picking a subset of high quality transcripts to form a large transcriptome. When compared to existing algorithms that return a single assembly directly, this strategy achieves comparable or increased accuracy as memory-efficient algorithms that can be used to process a large amount of RNA-Seq data, and comparable or decreased accuracy as memory-intensive algorithms that can only be used to construct small assemblies. Our divide-and-conquer strategy allows memory-intensive de novo transcriptome assembly algorithms to be utilized to construct large assemblies.
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Directory of Open Access Journals (Sweden)
Kai-Yu Peng
2014-01-01
Full Text Available A single-monolayered hexagonal self-assembled photonic crystal (PC pattern fabricated onto polyethylene terephthalate (PET films by using simple nanosphere lithography (NSL method has been demonstrated in this research work. The patterned nanostructures acted as a scattering medium to extract the trapped photons from substrate mode of optical-electronic device for improving the overall external quantum efficiency of the organic light-emitting diodes (OLEDs. With an optimum latex concentration, the distribution of self-assembled polystyrene (PS nanosphere patterns on PET films can be easily controlled by adjusting the rotation speed of spin-coater. After attaching the PS nanosphere array brightness enhancement film (BEF sheet as a photonic crystal pattern onto the device, the luminous intensity of OLEDs in the normal viewing direction is 161% higher than the one without any BEF attachment. The electroluminescent (EL spectrum of OLEDs with PS patterned BEF attachment also showed minor color offset and superior color stabilization characteristics, and thus it possessed the potential applications in all kinds of display technology and solid-state optical-electronic devices.
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El Malah, Tamer; Ciesielski, Artur; Piot, Luc; Troyanov, Sergey I; Mueller, Uwe; Weidner, Steffen; Samorì, Paolo; Hecht, Stefan
2012-01-21
Efficient Cu-catalyzed 1,3-dipolar cycloaddition reactions have been used to prepare two series of three regioisomers of G-1 and G-2 poly(triazole-pyridine) dendrons. The G-1 and G-2 dendrons consist of branched yet conformationally pre-organized 2,6-bis(phenyl/pyridyl-1,2,3-triazol-4-yl)pyridine (BPTP) monomeric and trimeric cores, respectively, carrying one focal and either two or four peripheral alkyl side chains. In the solid state, the conformation and supramolecular organization were studied by means of a single crystal X-ray structure analysis of one derivative. At the liquid-solid interface, the self-assembly behavior was investigated by scanning tunneling microscopy (STM) on graphite surfaces. Based on the observed supramolecular organization, it appears that the subtle balance between conformational preferences inherent in the dendritic backbone on the one side and the adsorption and packing of the alkyl side chains on the graphite substrate on the other side dictate the overall structure formation in 2D.
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Percec, Virgil; Bera, Tushar K; Glodde, Martin; Fu, Qiongying; Balagurusamy, Venkatachalapathy S K; Heiney, Paul A
2003-02-17
The synthesis and structural analysis of the twin-dendritic benzamide 10, based on the first-generation, self-assembling, tapered dendrons 3,4,5-tris(4'-dodecyloxybenzyloxy)benzoic acid and 3,4,5-tris(4'-dodecyloxybenzyloxy)-1-aminobenzene, and the polymethacrylate, 20, which contains 10 as side groups, are presented. Benzamide 10 self-assembles into a supramolecular cylindrical dendrimer that self-organizes into a columnar hexagonal (Phi(h)) liquid crystalline (LC) phase. Polymer 20 self-assembles into an imperfect four-cylinder-bundle supramolecular dendrimer, and creates a giant vesicular supercylinder that self-organizes into a columnar nematic (N(c)) LC phase which displays short-range hexagonal order. In mixtures of 20 and 10, 10 acts as a guest and 20 as a host to create a perfect four-cylinder-bundle host-guest supramolecular dendrimer that coorganizes with 10. A diversity of Phi(h), simple rectangular columnar (Phi(r-s)) and centered rectangular columnar (Phi(r-c)), superlattices are produced at different ratios between 20 and 10. This diversity of LC lattices and superlattices is facilitated by the architecture of the twin-dendritic building block, polymethacrylate, the host-guest supramolecular assembly, and by hydrogen bonding along the center of the supramolecular cylinders generated from 10 and 20.
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Quantum-Chemical Insights into the Self-Assembly of Carbon-Based Supramolecular Complexes
Directory of Open Access Journals (Sweden)
Joaquín Calbo
2018-01-01
Full Text Available Understanding how molecular systems self-assemble to form well-organized superstructures governed by noncovalent interactions is essential in the field of supramolecular chemistry. In the nanoscience context, the self-assembly of different carbon-based nanoforms (fullerenes, carbon nanotubes and graphene with, in general, electron-donor molecular systems, has received increasing attention as a means of generating potential candidates for technological applications. In these carbon-based systems, a deep characterization of the supramolecular organization is crucial to establish an intimate relation between supramolecular structure and functionality. Detailed structural information on the self-assembly of these carbon-based nanoforms is however not always accessible from experimental techniques. In this regard, quantum chemistry has demonstrated to be key to gain a deep insight into the supramolecular organization of molecular systems of high interest. In this review, we intend to highlight the fundamental role that quantum-chemical calculations can play to understand the supramolecular self-assembly of carbon-based nanoforms through a limited selection of supramolecular assemblies involving fullerene, fullerene fragments, nanotubes and graphene with several electron-rich π-conjugated systems.
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Patil, Avinash J; Li, Mei; Mann, Stephen
2013-08-21
Synthesis of functional hybrid nanoscale objects has been a core focus of the rapidly progressing field of nanomaterials science. In particular, there has been significant interest in the integration of evolutionally optimized biological systems such as proteins, DNA, virus particles and cells with functional inorganic building blocks to construct mesoscopic architectures and nanostructured materials. However, in many cases the fragile nature of the biomolecules seriously constrains their potential applications. As a consequence, there is an on-going quest for the development of novel strategies to modulate the thermal and chemical stabilities, and performance of biomolecules under adverse conditions. This feature article highlights new methods of "inorganic molecular wrapping" of single or multiple protein molecules, individual double-stranded DNA helices, lipid bilayer vesicles and self-assembled organic dye superstructures using inorganic building blocks to produce bio-inorganic nanoconstructs with core-shell type structures. We show that spatial isolation of the functional biological nanostructures as "armour-plated" enzyme molecules or polynucleotide strands not only maintains their intact structure and biochemical properties, but also enables the fabrication of novel hybrid nanomaterials for potential applications in diverse areas of bionanotechnology.
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Patil, Avinash J.; Li, Mei; Mann, Stephen
2013-07-01
Synthesis of functional hybrid nanoscale objects has been a core focus of the rapidly progressing field of nanomaterials science. In particular, there has been significant interest in the integration of evolutionally optimized biological systems such as proteins, DNA, virus particles and cells with functional inorganic building blocks to construct mesoscopic architectures and nanostructured materials. However, in many cases the fragile nature of the biomolecules seriously constrains their potential applications. As a consequence, there is an on-going quest for the development of novel strategies to modulate the thermal and chemical stabilities, and performance of biomolecules under adverse conditions. This feature article highlights new methods of ``inorganic molecular wrapping'' of single or multiple protein molecules, individual double-stranded DNA helices, lipid bilayer vesicles and self-assembled organic dye superstructures using inorganic building blocks to produce bio-inorganic nanoconstructs with core-shell type structures. We show that spatial isolation of the functional biological nanostructures as ``armour-plated'' enzyme molecules or polynucleotide strands not only maintains their intact structure and biochemical properties, but also enables the fabrication of novel hybrid nanomaterials for potential applications in diverse areas of bionanotechnology.
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International Nuclear Information System (INIS)
Nam, K.O.; Park, H.K.; Kim, D.J.; Ahn, H.J.; Kim, K.K.; Im, K.; Shaw, R.
2010-01-01
The final assembly of main components of the International Thermonuclear Experimental Reactor (ITER) tokamak, Vacuum Vessel (VV) and Toroidal Field Coils (TFCs), is achieved by the sequential assembly of the nine sub-assembled 40 o sectors in tokamak pit. Each sub-assembled 40 o sector is composed of one VV 40 o sector, two TFCs, and in-between Vacuum Vessel Thermal Shield (VVTS) segments. Sub-assembly is carried out in the assembly building and then the sub-assembled sectors are transferred into tokamak pit, in sequence, to complete sector assembly. The role of in-pit assembly tool is to support and align the sub-assembled sectors in tokamak pit. It also plays the role of reference datum during assembly until the completion of main components assembly. Korea Domestic Agency (KO DA) has developed the conceptual design of most ITER purpose-built assembly tools under the collaboration with the ITER Organization. Among the conceptual designs carried out, this paper describes the function, the structure, the selected material and the design results of the in-pit assembly tools comprising central column, radial beams and their supports, TF inner supports and in-pit working floor. The results of structural analysis using ANSYS for the various loading cases are given as well. The resultant stresses and deflections turned out to fall within the allowable ranges.
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Pressure effects on lipids and bio-membrane assemblies
Directory of Open Access Journals (Sweden)
Nicholas J. Brooks
2014-11-01
Full Text Available Membranes are amongst the most important biological structures; they maintain the fundamental integrity of cells, compartmentalize regions within them and play an active role in a wide range of cellular processes. Pressure can play a key role in probing the structure and dynamics of membrane assemblies, and is also critical to the biology and adaptation of deep-sea organisms. This article presents an overview of the effect of pressure on the mesostructure of lipid membranes, bilayer organization and lipid–protein assemblies. It also summarizes recent developments in high-pressure structural instrumentation suitable for experiments on membranes.
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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.
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International Nuclear Information System (INIS)
Li Yun; Pan Lijia; Pu Lin; Shi Yi; Liu Chuan; Tsukagoshi, Kazuhito
2012-01-01
Charge trapping at organic/self-assembly molecule (SAM) interfaces is studied by the electrical switching behaviour in a crosspoint structure, where interfacial charge trapping tunes the potential barrier of the SAM layer. The sample with rubrene exhibits the write-once read-many-times memory effect, which is due to the interfacial charges trapped at deep states. On the other hand, the sample with 2-amino-4,5-dicyanoimidazole presents recyclable conduction transition, which results from the trapped charges distributed at shallow states. Moreover, the percentage of the charges trapped at shallow states can be estimated from electrical transition levels. (paper)
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Li, Yun; Liu, Chuan; Pan, Lijia; Pu, Lin; Tsukagoshi, Kazuhito; Shi, Yi
2012-01-01
Charge trapping at organic/self-assembly molecule (SAM) interfaces is studied by the electrical switching behaviour in a crosspoint structure, where interfacial charge trapping tunes the potential barrier of the SAM layer. The sample with rubrene exhibits the write-once read-many-times memory effect, which is due to the interfacial charges trapped at deep states. On the other hand, the sample with 2-amino-4,5-dicyanoimidazole presents recyclable conduction transition, which results from the trapped charges distributed at shallow states. Moreover, the percentage of the charges trapped at shallow states can be estimated from electrical transition levels.
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Predicting supramolecular self-assembly on reconstructed metal surfaces
Roussel, Thomas J.; Barrena, Esther; Ocal, Carmen; Faraudo, Jordi
2014-06-01
The prediction of supramolecular self-assembly onto solid surfaces is still challenging in many situations of interest for nanoscience. In particular, no previous simulation approach has been capable to simulate large self-assembly patterns of organic molecules over reconstructed surfaces (which have periodicities over large distances) due to the large number of surface atoms and adsorbing molecules involved. Using a novel simulation technique, we report here large scale simulations of the self-assembly patterns of an organic molecule (DIP) over different reconstructions of the Au(111) surface. We show that on particular reconstructions, the molecule-molecule interactions are enhanced in a way that long-range order is promoted. Also, the presence of a distortion in a reconstructed surface pattern not only induces the presence of long-range order but also is able to drive the organization of DIP into two coexisting homochiral domains, in quantitative agreement with STM experiments. On the other hand, only short range order is obtained in other reconstructions of the Au(111) surface. The simulation strategy opens interesting perspectives to tune the supramolecular structure by simulation design and surface engineering if choosing the right molecular building blocks and stabilising the chosen reconstruction pattern.The prediction of supramolecular self-assembly onto solid surfaces is still challenging in many situations of interest for nanoscience. In particular, no previous simulation approach has been capable to simulate large self-assembly patterns of organic molecules over reconstructed surfaces (which have periodicities over large distances) due to the large number of surface atoms and adsorbing molecules involved. Using a novel simulation technique, we report here large scale simulations of the self-assembly patterns of an organic molecule (DIP) over different reconstructions of the Au(111) surface. We show that on particular reconstructions, the molecule
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Nanoparticle assemblies and superstructures
National Research Council Canada - National Science Library
Kotov, Nicholas A
2006-01-01
... building blocks of larger and more complex systems. Therefore, the present challenge of nanoscale science is to shift from making certain building blocks to organizing them in one-, two-, and three-dimensional structures. Such assemblies and superstructures are the next logical step in the development of nanoscience and nanotechnology. In this re...
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Large branched self-assembled DNA complexes
International Nuclear Information System (INIS)
Tosch, Paul; Waelti, Christoph; Middelberg, Anton P J; Davies, A Giles
2007-01-01
Many biological molecules have been demonstrated to self-assemble into complex structures and networks by using their very efficient and selective molecular recognition processes. The use of biological molecules as scaffolds for the construction of functional devices by self-assembling nanoscale complexes onto the scaffolds has recently attracted significant attention and many different applications in this field have emerged. In particular DNA, owing to its inherent sophisticated self-organization and molecular recognition properties, has served widely as a scaffold for various nanotechnological self-assembly applications, with metallic and semiconducting nanoparticles, proteins, macromolecular complexes, inter alia, being assembled onto designed DNA scaffolds. Such scaffolds may typically contain multiple branch-points and comprise a number of DNA molecules selfassembled into the desired configuration. Previously, several studies have used synthetic methods to produce the constituent DNA of the scaffolds, but this typically constrains the size of the complexes. For applications that require larger self-assembling DNA complexes, several tens of nanometers or more, other techniques need to be employed. In this article, we discuss a generic technique to generate large branched DNA macromolecular complexes
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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.
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Yoshida, Satoru; Takinoue, Masahiro; Iwase, Eiji; Onoe, Hiroaki
2016-08-01
This paper describes a system through which the self-assembly of anisotropic hydrogel microparticles is achieved, which also enables dynamic transformation of the assembled structures. Using a centrifuge-based microfluidic device, anisotropic hydrogel microparticles encapsulating superparamagnetic materials on one side are fabricated, which respond to a magnetic field. We successfully achieve dynamic assembly using these hydrogel microparticles and realize three different self-assembled structures (single and double pearl chain structures, and close-packed structures), which can be transformed to other structures dynamically via tuning of the precessional magnetic field. We believe that the developed system has potential application as an effective platform for a dynamic cell manipulation and cultivation system, in biomimetic autonomous microrobot organization, and that it can facilitate further understanding of the self-organization and complex systems observed in nature.
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Zhang, Lianbin
2012-01-01
In this study, three-dimensional (3D) graphene assemblies are prepared from graphene oxide (GO) by a facile in situ reduction-assembly method, using a novel, low-cost, and environment-friendly reducing medium which is a combination of oxalic acid (OA) and sodium iodide (NaI). It is demonstrated that the combination of a reducing acid, OA, and NaI is indispensable for effective reduction of GO in the current study and this unique combination (1) allows for tunable control over the volume of the thus-prepared graphene assemblies and (2) enables 3D graphene assemblies to be prepared from the GO suspension with a wide range of concentrations (0.1 to 4.5 mg mL-1). To the best of our knowledge, the GO concentration of 0.1 mg mL-1 is the lowest GO concentration ever reported for preparation of 3D graphene assemblies. The thus-prepared 3D graphene assemblies exhibit low density, highly porous structures, and electrically conducting properties. As a proof of concept, we show that by infiltrating a responsive polymer of polydimethylsiloxane (PDMS) into the as-resulted 3D conducting network of graphene, a conducting composite is obtained, which can be used as a sensing device for differentiating organic solvents with different polarity. © 2012 The Royal Society of Chemistry.
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DEFF Research Database (Denmark)
Pedersen, Lotte B; Veland, Iben R; Schrøder, Jacob M
2008-01-01
knowledge about IFT is based on studies performed in Chlamydomonas and Caenorhabditis elegans. Therefore, our review of the IFT literature includes studies performed in these two model organisms. The role of several non-IFT proteins (e.g., centrosomal proteins) in the ciliary assembly process is also...... discussed. Developmental Dynamics, 2008. (c) 2008 Wiley-Liss, Inc....
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In Vitro Assembly of Catalase*
Baureder, Michael; Barane, Elisabeth; Hederstedt, Lars
2014-01-01
Most aerobic organisms contain catalase, which functions to decompose hydrogen peroxide. Typical catalases are structurally complex homo-tetrameric enzymes with one heme prosthetic group buried in each subunit. It is not known how catalase in the cell is assembled from its constituents. The bacterium Enterococcus faecalis cannot synthesize heme but can acquire it from the environment to form a cytoplasmic catalase. We have in E. faecalis monitored production of the enzyme polypeptide (KatA) depending on the availability of heme and used our findings to devise a procedure for the purification of preparative amounts of in vivo-synthesized apocatalase. We show that fully active catalase can be obtained in vitro by incubating isolated apoprotein with hemin. We have characterized features of the assembly process and describe a temperature-trapped hemylated intermediate of the enzyme maturation process. Hemylation of apocatalase does not require auxiliary cell components, but rapid assembly of active enzyme seemingly is assisted in the cell. Our findings provide insight about catalase assembly and offer new experimental possibilities for detailed studies of this process. PMID:25148685
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Wang, Zhihua; Teng, Xu; Lu, Chao
2013-02-19
In this work, a universal chemiluminescence (CL) flow-through device suitable for various CL resonance energy transfer (CRET) systems has been successfully fabricated. Highly efficient CRET in solid-state photoactive organic molecules can be achieved by assembling them on the surface of layered double hydroxides (LDHs). We attribute these observations to the suppression of the intermolecular π-π stacking interactions among aromatic rings and the improvement of molecular orientation and planarity in the LDH matrix, enabling a remarkable increase in fluorescence lifetime and quantum yield of organic molecules. Under optimal conditions, using peroxynitrous acid-fluorescein dianion (FLUD) as a model CRET system, trace FLUD (10 μM) was assembled on the surface of LDHs. Peroxynitrous acid/nitrite could be assayed in the range of 1.0-500 μM, and the detection limit for peroxynitrous acid/nitrite (S/N = 3) was 0.6 μM. This CL flow-through device exhibited operational stability, high reproducibility, and long lifetime. While LDHs were immobilized in a flow-through device in the absence of FLUD, the detection limit for peroxynitrous acid/nitrite was 100 μM. On the other hand, FLUD at the same concentration can not enhance the CL intensity of peroxynitrous acid system. This fabricated CL flow-through column has been successfully applied to determine nitrite in sausage samples with recoveries of 98-102%. These satisfactory results demonstrated that our studies pave a novel way toward flow-through column-based CRET using solid-state organic molecules as acceptors for signal amplification.
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Ultrafine luminescent structures through nanoparticle self-assembly
International Nuclear Information System (INIS)
Prabhakaran, K; Goetzinger, S; Shafi, K V P M; Mazzei, A; Schietinger, S; Benson, O
2006-01-01
We report the fabrication of ultrafine structures consisting of regular arrays of nanoemitters through the self-assembly of luminescent nanoparticles on a silicon wafer. Nanoparticles of yttrium aluminium garnet (YAG) doped with Eu 3+ ions were synthesized by a sonochemical technique. These particles, suspended in ethanol, are introduced onto a pre-patterned silicon wafer, covered with a thin oxide layer. On annealing the sample in an ultrahigh-vacuum chamber, the nanoparticles self-assemble along the pattern. We demonstrate this 'chemical lithography' by assembling the nanoparticles along a variety of patterns. We believe that such self-organized nanopatterning of functional structures is important for the realization of nanodevices
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"Supersaturated" self-assembled charge-selective interfacial layers for organic solar cells.
Song, Charles Kiseok; Luck, Kyle A; Zhou, Nanjia; Zeng, Li; Heitzer, Henry M; Manley, Eric F; Goldman, Samuel; Chen, Lin X; Ratner, Mark A; Bedzyk, Michael J; Chang, Robert P H; Hersam, Mark C; Marks, Tobin J
2014-12-24
To achieve densely packed charge-selective organosilane-based interfacial layers (IFLs) on the tin-doped indium oxide (ITO) anodes of organic photovoltaic (OPV) cells, a series of Ar2N-(CH2)n-SiCl3 precursors with Ar = 3,4-difluorophenyl, n = 3, 6, 10, and 18, was synthesized, characterized, and chemisorbed on OPV anodes to serve as IFLs. To minimize lateral nonbonded -NAr2···Ar2N- repulsions which likely limit IFL packing densities in the resulting self-assembled monolayers (SAMs), precursor mixtures having both small and large n values are simultaneously deposited. These "heterogeneous" SAMs are characterized by a battery of techniques: contact angle measurements, X-ray reflectivity, X-ray photoelectron spectroscopy, ultraviolet photoelectron spectroscopy (UPS), cyclic voltammetry, and DFT computation. It is found that the headgroup densities of these "supersaturated" heterogeneous SAMs (SHSAMs) are enhanced by as much as 17% versus their homogeneous counterparts. Supersaturation significantly modifies the IFL properties including the work function (as much as 16%) and areal dipole moment (as much as 49%). Bulk-heterojunction OPV devices are fabricated with these SHSAMs: ITO/IFL/poly[[4,8-bis[(2-ethylhexyl)oxy]benzo[1,2-b:4,5-b']dithiophene-2,6-diyl][2-[[(2-ethylhexyl)oxy]carbonyl]-3-fluorothieno[3,4-b]thiophenediyl
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Liascukiene, Irma; Steffenhagen, Marie; Asadauskas, Svajus J; Lambert, Jean-François; Landoulsi, Jessem
2014-05-27
The self-assembly of fatty acids (FA) on the surfaces of inorganic materials is a relevant way to control their wetting properties. While the mechanism of adsorption on model flat substrate is well described in the literature, interfacial processes remain poorly documented on nanostructured surfaces. In this study, we report the self-assembly of a variety of FA on a hydroxylated Al surface which exhibits a random nanoscale organization. Our results revealed a peculiar fingerprint due to the FA self-assembly which consists in the formation of aligned nanopatterns in a state of hierarchical nanostructuration, regardless of the molecular structure of the FA (chain length, level of unsaturation). After a significant removal of adsorbed FA using UV/O3 treatment, a complete wetting was reached, and a noticeable disturbance of the surface morphology was observed, evidencing the pivotal role of FA molecules to maintain these nanostructures. The origin of wetting properties was investigated prior to and after conditioning of FA-modified samples taking into account key parameters, namely the surface roughness and its composition. For this purpose, the Wenzel roughness, defined as the third moment of power spectral density, was used, as it is sensitive to high spatial frequency and thus to the obtained hierarchical level of nanostructuration. Our results revealed that no correlation can be made between water contact angles (θ(w)) and the Wenzel roughness. By contrast, θ(w) strongly increased with the amount of -CHx- groups exhibited by adsorbed FA. These findings suggest that the main origin of hydrophobization is the presence of self-assembled molecules and that the surface roughness has only a small contribution to the wettability.
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Unknown Aspects of Self-Assembly of PbS Microscale Superstructures
Querejeta-Fernández, Ana; Hernández-Garrido, Juan C.; Yang, Hengxi; Zhou, Yunlong; Varela, Aurea; Parras, Marina; Calvino-Gámez, José J.; González-Calbet, Jose M.; Green, Peter F.; Kotov, Nicholas A.
2012-01-01
A lot of interesting and sophisticated examples of nanoparticle (NP) self-assembly (SA) are known. From both fundamental and technological standpoints this field requires advancements in three principle directions: a) understanding the mechanism and driving forces of three-dimensional (3D) SA with both nano- and micro-levels of organization; b) understanding of disassembly/deconstruction processes; and c) finding synthetic methods of assembly into continuous superstructures without insulating barriers. From this perspective, we investigated the formation of well-known star-like PbS superstructures and found a number of previously unknown or overlooked aspects that can advance the knowledge of NP self-assembly in these three directions. The primary one is that the formation of large seemingly monocrystalline PbS superstructures with multiple levels of octahedral symmetry can be explained only by SA of small octahedral NPs. We found five distinct periods in the formation PbS hyperbranched stars: 1) nucleation of early PbS NPs with an average diameter of 31 nm; 2) assembly into 100–500 nm octahedral mesocrystals; 3) assembly into 1000–2500 nm hyperbranched stars; 4) assembly and ionic recrystallization into six-arm rods accompanied by disappearance of fine nanoscale structure; 5) deconstruction into rods and cubooctahedral NPs. The switches in assembly patterns between the periods occur due to variable dominance of pattern–determining forces that include vander Waals and electrostatic (charge-charge, dipole-dipole, and polarization) interactions. The superstructure deconstruction is triggered by chemical changes in the deep eutectic solvent (DES) used as the media. PbS superstructures can be excellent models for fundamental studies of nanoscale organization and SA manufacturing of (opto)electronics and energy harvesting devices which require organization of PbS components at multiple scales. PMID:22515512
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HapCol: Accurate and Memory-efficient Haplotype Assembly from Long Reads
Y. Pirola (Yuri); S. Zaccaria (Simone); R. Dondi (Riccardo); G.W. Klau (Gunnar); N. Pisanti (Nadia); P. Bonizzoni (Paola)
2015-01-01
htmlabstractMotivation: Haplotype assembly is the computational problem of reconstructing haplotypes in diploid organisms and is of fundamental importance for characterizing the effects of single-nucleotide polymorphisms on the expression of phenotypic traits. Haplotype assembly highly benefits from
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A self-assembled monolayer-assisted surface microfabrication and release technique
Kim, B.J.; Liebau, M.; Huskens, Jurriaan; Reinhoudt, David; Brugger, J.P.
2001-01-01
This paper describes a method of thin film and MEMS processing which uses self-assembled monolayers as ultra-thin organic surface coating to enable a simple removal of microfabricated devices off the surface without wet chemical etching. A 1.5-nm thick self-assembled monolayer of
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Comparing de novo assemblers for 454 transcriptome data.
Kumar, Sujai; Blaxter, Mark L
2010-10-16
Roche 454 pyrosequencing has become a method of choice for generating transcriptome data from non-model organisms. Once the tens to hundreds of thousands of short (250-450 base) reads have been produced, it is important to correctly assemble these to estimate the sequence of all the transcripts. Most transcriptome assembly projects use only one program for assembling 454 pyrosequencing reads, but there is no evidence that the programs used to date are optimal. We have carried out a systematic comparison of five assemblers (CAP3, MIRA, Newbler, SeqMan and CLC) to establish best practices for transcriptome assemblies, using a new dataset from the parasitic nematode Litomosoides sigmodontis. Although no single assembler performed best on all our criteria, Newbler 2.5 gave longer contigs, better alignments to some reference sequences, and was fast and easy to use. SeqMan assemblies performed best on the criterion of recapitulating known transcripts, and had more novel sequence than the other assemblers, but generated an excess of small, redundant contigs. The remaining assemblers all performed almost as well, with the exception of Newbler 2.3 (the version currently used by most assembly projects), which generated assemblies that had significantly lower total length. As different assemblers use different underlying algorithms to generate contigs, we also explored merging of assemblies and found that the merged datasets not only aligned better to reference sequences than individual assemblies, but were also more consistent in the number and size of contigs. Transcriptome assemblies are smaller than genome assemblies and thus should be more computationally tractable, but are often harder because individual contigs can have highly variable read coverage. Comparing single assemblers, Newbler 2.5 performed best on our trial data set, but other assemblers were closely comparable. Combining differently optimal assemblies from different programs however gave a more credible
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Babur, Betul Kul; Kabiri, Mahboubeh; Klein, Travis Jacob; Lott, William B; Doran, Michael Robert
2015-01-01
We and others have published on the rapid manufacture of micropellet tissues, typically formed from 100-500 cells each. The micropellet geometry enhances cellular biological properties, and in many cases the micropellets can subsequently be utilized as building blocks to assemble complex macrotissues. Generally, micropellets are formed from cells alone, however when replicating matrix-rich tissues such as cartilage it would be ideal if matrix or biomaterials supplements could be incorporated directly into the micropellet during the manufacturing process. Herein we describe a method to efficiently incorporate donor cartilage matrix into tissue engineered cartilage micropellets. We lyophilized bovine cartilage matrix, and then shattered it into microscopic pieces having average dimensions manufacture of thousands of replica composite micropellets, with each micropellet having a material/CD core and a cellular surface. This micropellet organization enabled the rapid bulking up of the micropellet core matrix content, and left an adhesive cellular outer surface. This morphological organization enabled the ready assembly of the composite micropellets into macroscopic tissues. Generically, this is a versatile method that enables the rapid and uniform integration of biomaterials into multicellular micropellets that can then be used as tissue building blocks. In this study, the addition of CD resulted in an approximate 8-fold volume increase in the micropellets, with the donor matrix functioning to contribute to an increase in total cartilage matrix content. Composite micropellets were readily assembled into macroscopic cartilage tissues; the incorporation of CD enhanced tissue size and matrix content, but did not enhance chondrogenic gene expression.
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HapCol : Accurate and memory-efficient haplotype assembly from long reads
Pirola, Yuri; Zaccaria, Simone; Dondi, Riccardo; Klau, Gunnar W.; Pisanti, Nadia; Bonizzoni, Paola
2016-01-01
Motivation: Haplotype assembly is the computational problem of reconstructing haplotypes in diploid organisms and is of fundamental importance for characterizing the effects of single-nucleotide polymorphisms on the expression of phenotypic traits. Haplotype assembly highly benefits from the advent
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World Health Organization global policy for improvement of oral health--World Health Assembly 2007
DEFF Research Database (Denmark)
Petersen, Poul Erik
2008-01-01
The World Health Organization (WHO) Global Oral Health Programme has worked hard over the past five years to increase the awareness of oral health worldwide as an important component of general health and quality of life. Meanwhile, oral disease is still a major public health problem in high income...... countries and the burden of oral disease is growing in many low- and middle income countries. In the World Oral Health Report 2003, the WHO Global Oral Health Programme formulated the policies and the necessary actions for the improvement of oral health. The strategy is that oral disease prevention...... and the promotion of oral health needs to be integrated with chronic disease prevention and general health promotion as the risks to health are linked. The World Health Assembly (WHA) and the Executive Board (EB) are supreme governance bodies of WHO and for the first time in 25 years oral health was subject...
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Self-assembly of a double-helical complex of sodium.
Bell, T W; Jousselin, H
1994-02-03
Spontaneous self-organization of helical and multiple-helical molecular structures occurs on several levels in living organisms. Key examples are alpha-helical polypeptides, double-helical nucleic acids and helical protein structures, including F-actin, microtubules and the protein sheath of the tobacco mosaic virus. Although the self-assembly of double-helical transition-metal complexes bears some resemblance to the molecular organization of double-stranded DNA, selection between monohelical, double-helical and triple-helical structures is determined largely by the size and geometrical preference of the tightly bound metal. Here we present an example of double-helical assembly induced by the weaker and non-directional interactions of an alkali-metal ion with an organic ligand that is pre-organized into a coil. We have characterized the resulting complex by two-dimensional NMR and fast-atom-bombardment mass spectrometry. These results provide a step toward the creation of molecular tubes or ion channels consisting of intertwined coils.
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Applications of self-assembled monolayers in materials chemistry
Indian Academy of Sciences (India)
Unknown
Physical and Materials Chemistry Division, National Chemical Laboratory,. Pune 411 008, India e-mail: viji@ems.ncl.res.in. Abstract. Self-assembly provides a simple route to organise suitable organic molecules on noble metal and selected nanocluster surfaces by using monolayers of long chain organic molecules with ...
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Nakamura, Eiichi
2017-06-20
A molecule is a quantum mechanical entity. "Watching motions and reactions of a molecule with our eyes" has therefore been a dream of chemists for a century. This dream has come true with the aid of the movies of atomic-resolution transmission electron microscopic (AR-TEM) molecular images through real-time observation of dynamic motions of single organic molecules (denoted hereafter as single-molecule atomic-resolution real-time (SMART) TEM imaging). Since 2007, we have reported movies of a variety of single organic molecules, organometallic molecules, and their assemblies, which are rotating, stretching, and reacting. Like movies in the theater, the atomic-resolution molecular movies provide us information on the 3-D structures of the molecules and also their time evolution. The success of the SMART-TEM imaging crucially depends on the development of "chemical fishhooks" with which fish (organic molecules) in solution can be captured on a single-walled carbon nanotube (CNT, serving as a "fishing rod"). The captured molecules are connected to a slowly vibrating CNT, and their motions are displayed on a monitor in real time. A "fishing line" connecting the fish and the rod may be a σ-bond, a van der Waals force, or other weak connections. Here, the molecule/CNT system behaves as a coupled oscillator, where the low-frequency anisotropic vibration of the CNT is transmitted to the molecules via the weak chemical connections that act as an energy filter. Interpretation of the observed motions of the molecules at atomic resolution needs us to consider the quantum mechanical nature of electrons as well as bond rotation, letting us deviate from the conventional statistical world of chemistry. What new horizons can we explore? We have so far carried out conformational studies of individual molecules, assigning anti or gauche conformations to each C-C bond in conformers that we saw. We can also determine the structures of van der Waals assemblies of organic molecules
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Energy Technology Data Exchange (ETDEWEB)
Bae, S.-S.; Lim, D.K.; Park, J.-I.; Kim, S. [Korea Advanced Institute of Science and Technology, Department of Chemistry and School of Molecular Science (BK 21), Daejeon (Korea); Cheon, J. [Yonsei University, Department of Chemistry, College of Sciences, Seoul (Korea); Jeon, I.C. [Chonbuk National University, Department of Chemistry, College of Natural Sciences, Chonbuk (Korea)
2005-03-01
We present a new strategy to fabricate a monolayer assembly of Br-terminated Co nanoparticles on functionalized Si surfaces by using chemical covalent bonding and microcontact printing method. Self-assembled monolayers (SAMs) of the Co nanoparticles formed on the hydroxyl-terminated Si surface exhibit two-dimensional island networks with locally ordered arrays via covalent linkage between nanoparticles and surface. On the other hand, SAMs of the nanoparticles on the aminopropyl-terminated Si surface show an individual and random distribution over an entire surface. Furthermore, we have fabricated striped architectures of Co nanoparticles using a combination of microcontact printing and covalent linkage. Microcontact printing of octadecyltrichlorosilane and selective covalent linkage between nanoparticles and functionalized Si surfaces lead to a hybrid nanostructure with selectively assembled nanoparticles stripes on the patterned functionalized Si surfaces. (orig.)
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Nowrousian, Minou; Stajich, Jason E; Chu, Meiling; Engh, Ines; Espagne, Eric; Halliday, Karen; Kamerewerd, Jens; Kempken, Frank; Knab, Birgit; Kuo, Hsiao-Che; Osiewacz, Heinz D; Pöggeler, Stefanie; Read, Nick D; Seiler, Stephan; Smith, Kristina M; Zickler, Denise; Kück, Ulrich; Freitag, Michael
2010-04-08
Filamentous fungi are of great importance in ecology, agriculture, medicine, and biotechnology. Thus, it is not surprising that genomes for more than 100 filamentous fungi have been sequenced, most of them by Sanger sequencing. While next-generation sequencing techniques have revolutionized genome resequencing, e.g. for strain comparisons, genetic mapping, or transcriptome and ChIP analyses, de novo assembly of eukaryotic genomes still presents significant hurdles, because of their large size and stretches of repetitive sequences. Filamentous fungi contain few repetitive regions in their 30-90 Mb genomes and thus are suitable candidates to test de novo genome assembly from short sequence reads. Here, we present a high-quality draft sequence of the Sordaria macrospora genome that was obtained by a combination of Illumina/Solexa and Roche/454 sequencing. Paired-end Solexa sequencing of genomic DNA to 85-fold coverage and an additional 10-fold coverage by single-end 454 sequencing resulted in approximately 4 Gb of DNA sequence. Reads were assembled to a 40 Mb draft version (N50 of 117 kb) with the Velvet assembler. Comparative analysis with Neurospora genomes increased the N50 to 498 kb. The S. macrospora genome contains even fewer repeat regions than its closest sequenced relative, Neurospora crassa. Comparison with genomes of other fungi showed that S. macrospora, a model organism for morphogenesis and meiosis, harbors duplications of several genes involved in self/nonself-recognition. Furthermore, S. macrospora contains more polyketide biosynthesis genes than N. crassa. Phylogenetic analyses suggest that some of these genes may have been acquired by horizontal gene transfer from a distantly related ascomycete group. Our study shows that, for typical filamentous fungi, de novo assembly of genomes from short sequence reads alone is feasible, that a mixture of Solexa and 454 sequencing substantially improves the assembly, and that the resulting data can be used for
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Directory of Open Access Journals (Sweden)
Minou Nowrousian
2010-04-01
Full Text Available Filamentous fungi are of great importance in ecology, agriculture, medicine, and biotechnology. Thus, it is not surprising that genomes for more than 100 filamentous fungi have been sequenced, most of them by Sanger sequencing. While next-generation sequencing techniques have revolutionized genome resequencing, e.g. for strain comparisons, genetic mapping, or transcriptome and ChIP analyses, de novo assembly of eukaryotic genomes still presents significant hurdles, because of their large size and stretches of repetitive sequences. Filamentous fungi contain few repetitive regions in their 30-90 Mb genomes and thus are suitable candidates to test de novo genome assembly from short sequence reads. Here, we present a high-quality draft sequence of the Sordaria macrospora genome that was obtained by a combination of Illumina/Solexa and Roche/454 sequencing. Paired-end Solexa sequencing of genomic DNA to 85-fold coverage and an additional 10-fold coverage by single-end 454 sequencing resulted in approximately 4 Gb of DNA sequence. Reads were assembled to a 40 Mb draft version (N50 of 117 kb with the Velvet assembler. Comparative analysis with Neurospora genomes increased the N50 to 498 kb. The S. macrospora genome contains even fewer repeat regions than its closest sequenced relative, Neurospora crassa. Comparison with genomes of other fungi showed that S. macrospora, a model organism for morphogenesis and meiosis, harbors duplications of several genes involved in self/nonself-recognition. Furthermore, S. macrospora contains more polyketide biosynthesis genes than N. crassa. Phylogenetic analyses suggest that some of these genes may have been acquired by horizontal gene transfer from a distantly related ascomycete group. Our study shows that, for typical filamentous fungi, de novo assembly of genomes from short sequence reads alone is feasible, that a mixture of Solexa and 454 sequencing substantially improves the assembly, and that the resulting data
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Supramolecular domains in mixed peptide self-assembled monolayers on gold nanoparticles.
Duchesne, Laurence; Wells, Geoff; Fernig, David G; Harris, Sarah A; Lévy, Raphaël
2008-09-01
Self-organization in mixed self-assembled monolayers of small molecules provides a route towards nanoparticles with complex molecular structures. Inspired by structural biology, a strategy based on chemical cross-linking is introduced to probe proximity between functional peptides embedded in a mixed self-assembled monolayer at the surface of a nanoparticle. The physical basis of the proximity measurement is a transition from intramolecular to intermolecular cross-linking as the functional peptides get closer. Experimental investigations of a binary peptide self-assembled monolayer show that this transition happens at an extremely low molar ratio of the functional versus matrix peptide. Molecular dynamics simulations of the peptide self-assembled monolayer are used to calculate the volume explored by the reactive groups. Comparison of the experimental results with a probabilistic model demonstrates that the peptides are not randomly distributed at the surface of the nanoparticle, but rather self-organize into supramolecular domains.
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In vitro assembly of catalase.
Baureder, Michael; Barane, Elisabeth; Hederstedt, Lars
2014-10-10
Most aerobic organisms contain catalase, which functions to decompose hydrogen peroxide. Typical catalases are structurally complex homo-tetrameric enzymes with one heme prosthetic group buried in each subunit. It is not known how catalase in the cell is assembled from its constituents. The bacterium Enterococcus faecalis cannot synthesize heme but can acquire it from the environment to form a cytoplasmic catalase. We have in E. faecalis monitored production of the enzyme polypeptide (KatA) depending on the availability of heme and used our findings to devise a procedure for the purification of preparative amounts of in vivo-synthesized apocatalase. We show that fully active catalase can be obtained in vitro by incubating isolated apoprotein with hemin. We have characterized features of the assembly process and describe a temperature-trapped hemylated intermediate of the enzyme maturation process. Hemylation of apocatalase does not require auxiliary cell components, but rapid assembly of active enzyme seemingly is assisted in the cell. Our findings provide insight about catalase assembly and offer new experimental possibilities for detailed studies of this process. © 2014 by The American Society for Biochemistry and Molecular Biology, Inc.
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Evaluating de Bruijn graph assemblers on 454 transcriptomic data.
Directory of Open Access Journals (Sweden)
Xianwen Ren
Full Text Available Next generation sequencing (NGS technologies have greatly changed the landscape of transcriptomic studies of non-model organisms. Since there is no reference genome available, de novo assembly methods play key roles in the analysis of these data sets. Because of the huge amount of data generated by NGS technologies for each run, many assemblers, e.g., ABySS, Velvet and Trinity, are developed based on a de Bruijn graph due to its time- and space-efficiency. However, most of these assemblers were developed initially for the Illumina/Solexa platform. The performance of these assemblers on 454 transcriptomic data is unknown. In this study, we evaluated and compared the relative performance of these de Bruijn graph based assemblers on both simulated and real 454 transcriptomic data. The results suggest that Trinity, the Illumina/Solexa-specialized transcriptomic assembler, performs the best among the multiple de Bruijn graph assemblers, comparable to or even outperforming the standard 454 assembler Newbler which is based on the overlap-layout-consensus algorithm. Our evaluation is expected to provide helpful guidance for researchers to choose assemblers when analyzing 454 transcriptomic data.
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Controlled short-linkage assembly of functional nano-objects
Energy Technology Data Exchange (ETDEWEB)
Chaudhary, Shilpi; Kamra, Tripta [Division of Pure and Applied Biochemistry, Lund University, Box 124, 221 00 Lund (Sweden); ENI AB, Malmö (Sweden); Division of Synchrotron Radiation Research, Lund University, Box 118, 221 00 Lund (Sweden); Uddin, Khan Mohammad Ahsan [Division of Pure and Applied Biochemistry, Lund University, Box 124, 221 00 Lund (Sweden); Snezhkova, Olesia [Division of Synchrotron Radiation Research, Lund University, Box 118, 221 00 Lund (Sweden); Jayawardena, H. Surangi N. [Department of Chemistry, University of Massachusetts Lowell, 1 University Ave., Lowell, MA 01854 (United States); Yan, Mingdi [Department of Chemistry, University of Massachusetts Lowell, 1 University Ave., Lowell, MA 01854 (United States); Department of Chemistry, KTH – Royal Institute of Technology, Teknikringen 30, S-10044 Stockholm (Sweden); Montelius, Lars [ENI AB, Malmö (Sweden); Schnadt, Joachim, E-mail: joachim.schnadt@sljus.lu.se [Division of Synchrotron Radiation Research, Lund University, Box 118, 221 00 Lund (Sweden); Ye, Lei, E-mail: lei.ye@tbiokem.lth.se [Division of Pure and Applied Biochemistry, Lund University, Box 124, 221 00 Lund (Sweden)
2014-05-01
Graphical abstract: - Highlights: • Fast photoconjugation of nanoparticles on surface. • Non-destructive feature guarantees intact function of nanoparticles. • Direct contact between nano-objects allows efficient photon and electron transfer. • Possibility of generating patterned nanoparticle assemblies on surface. • Open new opportunities for assembling chemical sensors. - Abstract: In this work, we report a method that allows the deterministic, photo-controlled covalent assembly of nanoparticles directly on surface. As a model system, we study the conjugation of molecularly imprinted polymer (MIP) nanoparticles on a glass surface and confirm that the immobilized nanoparticles maintain their molecular recognition functionality. The glass slide was first modified with perfluorophenylazide and then used to bind MIP nanoparticles under UV irradiation. After each step the surface was analyzed by water contact angle measurement, fluorescence microscopy, scanning electron microscopy, and/or synchrotron-based X-ray photoelectron spectroscopy. The MIP nanoparticles immobilized on the glass surface remained stable and maintained specific binding for the template molecule, propranolol. The method developed in this work allows MIP nanoparticles to be directly coupled to a flat surface, offering a straightforward means to construct robust chemical sensors. Using the reported photo conjugation method, it is possible to generate patterned assembly of nanoparticles using a photomask. Since perfluorophenylazide-based photochemistry works with all kinds of organic material, the method developed in this work is expected to enable immobilization of not only MIPs but also other kinds of organic and inorganic–organic core–shell particles for various applications involving photon or electron transfer.
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Controlled short-linkage assembly of functional nano-objects
International Nuclear Information System (INIS)
Chaudhary, Shilpi; Kamra, Tripta; Uddin, Khan Mohammad Ahsan; Snezhkova, Olesia; Jayawardena, H. Surangi N.; Yan, Mingdi; Montelius, Lars; Schnadt, Joachim; Ye, Lei
2014-01-01
Graphical abstract: - Highlights: • Fast photoconjugation of nanoparticles on surface. • Non-destructive feature guarantees intact function of nanoparticles. • Direct contact between nano-objects allows efficient photon and electron transfer. • Possibility of generating patterned nanoparticle assemblies on surface. • Open new opportunities for assembling chemical sensors. - Abstract: In this work, we report a method that allows the deterministic, photo-controlled covalent assembly of nanoparticles directly on surface. As a model system, we study the conjugation of molecularly imprinted polymer (MIP) nanoparticles on a glass surface and confirm that the immobilized nanoparticles maintain their molecular recognition functionality. The glass slide was first modified with perfluorophenylazide and then used to bind MIP nanoparticles under UV irradiation. After each step the surface was analyzed by water contact angle measurement, fluorescence microscopy, scanning electron microscopy, and/or synchrotron-based X-ray photoelectron spectroscopy. The MIP nanoparticles immobilized on the glass surface remained stable and maintained specific binding for the template molecule, propranolol. The method developed in this work allows MIP nanoparticles to be directly coupled to a flat surface, offering a straightforward means to construct robust chemical sensors. Using the reported photo conjugation method, it is possible to generate patterned assembly of nanoparticles using a photomask. Since perfluorophenylazide-based photochemistry works with all kinds of organic material, the method developed in this work is expected to enable immobilization of not only MIPs but also other kinds of organic and inorganic–organic core–shell particles for various applications involving photon or electron transfer
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Jin, Shouwen; Wang, Daqi
2014-05-01
Eight crystalline organic acid-base adducts derived from alkane bridged bis(N-benzimidazole) and organic acids (2,4,6-trinitrophenol, p-nitrobenzoic acid, m-nitrobenzoic acid, 3,5-dinitrobenzoic acid, 5-sulfosalicylic acid and oxalic acid) were prepared and characterized by X-ray diffraction analysis, IR, mp, and elemental analysis. Of the eight compounds five are organic salts (1, 4, 6, 7 and 8) and the other three (2, 3, and 5) are cocrystals. In all of the adducts except 1 and 8, the ratio of the acid and the base is 2:1. All eight supramolecular assemblies involve extensive intermolecular classical hydrogen bonds as well as other noncovalent interactions. The role of weak and strong noncovalent interactions in the crystal packing is ascertained. These weak interactions combined, all the complexes displayed 3D framework structure. The results presented herein indicate that the strength and directionality of the classical N+-H⋯O-, O-H⋯O, and O-H⋯N hydrogen bonds (ionic or neutral) and other nonbonding associations between acids and ditopic benzimidazoles are sufficient to bring about the formation of cocrystals or organic salts.
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Superlattices assembled through shape-induced directional binding
Lu, Fang; Yager, Kevin G.; Zhang, Yugang; Xin, Huolin; Gang, Oleg
2015-04-01
Organization of spherical particles into lattices is typically driven by packing considerations. Although the addition of directional binding can significantly broaden structural diversity, nanoscale implementation remains challenging. Here we investigate the assembly of clusters and lattices in which anisotropic polyhedral blocks coordinate isotropic spherical nanoparticles via shape-induced directional interactions facilitated by DNA recognition. We show that these polyhedral blocks--cubes and octahedrons--when mixed with spheres, promote the assembly of clusters with architecture determined by polyhedron symmetry. Moreover, three-dimensional binary superlattices are formed when DNA shells accommodate the shape disparity between nanoparticle interfaces. The crystallographic symmetry of assembled lattices is determined by the spatial symmetry of the block's facets, while structural order depends on DNA-tuned interactions and particle size ratio. The presented lattice assembly strategy, exploiting shape for defining the global structure and DNA-mediation locally, opens novel possibilities for by-design fabrication of binary lattices.
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Directory of Open Access Journals (Sweden)
Joanna eMoreton
2014-06-01
Full Text Available For vertebrate organisms where a reference genome is not available, de novo transcriptome assembly enables a cost effective insight into the identification of tissue specific or differentially expressed genes and variation of the coding part of the genome. However, since there are a number of different tools and parameters that can be used to reconstruct transcripts, it is difficult to determine an optimal method. Here we suggest a pipeline based on (1 assessing the performance of three different assembly tools (2 using both single and multiple k-mer approaches (3 examining the influence of the number of reads used in the assembly (4 merging assemblies from different tools. We use an example dataset from the vertebrate Anas platyrhynchos domestica (Pekin duck. We find that taking a subset of data enables a robust assembly to be produced by multiple methods without the need for very high memory capacity. The use of reads mapped back to transcripts (RMBT and CEGMA (Core Eukaryotic Genes Mapping Approach provides useful metrics to determine the completeness of assembly obtained. For this dataset the use of multiple k-mers in the assembly generated a more complete assembly as measured by greater number of RMBT and CEGMA score. Merged single k-mer assemblies are generally smaller but consist of longer transcripts, suggesting an assembly consisting of fewer fragmented transcripts. We suggest that the use of a subset of reads during assembly allows the relatively rapid investigation of assembly characteristics and can guide the user to the most appropriate transcriptome for particular downstream use. Transcriptomes generated by the compared assembly methods and the final merged assembly are freely available for download at http://dx.doi.org/10.6084/m9.figshare.1032613.
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Comparing de novo assemblers for 454 transcriptome data
Directory of Open Access Journals (Sweden)
Blaxter Mark L
2010-10-01
Full Text Available Abstract Background Roche 454 pyrosequencing has become a method of choice for generating transcriptome data from non-model organisms. Once the tens to hundreds of thousands of short (250-450 base reads have been produced, it is important to correctly assemble these to estimate the sequence of all the transcripts. Most transcriptome assembly projects use only one program for assembling 454 pyrosequencing reads, but there is no evidence that the programs used to date are optimal. We have carried out a systematic comparison of five assemblers (CAP3, MIRA, Newbler, SeqMan and CLC to establish best practices for transcriptome assemblies, using a new dataset from the parasitic nematode Litomosoides sigmodontis. Results Although no single assembler performed best on all our criteria, Newbler 2.5 gave longer contigs, better alignments to some reference sequences, and was fast and easy to use. SeqMan assemblies performed best on the criterion of recapitulating known transcripts, and had more novel sequence than the other assemblers, but generated an excess of small, redundant contigs. The remaining assemblers all performed almost as well, with the exception of Newbler 2.3 (the version currently used by most assembly projects, which generated assemblies that had significantly lower total length. As different assemblers use different underlying algorithms to generate contigs, we also explored merging of assemblies and found that the merged datasets not only aligned better to reference sequences than individual assemblies, but were also more consistent in the number and size of contigs. Conclusions Transcriptome assemblies are smaller than genome assemblies and thus should be more computationally tractable, but are often harder because individual contigs can have highly variable read coverage. Comparing single assemblers, Newbler 2.5 performed best on our trial data set, but other assemblers were closely comparable. Combining differently optimal assemblies
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Samanta, Suman K; Bhattacharya, Santanu
2012-12-03
We have synthesized two new low-molecular-mass organogelators based on tri-p-phenylene vinylene derivatives, one of which could be designated as the donor whereas the other one is an acceptor. These were prepared specifically to show the intergelator interactions at the molecular level by using donor-acceptor self-assembly to achieve appropriate control over their macroscopic properties. Intermolecular hydrogen-bonding, π-stacking, and van der Waals interactions operate for both the individual components and the mixtures, leading to the formation of gels in the chosen organic solvents. Evidence for intergelator interactions was acquired from various spectroscopic, microscopic, thermal, and mechanical investigations. Due to the photochromic nature of these molecules, interesting photophysical properties, such as solvatochromism and J-type aggregation, were clearly observed. An efficient energy transfer was exhibited by the mixture of donor-acceptor assemblies. An array of four chromophores was built up by inclusion of two known dyes (anthracene and rhodamine 6G) for the energy-transfer studies. Interestingly, an energy-transfer cascade was observed in the assembly of four chromophores in a particular order (anthracene-donor-acceptor-rhodamine 6G), and if one of the components was removed from the assembly the energy transfer process was discontinued. This allowed the build up of a light-harvesting process with a wide range. Excitation at one end produces an emission at the other end of the assembly. Copyright © 2012 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.
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Toward high throughput optical metamaterial assemblies.
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.
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Predominantly ligand guided non-covalently linked assemblies of ...
Indian Academy of Sciences (India)
JUBARAJ B BARUAH
2018-05-12
May 12, 2018 ... Abstract. Various non-covalently linked inorganic self-assemblies formed by the supramolecular interacting .... metal-organic frameworks.59 Inorganic chemists rou- ...... two-dimensional organic–inorganic layered perovskite.
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Bourcey, N; López, R; Poncet, A; Parma, V
2007-01-01
After 4 years of activity, the assembly of approximately 500 Short Straight Sections (SSS) for the LHC has come to an end at the beginning of 2007. This activity, which was initially foreseen in European industry, was in-sourced at CERN because of the insolvency of the prime contractor. While the quadrupole cold masses were produced in industry, the assembly within their cryostats was transferred to CERN and executed by an external company under a result-oriented contract. CERN procured cryostat components, set up a dedicated 2000 m2 assembly hall with all the specific assembly equipment and tooling and defined the assembly and testing procedures. The contractor took up responsibility for the delivery, on time, of assemblies according to the required quality. A dedicated CERN production and quality assurance team was constituted. A specific quality assurance plan was set up involving 2 additional contractors responsible for weld inspections on a total of about 20'000 assembly welds and the execution of about ...
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Molecular Architecture of the Human Mediator–RNA Polymerase II–TFIIF Assembly
Bernecky, Carrie; Grob, Patricia; Ebmeier, Christopher C.; Nogales, Eva; Taatjes, Dylan J.
2011-01-01
The macromolecular assembly required to initiate transcription of protein-coding genes, known as the Pre-Initiation Complex (PIC), consists of multiple protein complexes and is approximately 3.5 MDa in size. At the heart of this assembly is the Mediator complex, which helps regulate PIC activity and interacts with the RNA polymerase II (pol II) enzyme. The structure of the human Mediator–pol II interface is not well-characterized, whereas attempts to structurally define the Mediator–pol II interaction in yeast have relied on incomplete assemblies of Mediator and/or pol II and have yielded inconsistent interpretations. We have assembled the complete, 1.9 MDa human Mediator–pol II–TFIIF complex from purified components and have characterized its structural organization using cryo-electron microscopy and single-particle reconstruction techniques. The orientation of pol II within this assembly was determined by crystal structure docking and further validated with projection matching experiments, allowing the structural organization of the entire human PIC to be envisioned. Significantly, pol II orientation within the Mediator–pol II–TFIIF assembly can be reconciled with past studies that determined the location of other PIC components relative to pol II itself. Pol II surfaces required for interacting with TFIIB, TFIIE, and promoter DNA (i.e., the pol II cleft) are exposed within the Mediator–pol II–TFIIF structure; RNA exit is unhindered along the RPB4/7 subunits; upstream and downstream DNA is accessible for binding additional factors; and no major structural re-organization is necessary to accommodate the large, multi-subunit TFIIH or TFIID complexes. The data also reveal how pol II binding excludes Mediator–CDK8 subcomplex interactions and provide a structural basis for Mediator-dependent control of PIC assembly and function. Finally, parallel structural analysis of Mediator–pol II complexes lacking TFIIF reveal that TFIIF plays a key role in
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Surface mediated assembly of small, metastable gold nanoclusters
Pettibone, John M.; Osborn, William A.; Rykaczewski, Konrad; Talin, A. Alec; Bonevich, John E.; Hudgens, Jeffrey W.; Allendorf, Mark D.
2013-06-01
The unique properties of metallic nanoclusters are attractive for numerous commercial and industrial applications but are generally less stable than nanocrystals. Thus, developing methodologies for stabilizing nanoclusters and retaining their enhanced functionality is of great interest. We report the assembly of PPh3-protected Au9 clusters from a heterogeneous mixture into films consisting of sub 3 nm nanocluster assemblies. The depositing nanoclusters are metastable in solution, but the resulting nanocluster assemblies are stabilized indefinitely in air or fresh solvent. The films exhibit distinct structure from Au nanoparticles observed by X-ray diffraction, and film dissolution data support the preservation of small nanoclusters. UV-Vis spectroscopy, electrospray ionization mass spectrometry, X-ray photoelectron spectroscopy and electron microscopy are used to elucidate information regarding the nanocluster formation and assembly mechanism. Preferential deposition of nanocluster assemblies can be achieved on multiple substrates, including polymer, Cr, Si, SiO2, SiNx, and metal-organic frameworks (MOFs). Unlike other vapor phase coating processes, nanocluster assembly on the MIL-68(In) MOF crystal is capable of preferentially coating the external surface and stabilizing the crystal structure in hydrothermal conditions, which should enhance their storage, separation and delivery capabilities.The unique properties of metallic nanoclusters are attractive for numerous commercial and industrial applications but are generally less stable than nanocrystals. Thus, developing methodologies for stabilizing nanoclusters and retaining their enhanced functionality is of great interest. We report the assembly of PPh3-protected Au9 clusters from a heterogeneous mixture into films consisting of sub 3 nm nanocluster assemblies. The depositing nanoclusters are metastable in solution, but the resulting nanocluster assemblies are stabilized indefinitely in air or fresh solvent. The
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Status of Preliminary Design on the Assembly Tools for ITER Tokamak Machine
International Nuclear Information System (INIS)
Nam, Kyoung O; Park, Hyun Ki; Kim, Dong Jin; Moon, Jae Hwan; Kim, Byung Seok; Lee, Jae Hyuk; Shaw, Robert
2012-01-01
The ITER Tokamak device is principally composed of nine 40 .deg. sectors. Each 40 .deg. sector is made up of one 40 .deg. vacuum vessel (VV), two 20 .deg. toroidal filed coils (TFC) and associated vacuum vessel thermal shield (VVTS) segments which consist of one inboard and two outboard vacuum vessel thermal shields. Based on the design description document and final report prepared by the ITER organization (IO) and conceptual design, Korea has carried out the preliminary design of these assembly tools. The assembly strategy and relevant tools for the 40 .deg. sector sub-assembly and sector assembly at in-pit should be developed to satisfy the basic assembly requirements of the ITER Tokamak machine. Assembly strategy, preliminary design of the sector sub-assembly and assembly tools are described in this paper
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DEFF Research Database (Denmark)
Weissbuch, I.; Buller, R.; Kjær, K.
2002-01-01
The advent of intense X-rays from synchrotron sources made possible to probe, at the molecular level, the structural aspects of self-assemblies generated at interfaces. Here we present the two-dimensional (2-D) packing arrangements of two-, three- and multi-component organo-metallic self......-assemblies formed via interfacial reaction at the air-aqueous solution interface, as determined by grazing incidence X-ray diffraction (GIRD) and X-ray specular reflectivity techniques. GIXD yields structural information on the crystalline part of the Langmuir film, including the ions and counterions lateral order...... of metal ions bound to the polar head groups of amphipilic molecules; use of bolaamphiphiles to generate oriented thin films with metal ions arranged in periodic layers; delineation of differences in the lateral organization of metal ions at interfaces as induced by racemates and enantiomerically pure...
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Self-assembly strategies for the synthesis of functional nanostructured materials
Perego, M.; Seguini, G.
2016-06-01
Self-assembly is the autonomous organization of components into patterns or structures without human intervention. This is the approach followed by nature to generate living cells and represents one of the practical strategies to fabricate ensembles of nanostructures. In static self-assembly the formation of ordered structures could require energy but once formed the structures are stable. The introduction of additional regular features in the environment could be used to template the self-assembly guiding the organization of the components and determining the final structure they form. In this regard self-assembly of block copolymers represents a potent platform for fundamental studies at the nanoscale and for application-driven investigation as a tool to fabricate functional nanostructured materials. Block copolymers can hierarchically assemble into chemically distinct domains with size and periodicity on the order of 10nm or below, offering a potentially inexpensive route to generate large-area nanostructured materials. The final structure characteristics of these materials are dictated by the properties of the elementary block copolymers, like chain length, volume fraction or degree of block incompatibility. Modern synthetic chemistry offers the possibility to design these macromolecules with very specific length scales and geometries, directly embodying in the block copolymers the code that drives their self- assembling process. The understanding of the kinetics and thermodynamics of the block copolymer self-assembly process in the bulk phase as well as in thin films represents a fundamental prerequisite toward the exploitation of these materials. Incorporating block copolymer into device fabrication procedures or directly into devices, as active elements, will lead to the development of a new generation of devices fabricated using the fundamental law of nature to our advantage in order to minimize cost and power consumption in the fabrication process
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Haplotype assembly in polyploid genomes and identical by descent shared tracts.
Aguiar, Derek; Istrail, Sorin
2013-07-01
Genome-wide haplotype reconstruction from sequence data, or haplotype assembly, is at the center of major challenges in molecular biology and life sciences. For complex eukaryotic organisms like humans, the genome is vast and the population samples are growing so rapidly that algorithms processing high-throughput sequencing data must scale favorably in terms of both accuracy and computational efficiency. Furthermore, current models and methodologies for haplotype assembly (i) do not consider individuals sharing haplotypes jointly, which reduces the size and accuracy of assembled haplotypes, and (ii) are unable to model genomes having more than two sets of homologous chromosomes (polyploidy). Polyploid organisms are increasingly becoming the target of many research groups interested in the genomics of disease, phylogenetics, botany and evolution but there is an absence of theory and methods for polyploid haplotype reconstruction. In this work, we present a number of results, extensions and generalizations of compass graphs and our HapCompass framework. We prove the theoretical complexity of two haplotype assembly optimizations, thereby motivating the use of heuristics. Furthermore, we present graph theory-based algorithms for the problem of haplotype assembly using our previously developed HapCompass framework for (i) novel implementations of haplotype assembly optimizations (minimum error correction), (ii) assembly of a pair of individuals sharing a haplotype tract identical by descent and (iii) assembly of polyploid genomes. We evaluate our methods on 1000 Genomes Project, Pacific Biosciences and simulated sequence data. HapCompass is available for download at http://www.brown.edu/Research/Istrail_Lab/. Supplementary data are available at Bioinformatics online.
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Mahboubi, Hicham; Koromilas, Antonis E; Stochaj, Ursula
2016-10-01
Eukaryotic cells assemble stress granules (SGs) when translation initiation is inhibited. Different cell signaling pathways regulate SG production. Particularly relevant to this process is 5'-AMP-activated protein kinase (AMPK), which functions as a stress sensor and is transiently activated by adverse physiologic conditions. Here, we dissected the role of AMPK for oxidant-induced SG formation. Our studies identified multiple steps of de novo SG assembly that are controlled by the kinase. Single-cell analyses demonstrated that pharmacological AMPK activation prior to stress exposure changed SG properties, because the granules became more abundant and smaller in size. These altered SG characteristics correlated with specific changes in cell survival, cell signaling, cytoskeletal organization, and the abundance of translation initiation factors. Specifically, AMPK activation increased stress-induced eukaryotic initiation factor (eIF) 2α phosphorylation and reduced the concentration of eIF4F complex subunits eIF4G and eIF4E. At the same time, the abundance of histone deacetylase 6 (HDAC6) was diminished. This loss of HDAC6 was accompanied by increased acetylation of α-tubulin on Lys40. Pharmacological studies further confirmed this novel AMPK-HDAC6 interplay and its importance for SG biology. Taken together, we provide mechanistic insights into the regulation of SG formation. We propose that AMPK activation stimulates oxidant-induced SG formation but limits their fusion into larger granules. Copyright © 2016 by The American Society for Pharmacology and Experimental Therapeutics.
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Exploration of Metagenome Assemblies with an Interactive Visualization Tool
Energy Technology Data Exchange (ETDEWEB)
Cantor, Michael; Nordberg, Henrik; Smirnova, Tatyana; Andersen, Evan; Tringe, Susannah; Hess, Matthias; Dubchak, Inna
2014-07-09
Metagenomics, one of the fastest growing areas of modern genomic science, is the genetic profiling of the entire community of microbial organisms present in an environmental sample. Elviz is a web-based tool for the interactive exploration of metagenome assemblies. Elviz can be used with publicly available data sets from the Joint Genome Institute or with custom user-loaded assemblies. Elviz is available at genome.jgi.doe.gov/viz
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International Nuclear Information System (INIS)
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 (GA 3 ) 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 GA 3 -amide derivatives efficiently nucleated and formed gold nanoparticles when heated to 60 deg. 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.
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Energy Technology Data Exchange (ETDEWEB)
Tavor, John [Johns Hopkins Univ., Baltimore, MD (United States)
2016-12-06
The realization of new supramolecular pi-conjugated organic structures inspired and driven by peptide-based self-assembly will offer a new approach to interface with the biotic environment in a way that will help to meet many DOE-recognized grand challenges. Previously, we developed pi-conjugated peptides that undergo supramolecular self-assembly into one-dimensional (1-D) organic electronic nanomaterials under benign aqueous conditions. The intermolecular interactions among the pi-conjugated organic segments within these nanomaterials lead to defined perturbations of their optoelectronic properties and yield nanoscale conduits that support energy transport within individual nanostructures and throughout bulk macroscopic collections of nanomaterials. Our objectives for future research are to construct and study biomimetic electronic materials for energy-related technology optimized for harsher non-biological environments where peptide-driven self-assembly enhances pi-stacking within nanostructured biomaterials, as detailed in the following specific tasks: (1) synthesis and detailed optoelectronic characterization of new pi-electron units to embed within homogeneous self assembling peptides, (2) molecular and data-driven modeling of the nanomaterial aggregates and their higher-order assemblies, and (3) development of new hierarchical assembly paradigms to organize multiple electronic subunits within the nanomaterials leading to heterogeneous electronic properties (i.e. gradients and localized electric fields). These intertwined research tasks will lead to the continued development and fundamental mechanistic understanding of a powerful bioinspired materials set capable of making connections between nanoscale electronic materials and macroscopic bulk interfaces, be they those of a cell, a protein or a device.
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Light-Controlled Swarming and Assembly of Colloidal Particles
Directory of Open Access Journals (Sweden)
Jianhua Zhang
2018-02-01
Full Text Available Swarms and assemblies are ubiquitous in nature and they can perform complex collective behaviors and cooperative functions that they cannot accomplish individually. In response to light, some colloidal particles (CPs, including light active and passive CPs, can mimic their counterparts in nature and organize into complex structures that exhibit collective functions with remote controllability and high temporospatial precision. In this review, we firstly analyze the structural characteristics of swarms and assemblies of CPs and point out that light-controlled swarming and assembly of CPs are generally achieved by constructing light-responsive interactions between CPs. Then, we summarize in detail the recent advances in light-controlled swarming and assembly of CPs based on the interactions arisen from optical forces, photochemical reactions, photothermal effects, and photoisomerizations, as well as their potential applications. In the end, we also envision some challenges and future prospects of light-controlled swarming and assembly of CPs. With the increasing innovations in mechanisms and control strategies with easy operation, low cost, and arbitrary applicability, light-controlled swarming and assembly of CPs may be employed to manufacture programmable materials and reconfigurable robots for cooperative grasping, collective cargo transportation, and micro- and nanoengineering.
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Directory of Open Access Journals (Sweden)
Betul Kul Babur
Full Text Available We and others have published on the rapid manufacture of micropellet tissues, typically formed from 100-500 cells each. The micropellet geometry enhances cellular biological properties, and in many cases the micropellets can subsequently be utilized as building blocks to assemble complex macrotissues. Generally, micropellets are formed from cells alone, however when replicating matrix-rich tissues such as cartilage it would be ideal if matrix or biomaterials supplements could be incorporated directly into the micropellet during the manufacturing process. Herein we describe a method to efficiently incorporate donor cartilage matrix into tissue engineered cartilage micropellets. We lyophilized bovine cartilage matrix, and then shattered it into microscopic pieces having average dimensions < 10 μm diameter; we termed this microscopic donor matrix "cartilage dust (CD". Using a microwell platform, we show that ~0.83 μg CD can be rapidly and efficiently incorporated into single multicellular aggregates formed from 180 bone marrow mesenchymal stem/stromal cells (MSC each. The microwell platform enabled the rapid manufacture of thousands of replica composite micropellets, with each micropellet having a material/CD core and a cellular surface. This micropellet organization enabled the rapid bulking up of the micropellet core matrix content, and left an adhesive cellular outer surface. This morphological organization enabled the ready assembly of the composite micropellets into macroscopic tissues. Generically, this is a versatile method that enables the rapid and uniform integration of biomaterials into multicellular micropellets that can then be used as tissue building blocks. In this study, the addition of CD resulted in an approximate 8-fold volume increase in the micropellets, with the donor matrix functioning to contribute to an increase in total cartilage matrix content. Composite micropellets were readily assembled into macroscopic cartilage
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The self-assembling process and applications in tissue engineering
Lee, Jennifer K.; Link, Jarrett M.; Hu, Jerry C. Y.; Athanasiou, Kyriacos A.
2018-01-01
Tissue engineering strives to create neotissues capable of restoring function. Scaffold-free technologies have emerged that can recapitulate native tissue function without the use of an exogenous scaffold. This chapter will survey, in particular, the self-assembling and self-organization processes as scaffold-free techniques. Characteristics and benefits of each process are described, and key examples of tissues created using these scaffold-free processes are examined to provide guidance for future tissue engineering developments. This chapter aims to explore the potential of self-assembly and self-organization scaffold-free approaches, detailing the recent progress in the in vitro tissue engineering of biomimetic tissues with these methods, toward generating functional tissue replacements. PMID:28348174
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A Structural analysis of M protein in coronavirus assembly and morphology
DEFF Research Database (Denmark)
W. Neuman, Benjamin; Kiss, Gabriella; H. Kunding, Andreas
2011-01-01
The M protein of coronavirus plays a central role in virus assembly, turning cellular membranes into workshops where virus and host factors come together to make new virus particles. We investigated how M structure and organization is related to virus shape and size using cryo-electron microscopy...... protein functions to promote virus assembly....
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Principles of assembly reveal a periodic table of protein complexes.
Ahnert, Sebastian E; Marsh, Joseph A; Hernández, Helena; Robinson, Carol V; Teichmann, Sarah A
2015-12-11
Structural insights into protein complexes have had a broad impact on our understanding of biological function and evolution. In this work, we sought a comprehensive understanding of the general principles underlying quaternary structure organization in protein complexes. We first examined the fundamental steps by which protein complexes can assemble, using experimental and structure-based characterization of assembly pathways. Most assembly transitions can be classified into three basic types, which can then be used to exhaustively enumerate a large set of possible quaternary structure topologies. These topologies, which include the vast majority of observed protein complex structures, enable a natural organization of protein complexes into a periodic table. On the basis of this table, we can accurately predict the expected frequencies of quaternary structure topologies, including those not yet observed. These results have important implications for quaternary structure prediction, modeling, and engineering. Copyright © 2015, American Association for the Advancement of Science.
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Jayakumar, Vasanthan; Sakakibara, Yasubumi
2017-11-03
Long reads obtained from third-generation sequencing platforms can help overcome the long-standing challenge of the de novo assembly of sequences for the genomic analysis of non-model eukaryotic organisms. Numerous long-read-aided de novo assemblies have been published recently, which exhibited superior quality of the assembled genomes in comparison with those achieved using earlier second-generation sequencing technologies. Evaluating assemblies is important in guiding the appropriate choice for specific research needs. In this study, we evaluated 10 long-read assemblers using a variety of metrics on Pacific Biosciences (PacBio) data sets from different taxonomic categories with considerable differences in genome size. The results allowed us to narrow down the list to a few assemblers that can be effectively applied to eukaryotic assembly projects. Moreover, we highlight how best to use limited genomic resources for effectively evaluating the genome assemblies of non-model organisms. © The Author 2017. Published by Oxford University Press.
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Capillary Assembly of Colloids: Interactions on Planar and Curved Interfaces
Liu, Iris B.; Sharifi-Mood, Nima; Stebe, Kathleen J.
2018-03-01
In directed assembly, small building blocks are assembled into an organized structure under the influence of guiding fields. Capillary interactions provide a versatile route for structure formation. Colloids adsorbed on fluid interfaces distort the interface, which creates an associated energy field. When neighboring distortions overlap, colloids interact to minimize interfacial area. Contact line pinning, particle shape, and surface chemistry play important roles in structure formation. Interface curvature acts like an external field; particles migrate and assemble in patterns dictated by curvature gradients. We review basic analysis and recent findings in this rapidly evolving literature. Understanding the roles of assembly is essential for tuning the mechanical, physical, and optical properties of the structure.
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Architecture and assembly of the Bacillus subtilis spore coat.
Plomp, Marco; Carroll, Alicia Monroe; Setlow, Peter; Malkin, Alexander J
2014-01-01
Bacillus spores are encased in a multilayer, proteinaceous self-assembled coat structure that assists in protecting the bacterial genome from stresses and consists of at least 70 proteins. The elucidation of Bacillus spore coat assembly, architecture, and function is critical to determining mechanisms of spore pathogenesis, environmental resistance, immune response, and physicochemical properties. Recently, genetic, biochemical and microscopy methods have provided new insight into spore coat architecture, assembly, structure and function. However, detailed spore coat architecture and assembly, comprehensive understanding of the proteomic composition of coat layers, and specific roles of coat proteins in coat assembly and their precise localization within the coat remain in question. In this study, atomic force microscopy was used to probe the coat structure of Bacillus subtilis wild type and cotA, cotB, safA, cotH, cotO, cotE, gerE, and cotE gerE spores. This approach provided high-resolution visualization of the various spore coat structures, new insight into the function of specific coat proteins, and enabled the development of a detailed model of spore coat architecture. This model is consistent with a recently reported four-layer coat assembly and further adds several coat layers not reported previously. The coat is organized starting from the outside into an outermost amorphous (crust) layer, a rodlet layer, a honeycomb layer, a fibrous layer, a layer of "nanodot" particles, a multilayer assembly, and finally the undercoat/basement layer. We propose that the assembly of the previously unreported fibrous layer, which we link to the darkly stained outer coat seen by electron microscopy, and the nanodot layer are cotH- and cotE- dependent and cotE-specific respectively. We further propose that the inner coat multilayer structure is crystalline with its apparent two-dimensional (2D) nuclei being the first example of a non-mineral 2D nucleation crystallization
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Architecture and Assembly of the Bacillus subtilis Spore Coat
Plomp, Marco; Carroll, Alicia Monroe; Setlow, Peter; Malkin, Alexander J.
2014-01-01
Bacillus spores are encased in a multilayer, proteinaceous self-assembled coat structure that assists in protecting the bacterial genome from stresses and consists of at least 70 proteins. The elucidation of Bacillus spore coat assembly, architecture, and function is critical to determining mechanisms of spore pathogenesis, environmental resistance, immune response, and physicochemical properties. Recently, genetic, biochemical and microscopy methods have provided new insight into spore coat architecture, assembly, structure and function. However, detailed spore coat architecture and assembly, comprehensive understanding of the proteomic composition of coat layers, and specific roles of coat proteins in coat assembly and their precise localization within the coat remain in question. In this study, atomic force microscopy was used to probe the coat structure of Bacillus subtilis wild type and cotA, cotB, safA, cotH, cotO, cotE, gerE, and cotE gerE spores. This approach provided high-resolution visualization of the various spore coat structures, new insight into the function of specific coat proteins, and enabled the development of a detailed model of spore coat architecture. This model is consistent with a recently reported four-layer coat assembly and further adds several coat layers not reported previously. The coat is organized starting from the outside into an outermost amorphous (crust) layer, a rodlet layer, a honeycomb layer, a fibrous layer, a layer of “nanodot” particles, a multilayer assembly, and finally the undercoat/basement layer. We propose that the assembly of the previously unreported fibrous layer, which we link to the darkly stained outer coat seen by electron microscopy, and the nanodot layer are cotH- and cotE- dependent and cotE-specific respectively. We further propose that the inner coat multilayer structure is crystalline with its apparent two-dimensional (2D) nuclei being the first example of a non-mineral 2D nucleation crystallization
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Dinesh, Bhimareddy; Squillaci, Marco A; Ménard-Moyon, Cécilia; Samorì, Paolo; Bianco, Alberto
2015-10-14
The integration of carbon nanotubes (CNTs) into organized nanostructures is of great interest for applications in materials science and biomedicine. In this work we studied the self-assembly of β and γ homologues of diphenylalanine peptides under different solvent and pH conditions. We aimed to investigate the role of peptide backbone in tuning the formation of different types of nanostructures alone or in combination with carbon nanotubes. In spite of having the same side chain, β and γ peptides formed distinctively different nanofibers, a clear indication of the role played by the backbone homologation on the self-assembly. The variation of the pH allowed to transform the nanofibers into spherical structures. Moreover, the co-assembly of β and γ peptides with carbon nanotubes covalently functionalized with the same peptide generated unique dendritic assemblies. This comparative study on self-assembly using diphenylalanine backbone homologues and of the co-assembly with CNT covalent conjugates is the first example exploring the capacity of β and γ peptides to adopt precise nanostructures, particularly in combination with carbon nanotubes. The dendritic organization obtained by mixing carbon nanotubes and peptides might find interesting applications in tissue engineering and neuronal interfacing.
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Oxide nanostructures through self-assembly
Aggarwal, S.; Ogale, S. B.; Ganpule, C. S.; Shinde, S. R.; Novikov, V. A.; Monga, A. P.; Burr, M. R.; Ramesh, R.; Ballarotto, V.; Williams, E. D.
2001-03-01
A prominent theme in inorganic materials research is the creation of uniformly flat thin films and heterostructures over large wafers, which can subsequently be lithographically processed into functional devices. This letter proposes an approach that will lead to thin film topographies that are directly counter to the above-mentioned philosophy. Recent years have witnessed considerable research activity in the area of self-assembly of materials, stimulated by observations of self-organized behavior in biological systems. We have fabricated uniform arrays of nonplanar surface features by a spontaneous assembly process involving the oxidation of simple metals, especially under constrained conditions on a variety of substrates, including glass and Si. In this letter we demonstrate the pervasiveness of this process through examples involving the oxidation of Pd, Cu, Fe, and In. The feature sizes can be controlled through the grain size and thickness of the starting metal thin film. Finally, we demonstrate how such submicron scale arrays can serve as templates for the design and development of self-assembled, nanoelectronic devices.
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Mind the gap; seven reasons to close fragmented genome assemblies.
Thomma, Bart P H J; Seidl, Michael F; Shi-Kunne, Xiaoqian; Cook, David E; Bolton, Melvin D; van Kan, Jan A L; Faino, Luigi
2016-05-01
Like other domains of life, research into the biology of filamentous microbes has greatly benefited from the advent of whole-genome sequencing. Next-generation sequencing (NGS) technologies have revolutionized sequencing, making genomic sciences accessible to many academic laboratories including those that study non-model organisms. Thus, hundreds of fungal genomes have been sequenced and are publically available today, although these initiatives have typically yielded considerably fragmented genome assemblies that often lack large contiguous genomic regions. Many important genomic features are contained in intergenic DNA that is often missing in current genome assemblies, and recent studies underscore the significance of non-coding regions and repetitive elements for the life style, adaptability and evolution of many organisms. The study of particular types of genetic elements, such as telomeres, centromeres, repetitive elements, effectors, and clusters of co-regulated genes, but also of phenomena such as structural rearrangements, genome compartmentalization and epigenetics, greatly benefits from having a contiguous and high-quality, preferably even complete and gapless, genome assembly. Here we discuss a number of important reasons to produce gapless, finished, genome assemblies to help answer important biological questions. Copyright © 2015 Elsevier Inc. All rights reserved.
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International Nuclear Information System (INIS)
Cao, Jing; Liu, Jia-Cheng; Deng, Wen-Ting; Li, Ren-Zhi; Jin, Neng-Zhi
2013-01-01
Graphical abstract: An innovative type of self-assembly based on acetohydrazide zinc porphyrin coordination polymer has been prepared in supramolecular solar cells. - Highlights: • A novel assembly with acetohydrazide porphyrin coordination polymer. • The assembly based on porphyrin is prepared as parallel sample. • Coordination polymer-based assembly shows enhanced photoelectronic behavior. • A series of different organic acid ligands as anchoring groups are prepared. - Abstract: In this work, a novel acetohydrazide zinc porphyrin-based coordination polymer (CP)-isonicotinic acid self-assembly by metal-ligand axial coordination to modify the nano-structured TiO 2 electrode surface has been investigated in photoelectrochemical device. Compared to the assembly based on corresponding zinc porphyrin combined with isonicotinic acid by metal-ligand axial coordination, CP-isonicotinic acid assembly exhibits a significantly enhanced photoelectronic behavior. In addition, a series of different organic acid ligands were prepared to probe the impact of their structures on the photoelectronic performances of their corresponding assemblies-sensitized cells. This study affords a novel type of self-assembly to functionalize the nanostructured TiO 2 electrode surface in supramolecular solar cells
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Assembly and disassembly of the nucleolus during the cell cycle.
Hernandez-Verdun, Danièle
2011-01-01
The nucleolus is a large nuclear domain in which transcription, maturation and assembly of ribosomes take place. In higher eukaryotes, nucleolar organization in three sub-domains reflects the compartmentation of the machineries related to active or inactive transcription of the ribosomal DNA, ribosomal RNA processing and assembly with ribosomal proteins of the two (40S and 60S) ribosomal subunits. The assembly of the nucleoli during telophase/early G(1) depends on pre-existing machineries inactivated during prophase (the transcription machinery and RNP processing complexes) and on partially processed 45S rRNAs inherited throughout mitosis. In telophase, the 45S rRNAs nucleate the prenucleolar bodies and order the dynamics of nucleolar assembly. The assembly/disassembly processes of the nucleolus depend on the equilibrium between phosphorylation/dephosphorylation of the transcription machinery and on the RNP processing complexes under the control of the CDK1-cyclin B kinase and PP1 phosphatases. The dynamics of assembly/disassembly of the nucleolus is time and space regulated.
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HOW ECOLOGICAL COMMUNITIES ARE STRUCTURED: A REVIEW ON ECOLOGICAL ASSEMBLY RULES
Directory of Open Access Journals (Sweden)
Gabriel Jaime Colorado Zuluaga
Full Text Available Whether biological communities are deterministic or stochastic assemblages of species has long been a central topic of ecology. The widely demonstrated presence of structural patterns in nature may imply the existence of rules that regulate the organization of ecological communities. In this review, I present a compilation of major assembly rules that fundament, in a great proportion, the community assembly theory. Initially, I present a general overview of key concepts associated to the assembly of communities, in particular the origin of assembly rules, definition, the problem of scale and underlying mechanisms in the structure of ecological communities. Subsequently, two major approaches or paradigms (i.e. species-based and trait-based for the assembly of communities are discussed. Finally, major tested assembly rules are explored and discussed under the light of available published literature.
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Molecular automata assembly: principles and simulation of bacterial membrane construction.
Lahoz-Beltra, R
1997-01-01
The motivation to understand the basic rules and principles governing molecular self-assembly may be relevant to explain in the context of molecular biology the self-organization and biological functions exhibited within cells. This paper presents a molecular automata model to simulate molecular self-assembly introducing the concept of molecular programming to simulate the biological function or operation performed by an assembled molecular state machine. The method is illustrated modelling Escherichia coli membrane construction including the assembly and operation of ATP synthase as well as the assembly of the bacterial flagellar motor. Flagellar motor operation was simulated using a different approach based on state machine definition used in virtual reality systems. The proposed methodology provides a modelling framework for simulation of biological functions performed by cellular components and other biological systems suitable to be modelled as molecular state machines.
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Self-assembling organomodified Co/Al based layered double hydroxides (LDH) via one-step route
Institute of Scientific and Technical Information of China (English)
WANG De-yi; A.LEUTERITZ; U.WAGENKNECHT; G.HEINRICH
2009-01-01
The preparation of self-assembling organomodified Co/Al-layered double hydroxide (LDH) via one-step route was studied.A common surfactant,sodium dodecylbenzenesulfonate (DBS),was employed as an organic modifier.The behavior and structure of self-assembled intercalated organic Co/Al-LDH were investigated by FTIR,SEM,WAXS,element analysis and TGA.Based upon the WAXS results and calculation by Bragg equation,the interlayer distance (d value) for organic Co/Al-LDH is enlarged from 0.75 nm to 3.10 nm,showing that the self-assembling behavior has been carried out successfully.Considering the observation from SEM,the product shows the morphology of organic Co/Al-LDH of a layered structure.In addition,FTIR,element analysis and TGA analysis show that the modifier is intercalated into the gallery of the Co/Al-LDH.Since organic modification for nanofiller is deemed to be necessary before applying it into polymer,the successful preparation of organomodified Co/Al-LDH will be significantly beneficial to the preparation and investigation of novel polymer/LDH nanocomposite.
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Development of anti-debris filter for WWER-440 working fuel assembly
International Nuclear Information System (INIS)
Kolosovsky, V.; Aksyonov, P.; Kukushkin, Y.; Molchanov, V.; Kolobaev, A.
2006-01-01
Mechanical damaging of the fuel rod claddings caused by debris is one of the main reasons for fuel assembly failures. The paper focuses on the program and results of experimental and design activities carried out by Russian organizations relating to the development and investigation of operational characteristics of anti-debris filters for WWER-440 working fuel assemblies. Lead working fuel assemblies equipped with anti-debris filters have been loaded in the core of Kola-2 NPP. The results obtained can be used for making the decision concerning the application of anti-debris filter for WWER-440 working fuel assemblies with the purpose of enhancing their debris-resistance properties. (authors)
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PREFACE The physics of virus assembly The physics of virus assembly
Stockley, Peter G.; Twarock, Reidun
2010-12-01
Viruses are pathogens in every kingdom of life and are major causes of human disease and suffering. They are known to encompass a size range that overlaps with that of the smallest bacterial cells, and the largest viruses now seem to be hosts of their own viral pathogens. Recent genomic sequencing efforts show that many organisms have genes that are likely to be descended in evolution from viral progenitors. Even more astonishingly, analysis of the world's oceans has shown that some of the simplest viruses, the tailed dsDNA phages, are the most common biological entities on the planet, with estimates of their numbers ranging up to 1031, with ~ 1021 infection events every second, leading to a turnover of around 20% of the biomass in the sea every few days. These cycles of infection and lysis of oceanic bacteria and algae provide the nutrients for the smallest organisms lying at the bottom of the food chain. Without viruses, therefore, life on Earth would probably not be sustainable. These are remarkable facts for systems that are non-living in the strict sense, and are composed of simple materials—nucleic acids, proteins and lipids. Many viruses consist of little more than a protective protein coat surrounding their genomic nucleic acids, which can be either DNA or RNA. Their simplicity leads to highly symmetrical structures with protein containers based on helical or icosahedral lattices. Many simple viruses self-assemble rapidly and with great fidelity, and many groups are busy trying to exploit these properties to make virus-like particles for a wide range of applications, including targeted drug-delivery, medical imaging and even novel materials. This issue of Physical Biology contains a series of papers describing some of the latest experimental and theoretical research on viruses, their structures and assembly, as well as their regulated disassembly during infection. These range from a dissection of the in vivo assembly mechanism of a filamentous virus
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Self-assembly strategies for the synthesis of functional nanostructured materials
International Nuclear Information System (INIS)
Perego, M.; Seguini, G.
2016-01-01
Self-assembly is the autonomous organization of components into patterns or structures without human intervention. This is the approach followed by nature to generate living cells and represents one of the practical strategies to fabricate ensembles of nanostructures. In static self-assembly the formation of ordered structures could require energy but once formed the structures are stable. The introduction of additional regular features in the environment could be used to template the self-assembly guiding the organization of the components and determining the final structure they form. In this regard self-assembly of block copolymers represents a potent platform for fundamental studies at the nanoscale and for application-driven investigation as a tool to fabricate functional nanostructured materials. Block copolymers can hierarchically assemble into chemically distinct domains with size and periodicity on the order of 10 nm or below, offering a potentially inexpensive route to generate large-area nanostructured materials. The final structure characteristics of these materials are dictated by the properties of the elementary block copolymers, like chain length, volume fraction or degree of block incompatibility. Modern synthetic chemistry offers the possibility to design these macromolecules with very specific length scales and geometries, directly embodying in the block copolymers the code that drives their self- assembling process. The understanding of the kinetics and thermodynamics of the block copolymer selfassembly process in the bulk phase as well as in thin films represents a fundamental prerequisite toward the exploitation of these materials. Incorporating block copolymer into device fabrication procedures or directly into devices, as active elements, will lead to the development of a new generation of devices fabricated using the fundamental law of nature to our advantage in order to minimize cost and power consumption in the fabrication process
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Multilayer Thin Films Sequential Assembly of Nanocomposite Materials
Decher, Gero
2012-01-01
This second, comprehensive edition of the pioneering book in this field has been completely revised and extended, now stretching to two volumes. The result is a comprehensive summary of layer-by-layer assembled, truly hybrid nanomaterials and thin films, covering organic, inorganic, colloidal, macromolecular and biological components, plus the assembly of nanoscale films derived from them on surfaces. Praise for the first edition: "... highly recommended to anyone interested in the field... and to scientists and researchers active in materials development..." –Polymer News With contri
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Tozawa, Tomokazu; Jones, James T. A.; Swamy, Shashikala I.; Jiang, Shan; Adams, Dave J.; Shakespeare, Stephen; Clowes, Rob; Bradshaw, Darren; Hasell, Tom; Chong, Samantha Y.; Tang, Chiu; Thompson, Stephen; Parker, Julia; Trewin, Abbie; Bacsa, John; Slawin, Alexandra M. Z.; Steiner, Alexander; Cooper, Andrew I.
2009-12-01
Porous materials are important in a wide range of applications including molecular separations and catalysis. We demonstrate that covalently bonded organic cages can assemble into crystalline microporous materials. The porosity is prefabricated and intrinsic to the molecular cage structure, as opposed to being formed by non-covalent self-assembly of non-porous sub-units. The three-dimensional connectivity between the cage windows is controlled by varying the chemical functionality such that either non-porous or permanently porous assemblies can be produced. Surface areas and gas uptakes for the latter exceed comparable molecular solids. One of the cages can be converted by recrystallization to produce either porous or non-porous polymorphs with apparent Brunauer-Emmett-Teller surface areas of 550 and 23m2g-1, respectively. These results suggest design principles for responsive porous organic solids and for the modular construction of extended materials from prefabricated molecular pores.
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Theory of Connectivity: Nature and Nurture of Cell Assemblies and Cognitive Computation.
Li, Meng; Liu, Jun; Tsien, Joe Z
2016-01-01
Richard Semon and Donald Hebb are among the firsts to put forth the notion of cell assembly-a group of coherently or sequentially-activated neurons-to represent percept, memory, or concept. Despite the rekindled interest in this century-old idea, the concept of cell assembly still remains ill-defined and its operational principle is poorly understood. What is the size of a cell assembly? How should a cell assembly be organized? What is the computational logic underlying Hebbian cell assemblies? How might Nature vs. Nurture interact at the level of a cell assembly? In contrast to the widely assumed randomness within the mature but naïve cell assembly, the Theory of Connectivity postulates that the brain consists of the developmentally pre-programmed cell assemblies known as the functional connectivity motif (FCM). Principal cells within such FCM is organized by the power-of-two-based mathematical principle that guides the construction of specific-to-general combinatorial connectivity patterns in neuronal circuits, giving rise to a full range of specific features, various relational patterns, and generalized knowledge. This pre-configured canonical computation is predicted to be evolutionarily conserved across many circuits, ranging from these encoding memory engrams and imagination to decision-making and motor control. Although the power-of-two-based wiring and computational logic places a mathematical boundary on an individual's cognitive capacity, the fullest intellectual potential can be brought about by optimized nature and nurture. This theory may also open up a new avenue to examining how genetic mutations and various drugs might impair or improve the computational logic of brain circuits.
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Cellular self-assembly and biomaterials-based organoid models of development and diseases.
Shah, Shivem B; Singh, Ankur
2017-04-15
Organogenesis and morphogenesis have informed our understanding of physiology, pathophysiology, and avenues to create new curative and regenerative therapies. Thus far, this understanding has been hindered by the lack of a physiologically relevant yet accessible model that affords biological control. Recently, three-dimensional ex vivo cellular cultures created through cellular self-assembly under natural extracellular matrix cues or through biomaterial-based directed assembly have been shown to physically resemble and recapture some functionality of target organs. These "organoids" have garnered momentum for their applications in modeling human development and disease, drug screening, and future therapy design or even organ replacement. This review first discusses the self-organizing organoids as materials with emergent properties and their advantages and limitations. We subsequently describe biomaterials-based strategies used to afford more control of the organoid's microenvironment and ensuing cellular composition and organization. In this review, we also offer our perspective on how multifunctional biomaterials with precise spatial and temporal control could ultimately bridge the gap between in vitro organoid platforms and their in vivo counterparts. Several notable reviews have highlighted PSC-derived organoids and 3D aggregates, including embryoid bodies, from a development and cellular assembly perspective. The focus of this review is to highlight the materials-based approaches that cells, including PSCs and others, adopt for self-assembly and the controlled development of complex tissues, such as that of the brain, gut, and immune system. Copyright © 2017 Acta Materialia Inc. Published by Elsevier Ltd. All rights reserved.
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Self-assembling layers created by membrane proteins on gold.
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.
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Integrating DNA strand-displacement circuitry with DNA tile self-assembly
Zhang, David Yu; Hariadi, Rizal F.; Choi, Harry M.T.; Winfree, Erik
2013-01-01
DNA nanotechnology has emerged as a reliable and programmable way of controlling matter at the nanoscale through the specificity of Watson–Crick base pairing, allowing both complex self-assembled structures with nanometer precision and complex reaction networks implementing digital and analog behaviors. Here we show how two well-developed frameworks, DNA tile self-assembly and DNA strand-displacement circuits, can be systematically integrated to provide programmable kinetic control of self-assembly. We demonstrate the triggered and catalytic isothermal self-assembly of DNA nanotubes over 10 μm long from precursor DNA double-crossover tiles activated by an upstream DNA catalyst network. Integrating more sophisticated control circuits and tile systems could enable precise spatial and temporal organization of dynamic molecular structures. PMID:23756381
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The Dit nuclear fuel assembly physics design code
International Nuclear Information System (INIS)
Jonsson, A.
1987-01-01
DIT is the Combustion Engineering, Inc. (C-E) nuclear fuel assembly design code. It belongs to a class of codes, all similar in structure and strategy, which may be characterized by the spectrum and spatial calculations being performed in 2D and in a single job step for the entire assembly. The forerunner of this class of codes is the U.K.A.E.A. WIMS code, the first version of which was completed 25 years ago. The structure and strategy of assembly spectrum codes have remained remarkably similar to the original concept thus proving its usefulness. As other organizations, including C-E, have developed their own versions of the concept, many important variations have been added which significantly influence the accuracy and performance of the resulting computational tool. This paper describes and discusses those features which are unique to the DIT code and which might be of interest to the community of fuel assembly physics design code users and developers
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The DIT nuclear fuel assembly physics design code
International Nuclear Information System (INIS)
Jonsson, A.
1988-01-01
The DIT code is the Combustion Engineering, Inc. (C-E) nuclear fuel assembly design code. It belongs to a class of codes, all similar in structure and strategy, that may be characterized by the spectrum and spatial calculations being performed in two dimensions and in a single job step for the entire assembly. The forerunner of this class of codes is the United Kingdom Atomic Energy Authority WIMS code, the first version of which was completed 25 yr ago. The structure and strategy of assembly spectrum codes have remained remarkably similar to the original concept thus proving its usefulness. As other organizations, including C-E, have developed their own versions of the concept, many important variations have been added that significantly influence the accuracy and performance of the resulting computational tool. Those features, which are unique to the DIT code and which might be of interest to the community of fuel assembly physics design code users and developers, are described and discussed
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Design of novel supramolecular self-assembly creating ...
Indian Academy of Sciences (India)
Administrator
Metal–organic composite materials with appropriate building blocks which can assemble into structures with specific and desired frameworks are challenging both for their solid state technology and for their chemical architecture. Of special interest is the construction of a microporous network that can exhibit reversible guest ...
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A Neural Assembly-Based View on Word Production: The Bilingual Test Case
Strijkers, Kristof
2016-01-01
I will propose a tentative framework of how words in two languages could be organized in the cerebral cortex based on neural assembly theory, according to which neurons that fire synchronously are bound into large-scale distributed functional units (assemblies), which represent a mental event as a whole ("gestalt"). For language this…
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Self-assembly of dodecaphenyl POSS thin films
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.
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Exploring the properties and possibilities of self-assembling
DEFF Research Database (Denmark)
Andersen, Karsten Brandt; Castillo, Jaime
2013-01-01
structures ranging from piezo electricity over semi conductance to fluorescence. If such peptide nanotubes could be controlled and incorporated in sensors such as a biological field effect transistor it would greatly reduce the fabrication costs while at the same time providing researchers with new...... and exciting possibilities. The major driving forces supporting the interest in the peptide nanotubes is the fast and simple assembly process combined with their remarkable stability towards alcohols, organic solvents, and biological analytes that was presented shortly after the self-assembling properties...... and illustrated their potential use as sensitive temperature sensor....
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Templated Biomineralization on Self-Assembled Protein Fibers
Energy Technology Data Exchange (ETDEWEB)
Subburaman,K.; Pernodet, N.; Kwak, S.; DiMasi, E.; Ge, S.; Zaitsev, V.; Ba, X.; Yang, N.; Rafailovich, M.
2006-01-01
Biological mineralization of tissues in living organisms relies on proteins that preferentially nucleate minerals and control their growth. This process is often referred to as 'templating', but this term has become generic, denoting various proposed mineral-organic interactions including both chemical and structural affinities. Here, we present an approach using self-assembled networks of elastin and fibronectin fibers, similar to the extracellular matrix. When induced onto negatively charged sulfonated polystyrene surfaces, these proteins form fiber networks of {approx}10-{mu}m spacing, leaving open regions of disorganized protein between them. We introduce an atomic force microscopy-based technique to measure the elastic modulus of both structured and disorganized protein before and during calcium carbonate mineralization. Mineral-induced thickening and stiffening of the protein fibers during early stages of mineralization is clearly demonstrated, well before discrete mineral crystals are large enough to image by atomic force microscopy. Calcium carbonate stiffens the protein fibers selectively without affecting the regions between them, emphasizing interactions between the mineral and the organized protein fibers. Late-stage observations by optical microscopy and secondary ion mass spectroscopy reveal that Ca is concentrated along the protein fibers and that crystals form preferentially on the fiber crossings. We demonstrate that organized versus unstructured proteins can be assembled mere nanometers apart and probed in identical environments, where mineralization is proved to require the structural organization imposed by fibrillogenesis of the extracellular matrix.
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Plasmonic organic solar cells employing nanobump assembly via aerosol-derived nanoparticles.
Jung, Kinam; Song, Hyung-Jun; Lee, Gunhee; Ko, Youngjun; Ahn, KwangJun; Choi, Hoseop; Kim, Jun Young; Ha, Kyungyeon; Song, Jiyun; Lee, Jong-Kwon; Lee, Changhee; Choi, Mansoo
2014-03-25
We report the effect of a nanobump assembly (NBA) constructed with molybdenum oxide (MoO3) covering Ag nanoparticles (NPs) under the active layer on the efficiency of plasmonic polymer solar cells. Here, the NPs with precisely controlled concentration and size have been generated by an atmospheric evaporation/condensation method and a differential mobility classification and then deposited on an indium tin oxide electrode via room temperature aerosol method. NBA structure is made by enclosing NPs with MoO3 layer via vacuum thermal evaporation to isolate the undulated active layer formed onto the underlying protruded NBA. Simulated scattering cross sections of the NBA structure reveal higher intensities with a strong forward scattering effect than those from the flat buffer cases. Experimental results of the device containing the NBA show 24% enhancement in short-circuit current density and 18% in power conversion efficiency compared to the device with the flat MoO3 without the NPs. The observed improvements are attributed to the enhanced light scattering and multireflection effects arising from the NBA structure combined with the undulated active layer in the visible and near-infrared regions. Moreover, we demonstrate that the NBA adopted devices show better performance with longer exciton lifetime and higher light absorption in comparison with the devices with Ag NPs incorporated flat poly(3,4-ethylenedioxythiophene):poly(styrenesulfonate) (PEDOT:PSS). Thus, the suggested approach provides a reliable and efficient light harvesting in a broad range of wavelength, which consequently enhances the performance of various organic solar cells.
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Mann, Stephen
2009-10-01
Understanding how chemically derived processes control the construction and organization of matter across extended and multiple length scales is of growing interest in many areas of materials research. Here we review present equilibrium and non-equilibrium self-assembly approaches to the synthetic construction of discrete hybrid (inorganic-organic) nano-objects and higher-level nanostructured networks. We examine a range of synthetic modalities under equilibrium conditions that give rise to integrative self-assembly (supramolecular wrapping, nanoscale incarceration and nanostructure templating) or higher-order self-assembly (programmed/directed aggregation). We contrast these strategies with processes of transformative self-assembly that use self-organizing media, reaction-diffusion systems and coupled mesophases to produce higher-level hybrid structures under non-equilibrium conditions. Key elements of the constructional codes associated with these processes are identified with regard to existing theoretical knowledge, and presented as a heuristic guideline for the rational design of hybrid nano-objects and nanomaterials.
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Status of Conceptual Design Progress for ITER Sector Sub-assembly Tools
Energy Technology Data Exchange (ETDEWEB)
Nam, Kyoung O; Park, Hyun Ki; Kim, Dong Jin [National Fusion Research Institute, Daejeon (Korea, Republic of); Lee, Jae Hyuk; Kim, Kyung Kyu [SFA Engineering Corp., Changwon (Korea, Republic of); Im, Ki Hak; Robert, Shaw [ITER Organization, Paul lez Durance (France)
2010-05-15
The ITER (International Thermonuclear Experimental Reactor) Tokamak assembly tools are purpose-built tools to complete the ITER Tokamak machine which includes the cryostat and the components contained therein. Based on the design description document prepared by the ITER organization, Korea has carried out the conceptual design of assembly tools. The 40 .deg. sector assemblies sub-assembled at assembly hall are transferred to Tokamak hall using the lifting tool operated by Tokamak main cranes. In-pit assembly tools are the purpose-built assembly tools for the completion of final sector assembly at Tokamak hall. The 40 .deg. sector sub-assembly tools are composed of the upending tool, the sector sub-assembly tool, the sector lifting tool and the vacuum vessel support and bracing tools. The process of the ITER sector sub-assembly at assembly hall and status of research and development are described in this paper. The ITER Tokamak device is composed of 9 vacuum vessel (VV)/toroidal field coils (TFCs)/vacuum vessel thermal shields (VVTS) 40 .deg. sectors. Each VV/TFCs/VVTS 40 .deg. sector is made up of one 40 .deg. VV, two 20 .deg. TFCs and associated VVTS segments. The 40 .deg. sectors are sub-assembled at assembly hall respectively and then 9 sectors which sub-assembled at assembly hall are finally assembled at Tokamak hall. As a basic assembly component, the assembly strategy and tools for the 40 .deg. sector sub-assembly and final assembly at inpit should be developed to satisfy the basic assembly requirements of the ITER Tokamak device. Accordingly, the purpose-built assembly tools should be designed and manufactured considering assembly plan, available space, safety, easy operation, efficient maintenance, and so on. The 40 .deg. sector assembly tools are classified into 2 groups. One group is the sub-assembly tools including upending tool, lifting tool, sub-assembly tool, VV supports and bracing tools used at assembly hall and the other group is the in
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International Nuclear Information System (INIS)
O'Riordan, A; Iacopino, D; Lovera, P; Floyd, L; Reynolds, K; Redmond, G
2011-01-01
Conjugated polymer based 1D nanostructures are attractive building blocks for future opto-electronic nanoscale devices and systems. However, a critical challenge remains the lack of manipulation methods that enable controlled and reliable positioning and orientation of organic nanostructures in a fast, reliable and scalable manner. To address this challenge, we explore dielectrophoretic assembly of discrete poly(9,9-dioctylfluorene) nanofibres and demonstrate site selective assembly and orientation of these fibres. Nanofibre arrays were assembled preferentially at receptor electrode edges, being aligned parallel to the applied electric field with a high order parameter fit (∼0.9) and exhibiting an emission dichroic ratio of ∼ 4.0. As such, the dielectrophoretic method represents a fast, reliable and scalable self-assembly approach for manipulation of 1D organic nanostructures. The ability to fabricate nanofibre arrays in this manner could be potentially important for exploration and development of future nanoscale opto-electronic devices and systems.
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Porous Hydrogen-Bonded Organic Frameworks
Directory of Open Access Journals (Sweden)
Yi-Fei Han
2017-02-01
Full Text Available Ordered porous solid-state architectures constructed via non-covalent supramolecular self-assembly have attracted increasing interest due to their unique advantages and potential applications. Porous metal-coordination organic frameworks (MOFs are generated by the assembly of metal coordination centers and organic linkers. Compared to MOFs, porous hydrogen-bonded organic frameworks (HOFs are readily purified and recovered via simple recrystallization. However, due to lacking of sufficiently ability to orientate self-aggregation of building motifs in predictable manners, rational design and preparation of porous HOFs are still challenging. Herein, we summarize recent developments about porous HOFs and attempt to gain deeper insights into the design strategies of basic building motifs.
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A Strategic Study of Assembly Plant Establishment in the Kingdom of Saudi Arabia
Santamaria, Scott
2001-01-01
Preface: Traditionally, assembly plant establishment in foreign countries has been a way for corporations to avoid high import duties and/or gain access to free-trade zones. With World Trade Organization (WTO) membership rising, and consequently import duties falling, the role of the assembly plant is changing. Purpose Statement: This thesis concentrates on companies that contemplate on, or have ambitions of establishing industrial assembly facilities in the country of Saudi Arabia. The main ...
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Theory of Connectivity: Nature and Nurture of Cell Assemblies and Cognitive Computation
Directory of Open Access Journals (Sweden)
Meng eLi
2016-04-01
Full Text Available Richard Semon and Donald Hebb are among the firsts to put forth the notion of cell assembly – a group of coherently or sequentially-activated neurons– to represent percept, memory, or concept. Despite the rekindled interest in this age-old idea, the concept of cell assembly still remains ill-defined and its operational principle is poorly understood. What is the size of a cell assembly? How should a cell assembly be organized? What is the computational logic underlying Hebbian cell assemblies? How might Nature vs Nurture interact at the level of a cell assembly? In contrast to the widely assumed local randomness within the mature but naïve cell assembly, the recent Theory of Connectivity postulates that the brain consists of the developmentally pre-programmed cell assemblies known as the functional connectivity motif (FCM. Principal cells within such FCM is organized by the power-of-two-based mathematical principle that guides the construction of specific-to-general combinatorial connectivity patterns in neuronal circuits, giving rise to a full range of specific features, various relational patterns, and generalized knowledge. This pre-configured canonical computation is predicted to be evolutionarily conserved across many circuits, ranging from these encoding memory engrams and imagination to decision-making and motor control. Although the power-of-two-based wiring and computational logic places a mathematical boundary on an individual’s cognitive capacity, the fullest intellectual potential can be brought about by optimized nature and nurture. This theory may also open up a new avenue to examining how genetic mutations and various drugs might impair or enhance the computational logic of brain circuits.
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Robotically Assembled Aerospace Structures: Digital Material Assembly using a Gantry-Type Assembler
Trinh, Greenfield; Copplestone, Grace; O'Connor, Molly; Hu, Steven; Nowak, Sebastian; Cheung, Kenneth; Jenett, Benjamin; Cellucci, Daniel
2017-01-01
This paper evaluates the development of automated assembly techniques for discrete lattice structures using a multi-axis gantry type CNC machine. These lattices are made of discrete components called "digital materials." We present the development of a specialized end effector that works in conjunction with the CNC machine to assemble these lattices. With this configuration we are able to place voxels at a rate of 1.5 per minute. The scalability of digital material structures due to the incremental modular assembly is one of its key traits and an important metric of interest. We investigate the build times of a 5x5 beam structure on the scale of 1 meter (325 parts), 10 meters (3,250 parts), and 30 meters (9,750 parts). Utilizing the current configuration with a single end effector, performing serial assembly with a globally fixed feed station at the edge of the build volume, the build time increases according to a scaling law of n4, where n is the build scale. Build times can be reduced significantly by integrating feed systems into the gantry itself, resulting in a scaling law of n3. A completely serial assembly process will encounter time limitations as build scale increases. Automated assembly for digital materials can assemble high performance structures from discrete parts, and techniques such as built in feed systems, parallelization, and optimization of the fastening process will yield much higher throughput.
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Layer-by-Layer-Assembled High-Performance Broadband Antireflection Coatings
Shimomura, Hiroomi; Gemici, Zekeriyya; Cohen, Robert E.; Rubner, Michael F.
2010-01-01
uniformity, thickness control, roughness control, mechanical durability, and incorporation of a diverse set of functional organic molecules into nanoparticle thin films are major challenges. We have used the electrostatic layer-by-layer assembly technique
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Simulating three dimensional self-assembly of shape modified particles using magnetic dipolar forces
Alink, Laurens; Marsman, G.H. (Mathijs); Woldering, L.A.; Abelmann, Leon
2011-01-01
The feasibility of 3D self-assembly of milli-magnetic particles that interact via magnetic dipolar forces is investigated. Typically magnetic particles, such as isotropic spheres, self-organize in stable 2D configurations. By modifying the shape of the particles, 3D self-assembly may be enabled. The
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Wang, Shuang; Belmabkhout, Youssef; Cairns, Amy J; Li, Guanghua; Huo, Qisheng; Liu, Yunling; Eddaoudi, Mohamed
2017-10-04
A strategy based on metal-ligand directed assembly of metal-organic squares (MOSs), built-up from four-membered ring (4MR) secondary building units (SBUs), has been employed for the design and construction of isoreticular zeolite-like supramolecular assemblies (ZSAs). Four porous Co-based ZSAs having the same underlying gis topology, but differing only with respect to the capping and bridging linkers, were successfully isolated and fully characterized. In this series, each MOS in ZSA-3-ZSA-6 possess an ideal square geometry and is connected to four neighboring MOS via a total of 16 hydrogen bonds to give a 3-periodic porous network.To systematically assess the effect of the pore system (size and functionality) on the gas adsorption properties, we evaluated the MOSs for their affinity for different probe molecules such as CO 2 and light hydrocarbons. ZSA-3-ZSA-6 showed high thermal stability (up to 300 °C) and was proven highly porous as evidenced by gas adsorption studies. Notably, alkyl-functionalized MOSs were found to offer potential for selective separation of CO 2 , C 3 H 6 , and C 3 H 8 from CH 4 and H 2 containing gas stream, such as natural gas and refinery-off gases.
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Wang, Shuang
2017-07-11
A strategy based on metal-ligand directed assembly of metal-organic squares (MOSs), built-up from four-membered ring (4MR) secondary building units (SBUs), has been employed for the design and construction of isoreticular zeolite-like supramolecular assemblies (ZSAs). Four porous Co-based ZSAs having the same underlying gis topology, but differing only with respect to the capping and bridging linkers, were successfully isolated and fully characterized. In this series, each MOS in ZSA-3-ZSA-6 possess an ideal square geometry and is connected to four neighboring MOS via a total of 16 hydrogen bonds to give a 3-periodic porous network.To systematically assess the effect of the pore system (size and functionality) on the gas adsorption properties, we evaluated the MOSs for their affinity for different probe molecules such as CO2 and light hydrocarbons. ZSA-3-ZSA-6 showed high thermal stability (up to 300 °C) and was proven highly porous as evidenced by gas adsorption studies. Notably, alkyl-functionalized MOSs were found to offer potential for selective separation of CO2, C3H6, and C3H8 from CH4 and H2 containing gas stream, such as natural gas and refinery-off gases.
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DEFF Research Database (Denmark)
Scheibye-Alsing, Karsten; Hoffmann, S.; Frankel, Annett Maria
2009-01-01
Despite the rapidly increasing number of sequenced and re-sequenced genomes, many issues regarding the computational assembly of large-scale sequencing data have remain unresolved. Computational assembly is crucial in large genome projects as well for the evolving high-throughput technologies and...... in genomic DNA, highly expressed genes and alternative transcripts in EST sequences. We summarize existing comparisons of different assemblers and provide a detailed descriptions and directions for download of assembly programs at: http://genome.ku.dk/resources/assembly/methods.html....
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Enabling complex nanoscale pattern customization using directed self-assembly.
Doerk, Gregory S; Cheng, Joy Y; Singh, Gurpreet; Rettner, Charles T; Pitera, Jed W; Balakrishnan, Srinivasan; Arellano, Noel; Sanders, Daniel P
2014-12-16
Block copolymer directed self-assembly is an attractive method to fabricate highly uniform nanoscale features for various technological applications, but the dense periodicity of block copolymer features limits the complexity of the resulting patterns and their potential utility. Therefore, customizability of nanoscale patterns has been a long-standing goal for using directed self-assembly in device fabrication. Here we show that a hybrid organic/inorganic chemical pattern serves as a guiding pattern for self-assembly as well as a self-aligned mask for pattern customization through cotransfer of aligned block copolymer features and an inorganic prepattern. As informed by a phenomenological model, deliberate process engineering is implemented to maintain global alignment of block copolymer features over arbitrarily shaped, 'masking' features incorporated into the chemical patterns. These hybrid chemical patterns with embedded customization information enable deterministic, complex two-dimensional nanoscale pattern customization through directed self-assembly.
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Drosophila parthenogenesis: A tool to decipher centrosomal vs acentrosomal spindle assembly pathways
International Nuclear Information System (INIS)
Riparbelli, Maria Giovanna; Callaini, Giuliano
2008-01-01
Development of unfertilized eggs in the parthenogenetic strain K23-O-im of Drosophila mercatorum requires the stochastic interactions of self-assembled centrosomes with the female chromatin. In a portion of the unfertilized eggs that do not assemble centrosomes, microtubules organize a bipolar anastral mitotic spindle around the chromatin like the one formed during the first female meiosis, suggesting that similar pathways may be operative. In the cytoplasm of eggs in which centrosomes do form, monastral and biastral spindles are found. Analysis by laser scanning confocal microscopy suggests that these spindles are derived from the stochastic interaction of astral microtubules directly with kinetochore regions or indirectly with kinetochore microtubules. Our findings are consistent with the idea that mitotic spindle assembly requires both acentrosomal and centrosomal pathways, strengthening the hypothesis that astral microtubules can dictate the organization of the spindle by capturing kinetochore microtubules
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Dai, Fangna; Dou, Jianmin; He, Haiyan; Zhao, Xiaoliang; Sun, Daofeng
2010-05-03
To assemble metal-organic supramolecules such as a metallamacrocycle and metal-organic coordination cage (MOCC), a series of flexible dicarboxylate ligands with the appropriate angle, 2,2'-(2,3,5,6-tetramethyl-1,4-phenylene)bis(methylene)bis(sulfanediyl)dibenzoic acid (H(2)L(1)), 2,2'-(2,5-dimethyl-1,4-phenylene)bis(methylene)bis(sulfanediyl)dibenzoic acid (H(2)L(2)), 2,2'-(2,4,6-trimethyl-1,3-phenylene)bis(methylene)bis(sulfanediyl)dinicotinic acid (H(2)L(3)), and 2,2'-(2,4,6-trimethyl-1,3-phenylene)bis(methylene)bis(sulfanediyl)dibenzoic acid (H(2)L(4)), have been designed and synthesized. Using these flexible ligands to assemble with metal ions, six metal-organic supramolecules, Cd(2)(L(1))(2)(dmf)(4)(H(2)O)(2).H(2)O (1), Mn(3)((1)L(2))(2)((2)L(2))(dmf)(2)(H(2)O)(2).5dmf (2), Cu(4)(L(3))(4)(H(2)O)(4).3dmf (3), Cu(4)(L(4))(4)(dmf)(2)(EtOH)(2).8dmf.6H(2)O (4), Mn(4)(L(4))(4)(dmf)(4)(H(2)O)(4).6dmf.H(2)O (5), and Mn(3)(L(4))(3)(dmf)(4).2dmf.3H(2)O (6), possessing a rectangular macrocycle, MOCCs or their extensions, and 1D or 2D coordination polymers, have been isolated. All complexes have been characterized by single-crystal X-ray diffraction, elemental analysis, and thermogravimetric analysis. Complex 1 is a discrete rectangular macrocycle, while complex 2 is a 2D macrocycle-based coordination polymer in which the L(2) ligand adopts both syn and anti conformations. Complexes 3-5 are discrete MOCCs in which two binuclear metal clusters are engaged by four organic ligands. The different geometries of the secondary building units (SBUs) and the axial coordinated solvates on the SBUs result in their different symmetries. Complex 6 is a 1D coordination polymer, extended from a MOCC made up of two metal ions and three L(4) ligands. All of the flexible dicarboxylate ligands adopt a syn conformation except that in complex 2, indicating that the syn conformational ligand is helpful for the formation of a metallamacrocycle and a MOCC. The magnetic properties of complexes 5
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Zhao, Kui
2015-09-07
The mechanistic understanding of the intrinsic molecular self-assembly of conjugated polymers is of immense importance to controlling the microstructure development in organic semiconducting thin films, with meaningful impact on charge transport and optoelectronic properties. Yet, to date the vast majority of studies have focused on the fast solution process itself, with studies of slower intrinsic molecular self-assembly in formulations lagging behind. Here we have investigated molecular self-assembly during spontaneous organization and uncovered how changes in formulation influence the microstructure, morphology and transport properties of conjugated polymer thin films. Our results suggest that the polymer-solvent interaction is the key factor for the molecular self-assembly and changes in macroscopic charge transport, which is in contrast with most solution processes, such as spin-coating and blade coating, where solvent drying kinetics dominates the aggregation and crystallization processes. Energetically favourable interactions between the polymer and its solvent are shown to cause chain expansion, resulting in a large hydrodynamic volume and few chain entanglements in solution. This provides molecular freedom for self-assembly and is shown to greatly enhance the local and long range order of the polymer, intra-chain backbone planarity and crystallite size. These improvements, in turn, are shown to endow the conjugated polymer with high carrier transport, as demonstrated by organic thin film transistors.
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Aghamohammadi, Mahdieh; Rödel, Reinhold; Zschieschang, Ute; Ocal, Carmen; Boschker, Hans; Weitz, R Thomas; Barrena, Esther; Klauk, Hagen
2015-10-21
The mechanisms behind the threshold-voltage shift in organic transistors due to functionalizing of the gate dielectric with self-assembled monolayers (SAMs) are still under debate. We address the mechanisms by which SAMs determine the threshold voltage, by analyzing whether the threshold voltage depends on the gate-dielectric capacitance. We have investigated transistors based on five oxide thicknesses and two SAMs with rather diverse chemical properties, using the benchmark organic semiconductor dinaphtho[2,3-b:2',3'-f]thieno[3,2-b]thiophene. Unlike several previous studies, we have found that the dependence of the threshold voltage on the gate-dielectric capacitance is completely different for the two SAMs. In transistors with an alkyl SAM, the threshold voltage does not depend on the gate-dielectric capacitance and is determined mainly by the dipolar character of the SAM, whereas in transistors with a fluoroalkyl SAM the threshold voltages exhibit a linear dependence on the inverse of the gate-dielectric capacitance. Kelvin probe force microscopy measurements indicate this behavior is attributed to an electronic coupling between the fluoroalkyl SAM and the organic semiconductor.
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Directory of Open Access Journals (Sweden)
Anastasia A. Aksyuk
2011-02-01
Full Text Available Bacteriophages have been a model system to study assembly processes for over half a century. Formation of infectious phage particles involves specific protein-protein and protein-nucleic acid interactions, as well as large conformational changes of assembly precursors. The sequence and molecular mechanisms of phage assembly have been elucidated by a variety of methods. Differences and similarities of assembly processes in several different groups of bacteriophages are discussed in this review. The general principles of phage assembly are applicable to many macromolecular complexes.
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Xing, Pengyao; Zhao, Zhuo; Hao, Aiyou; Zhao, Yanli
2016-01-21
Structural matching of two organic building blocks bearing glutamate units and different luminophores assembled into unilamellar nanovesicles in aqueous media through a co-assembly process. Aggregation-induced energy transfer took place in the co-assembled system, leading to controllable generation of multiple luminescence colors including white light.
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Directory of Open Access Journals (Sweden)
Fengxi Yang
Full Text Available Cymbidium ensifolium belongs to the genus Cymbidium of the orchid family. Owing to its spectacular flower morphology, C. ensifolium has considerable ecological and cultural value. However, limited genetic data is available for this non-model plant, and the molecular mechanism underlying floral organ identity is still poorly understood. In this study, we characterize the floral transcriptome of C. ensifolium and present, for the first time, extensive sequence and transcript abundance data of individual floral organs. After sequencing, over 10 Gb clean sequence data were generated and assembled into 111,892 unigenes with an average length of 932.03 base pairs, including 1,227 clusters and 110,665 singletons. Assembled sequences were annotated with gene descriptions, gene ontology, clusters of orthologous group terms, the Kyoto Encyclopedia of Genes and Genomes, and the plant transcription factor database. From these annotations, 131 flowering-associated unigenes, 61 CONSTANS-LIKE (COL unigenes and 90 floral homeotic genes were identified. In addition, four digital gene expression libraries were constructed for the sepal, petal, labellum and gynostemium, and 1,058 genes corresponding to individual floral organ development were identified. Among them, eight MADS-box genes were further investigated by full-length cDNA sequence analysis and expression validation, which revealed two APETALA1/AGL9-like MADS-box genes preferentially expressed in the sepal and petal, two AGAMOUS-like genes particularly restricted to the gynostemium, and four DEF-like genes distinctively expressed in different floral organs. The spatial expression of these genes varied distinctly in different floral mutant corresponding to different floral morphogenesis, which validated the specialized roles of them in floral patterning and further supported the effectiveness of our in silico analysis. This dataset generated in our study provides new insights into the molecular mechanisms
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Wang, Peng
2012-02-08
Direct photoelectrochemical conversion of toluene (TL) to methylcyclohexane (MC) with water has been examined as an organic hydride conversion using light irradiation. The production of MC from TL was observed on Pt/CdS/Cu 2ZnSnS 4/Mo photoelectrodes with anion-type ionomer membrane assemblies. A cathodic photocurrent was observed below 0.7 V vs RHE (V RHE) in 0.1 M Na 2SO 4/NaOH (pH 9.5) aqueous solution, and an apparent photocurrent density of 0.5 mA cm -2 was obtained at 0 V RHE under the irradiation of a 300 W Xe lamp with a 420 nm cutoff filter. The yield of MC was measured by gas chromatography, and an 88% faradaic efficiency was estimated. This study suggests the possibility of direct energy conversion from solar energy to MC as an energy carrier of organic hydrides. © 2012 American Chemical Society.
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Opal-like Multicolor Appearance of Self-Assembled Photonic Array.
Arnon, Zohar A; Pinotsi, Dorothea; Schmidt, Matthias; Gilead, Sharon; Guterman, Tom; Sadhanala, Aditya; Ahmad, Shahab; Levin, Aviad; Walther, Paul; Kaminski, Clemens F; Fändrich, Marcus; Kaminski Schierle, Gabriele S; Adler-Abramovich, Lihi; Shimon, Linda J W; Gazit, Ehud
2018-06-20
Molecular self-assembly of short peptide building blocks leads to the formation of various material architectures that may possess unique physical properties. Recent studies had confirmed the key role of biaromaticity in peptide self-assembly, with the diphenylalanine (FF) structural family as an archetypal model. Another significant direction in the molecular engineering of peptide building blocks is the use of fluorenylmethoxycarbonyl (Fmoc) modification, which promotes the assembly process and may result in nanostructures with distinctive features and macroscopic hydrogel with supramolecular features and nanoscale order. Here, we explored the self-assembly of the protected, noncoded fluorenylmethoxycarbonyl-β,β-diphenyl-Ala-OH (Fmoc-Dip) amino acid. This process results in the formation of elongated needle-like crystals with notable aromatic continuity. By altering the assembly conditions, arrays of spherical particles were formed that exhibit strong light scattering. These arrays display vivid coloration, strongly resembling the appearance of opal gemstones. However, unlike the Rayleigh scattering effect produced by the arrangement of opal, the described optical phenomenon is attributed to Mie scattering. Moreover, by controlling the solution evaporation rate, i.e., the assembly kinetics, we were able to manipulate the resulting coloration. This work demonstrates a bottom-up approach, utilizing self-assembly of a protected amino acid minimal building block, to create arrays of organic, light-scattering colorful surfaces.
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Layer-by-layer assembly of nanostructured composites: Mechanics and applications
Podsiadlo, Paul
The development of efficient methods for preparation of nanometer-sized materials and our evolving ability to manipulate the nanoscale objects have brought about a scientific and technological revolution called: nanotechnology. This revolution has been especially driven by discovery of unique nanoscale properties of the nanomaterials which are governed by their inherent size. Today, the total societal impact of nanotechnology is expected to be greater than the combined influences that the silicon integrated circuit, medical imaging, computer-aided engineering, and man-made polymers have had in the last century. Many nanomaterials were also found to possess exceptional mechanical properties. This led to tremendous interest into developing composite materials by exploiting the mechanical properties of these building blocks. In spite of a tremendous volume of work done in the field, preparation of such nanocomposites (NCs) has proven to be elusive due to inability of traditional "top-down" fabrication approaches to effectively harness properties of the nano-scale building blocks. This thesis focuses on preparation of organic/inorganic and solely organic NCs via a bottom-up nano-manufacturing approach called the layer-by-layer (LBL) assembly. Two natural and inexpensive nanoscale building blocks are explored: nanosheets of Na+-montmorillonite clay (MTM) and rod-shaped nanocrystals of cellulose (CNRs). In the first part of the thesis, we present results from systematic study of mechanics of MTM-based NCs. Different compositions are explored with a goal of understanding the nanoscale mechanics. Ultimately, development of a transparent composite with record-high strength and stiffness is presented. In the second part, we present results from LBL assembly of the CNRs. We demonstrate feasibility of assembly and mechanical properties of the resulting films. We also demonstrate preparation of LBL films with anti- reflective properties from tunicate (a sea animal) CNRs. In the
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N-Type self-assembled monolayer field-effect transistors for flexible organic electronics
Ringk, A.; Roelofs, Christian; Smits, E.C.P.; van der Marel, C.; Salzmann, I.; Neuhold, A.; Gelinck, G.H.; Resel, R.; de Leeuw, D.M.; Strohriegl, P.
Within this work we present n-type self-assembled monolayer field-effect transistors (SAMFETs) based on a novel perylene bisimide. The molecule spontaneously forms a covalently fixed monolayer on top of an aluminium oxide dielectric via a phosphonic acid anchor group. Detailed studies revealed an
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Haynes, S L; Shuttleworth, C A; Kielty, C M
1997-07-01
Fibrillin-containing microfibrils are key architectural structures of the upper dermis and integral components of the dermal elastic fibre network. Microfibril bundles intercalate into the dermal-epithelial junction and provide an elastic connection between the dermal elastic fibre network and the epidermis. Immunohistochemical studies have suggested that they are laid down both at the dermal-epithelial junction and in the deep dermis. While dermal fibroblasts are responsible for deposition of the elastin and microfibrillar components that comprise the elastic fibres of the deep dermis, the cellular origin of the microfibril bundles that extrude from the dermal-epithelial junction is not well defined. We have used fresh tissues, freshly isolated epidermis and primary human and porcine keratinocyte cultures to investigate the possibility that keratinocytes are responsible for deposition of these microfibrils. We have shown that keratinocytes in vivo and in vitro synthesize both fibrillin-1 and fibrillin-2, and assemble beaded microfibrils concurrently with expression of basement membrane collagen. These observations suggest that keratinocytes co-ordinate the secretion, deposition and assembly of these distinct structural elements of the dermal matrix, and have important implications for skin remodelling.
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Wu, Kunjie; Li, Hongwei; Li, Liqiang; Zhang, Suna; Chen, Xiaosong; Xu, Zeyang; Zhang, Xi; Hu, Wenping; Chi, Lifeng; Gao, Xike; Meng, Yancheng
2016-06-28
Ultrathin film with thickness below 15 nm of organic semiconductors provides excellent platform for some fundamental research and practical applications in the field of organic electronics. However, it is quite challenging to develop a general principle for the growth of uniform and continuous ultrathin film over large area. Dip-coating is a useful technique to prepare diverse structures of organic semiconductors, but the assembly of organic semiconductors in dip-coating is quite complicated, and there are no reports about the core rules for the growth of ultrathin film via dip-coating until now. In this work, we develop a general strategy for the growth of ultrathin film of organic semiconductor via dip-coating, which provides a relatively facile model to analyze the growth behavior. The balance between the three direct factors (nucleation rate, assembly rate, and recession rate) is the key to determine the growth of ultrathin film. Under the direction of this rule, ultrathin films of four organic semiconductors are obtained. The field-effect transistors constructed on the ultrathin film show good field-effect property. This work provides a general principle and systematic guideline to prepare ultrathin film of organic semiconductors via dip-coating, which would be highly meaningful for organic electronics as well as for the assembly of other materials via solution processes.
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Directory of Open Access Journals (Sweden)
Shu Chen
2015-03-01
Full Text Available Due to rapid advances in sequencing technology, increasing amounts of genomic and transcriptomic data are available for plant species, presenting enormous challenges for biocomputing analysis. A crucial first step for a successful transcriptomics-based study is the building of a high-quality assembly. Here, we utilized three different de novo assemblers (Trinity, Velvet, and CLC and the EvidentialGene pipeline tr2aacds to assemble two optimized transcript sets for the notorious weed species, . Two RNA sequencing (RNA-seq datasets from leaf and aboveground seedlings were processed using three assemblers, which resulted in 20 assemblies for each dataset. The contig numbers and N50 values of each assembly were compared to study the effect of read number, k-mer size, and in silico normalization on assembly output. The 20 assemblies were then processed through the tr2aacds pipeline to remove redundant transcripts and to select the transcript set with the best coding potential. Each assembly contributed a considerable proportion to the final transcript combination with the exception of the CLC-k14. Thus each assembler and parameter set did assemble better contigs for certain transcripts. The redundancy, total contig number, N50, fully assembled contig number, and transcripts related to target-site herbicide resistance were evaluated for the EvidentialGene and Trinity assemblies. Comparing the EvidentialGene set with the Trinity assembly revealed improved quality and reduced redundancy in both leaf and seedling EvidentialGene sets. The optimized transcriptome references will be useful for studying herbicide resistance in and the evolutionary process in the three allotetraploid offspring.
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Energy Technology Data Exchange (ETDEWEB)
Dutta, Tanushree [Department of Civil & Environmental Engineering, Hanyang University, 222 Wangsimni-Ro, Seoul 04763 (Korea, Republic of); Kim, Ki-Hyun, E-mail: kkim61@hanyang.ac.kr [Department of Civil & Environmental Engineering, Hanyang University, 222 Wangsimni-Ro, Seoul 04763 (Korea, Republic of); Uchimiya, Minori [USDA-ARS Southern Regional Research Center, 1100 Robert E. Lee Boulevard, New Orleans, LA 70124 (United States); Kumar, Pawan [Department of Chemical Engineering, Indian Institute of Technology, Hauz Khas, New Delhi 11016 (India); Das, Subhasish; Bhattacharya, Satya Sundar [Soil & Agro-Bioengineering Lab, Department of Environmental Science, Tezpur University, Napaam 784028 (India); Szulejko, Jan [Department of Civil & Environmental Engineering, Hanyang University, 222 Wangsimni-Ro, Seoul 04763 (Korea, Republic of)
2016-11-15
Large-scale assemblies of people in a confined space can exert significant impacts on the local air chemistry due to human emissions of volatile organics. Variations of air-quality in such small scale can be studied by quantifying fingerprint volatile organic compounds (VOCs) such as acetone, toluene, and isoprene produced during concerts, movie screenings, and sport events (like the Olympics and the World Cup). This review summarizes the extent of VOC accumulation resulting from a large population in a confined area or in a small open area during sporting and other recreational activities. Apart from VOCs emitted directly from human bodies (e.g., perspiration and exhaled breath), those released indirectly from other related sources (e.g., smoking, waste disposal, discharge of food-waste, and use of personal-care products) are also discussed. Although direct and indirect emissions of VOCs from human may constitute <1% of the global atmospheric VOCs budget, unique spatiotemporal variations in VOCs species within a confined space can have unforeseen impacts on the local atmosphere to lead to acute human exposure to harmful pollutants.
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International Nuclear Information System (INIS)
Dutta, Tanushree; Kim, Ki-Hyun; Uchimiya, Minori; Kumar, Pawan; Das, Subhasish; Bhattacharya, Satya Sundar; Szulejko, Jan
2016-01-01
Large-scale assemblies of people in a confined space can exert significant impacts on the local air chemistry due to human emissions of volatile organics. Variations of air-quality in such small scale can be studied by quantifying fingerprint volatile organic compounds (VOCs) such as acetone, toluene, and isoprene produced during concerts, movie screenings, and sport events (like the Olympics and the World Cup). This review summarizes the extent of VOC accumulation resulting from a large population in a confined area or in a small open area during sporting and other recreational activities. Apart from VOCs emitted directly from human bodies (e.g., perspiration and exhaled breath), those released indirectly from other related sources (e.g., smoking, waste disposal, discharge of food-waste, and use of personal-care products) are also discussed. Although direct and indirect emissions of VOCs from human may constitute <1% of the global atmospheric VOCs budget, unique spatiotemporal variations in VOCs species within a confined space can have unforeseen impacts on the local atmosphere to lead to acute human exposure to harmful pollutants.
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International Nuclear Information System (INIS)
Oliveira, I. S. S. de; Miwa, R. H.
2015-01-01
We use ab initio simulations to investigate the adsorption and the self-assembly processes of tetracyanoquinodimethane (TCNQ), tetrafluoro-tetracyanoquinodimethane (F4-TCNQ), and tetrasodium 1,3,6,8-pyrenetetrasulfonic acid (TPA) on the graphene surface. We find that there are no chemical bonds at the molecule–graphene interface, even at the presence of grain boundaries on the graphene surface. The molecules bond to graphene through van der Waals interactions. In addition to the molecule–graphene interaction, we performed a detailed study of the role played by the (lateral) molecule–molecule interaction in the formation of the, experimentally verified, self-assembled layers of TCNQ and TPA on graphene. Regarding the electronic properties, we calculate the electronic charge transfer from the graphene sheet to the TCNQ and F4-TCNQ molecules, leading to a p-doping of graphene. Meanwhile, such charge transfer is reduced by an order of magnitude for TPA molecules on graphene. In this case, it is not expected a significant doping process upon the formation of self-assembled layer of TPA molecules on the graphene sheet
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Self-assembly of silver nanoparticles and bacteriophage
Directory of Open Access Journals (Sweden)
Santi Scibilia
2016-03-01
Full Text Available Biohybrid nanostructured materials, composed of both inorganic nanoparticles and biomolecules, offer prospects for many new applications in extremely diverse fields such as chemistry, physics, engineering, medicine and nanobiotechnology. In the recent years, Phage display technique has been extensively used to generate phage clones displaying surface peptides with functionality towards organic materials. Screening and selection of phage displayed material binding peptides has attracted great interest because of their use for development of hybrid materials with multiple functionalities. Here, we present a self-assembly approach for the construction of hybrid nanostructured networks consisting of M13 P9b phage clone, specific for Pseudomonas aeruginosa, selected by Phage display technology, directly assembled with silver nanoparticles (AgNPs, previously prepared by pulsed laser ablation. These networks are characterized by UV–vis optical spectroscopy, scanning/transmission electron microscopies and Raman spectroscopy. We investigated the influence of different ions and medium pH on self-assembly by evaluating different phage suspension buffers. The assembly of these networks is controlled by electrostatic interactions between the phage pVIII major capsid proteins and the AgNPs. The formation of the AgNPs-phage networks was obtained only in two types of tested buffers at a pH value near the isoelectric point of each pVIII proteins displayed on the surface of the clone. This systematic study allowed to optimize the synthesis procedure to assembly AgNPs and bacteriophage. Such networks find application in the biomedical field of advanced biosensing and targeted gene and drug delivery. Keywords: Phage display, Silver nanoparticles, Self-assembly, Hybrid architecture, Raman spectroscopy
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Directory of Open Access Journals (Sweden)
Jinny L. Liu
2009-08-01
Full Text Available Bacteriophage T4 nanoparticles possess characteristics that make them ideal candidates as materials for sensors, particularly as sensor probes. Their surface can be modified, either through genetic engineering or direct chemical conjugation to display functional moieties such as antibodies or other proteins to recognize a specific target. However, in order for T4 nanoparticles to be utilized as a sensor probe, it is necessary to understand and control the variables that determine their assembly and organization on a surface. The aim of this work is to discuss some of variables that we have identified as influencing the behavior of T4 nanoparticles on surfaces. The effect of pH, ionic strength, substrate characteristics, nanoparticle concentration and charge was addressed qualitatively using atomic force microscopy (AFM.
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Self-Assembly, Pattern Formation and Growth Phenomena in Nano-Systems
Nepomnyashchy, Alexander A
2006-01-01
Nano-science and nano-technology are rapidly developing scientific and technological areas that deal with physical, chemical and biological processes that occur on nano-meter scale – one millionth of a millimeter. Self-organization and pattern formation play crucial role on nano-scales and promise new, effective routes to control various nano-scales processes. This book contains lecture notes written by the lecturers of the NATO Advanced Study Institute "Self-Assembly, Pattern Formation and Growth Phenomena in Nano-Systems" that took place in St Etienne de Tinee, France, in the fall 2004. They give examples of self-organization phenomena on micro- and nano-scale as well as examples of the interplay between phenomena on nano- and macro-scales leading to complex behavior in various physical, chemical and biological systems. They discuss such fascinating nano-scale self-organization phenomena as self-assembly of quantum dots in thin solid films, pattern formation in liquid crystals caused by light, self-organi...
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Supramolecule-to-supramolecule transformations of coordination-driven self-assembled polygons.
Zhao, Liang; Northrop, Brian H; Stang, Peter J
2008-09-10
Two types of supramolecular transformations, wherein a self-assembled Pt(II)-pyridyl metal-organic polygon is controllably converted into an alternative polygon, have been achieved through the reaction between cobalt carbonyl and the acetylene moiety of a dipyridyl donor ligand. A [6 + 6] hexagon is transformed into two [3 + 3] hexagons, and a triangle-square mixture is converted into [2 + 2] rhomboids. 1H and 31P NMR spectra are used to track the transformation process and evaluate the yield of new self-assembled polygons. Such transformed species are identified by electrospray ionization (ESI) mass spectrometry. This new kind of supramolecule-to-supramolecule transformations provides a viable means for constructing, and then converting, new self-assembled polygons.
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Engineering self-assembled bioreactors from protein microcompartments
Energy Technology Data Exchange (ETDEWEB)
Savage, David [Univ. of California, Berkeley, CA (United States)
2016-10-12
The goals of this research are to understand how organisms such as bacteria segregate certain metabolic processes inside of specific structures, or “microcompartments,” in the cell and apply this knowledge to develop novel engineered microcompartments for use in nanotechnology and metabolic engineering. For example, in some bacteria, self-assembling protein microcompartments called carboxysomes encapsulate the enzymes involved in carbon fixation, enabling the cell to utilize carbon dioxide more effectively than if the enzymes were free in the cell. The proposed research will determine how structures such as carboxysomes assemble and function in bacteria and develop a means for creating novel, synthetic microcompartments for optimizing production of specific energy-rich compounds.
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International Nuclear Information System (INIS)
Nakatsuka, Masafumi.
1979-01-01
Purpose: To prevent scattering of gaseous fission products released from fuel assemblies stored in an fbr type reactor. Constitution; A cap provided with means capable of storing gas is adapted to amount to the assembly handling head, for example, by way of threading in a storage rack of spent fuel assemblies consisting of a bottom plate, a top plate and an assembly support mechanism. By previously eliminating the gas inside of the assembly and the cap in the storage rack, gaseous fission products upon loading, if released from fuel rods during storage, are stored in the cap and do not scatter in the storage rack. (Horiuchi, T.)
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Directory of Open Access Journals (Sweden)
Tatjana Ladnorg
2013-10-01
Full Text Available Surface anchored metal-organic frameworks, SURMOFs, are highly porous materials, which can be grown on modified substrates as highly oriented, crystalline coatings by a quasi-epitaxial layer-by-layer method (liquid-phase epitaxy, or LPE. The chemical termination of the supporting substrate is crucial, because the most convenient method for substrate modification is the formation of a suitable self-assembled monolayer. The choice of a particular SAM also allows for control over the orientation of the SURMOF. Here, we demonstrate for the first time the site-selective growth of the SURMOF HKUST-1 on thiol-based self-assembled monolayers patterned by the nanografting technique, with an atomic force microscope as a structuring tool. Two different approaches were applied: The first one is based on 3-mercaptopropionic acid molecules which are grafted in a 1-decanethiolate SAM, which serves as a matrix for this nanolithography. The second approach uses 16-mercaptohexadecanoic acid, which is grafted in a matrix of an 1-octadecanethiolate SAM. In both cases a site-selective growth of the SURMOF is observed. In the latter case the roughness of the HKUST-1 is found to be significantly higher than for the 1-mercaptopropionic acid. The successful grafting process was verified by time-of-flight secondary ion mass spectrometry and atomic force microscopy. The SURMOF structures grown via LPE were investigated and characterized by atomic force microscopy and Fourier-transform infrared microscopy.
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Ladnorg, Tatjana; Welle, Alexander; Heißler, Stefan; Wöll, Christof
2013-01-01
Summary Surface anchored metal-organic frameworks, SURMOFs, are highly porous materials, which can be grown on modified substrates as highly oriented, crystalline coatings by a quasi-epitaxial layer-by-layer method (liquid-phase epitaxy, or LPE). The chemical termination of the supporting substrate is crucial, because the most convenient method for substrate modification is the formation of a suitable self-assembled monolayer. The choice of a particular SAM also allows for control over the orientation of the SURMOF. Here, we demonstrate for the first time the site-selective growth of the SURMOF HKUST-1 on thiol-based self-assembled monolayers patterned by the nanografting technique, with an atomic force microscope as a structuring tool. Two different approaches were applied: The first one is based on 3-mercaptopropionic acid molecules which are grafted in a 1-decanethiolate SAM, which serves as a matrix for this nanolithography. The second approach uses 16-mercaptohexadecanoic acid, which is grafted in a matrix of an 1-octadecanethiolate SAM. In both cases a site-selective growth of the SURMOF is observed. In the latter case the roughness of the HKUST-1 is found to be significantly higher than for the 1-mercaptopropionic acid. The successful grafting process was verified by time-of-flight secondary ion mass spectrometry and atomic force microscopy. The SURMOF structures grown via LPE were investigated and characterized by atomic force microscopy and Fourier-transform infrared microscopy. PMID:24205458
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Electrochemical cell and method of assembly
Shimotake, Hiroshi; Voss, Ernst C. H.; Bartholme, Louis G.
1979-01-01
A method of preparing an electrochemical cell is disclosed which permits the assembly to be accomplished in air. The cell includes a metal sulfide as the positive electrode reactant, lithium alloy as the negative electrode reactant and an alkali metal, molten salt electrolyte. Positive electrode reactant is introduced as Li.sub.2 FeS.sub.2, a single-phase compound produced by the reaction of Li.sub.2 S and FeS. The use of this compound permits introduction of lithium in an oxidized form. Additional lithium can be introduced in the negative electrode structure enclosed within an aluminum foil envelope between layers of porous aluminum. Molten salt electrolyte is added after assembly and evacuation of the cell by including an interelectrode separator that has been prewet with an organic solution of KCl.
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Hughes, Robert A.; Menumerov, Eredzhep; Neretina, Svetlana
2017-07-01
One of the foremost challenges in nanofabrication is the establishment of a processing science that integrates wafer-based materials, techniques, and devices with the extraordinary physicochemical properties accessible when materials are reduced to nanoscale dimensions. Such a merger would allow for exacting controls on nanostructure positioning, promote cooperative phenomenon between adjacent nanostructures and/or substrate materials, and allow for electrical contact to individual or groups of nanostructures. With neither self-assembly nor top-down lithographic processes being able to adequately meet this challenge, advancements have often relied on a hybrid strategy that utilizes lithographically-defined features to direct the assembly of nanostructures into organized patterns. While these so-called directed assembly techniques have proven viable, much of this effort has focused on the assembly of periodic arrays of spherical or near-spherical nanostructures comprised of a single element. Work directed toward the fabrication of more complex nanostructures, while still at a nascent stage, has nevertheless demonstrated the possibility of forming arrays of nanocubes, nanorods, nanoprisms, nanoshells, nanocages, nanoframes, core-shell structures, Janus structures, and various alloys on the substrate surface. In this topical review, we describe the progress made in the directed assembly of periodic arrays of these complex metal nanostructures on planar and textured substrates. The review is divided into three broad strategies reliant on: (i) the deterministic positioning of colloidal structures, (ii) the reorganization of deposited metal films at elevated temperatures, and (iii) liquid-phase chemistry practiced directly on the substrate surface. These strategies collectively utilize a broad range of techniques including capillary assembly, microcontact printing, chemical surface modulation, templated dewetting, nanoimprint lithography, and dip-pen nanolithography and
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Semiconductor monolayer assemblies with oriented crystal faces
Ma, Guijun; Takata, Tsuyoshi; Katayama, Masao; Zhang, Fuxiang; Moriya, Yosuke; Takanabe, Kazuhiro; Kubota, Jun; Domen, Kazunari
2012-01-01
Fabrication of two-dimensional monolayers of crystalline oxide and oxynitride particles was attempted on glass plate substrates. X-Ray diffraction patterns of the assemblies show only specific crystal facets, indicative of the uniform orientation of the particles on the substrate. The selectivity afforded by this immobilization technique enables the organization of randomly distributed polycrystalline powders in a controlled manner.
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Assembling a game development scene? Uncovering Finland’s largest demo party
Directory of Open Access Journals (Sweden)
Heikki Tyni
2014-03-01
Full Text Available The study takes look at Assembly, a large-scale LAN and demo party founded in 1992 and organized annually in Helsinki, Finland. Assembly is used as a case study to explore the relationship between computer hobbyism – including gaming, demoscene and other related activities – and professional game development. Drawing from expert interviews, a visitor query and news coverage we ask what kind of functions Assembly has played for the scene in general, and on the formation and fostering of the Finnish game industry in particular. The conceptual contribution of the paper is constructed around the interrelated concepts of scene, technicity and gaming capital.
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Lipid-bilayer-assisted two-dimensional self-assembly of DNA origami nanostructures
Endo, Masayuki; Sugiyama, Hiroshi
2015-01-01
Self-assembly is a ubiquitous approach to the design and fabrication of novel supermolecular architectures. Here we report a strategy termed ‘lipid-bilayer-assisted self-assembly' that is used to assemble DNA origami nanostructures into two-dimensional lattices. DNA origami structures are electrostatically adsorbed onto a mica-supported zwitterionic lipid bilayer in the presence of divalent cations. We demonstrate that the bilayer-adsorbed origami units are mobile on the surface and self-assembled into large micrometre-sized lattices in their lateral dimensions. Using high-speed atomic force microscopy imaging, a variety of dynamic processes involved in the formation of the lattice, such as fusion, reorganization and defect filling, are successfully visualized. The surface modifiability of the assembled lattice is also demonstrated by in situ decoration with streptavidin molecules. Our approach provides a new strategy for preparing versatile scaffolds for nanofabrication and paves the way for organizing functional nanodevices in a micrometer space. PMID:26310995
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Lipid-bilayer-assisted two-dimensional self-assembly of DNA origami nanostructures
Suzuki, Yuki; Endo, Masayuki; Sugiyama, Hiroshi
2015-08-01
Self-assembly is a ubiquitous approach to the design and fabrication of novel supermolecular architectures. Here we report a strategy termed `lipid-bilayer-assisted self-assembly' that is used to assemble DNA origami nanostructures into two-dimensional lattices. DNA origami structures are electrostatically adsorbed onto a mica-supported zwitterionic lipid bilayer in the presence of divalent cations. We demonstrate that the bilayer-adsorbed origami units are mobile on the surface and self-assembled into large micrometre-sized lattices in their lateral dimensions. Using high-speed atomic force microscopy imaging, a variety of dynamic processes involved in the formation of the lattice, such as fusion, reorganization and defect filling, are successfully visualized. The surface modifiability of the assembled lattice is also demonstrated by in situ decoration with streptavidin molecules. Our approach provides a new strategy for preparing versatile scaffolds for nanofabrication and paves the way for organizing functional nanodevices in a micrometer space.
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Expanded Organic Building Units for the Construction of Highly Porous Metal-Organic Frameworks
Kong, G.Q.; Han, Z.D.; He, Y.; Qu, S.; Zhou, W.; Yildirim, T.; Krishna, R.; Zou, C.; Chen, B.; Wu, C.D.
2013-01-01
wo new organic building units that contain dicarboxylate sites for their self-assembly with paddlewheel [Cu2(CO2)4] units have been successfully developed to construct two isoreticular porous metal-organic frameworks (MOFs), ZJU-35 and ZJU-36, which have the same tbo topologies (Reticular Chemistry
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Hof, Fraser; Palmer, Liam C.; Rebek, Julius, Jr.
2001-11-01
While important to the biological and materials sciences, noncovalent interactions, self-folding, and self-assembly often receive little discussion in the undergraduate chemistry curriculum. The synthesis and NMR characterization of a molecular "tennis ball" in an advanced undergraduate organic chemistry laboratory is a simple and effective way to introduce the relevance of these concepts. In appropriate solvents, the monomer dimerizes through a seam of eight hydrogen bonds with encapsulation of a guest molecule and symmetry reminiscent of a tennis ball. The entire experiment can be completed in three lab periods, however large-scale synthetic preparation of the starting monomer by a teaching assistant would reduce the laboratory to a single lab period for NMR studies.
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Regulation of corneal stroma extracellular matrix assembly.
Chen, Shoujun; Mienaltowski, Michael J; Birk, David E
2015-04-01
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. Copyright © 2014 Elsevier Ltd. All rights reserved.
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Sensor mount assemblies and sensor assemblies
Miller, David H [Redondo Beach, CA
2012-04-10
Sensor mount assemblies and sensor assemblies are provided. In an embodiment, by way of example only, a sensor mount assembly includes a busbar, a main body, a backing surface, and a first finger. The busbar has a first end and a second end. The main body is overmolded onto the busbar. The backing surface extends radially outwardly relative to the main body. The first finger extends axially from the backing surface, and the first finger has a first end, a second end, and a tooth. The first end of the first finger is disposed on the backing surface, and the tooth is formed on the second end of the first finger.
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From one to many: dynamic assembly and collective behavior of self-propelled colloidal motors.
Wang, Wei; Duan, Wentao; Ahmed, Suzanne; Sen, Ayusman; Mallouk, Thomas E
2015-07-21
The assembly of complex structures from simpler, individual units is a hallmark of biology. Examples include the pairing of DNA strands, the assembly of protein chains into quaternary structures, the formation of tissues and organs from cells, and the self-organization of bacterial colonies, flocks of birds, and human beings in cities. While the individual behaviors of biomolecules, bacteria, birds, and humans are governed by relatively simple rules, groups assembled from many individuals exhibit complex collective behaviors and functions that do not exist in the absence of the hierarchically organized structure. Self-assembly is a familiar concept to chemists who study the formation and properties of monolayers, crystals, and supramolecular structures. In chemical self-assembly, disorder evolves to order as the system approaches equilibrium. In contrast, living assemblies are typically characterized by two additional features: (1) the system constantly dissipates energy and is not at thermodynamic equilibrium; (2) the structure is dynamic and can transform or disassemble in response to stimuli or changing conditions. To distinguish them from equilibrium self-assembled structures, living (or nonliving) assemblies of objects with these characteristics are referred to as active matter. In this Account, we focus on the powered assembly and collective behavior of self-propelled colloids. These nano- and microparticles, also called nano- and micromotors or microswimmers, autonomously convert energy available in the environment (in the form of chemical, electromagnetic, acoustic, or thermal energy) into mechanical motion. Collections of these colloids are a form of synthetic active matter. Because of the analogy to living swimmers of similar size such as bacteria, the dynamic interactions and collective behavior of self-propelled colloids are interesting in the context of understanding biological active matter and in the development of new applications. The progression
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The Use of Hebbian Cell Assemblies for Nonlinear Computation
DEFF Research Database (Denmark)
Tetzlaff, Christian; Dasgupta, Sakyasingha; Kulvicius, Tomas
2015-01-01
When learning a complex task our nervous system self-organizes large groups of neurons into coherent dynamic activity patterns. During this, a network with multiple, simultaneously active, and computationally powerful cell assemblies is created. How such ordered structures are formed while preser...... computing complex non-linear transforms and - for execution - must cooperate with each other without interference. This mechanism, thus, permits the self-organization of computationally powerful sub-structures in dynamic networks for behavior control....
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Chemical solution route to self-assembled epitaxial oxide nanostructures.
Obradors, X; Puig, T; Gibert, M; Queraltó, A; Zabaleta, J; Mestres, N
2014-04-07
Self-assembly of oxides as a bottom-up approach to functional nanostructures goes beyond the conventional nanostructure formation based on lithographic techniques. Particularly, chemical solution deposition (CSD) is an ex situ growth approach very promising for high throughput nanofabrication at low cost. Whereas strain engineering as a strategy to define nanostructures with tight control of size, shape and orientation has been widely used in metals and semiconductors, it has been rarely explored in the emergent field of functional complex oxides. Here we will show that thermodynamic modeling can be very useful to understand the principles controlling the growth of oxide nanostructures by CSD, and some attractive kinetic features will also be presented. The methodology of strain engineering is applied in a high degree of detail to form different sorts of nanostructures (nanodots, nanowires) of the oxide CeO2 with fluorite structure which then is used as a model system to identify the principles controlling self-assembly and self-organization in CSD grown oxides. We also present, more briefly, the application of these ideas to other oxides such as manganites or BaZrO3. We will show that the nucleation and growth steps are essentially understood and manipulated while the kinetic phenomena underlying the evolution of the self-organized networks are still less widely explored, even if very appealing effects have been already observed. Overall, our investigation based on a CSD approach has opened a new strategy towards a general use of self-assembly and self-organization which can now be widely spread to many functional oxide materials.
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RESEARCH ON RISK CLASSIFICATION METHOD OF ASSEMBLY OCCUPANCIES
Directory of Open Access Journals (Sweden)
Hao Yu
2017-10-01
Full Text Available Due to the densely population and mobility characteristics of the crowd, generally accidents happened in assembly occupancies will trigger a chain reaction, and then bring heavy casualties and property loss, and result disastrous consequences. In the context of safety regulation resources limited, building risk classification system of assembly occupancies is important for "scientific predicting, and hierarchical controlling” In this paper, a software with a graphical user interface is designed using MATLAB GUI to analyze and calculate risks of stampede accident caused by gathered crowds in the video. A velocity extraction method based on cross-correlation algorithm is adopted, and the risk characteristic parameters such as velocity variance is also applied. In this way, real-time analysis and early-warning for risks of stampede accident in time and space can be achieved. Also, the algorithm is applied to the surveillance video of the stampede in Shanghai and its feasibility is proved. Empirical research shows that, the assembly occupancies risk rating model built in this paper has good effectiveness, simplicity and practicability, applies to the government safety regulation and organization safety management, and can improve the safety situation of assembly occupancies effectively.
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Could a Proto-Ribosome Emerge Spontaneously in the Prebiotic World?
Directory of Open Access Journals (Sweden)
Ilana C. Agmon
2016-12-01
Full Text Available An indispensable prerequisite for establishing a scenario of life emerging by natural processes is the requirement that the first simple proto-molecules could have had a realistic probability of self-assembly from random molecular polymers in the prebiotic world. The vestige of the proto-ribosome, which is believed to be still embedded in the contemporary ribosome, is used to assess the feasibility of such spontaneous emergence. Three concentric structural elements of different magnitudes, having a dimeric nature derived from the symmetrical region of the ribosomal large subunit, were suggested to constitute the vestige of the proto-ribosome. It is assumed to have materialized spontaneously in the prebiotic world, catalyzing non-coded peptide bond formation and simple elongation. Probabilistic and energetic considerations are applied in order to evaluate the suitability of the three contenders for being the initial proto-ribosome. The analysis points to the simplest proto-ribosome, comprised of a dimer of tRNA-like molecules presently embedded in the core of the symmetrical region, as the only one having a realistic statistical likelihood of spontaneous emergence from random RNA chains. Hence it offers a feasible starting point for a continuous evolutionary path from the prebiotic matter, through natural processes, into the intricate modern translation system.
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Supramolecular ribbons from amphiphilic trisamides self-assembly.
García, Fátima; Buendía, Julia; Sánchez, Luis
2011-08-05
Two amphiphilic C(3)-symmetric OPE-based trisamides have been synthesized and their self-assembling features investigated in solution and on surface. Variable-temperature UV-vis experiments demonstrate the cooperative supramolecular polymerization of these trisamides that self-assemble by the operation of triple C═O···H-N H-bonding arrays between the amide functional groups and π-π stacking between the aromatic units. The helical organization of the aggregates has been demonstrated by circular dichroism at a concentration as low as 1 × 10(-4) M in acetonitrile. In the reported trisamides, the large hydrophobic aromatic core acts as a solvophobic module impeding the interaction between the polar TEG chains and the amide H-bonds. This strategy makes unnecessary the separation of the amide functional groups to the polar tri(ethylene glycol) chains by paraffinic fragments. Achiral trisamide 1 self-assembles into flat ribbon-like structures that experience an amplification of chirality by the addition of a small amount of chiral 2 that generates twisted stripes.
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The assembly of MreB, a prokaryotic homolog of actin.
Esue, Osigwe; Cordero, Maria; Wirtz, Denis; Tseng, Yiider
2005-01-28
MreB, a major component of the bacterial cytoskeleton, exhibits high structural homology to its eukaryotic counterpart actin. Live cell microscopy studies suggest that MreB molecules organize into large filamentous spirals that support the cell membrane and play a key shape-determining function. However, the basic properties of MreB filament assembly remain unknown. Here, we studied the assembly of Thermotoga maritima MreB triggered by ATP in vitro and compared it to the well-studied assembly of actin. These studies show that MreB filament ultrastructure and polymerization depend crucially on temperature as well as the ions present on solution. At the optimal growth temperature of T. maritima, MreB assembly proceeded much faster than that of actin, without nucleation (or nucleation is highly favorable and fast) and with little or no contribution from filament end-to-end annealing. MreB exhibited rates of ATP hydrolysis and phosphate release similar to that of F-actin, however, with a critical concentration of approximately 3 nm, which is approximately 100-fold lower than that of actin. Furthermore, MreB assembled into filamentous bundles that have the ability to spontaneously form ring-like structures without auxiliary proteins. These findings suggest that despite high structural homology, MreB and actin display significantly different assembly properties.
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Tugba Camic, B; Jeong Shin, Hee; Hasan Aslan, M; Basarir, Fevzihan; Choi, Hyosung
2018-02-15
Solution-processed transparent conducting electrodes (TCEs) were fabricated via the self-assembly deposition of silver nanowires (Ag NWs). Glass substrates modified with (3-aminopropyl)triethoxysilane (APTES) and (3-mercaptopropyl)trimethoxysilane (MPTES) were coated with Ag NWs for various deposition times, leading to three different Ag NWs samples (APTES-Ag NWs (PVP), MPTES-Ag NWs (PVP), and APTES-Ag NWs (COOH)). Controlling the deposition time produced Ag NWs monolayer thin films with different optical transmittance and sheet resistance. Post-annealing treatment improved their electrical conductivity. The Ag NWs films were successfully characterized using UV-Vis spectroscopy, field emission scanning electron microscopy, optical microscopy and four-point probe. Three Ag NWs films exhibited low sheet resistance of 4-19Ω/sq and high optical transmittance of 65-81% (at 550nm), which are comparable to those of commercial ITO electrode. We fabricated an organic photovoltaic device by using Ag NWs as the anode instead of ITO electrode, and optimized device with Ag NWs exhibited power conversion efficiency of 1.72%. Copyright © 2017 Elsevier Inc. All rights reserved.
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Modeling and simulation of bus assem-bling process using DES/ABS approach
Directory of Open Access Journals (Sweden)
Pawel PAWLEWSKI
2017-03-01
Full Text Available This paper presents the results of the project, which goal is to analyze the production process capability after reengineering the assembly process due to expansion of a bus production plant. The verification of the designed work organization for the new configuration of workstations on new production hall is necessary. To solve these problems authors propose a method based on mixing DES (Discrete Event Simulation and ABS (Agent Based Simulation approach. DES is using to model the main process – material flow (buses, ABS is using to model assembling operations of teams of workers.One of obtained goal is to build a simulation model, which presents the new assembly line in the factory, taking into ac-count the arrangement of workstations and work teams in the new production hall as well as the transport between workstations. Second goal is to present work organization of work teams and division of individual workers’ labor (who belongs to a particular work team and performs operations on buses in a particular workstation in order to determine the best allocation of tasks and the optimum size of individual work teams. Proposed solution enables to determine the effect of assembly interferences on the work of particular work teams and the efficiency of the whole production system, to define the efficiency of the designed assembly lines and proposing changes aimed at the quality improvement of the created conception.
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Avci, Civan; Imaz, Inhar; Carné-Sánchez, Arnau; Pariente, Jose Angel; Tasios, Nikos; Pérez-Carvajal, Javier; Alonso, Maria Isabel; Blanco, Alvaro; Dijkstra, M.; López, Cefe; Maspoch, Daniel
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
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Lipid self-assembly and lectin-induced reorganization of the plasma membrane.
Sych, Taras; Mély, Yves; Römer, Winfried
2018-05-26
The plasma membrane represents an outstanding example of self-organization in biology. It plays a vital role in protecting the integrity of the cell interior and regulates meticulously the import and export of diverse substances. Its major building blocks are proteins and lipids, which self-assemble to a fluid lipid bilayer driven mainly by hydrophobic forces. Even if the plasma membrane appears-globally speaking-homogeneous at physiological temperatures, the existence of specialized nano- to micrometre-sized domains of raft-type character within cellular and synthetic membrane systems has been reported. It is hypothesized that these domains are the origin of a plethora of cellular processes, such as signalling or vesicular trafficking. This review intends to highlight the driving forces of lipid self-assembly into a bilayer membrane and the formation of small, transient domains within the plasma membrane. The mechanisms of self-assembly depend on several factors, such as the lipid composition of the membrane and the geometry of lipids. Moreover, the dynamics and organization of glycosphingolipids into nanometre-sized clusters will be discussed, also in the context of multivalent lectins, which cluster several glycosphingolipid receptor molecules and thus create an asymmetric stress between the two membrane leaflets, leading to tubular plasma membrane invaginations.This article is part of the theme issue 'Self-organization in cell biology'. © 2018 The Author(s).
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X-ray structural analysis of two-dimensional assembling lead sulfide nanocrystals of different sizes
Ushakova, Elena V.; Golubkov, Valery V.; Litvin, Aleksandr P.; Parfenov, Peter S.; Cherevkov, Sergei A.; Fedorov, Anatoly V.; Baranov, Alexander V.
2016-08-01
We report on the structural investigation of self-organized assemblies of PbS nanocrystals (NCs) of different sizes, which were deposited on a glass substrate or embedded in a porous matrix. Regardless of the NC size and the type of the substrate and matrix, the assemblies were ordered in two-dimensional superlattices with densely packed NCs.
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Organ printing: from bioprinter to organ biofabrication line.
Mironov, Vladimir; Kasyanov, Vladimir; Markwald, Roger R
2011-10-01
Organ printing, or the layer by layer additive robotic biofabrication of functional three-dimensional tissue and organ constructs using self-assembling tissue spheroid building blocks, is a rapidly emerging technology that promises to transform tissue engineering into a commercially successful biomedical industry. It is increasingly obvious that similar well-established industries implement automated robotic systems on the path to commercial translation and economic success. The use of robotic bioprinters alone however is not sufficient for the development of large industrial scale organ biofabrication. The design and development of a fully integrated organ biofabrication line is imperative for the commercial translation of organ printing technology. This paper presents recent progress and challenges in the development of the essential components of an organ biofabrication line. Copyright © 2011 Elsevier Ltd. All rights reserved.
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Organic nanomaterials: synthesis, characterization, and device applications
Torres, Tomas
2013-01-01
Recent developments in nanoscience and nanotechnology have given rise to a new generation of functional organic nanomaterials with controlled morphology and well-defined properties, which enable a broad range of useful applications. This book explores some of the most important of these organic nanomaterials, describing how they are synthesized and characterized. Moreover, the book explains how researchers have incorporated organic nanomaterials into devices for real-world applications.Featuring contributions from an international team of leading nanoscientists, Organic Nanomaterials is divided into five parts:Part One introduces the fundamentals of nanomaterials and self-assembled nanostructuresPart Two examines carbon nanostructures—from fullerenes to carbon nanotubes to graphene—reporting on properties, theoretical studies, and applicationsPart Three investigates key aspects of some inorganic materials, self-assembled monolayers,...
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Chopra, Arsh; Ramirez, Gustavo A.; Vaishampayan, Parag A.; Venkateswaran, Kasthuri J.
2011-01-01
Spore forming bacteria, a common inhabitant of spacecraft assembly facilities, are known to tolerate extreme environmental conditions such as radiation, desiccation, and high temperatures. Since the Viking era (early 1970's), spores have been utilized to assess the degree and level of microbiological contamination on spacecraft and their associated spacecraft assembly facilities. There is a growing concern that desiccation and extreme radiation resistant spore forming microorganisms associated with spacecraft surfaces can withstand space environmental conditions and subsequently proliferate on another solar body. Such forward contamination would certainly jeopardize future life detection or sample return technologies. It is important to recognize that different classes of organisms are critical while calculating the probability of contamination, and methods must be devised to estimate their abundances. Microorganisms can be categorized based on radiation sensitivity as Type A, B, C, and D. Type C represents spores resistant to radiation (10% or greater survival above 0.8 Mrad gamma radiation). To address these questions we have purified 96 spore formers, isolated during planetary protection efforts of Mars Science Laboratory assembly for gamma radiation resistance. The spores purified and stored will be used to generate data that can be used further to model and predict the probability of forward contamination.
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Dewetting-mediated pattern formation in nanoparticle assemblies
International Nuclear Information System (INIS)
Stannard, Andrew
2011-01-01
The deposition of nanoparticles from solution onto solid substrates is a diverse subfield of current nanoscience research. Complex physical and chemical processes underpin the self-assembly and self-organization of colloidal nanoparticles at two-phase (solid-liquid, liquid-air) interfaces and three-phase (solid-liquid-air) contact lines. This review discusses key recent advances made in the understanding of nonequilibrium dewetting processes of nanoparticle-containing solutions, detailing how such an apparently simple experimental system can give rise to such a strikingly varied palette of two-dimensional self-organized nanoparticle array morphologies. Patterns discussed include worm-like domains, cellular networks, microscale rings, and fractal-like fingering structures. There remain many unresolved issues regarding the role of the solvent dewetting dynamics in assembly processes of this type, with a significant focus on how dewetting can be coerced to produce nanoparticle arrays with desirable characteristics such as long-range order. In addition to these topics, methods developed to control nanofluid dewetting through routes such as confining the geometries of drying solutions, depositing onto pre-patterned heterogeneous substrates, and post-dewetting pattern evolution via local or global manipulation are covered. (topical review)
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Dewetting-mediated pattern formation in nanoparticle assemblies.
Stannard, Andrew
2011-03-02
The deposition of nanoparticles from solution onto solid substrates is a diverse subfield of current nanoscience research. Complex physical and chemical processes underpin the self-assembly and self-organization of colloidal nanoparticles at two-phase (solid-liquid, liquid-air) interfaces and three-phase (solid-liquid-air) contact lines. This review discusses key recent advances made in the understanding of nonequilibrium dewetting processes of nanoparticle-containing solutions, detailing how such an apparently simple experimental system can give rise to such a strikingly varied palette of two-dimensional self-organized nanoparticle array morphologies. Patterns discussed include worm-like domains, cellular networks, microscale rings, and fractal-like fingering structures. There remain many unresolved issues regarding the role of the solvent dewetting dynamics in assembly processes of this type, with a significant focus on how dewetting can be coerced to produce nanoparticle arrays with desirable characteristics such as long-range order. In addition to these topics, methods developed to control nanofluid dewetting through routes such as confining the geometries of drying solutions, depositing onto pre-patterned heterogeneous substrates, and post-dewetting pattern evolution via local or global manipulation are covered.
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PREFACE: Self-organized nanostructures
Rousset, Sylvie; Ortega, Enrique
2006-04-01
In order to fabricate ordered arrays of nanostructures, two different strategies might be considered. The `top-down' approach consists of pushing the limit of lithography techniques down to the nanometre scale. However, beyond 10 nm lithography techniques will inevitably face major intrinsic limitations. An alternative method for elaborating ultimate-size nanostructures is based on the reverse `bottom-up' approach, i.e. building up nanostructures (and eventually assemble them to form functional circuits) from individual atoms or molecules. Scanning probe microscopies, including scanning tunnelling microscopy (STM) invented in 1982, have made it possible to create (and visualize) individual structures atom by atom. However, such individual atomic manipulation is not suitable for industrial applications. Self-assembly or self-organization of nanostructures on solid surfaces is a bottom-up approach that allows one to fabricate and assemble nanostructure arrays in a one-step process. For applications, such as high density magnetic storage, self-assembly appears to be the simplest alternative to lithography for massive, parallel fabrication of nanostructure arrays with regular sizes and spacings. These are also necessary for investigating the physical properties of individual nanostructures by means of averaging techniques, i.e. all those using light or particle beams. The state-of-the-art and the current developments in the field of self-organization and physical properties of assembled nanostructures are reviewed in this issue of Journal of Physics: Condensed Matter. The papers have been selected from among the invited and oral presentations of the recent summer workshop held in Cargese (Corsica, France, 17-23 July 2005). All authors are world-renowned in the field. The workshop has been funded by the Marie Curie Actions: Marie Curie Conferences and Training Courses series named `NanosciencesTech' supported by the VI Framework Programme of the European Community, by
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Mobius Assembly: A versatile Golden-Gate framework towards universal DNA assembly.
Directory of Open Access Journals (Sweden)
Andreas I Andreou
Full Text Available Synthetic biology builds upon the foundation of engineering principles, prompting innovation and improvement in biotechnology via a design-build-test-learn cycle. A community-wide standard in DNA assembly would enable bio-molecular engineering at the levels of predictivity and universality in design and construction that are comparable to other engineering fields. Golden Gate Assembly technology, with its robust capability to unidirectionally assemble numerous DNA fragments in a one-tube reaction, has the potential to deliver a universal standard framework for DNA assembly. While current Golden Gate Assembly frameworks (e.g. MoClo and Golden Braid render either high cloning capacity or vector toolkit simplicity, the technology can be made more versatile-simple, streamlined, and cost/labor-efficient, without compromising capacity. Here we report the development of a new Golden Gate Assembly framework named Mobius Assembly, which combines vector toolkit simplicity with high cloning capacity. It is based on a two-level, hierarchical approach and utilizes a low-frequency cutter to reduce domestication requirements. Mobius Assembly embraces the standard overhang designs designated by MoClo, Golden Braid, and Phytobricks and is largely compatible with already available Golden Gate part libraries. In addition, dropout cassettes encoding chromogenic proteins were implemented for cost-free visible cloning screening that color-code different cloning levels. As proofs of concept, we have successfully assembled up to 16 transcriptional units of various pigmentation genes in both operon and multigene arrangements. Taken together, Mobius Assembly delivers enhanced versatility and efficiency in DNA assembly, facilitating improved standardization and automation.
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Self-assembled Nanomaterials for Chemotherapeutic Applications
Shieh, Aileen
The self-assembly of short designed peptides into functional nanostructures is becoming a growing interest in a wide range of fields from optoelectronic devices to nanobiotechnology. In the medical field, self-assembled peptides have especially attracted attention with several of its attractive features for applications in drug delivery, tissue regeneration, biological engineering as well as cosmetic industry and also the antibiotics field. We here describe the self-assembly of peptide conjugated with organic chromophore to successfully deliver sequence independent micro RNAs into human non-small cell lung cancer cell lines. The nanofiber used as the delivery vehicle is completely non-toxic and biodegradable, and exhibit enhanced permeability effect for targeting malignant tumors. The transfection efficiency with nanofiber as the delivery vehicle is comparable to that of the commercially available RNAiMAX lipofectamine while the toxicity is significantly lower. We also conjugated the peptide sequence with camptothecin (CPT) and observed the self-assembly of nanotubes for chemotherapeutic applications. The peptide scaffold is non-toxic and biodegradable, and drug loading of CPT is high, which minimizes the issue of systemic toxicity caused by extensive burden from the elimination of drug carriers. In addition, the peptide assembly drastically increases the solubility and stability of CPT under physiological conditions in vitro, while active CPT is gradually released from the peptide chain under the slight acidic tumor cell environment. Cytotoxicity results on human colorectal cancer cells and non-small cell lung cancer cell lines display promising anti-cancer properties compared to the parental CPT drug, which cannot be used clinically due to its poor solubility and lack of stability in physiological conditions. Moreover, the peptide sequence conjugated with 5-fluorouracil formed a hydrogel with promising topical chemotherapeutic applications that also display
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Superhydrophobic and transparent coatings prepared by self-assembly of dual-sized silica particles
Xu, Qian-Feng; Wang, Jian-Nong
2010-06-01
Superhydrophobic and transparent coatings have been prepared by self-assembly of dual-sized silica particles from a mixed dispersion. The desirable micro/nano hierarchical structure for superhydrophobicity is constructed simply by adjusting the size and ratio of the dual-sized particles without organic/inorganic templates. The transparency of the prepared coatings is also researched, and the light scattering can be reduced by lowering the ratio of big sub-micro particles while the superhydrophobicity maintains unchanged. When nano particles with a diameter of 50 nm and sub-micro particles with a diameter of 350 nm are assembled, a superhydrophobic property with a water contact angle of 161° is achieved. Additionally, the coated glass is also very transparent. The highest transmittance of the coated glass can reach 85%. Compared to traditional colloid self-assembly approach, which often involves dozens of steps of layer-by-layer processing and organic/inorganic templates, the present approach is much simpler and has advantages for large-scale coating.
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Bridging-ligand-substitution strategy for the preparation of metal-organic polyhedra
Li, Jian-Rong; Zhou, Hong-Cai
2010-10-01
Metal-organic polyhedra-discrete molecular architectures constructed through the coordination of metal ions and organic linkers-have recently attracted considerable attention due to their intriguing structures, their potential for a variety of applications and their relevance to biological self-assembly. Several synthetic routes have been investigated to prepare these complexes. However, to date, these preparative methods have typically been based on the direct assembly of metal ions and organic linkers. Although these routes are convenient, it remains difficult to find suitable reaction conditions or to control the outcome of the assembly process. Here, we demonstrate a synthetic strategy based on the substitution of bridging ligands in soluble metal-organic polyhedra. The introduction of linkers with different properties from those of the initial metal-organic polyhedra can thus lead to new metal-organic polyhedra with distinct properties (including size and shape). Furthermore, partial substitution can also occur and form mixed-ligand species that may be difficult to access by means of other approaches.
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High-performance vertical organic transistors.
Kleemann, Hans; Günther, Alrun A; Leo, Karl; Lüssem, Björn
2013-11-11
Vertical organic thin-film transistors (VOTFTs) are promising devices to overcome the transconductance and cut-off frequency restrictions of horizontal organic thin-film transistors. The basic physical mechanisms of VOTFT operation, however, are not well understood and VOTFTs often require complex patterning techniques using self-assembly processes which impedes a future large-area production. In this contribution, high-performance vertical organic transistors comprising pentacene for p-type operation and C60 for n-type operation are presented. The static current-voltage behavior as well as the fundamental scaling laws of such transistors are studied, disclosing a remarkable transistor operation with a behavior limited by injection of charge carriers. The transistors are manufactured by photolithography, in contrast to other VOTFT concepts using self-assembled source electrodes. Fluorinated photoresist and solvent compounds allow for photolithographical patterning directly and strongly onto the organic materials, simplifying the fabrication protocol and making VOTFTs a prospective candidate for future high-performance applications of organic transistors. Copyright © 2013 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.
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Bioengineering towards self-assembly of particulate vaccines.
Rehm, Bernd H A
2017-12-01
There is an unmet demand for safe and efficient vaccines for prevention of various infectious diseases. Subunit vaccines comprise selected pathogen specific antigens are a safe alternative to whole organism vaccines. However they often lack immunogenicity. Natural and synthetic self-assembling polymers and proteins will be reviewed in view their use to encapsulate and/or display antigens to serve as immunogenic antigen carriers for induction of protective immunity. Recent advances made in in vivo assembly of antigen-displaying polyester inclusions will be a focus. Particulate vaccines are inherently immunogenic due to enhanced uptake by antigen presenting cells which process antigens mediating adaptive immune responses. Bioengineering approaches enable the design of tailor-made particulate vaccines to fine tune immune responses towards protective immunity. Copyright © 2017 Elsevier Ltd. All rights reserved.
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International Nuclear Information System (INIS)
Bhanjadeo, Madhabi M.; Nayak, Ashok K.; Subudhi, Umakanta
2017-01-01
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. - 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.
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Self-Assembling Organic Nanopores as Synthetic Transmembrane Channels with Tunable Functions
Wei, Xiaoxi
A long-standing goal in the area of supramolecular self-assembly involves the development of synthetic ion/water channels capable of mimicking the mass-transport characteristics of biological channels and pores. Few examples of artificial transmembrane channels with large lumen, high conductivity and selectivity are known. A review of pronounced biological transmembrane protein channels and some representative synthetic models have been provided in Chapter 1, followed by our discovery and initial investigation of shape-persistent oligoamide and phenylene ethynylene macrocycles as synthetic ion/water channels. In Chapter 2, the systematic structural modification of oligoamide macrocycles 1, the so-called first-generation of these shape-persistent macrocycles, has led to third-generation macrocycles 3. The third generation was found to exhibit unprecedented, strong intermolecular association in both the solid state and solution via multiple techniques including X-ray diffraction (XRD), SEM, and 1H NMR. Fluorescence spectroscopy paired with dynamic light scattering (DLS) revealed that macrocycles 3 can assemble into a singly dispersed nanotubular structure in solution. The resultant self-assembling pores consisting of 3 were examined by HPTS-LUVs assays and BLM studies (Chapter 3) and found to form cation-selective (PK+/PCl- = 69:1) transmembrane ion channels with large conductance (200 ˜ 2000 pS for alkali cations) and high stability with open times reaching to 103 seconds. Tuning the aggregation state of macrocycles by choosing an appropriate polar solvent mixture (i.e., 3:1, THF:DMF, v/v) and concentration led to the formation of ion channels with well-defined square top behavior. A parallel study using DLS to examine the size of aggregates was used in conjunction with channel activity assays (LUVs/BLM) to reveal the effects of the aggregation state on channel activity. Empirical evidence now clearly indicates that a preassembled state, perhaps that of a
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Customization and design of directed self-assembly using hybrid prepatterns
Cheng, Joy; Doerk, Gregory S.; Rettner, Charles T.; Singh, Gurpreet; Tjio, Melia; Truong, Hoa; Arellano, Noel; Balakrishnan, Srinivasan; Brink, Markus; Tsai, Hsinyu; Liu, Chi-Chun; Guillorn, Michael; Sanders, Daniel P.
2015-03-01
Diminishing error tolerance renders the customization of patterns created through directed self-assembly (DSA) extremely challenging at tighter pitch. A self-aligned customization scheme can be achieved using a hybrid prepattern comprising both organic and inorganic regions that serves as a guiding prepattern to direct the self-assembly of the block copolymers as well as a cut mask pattern for the DSA arrays aligned to it. In this paper, chemoepitaxy-based self-aligned customization is demonstrated using two types of organic-inorganic prepatterns. CHEETAH prepattern for "CHemoepitaxy Etch Trim using a self-Aligned Hardmask" of preferential hydrogen silsesquioxane (HSQ, inorganic resist), non-preferential organic underlayer is fabricated using electron beam lithography. Customized trench or hole arrays can be achieved through co-transfer of DSA-formed arrays and CHEETAH prepattern. Herein, we also introduce a tone-reversed version called reverse-CHEETAH (or rCHEETAH) in which customized line segments can be achieved through co-transfer of DSA-formed arrays formed on a prepattern wherein the inorganic HSQ regions are nonpreferential and the organic regions are PMMA preferential. Examples of two-dimensional self-aligned customization including 25nm pitch fin structures and an 8-bar "IBM" illustrate the versatility of this customization scheme using rCHEETAH.
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Lin, Tao
Organic molecules are envisioned as the building blocks for design and fabrication of functional devices in future, owing to their versatility, low cost and flexibility. Although some devices such as organic light-emitting diode (OLED) have been already applied in our daily lives, the field is still in its infancy and numerous challenges still remain. In particular, fundamental understanding of the process of organic material fabrication at a molecular level is highly desirable. This thesis focuses on the design and fabrication of supramolecular and macromolecular nanostructures on a Au(111) surface through self-assembly, polymerization and a combination of two. We used scanning tunneling microscopy (STM) as an experimental tool and Monte Carlo (MC) and kinetic Monte Carlo (KMC) simulations as theoretical tools to characterize the structures of these systems and to investigate the mechanisms of the self-assembly and polymerization processes at a single-molecular level. The results of this thesis consist of four parts as below: Part I addresses the mechanisms of two-dimensional multicomponent supramolecular self-assembly via pyridyl-Fe-terpyridyl coordination. Firstly, we studied four types of self-assembled metal-organic systems exhibiting different dimensionalities using specifically-designed molecular building blocks. We found that the two-dimensional system is under thermodynamic controls while the systems of lower dimension are under kinetic controls. Secondly, we studied the self-assembly of a series of cyclic supramolecular polygons. Our results indicate that the yield of on-surface cyclic polygon structures is very low independent of temperature and concentration and this phenomenon can be attributed to a subtle competition between kinetic and thermodynamic controls. These results shed light on thermodynamic and kinetic controls in on-surface coordination self-assembly. Part II addresses the two-dimensional supramolecular self-assembly of porphyrin
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Self-assembly of self-assembled molecular triangles
Indian Academy of Sciences (India)
While the solution state structure of 1 can be best described as a trinuclear complex, in the solidstate well-fashioned intermolecular - and CH- interactions are observed. Thus, in the solid-state further self-assembly of already self-assembled molecular triangle is witnessed. The triangular panels are arranged in a linear ...
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Chen, Chong; Li, Bingxue; Zhou, Lijin; Xia, Zefeng; Feng, Nengjie; Ding, Jing; Wang, Lei; Wan, Hui; Guan, Guofeng
2017-07-12
The HKUST-1@SBA-15 composites with hierarchical pore structure were constructed by in situ self-assembly of metal-organic framework (MOF) with mesoporous silica. The structure directing role of SBA-15 had an obvious impact on the growth of MOF crystals, which in turn affected the morphologies and structural properties of the composites. The pristine HKUST-1 and the composites with different content of SBA-15 were characterized by XRD, N 2 adsorption-desorption, SEM, TEM, FT-IR, TG, XPS, and CO 2 -TPD techniques. It was found that the composites were assembled by oriented growth of MOF nanocrystals on the surfaces of SBA-15 matrix. The interactions between surface silanol groups and metal centers induced structural changes and resulted in the increases in surface areas as well as micropore volumes of hybrid materials. Besides, the additional constraints from SBA-15 also restrained the expansion of HKUST-1, contributing to their smaller crystal sizes in the composites. The adsorption isotherms of CO 2 on the materials were measured and applied to calculate the isosteric heats of adsorption. The HS-1 composite exhibited an increase of 15.9% in CO 2 uptake capacity compared with that of HKUST-1. Moreover, its higher isosteric heats of CO 2 adsorption indicated the stronger interactions between the surfaces and CO 2 molecules. The adsorption rate of the composite was also improved due to the introduction of mesopores. Ten cycles of CO 2 adsorption-desorption experiments implied that the HS-1 had excellent reversibility of CO 2 adsorption. This study was intended to provide the possibility of assembling new composites with tailored properties based on MOF and mesoporous silica to satisfy the requirements of various applications.
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Evaluation of nine popular de novo assemblers in microbial genome assembly.
Forouzan, Esmaeil; Maleki, Masoumeh Sadat Mousavi; Karkhane, Ali Asghar; Yakhchali, Bagher
2017-12-01
Next generation sequencing (NGS) technologies are revolutionizing biology, with Illumina being the most popular NGS platform. Short read assembly is a critical part of most genome studies using NGS. Hence, in this study, the performance of nine well-known assemblers was evaluated in the assembly of seven different microbial genomes. Effect of different read coverage and k-mer parameters on the quality of the assembly were also evaluated on both simulated and actual read datasets. Our results show that the performance of assemblers on real and simulated datasets could be significantly different, mainly because of coverage bias. According to outputs on actual read datasets, for all studied read coverages (of 7×, 25× and 100×), SPAdes and IDBA-UD clearly outperformed other assemblers based on NGA50 and accuracy metrics. Velvet is the most conservative assembler with the lowest NGA50 and error rate. Copyright © 2017. Published by Elsevier B.V.
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International Nuclear Information System (INIS)
Naber, W J M; Faez, S; Wiel, W G van der
2007-01-01
We review the emerging field of organic spintronics, where organic materials are applied as a medium to transport and control spin-polarized signals. The contacts for injecting and detecting spins are formed by ferromagnetic metals, oxides, or inorganic semiconductors. First, the basic concepts of spintronics and organic electronics are addressed, and phenomena which are in particular relevant for organic spintronics are highlighted. Experiments using different organic materials, including carbon nanotubes, organic thin films, self-assembled monolayers and single molecules are then reviewed. Observed magnetoresistance points toward successful spin injection and detection, but spurious magnetoresistance effects can easily be confused with spin accumulation. A few studies report long spin relaxation times and lengths, which forms a promising basis for further research. We conclude with discussing outstanding questions and problems. (topical review)
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[The Assembly and the national priorities ].
1997-12-01
Social participation and attention to the actions of government have increased dramatically in Ecuador. It is crucial that political debate be broadened concerning the functioning of the National Assembly, thereby opening greater public opportunities for participation. All social groups should be guaranteed access to the debate; expansion of the public sphere is essential for development of effective mechanisms of social inclusion. Those with no capacity to defend their own interests must have a voice. The National Assembly, in addition to reforming the Constitution, must reinforce the role of public men and statesmen at all levels of government. Statesmen place the common interest over special interests and create coalitions to effect necessary changes. The National Assembly must reorient the emphasis of government activities to give all sectors equal opportunity and access to basic public services. The role of the government must be redefined, which includes being equipped with better tools for management and control and with mechanisms for accountability at a time when many believe that globalization and market forces by themselves should dictate the rhythms of political, economic, and social life. Diversity should be respected. Nongovernmental organizations can be of great assistance in fostering dialogue, cooperation, solidarity, and consensus. Ecuadorians must support the goal of human and sustainable development.
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Yu, Ziyi; Zheng, Yu; Parker, Richard M; Lan, Yang; Wu, Yuchao; Coulston, Roger J; Zhang, Jing; Scherman, Oren A; Abell, Chris
2016-04-06
Bottom-up hierarchical assembly has emerged as an elaborate and energy-efficient strategy for the fabrication of smart materials. Herein, we present a hierarchical assembly process, whereby linear amphiphilic block copolymers are self-assembled into micelles, which in turn are accommodated at the interface of microfluidic droplets via cucurbit[8]uril-mediated host-guest chemistry to form supramolecular microcapsules. The monodisperse microcapsules can be used for simultaneous carriage of both organic (Nile Red) and aqueous-soluble (fluorescein isothiocyanate-dextran) cargo. Furthermore, the well-defined compartmentalized structure benefits from the dynamic nature of the supramolecular interaction and offers synergistic delivery of cargos with triggered release or through photocontrolled porosity. This demonstration of premeditated hierarchical assembly, where interactions from the molecular to microscale are designed, illustrates the power of this route toward accessing the next generation of functional materials and encapsulation strategies.
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A conceptual design of assembly strategy and dedicated tools for assembly of 40o sector
International Nuclear Information System (INIS)
Park, H.K.; Nam, K.O.; Kim, D.J.; Ahn, H.J.; Lee, J.H.; Im, K.; Shaw, R.
2010-01-01
The International Thermanuclear Experimental Reactor (ITER) tokamak device is composed of 9 vacuum vessel (VV)/toroidal field coils (TFCs)/vacuum vessel thermal shields (VVTS) 40 o sectors. Each VV/TFCs/VVTS 40 o sector is made up of one 40 o VV, two 20 o TFCs and associated VVTS segments. The 40 o sectors are sub-assembled at assembly hall respectively and then nine 40 o sectors sub-assembled at assembly hall are finally assembled at tokamak in-pit hall. The assembly strategy and tools for the 40 o sector sub-assembly and final assembly should be developed to satisfy the basic assembly requirements of the ITER tokamak device. Accordingly, the purpose-built assembly tools should be designed and manufactured considering assembly plan, available space, cost, safety, easy operation, efficient maintenance, and so on. The 40 o sector assembly tools are classified into 2 groups. One group is the sub-assembly tools including upending tool, lifting tool, sub-assembly tool, VV supports and bracing tools used at assembly hall and the other group is the in-pit assembly tools including lifting tool, central column, radial beams and their supports. This paper describes the current status of the assembly strategy and major tools for the VV/TFCs/VVTS 40 o sector assembly at in-pit hall and assembly hall. The conceptual design of the major assembly tools and assembly process at assembly hall and tokamak in-pit hall are presented also.
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Directed self-assembled crystalline oligomer domains on graphene and graphite
DEFF Research Database (Denmark)
Balzer, Frank; Henrichsen, Henrik Hartmann; Klarskov, Mikkel Buster
2014-01-01
We observe the formation of thin films of fibre-like aggregates from the prototypical organic semiconductor molecule para-hexaphenylene (p-6P) on graphite thin flakes and on monolayer graphene. Using atomic force microscopy, scanning electron microscopy, x-ray diffraction, polarized fluorescence...... show that the graphene surface can be used as a growth substrate to direct the self-assembly of organic molecular thin films and nanofibres, both with and without lithographical processing....
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Fuel injection assembly for use in turbine engines and method of assembling same
Berry, Jonathan Dwight; Johnson, Thomas Edward; York, William David; Uhm, Jong Ho
2015-12-15
A fuel injection assembly for use in a turbine engine is provided. The fuel injection assembly includes an end cover, an endcap assembly, a fluid supply chamber, and a plurality of tube assemblies positioned at the endcap assembly. Each of the tube assemblies includes housing having a fuel plenum and a cooling fluid plenum. The cooling fluid plenum is positioned downstream from the fuel plenum and separated from the fuel plenum by an intermediate wall. The plurality of tube assemblies also include a plurality of tubes that extends through the housing. Each of the plurality of tubes is coupled in flow communication with the fluid supply chamber and a combustion chamber positioned downstream from the tube assembly. The plurality of tube assemblies further includes an aft plate at a downstream end of the cooling fluid plenum. The plate includes at least one aperture.
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GABenchToB: a genome assembly benchmark tuned on bacteria and benchtop sequencers.
Directory of Open Access Journals (Sweden)
Sebastian Jünemann
Full Text Available De novo genome assembly is the process of reconstructing a complete genomic sequence from countless small sequencing reads. Due to the complexity of this task, numerous genome assemblers have been developed to cope with different requirements and the different kinds of data provided by sequencers within the fast evolving field of next-generation sequencing technologies. In particular, the recently introduced generation of benchtop sequencers, like Illumina's MiSeq and Ion Torrent's Personal Genome Machine (PGM, popularized the easy, fast, and cheap sequencing of bacterial organisms to a broad range of academic and clinical institutions. With a strong pragmatic focus, here, we give a novel insight into the line of assembly evaluation surveys as we benchmark popular de novo genome assemblers based on bacterial data generated by benchtop sequencers. Therefore, single-library assemblies were generated, assembled, and compared to each other by metrics describing assembly contiguity and accuracy, and also by practice-oriented criteria as for instance computing time. In addition, we extensively analyzed the effect of the depth of coverage on the genome assemblies within reasonable ranges and the k-mer optimization problem of de Bruijn Graph assemblers. Our results show that, although both MiSeq and PGM allow for good genome assemblies, they require different approaches. They not only pair with different assembler types, but also affect assemblies differently regarding the depth of coverage where oversampling can become problematic. Assemblies vary greatly with respect to contiguity and accuracy but also by the requirement on the computing power. Consequently, no assembler can be rated best for all preconditions. Instead, the given kind of data, the demands on assembly quality, and the available computing infrastructure determines which assembler suits best. The data sets, scripts and all additional information needed to replicate our results are freely
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Dabić, Dario; Brkljačić, Lidija; Tandarić, Tana; Žinić, Mladen; Vianello, Robert; Frkanec, Leo; Kobetić, Renata
2018-01-01
Gels formed by self-assembly of small organic molecules are of wide interest as dynamic soft materials with numerous possible applications, especially in terms of nanotechnology for functional and responsive biomaterials, biosensors, and nanowires. Four bis-oxalamides were chosen to show if electrospray ionization mass spectrometry (ESI-MS) could be used as a prediction of a good gelator and also to shed light on the gelation processes. By inspecting the gelation of several solvent, we showed that bis(amino acid)oxalamide 1 proved to be the most efficient, also being able of forming the largest observable assemblies in the gas phase. The formation of singly charged assemblies holding from one up to six monomer units is the outcome of the strong intermolecular H-bonds, particularly among terminal carboxyl groups. The variation of solvents from polar aprotic towards polar protic did not have any significant effects on the size of the assemblies. The addition of a salt such as NaOAc or Mg(OAc)2, depending on the concentration, altered the assembling. Computational analysis at the DFT level aided in the interpretation of the observed trends and revealed that individual gelator molecules spontaneously assemble to higher aggregates, but the presence of the Na+ cation disrupts any gelator organization since it becomes significantly more favorable for gelator molecules to bind Na+ cations up to the 3:1 ratio than to self-assemble, being fully in line with experimental observations reported here. [Figure not available: see fulltext.
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A multi attribute decision making method for selection of optimal assembly line
Directory of Open Access Journals (Sweden)
B. Vijaya Ramnath
2011-01-01
Full Text Available With globalization, sweeping technological development, and increasing competition, customers are placing greater demands on manufacturers to increase quality, flexibility, on time delivery of product and less cost. Therefore, manufacturers must develop and maintain a high degree of coherence among competitive priorities, order winning criteria and improvement activities. Thus, the production managers are making an attempt to transform their organization by adopting familiar and beneficial management philosophies like cellular manufacturing (CM, lean manufacturing (LM, green manufacturing (GM, total quality management (TQM, agile manufacturing (AM, and just in time manufacturing (JIT. The main objective of this paper is to propose an optimal assembly method for an engine manufacturer’s assembly line in India. Currently, the Indian manufacturer is following traditional assembly method where the raw materials for assembly are kept along the sideways of conveyor line. It consumes more floor space, more work in process inventory, more operator's walking time and more operator's walking distance per day. In order to reduce the above mentioned wastes, lean kitting assembly is suggested by some managers. Another group of managers suggest JIT assembly as it consumes very less inventory cost compared to other types of assembly processes. Hence, a Multi-attribute decision making model namely analytical hierarchy process (AHP is applied to analyse the alternative assembly methods based on various important factors.
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AutoAssemblyD: a graphical user interface system for several genome assemblers.
Veras, Adonney Allan de Oliveira; de Sá, Pablo Henrique Caracciolo Gomes; Azevedo, Vasco; Silva, Artur; Ramos, Rommel Thiago Jucá
2013-01-01
Next-generation sequencing technologies have increased the amount of biological data generated. Thus, bioinformatics has become important because new methods and algorithms are necessary to manipulate and process such data. However, certain challenges have emerged, such as genome assembly using short reads and high-throughput platforms. In this context, several algorithms have been developed, such as Velvet, Abyss, Euler-SR, Mira, Edna, Maq, SHRiMP, Newbler, ALLPATHS, Bowtie and BWA. However, most such assemblers do not have a graphical interface, which makes their use difficult for users without computing experience given the complexity of the assembler syntax. Thus, to make the operation of such assemblers accessible to users without a computing background, we developed AutoAssemblyD, which is a graphical tool for genome assembly submission and remote management by multiple assemblers through XML templates. AssemblyD is freely available at https://sourceforge.net/projects/autoassemblyd. It requires Sun jdk 6 or higher.
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Out-of-equilibrium self-assembly approaches for new soft materials
Hendriksen, W.E.
2015-01-01
Living creatures exists for an important part out of soft material, such as skin, organs and cells, that are out-of-equilibrium formed by the self-assembly of molecular building blocks. Natural materials are continuously active with dynamic processes occurring, such as growth, shrinkage and
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Dynamic Self-Assembly of Homogenous Microcyclic Structures Controlled by a Silver-Coated Nanopore.
Gao, Rui; Lin, Yao; Ying, Yi-Lun; Liu, Xiao-Yuan; Shi, Xin; Hu, Yong-Xu; Long, Yi-Tao; Tian, He
2017-07-01
The self-assembly of nanoparticles is a challenging process for organizing precise structures with complicated and ingenious structures. In the past decades, a simple, high-efficiency, and reproducible self-assembly method from nanoscale to microscale has been pursued because of the promising and extensive application prospects in bioanalysis, catalysis, photonics, and energy storage. However, microscale self-assembly still faces big challenges including improving the stability and homogeneity as well as pursuing new assembly methods and templates for the uniform self-assembly. To address these obstacles, here, a novel silver-coated nanopore is developed which serves as a template for electrochemically generating microcyclic structures of gold nanoparticles at micrometers with highly homogenous size and remarkable reproducibility. Nanopore-induced microcyclic structures are further applied to visualize the diffusion profile of ionic flux. Based on this novel strategy, a nanopore could potentially facilitate the delivery of assembled structures for many practical applications including drug delivery, cellular detection, catalysis, and plasmonic sensing. © 2017 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.
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Swell Gels to Dumbbell Micelles: Construction of Materials and Nanostructure with Self-assembly
Pochan, Darrin
2007-03-01
Bionanotechnology, the emerging field of using biomolecular and biotechnological tools for nanostructure or nanotecnology development, provides exceptional opportunity in the design of new materials. Self-assembly of molecules is an attractive materials construction strategy due to its simplicity in application. By considering peptidic or charged synthetic polymer molecules in the bottom-up materials self-assembly design process, one can take advantage of inherently biomolecular attributes; intramolecular folding events, secondary structure, and electrostatic interactions; in addition to more traditional self-assembling molecular attributes such as amphiphilicty, to define hierarchical material structure and consequent properties. Several molecular systems will be discussed. Synthetic block copolymers with charged corona blocks can be assembled in dilute solution containing multivalent organic counterions to produce micelle structures such as toroids. These ring-like micelles are similar to the toroidal bundling of charged semiflexible biopolymers like DNA in the presence of multivalent counterions. Micelle structure can be tuned between toroids, cylinders, and disks simply by using different concentrations or molecular volumes of organic counterion. In addition, these charged blocks can consist of amino acids as monomers producing block copolypeptides. In addition to the above attributes, block copolypeptides provide the control of block secondary structure to further control self-assembly. Design strategies based on small (less than 24 amino acids) beta-hairpin peptides will be discussed. Self-assembly of the peptides is predicated on an intramolecular folding event caused by desired solution properties. Importantly, the intramolecular folding event impart a molecular-level mechanism for environmental responsiveness at the material level (e.g. infinite change in viscosity of a solution to a gel with changes in pH, ionic strength, temperature).
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Assembly, alignment and test of the Transiting Exoplanet Survey Satellite (TESS) optical assemblies
Balonek, Gregory; Brown, Joshua J.; Andre, James E.; Chesbrough, Christian D.; Chrisp, Michael P.; Dalpiaz, Michael; Lennon, Joseph; Richards, B. C.; Clark, Kristin E.
2017-08-01
The Transiting Exoplanet Survey Satellite (TESS) will carry four visible waveband, seven-element, refractive F/1.4 lenses, each with a 34 degree diagonal field of view. This paper describes the methods used for the assembly, alignment and test of the four flight optical assemblies. Prior to commencing the build of the four flight optical assemblies, a Risk Reduction Unit (RRU) was successfully assembled and tested [1]. The lessons learned from the RRU were applied to the build of the flight assemblies. The main modifications to the flight assemblies include the inking of the third lens element stray light mitigation, tighter alignment tolerances, and diamond turning for critical mechanical surfaces. Each of the optical assemblies was tested interferometrically and measured with a low coherence distance measuring interferometer (DMI) to predict the optimal shim thickness between the lens assembly and detector before -75°C environmental testing. In addition to individual test data, environmental test results from prior assemblies allow for the exploration of marginal performance differences between each of the optical assemblies.
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International Nuclear Information System (INIS)
Ibraev, S.
2000-01-01
The author points out, that ecological heritage of Semipalatinsk test site is not studied, scattered investigations does not give objective assessment about radiation situation in the region. Only operations of close down of wells on the base of inter-state agreement between Republic of Kazakhstan and the United States of America were carried out. There are following main rehabilitation measures on liquidation of nuclear tests consequences in the region: study, deactivation and re-cultivation of populated territories; study of radioactive contamination level in underground waters and definition radionuclides migration by biological chain for taking preventative measures. It is noted, that citizens of the region with gratitude took solution of 52-53 Sessions of United Nations Organization General Assembly 'On liquidation of nuclear tests consequences on Semipalatinsk nuclear test site
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SWAP-Assembler: scalable and efficient genome assembly towards thousands of cores.
Meng, Jintao; Wang, Bingqiang; Wei, Yanjie; Feng, Shengzhong; Balaji, Pavan
2014-01-01
There is a widening gap between the throughput of massive parallel sequencing machines and the ability to analyze these sequencing data. Traditional assembly methods requiring long execution time and large amount of memory on a single workstation limit their use on these massive data. This paper presents a highly scalable assembler named as SWAP-Assembler for processing massive sequencing data using thousands of cores, where SWAP is an acronym for Small World Asynchronous Parallel model. In the paper, a mathematical description of multi-step bi-directed graph (MSG) is provided to resolve the computational interdependence on merging edges, and a highly scalable computational framework for SWAP is developed to automatically preform the parallel computation of all operations. Graph cleaning and contig extension are also included for generating contigs with high quality. Experimental results show that SWAP-Assembler scales up to 2048 cores on Yanhuang dataset using only 26 minutes, which is better than several other parallel assemblers, such as ABySS, Ray, and PASHA. Results also show that SWAP-Assembler can generate high quality contigs with good N50 size and low error rate, especially it generated the longest N50 contig sizes for Fish and Yanhuang datasets. In this paper, we presented a highly scalable and efficient genome assembly software, SWAP-Assembler. Compared with several other assemblers, it showed very good performance in terms of scalability and contig quality. This software is available at: https://sourceforge.net/projects/swapassembler.
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Loquet, Antoine; Tolchard, James; Berbon, Melanie; Martinez, Denis; Habenstein, Birgit
2017-09-17
Supramolecular protein assemblies play fundamental roles in biological processes ranging from host-pathogen interaction, viral infection to the propagation of neurodegenerative disorders. Such assemblies consist in multiple protein subunits organized in a non-covalent way to form large macromolecular objects that can execute a variety of cellular functions or cause detrimental consequences. Atomic insights into the assembly mechanisms and the functioning of those macromolecular assemblies remain often scarce since their inherent insolubility and non-crystallinity often drastically reduces the quality of the data obtained from most techniques used in structural biology, such as X-ray crystallography and solution Nuclear Magnetic Resonance (NMR). We here present magic-angle spinning solid-state NMR spectroscopy (SSNMR) as a powerful method to investigate structures of macromolecular assemblies at atomic resolution. SSNMR can reveal atomic details on the assembled complex without size and solubility limitations. The protocol presented here describes the essential steps from the production of 13 C/ 15 N isotope-labeled macromolecular protein assemblies to the acquisition of standard SSNMR spectra and their analysis and interpretation. As an example, we show the pipeline of a SSNMR structural analysis of a filamentous protein assembly.
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International Nuclear Information System (INIS)
Kanamori, Naokazu; Nakahira, Masataka; Ohkawa, Yoshinao; Tada, Eisuke; Seki, Masahiro
1996-06-01
The reactor core of the International Thermonuclear Experimental Reactor (ITER) is assembled with a number of large and asymmetric components within a tight tolerance in order to assure the structural integrity for various loads and to provide the tritium confinement. In addition, the assembly procedure should be compatible with remote operation since the core structures will be activated by 14-MeV neutrons once it starts operation and thus personal access will be prohibited. Accordingly, the assembly procedure and tool design are quite essential and should be designed from the beginning to facilitate remote operation. According to the ITER Design Task Agreement, the Japan Atomic Energy Research Institute (JAERI) has performed design study to develop the assembly procedures and associated tool design for the ITER tokamak assembly. This report describes outlines of the assembly tools and the remaining issues obtained in this design study. (author)
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Production of solar chemicals: gaining selectivity with hybrid molecule/semiconductor assemblies.
Hennessey, Seán; Farràs, Pau
2018-05-29
Research on the production of solar fuels and chemicals has rocketed over the past decade, with a wide variety of systems proposed to harvest solar energy and drive chemical reactions. In this Feature Article we have focused on hybrid molecule/semiconductor assemblies in both powder and supported materials, summarising recent systems and highlighting the enormous possibilities offered by such assemblies to carry out highly demanding chemical reactions with industrial impact. Of relevance is the higher selectivity obtained in visible light-driven organic transformations when using molecular catalysts compared to photocatalytic materials.
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Organic Donor-Acceptor Complexes as Novel Organic Semiconductors.
Zhang, Jing; Xu, Wei; Sheng, Peng; Zhao, Guangyao; Zhu, Daoben
2017-07-18
Organic donor-acceptor (DA) complexes have attracted wide attention in recent decades, resulting in the rapid development of organic binary system electronics. The design and synthesis of organic DA complexes with a variety of component structures have mainly focused on metallicity (or even superconductivity), emission, or ferroelectricity studies. Further efforts have been made in high-performance electronic investigations. The chemical versatility of organic semiconductors provides DA complexes with a great number of possibilities for semiconducting applications. Organic DA complexes extend the semiconductor family and promote charge separation and transport in organic field-effect transistors (OFETs) and organic photovoltaics (OPVs). In OFETs, the organic complex serves as an active layer across extraordinary charge pathways, ensuring the efficient transport of induced charges. Although an increasing number of organic semiconductors have been reported to exhibit good p- or n-type properties (mobilities higher than 1 or even 10 cm 2 V -1 s -1 ), critical scientific challenges remain in utilizing the advantages of existing semiconductor materials for more and wider applications while maintaining less complicated synthetic or device fabrication processes. DA complex materials have revealed new insight: their unique molecular packing and structure-property relationships. The combination of donors and acceptors could offer practical advantages compared with their unimolecular materials. First, growing crystals of DA complexes with densely packed structures will reduce impurities and traps from the self-assembly process. Second, complexes based on the original structural components could form superior mixture stacking, which can facilitate charge transport depending on the driving force in the coassembly process. Third, the effective use of organic semiconductors can lead to tunable band structures, allowing the operation mode (p- or n-type) of the transistor to be
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Assembly of DNA Architectures in a Non-Aqueous Solution
Directory of Open Access Journals (Sweden)
Thomas J. Proctor
2012-08-01
Full Text Available In the present work, the procedures for the creation of self-assembled DNA nanostructures in aqueous and non-aqueous media are described. DNA-Surfactant complex formation renders the DNA soluble in organic solvents offering an exciting way to bridge the transition of DNA origami materials electronics applications. The DNA retains its structural features, and these unique geometries provide an interesting candidate for future electronics and nanofabrication applications with potential for new properties. The DNA architectures were first assembled under aqueous conditions, and then characterized in solution (using circular dichroism (CD spectroscopy and on the surface (using atomic force microscopy (AFM. Following aqueous assembly, the DNA nanostructures were transitioned to a non-aqueous environment, where butanol was chosen for optical compatibility and thermal properties. The retention of DNA hierarchical structure and thermal stability in non-aqueous conditions were confirmed via CD spectroscopy. The formation and characterization of these higher order DNA-surfactant complexes is described in this paper.
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Controlled assembly of jammed colloidal shells on fluid droplets
Subramaniam, Anand Bala; Abkarian, Manouk; Stone, Howard A.
2005-07-01
Assembly of colloidal particles on fluid interfaces is a promising technique for synthesizing two-dimensional microcrystalline materials useful in fields as diverse as biomedicine, materials science, mineral flotation and food processing. Current approaches rely on bulk emulsification methods, require further chemical and thermal treatments, and are restrictive with respect to the materials used. The development of methods that exploit the great potential of interfacial assembly for producing tailored materials have been hampered by the lack of understanding of the assembly process. Here we report a microfluidic method that allows direct visualization and understanding of the dynamics of colloidal crystal growth on curved interfaces. The crystals are periodically ejected to form stable jammed shells, which we refer to as colloidal armour. We propose that the energetic barriers to interfacial crystal growth and organization can be overcome by targeted delivery of colloidal particles through hydrodynamic flows. Our method allows an unprecedented degree of control over armour composition, size and stability.
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Nuclear fuel assembly with improved spectral shift-producing rods
International Nuclear Information System (INIS)
Ferrari, H.M.
1987-01-01
This patent describes a nuclear reactor having fuel assemblies and a moderator-coolant liquid flowing through the fuel assemblies, each fuel assembly including an organized array of nuclear fuel rods wherein the moderator-coolant liquid flows along the fuel rods, at least one improved spectral shift-producing rod disposed among the fuel rods. The spectra shift-producing rod consists of: (a) an elongated hollow hermetically-sealed tubular member; (b) a weakened region formed in a portion of the member, the portion being subject to rupture at a given level of internal pressure; and (c) burnable poison material contained in the member which generates gas in the member as operation of the reactor proceeds normally, the material being soluble in the moderator-coolant liquid when brought into contact therewith; (d) the given level of internal pressure being less than the maximum level of internal pressure normally expected to be generated within the member by the poison material by normal operation of the reactor
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Block copolymer templated self-assembly of disk-shaped molecules
Aragones, J. L.; Alexander-Katz, A.
2017-08-01
Stacking of disk-shaped organic molecules is a promising strategy to develop electronic and photovoltaic devices. Here, we investigate the capability of a soft block copolymer matrix that microphase separates into a cylindrical phase to direct the self-assembly of disk-shaped molecules by means of molecular simulations. We show that two disk molecules confined in the cylinder domain experience a depletion force, induced by the polymer chains, which results in the formation of stacks of disks. This entropic interaction and the soft confinement provided by the matrix are both responsible for the structures that can be self-assembled, which include slanted or columnar stacks. In addition, we evidence the transmission of stresses between the different minority domains of the microphase, which results in the establishment of a long-ranged interaction between disk molecules embedded in different domains; this interaction is of the order of the microphase periodicity and may be exploited to direct assembly of disks at larger scales.
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Drive piston assembly for a valve actuator assembly
Sun, Zongxuan
2010-02-23
A drive piston assembly is provided that is operable to selectively open a poppet valve. The drive piston assembly includes a cartridge defining a generally stepped bore. A drive piston is movable within the generally stepped bore and a boost sleeve is coaxially disposed with respect to the drive piston. A main fluid chamber is at least partially defined by the generally stepped bore, drive piston, and boost sleeve. First and second feedback chambers are at least partially defined by the drive piston and each are disposed at opposite ends of the drive piston. At least one of the drive piston and the boost sleeve is sufficiently configured to move within the generally stepped bore in response to fluid pressure within the main fluid chamber to selectively open the poppet valve. A valve actuator assembly and engine are also provided incorporating the disclosed drive piston assembly.
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Hybrid Wing Body Multi-Bay Test Article Analysis and Assembly Final Report
Velicki, Alexander; Hoffman, Krishna; Linton, Kim A.; Baraja, Jaime; Wu, Hsi-Yung T.; Thrash, Patrick
2017-01-01
This report summarizes work performed by The Boeing Company, through its Boeing Research & Technology organization located in Huntington Beach, California, under the Environmentally Responsible Aviation (ERA) project. The report documents work performed to structurally analyze and assemble a large-scale Multi-bay Box (MBB) Test Article capable of withstanding bending and internal pressure loadings representative of a Hybrid Wing Body (HWB) aircraft. The work included fabrication of tooling elements for use in the fabrication and assembly of the test article.
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International Nuclear Information System (INIS)
Lamb, Kristen; Lokesh, G.L.; Sherman, Michael; Watowich, Stanley
2010-01-01
Venezuelan equine encephalitis virus (VEEV) is a prototypical enveloped ssRNA virus of the family Togaviridae. To better understand alphavirus assembly, we analyzed newly formed nucleocapsid particles (termed pre-viral nucleocapsids) isolated from infected cells. These particles were intermediates along the virus assembly pathway, and ultimately bind membrane-associated viral glycoproteins to bud as mature infectious virus. Purified pre-viral nucleocapsids were spherical with a unimodal diameter distribution. The structure of one class of pre-viral nucleocapsids was determined with single particle reconstruction of cryo-electron microscopy images. These studies showed that pre-viral nucleocapsids assembled into an icosahedral structure with a capsid stoichiometry similar to the mature nucleocapsid. However, the individual capsomers were organized significantly differently within the pre-viral and mature nucleocapsids. The pre-viral nucleocapsid structure implies that nucleocapsids are highly plastic and undergo glycoprotein and/or lipid-driven rearrangements during virus self-assembly. This mechanism of self-assembly may be general for other enveloped viruses.
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Logical NAND and NOR Operations Using Algorithmic Self-assembly of DNA Molecules
Wang, Yanfeng; Cui, Guangzhao; Zhang, Xuncai; Zheng, Yan
DNA self-assembly is the most advanced and versatile system that has been experimentally demonstrated for programmable construction of patterned systems on the molecular scale. It has been demonstrated that the simple binary arithmetic and logical operations can be computed by the process of self assembly of DNA tiles. Here we report a one-dimensional algorithmic self-assembly of DNA triple-crossover molecules that can be used to execute five steps of a logical NAND and NOR operations on a string of binary bits. To achieve this, abstract tiles were translated into DNA tiles based on triple-crossover motifs. Serving as input for the computation, long single stranded DNA molecules were used to nucleate growth of tiles into algorithmic crystals. Our method shows that engineered DNA self-assembly can be treated as a bottom-up design techniques, and can be capable of designing DNA computer organization and architecture.
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Analysis of assembly serial number usage in domestic light-water reactors
International Nuclear Information System (INIS)
Reich, W.J.; Moore, R.S.
1991-05-01
Domestic light-water reactor (LWR) fuel assemblies are identified by a serial number that is placed on each assembly. These serial numbers are used as identifiers throughout the life of the fuel. The uniqueness of assembly serial numbers is important in determining their effectiveness as unambiguous identifiers. The purpose of this study is to determine what serial numbering schemes are used, the effectiveness of these schemes, and to quantify how many duplicate serial numbers occur on domestic LWR fuel assemblies. The serial numbering scheme adopted by the American National Standards Institute (ANSI) ensures uniqueness of assembly serial numbers. The latest numbering scheme adopted by General Electric (GE), was also found to be unique. Analysis of 70,971 fuel assembly serial numbers from permanently discharged fuel identified 11,948 serial number duplicates. Three duplicate serial numbers were found when analysis focused on duplication within the individual fuel inventory at each reactor site, but these were traced back to data entry errors and will be corrected by the Energy Information Administration (EIA). There were also three instances where the serial numbers used to identify assemblies used for hot cell studies differed from the serial numbers reported to the EIA. It is recommended that fuel fabricators and utilities adhere to the ANSI serial numbering scheme to ensure serial number uniqueness. In addition, organizations collecting serial number information, should request that all known serial numbers physically attached or associated with each assembly be reported and identified by the corresponding number scheme. 10 refs., 5 tabs
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Commercial Application of In-Space Assembly
Lymer, John; Hanson, Mark; Tadros, Al; Boccio, Joel; Hollenstein, Bruno; Emerick, Ken; Doughtery, Sean; Doggett, Bill; Dorsey, John T.; King, Bruce D.;
2016-01-01
In-Space assembly (ISA) expands the opportunities for cost effective emplacement of systems in space. Currently, spacecraft are launched into space and deploy into their operational configuration through a carefully choreographed sequence of operations. The deployment operation dictates the arrangement of the primary systems on the spacecraft, limiting the ability to take full advantage of launch vehicles volume and mass capability. ISA enables vastly different spacecraft architectures and emplacement scenarios to be achieved, including optimal launch configurations ranging from single launch and assembly to on-orbit aggregation of multiple launches at different orbital locations and times. The spacecraft can be visited at different orbital locations and times to effect expansion and maintenance of an operational capability. To date, the primary application of ISA has been in large programs funded by government organizations, such as the International Space Station. Recently, Space Systems Loral (SSL) led a study funded by the Defense Advanced Research Projects Agency (DARPA), called Dragonfly, to investigate the commercial applicability and economic advantages of ISA. In the study, it was shown that ISA enables SSL to double the capability of a commercial satellite system by taking advantage of alternate packaging approaches for the reflectors. The study included an ultra-light-weight robotic system, derived from Mars manipulator designs, to complete assembly of portions of the antenna system using a tool derived from DARPA orbital express and National Aeronautics and Space Administration (NASA) automated structural assembly experience. The mechanical connector that enables robotic ISA takes advantage of decades of development by NASA from the 1970's to 1980's during the Space Station Freedom program, the precursor to the ISS. The mechanical connector was originally designed for rapid astronaut assembly while also providing a high quality structural connection
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Gutsmann, Thomas; Fantner, Georg E.; Kindt, Johannes H.; Venturoni, Manuela; Danielsen, Signe; Hansma, Paul K.
2004-01-01
Tendons are composed of collagen and other molecules in a highly organized hierarchical assembly, leading to extraordinary mechanical properties. To probe the cross-links on the lower level of organization, we used a cantilever to pull substructures out of the assembly. Advanced force probe technology, using small cantilevers (length
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Self-Assembly of Hierarchical DNA Nanotube Architectures with Well-Defined Geometries.
Jorgenson, Tyler D; Mohammed, Abdul M; Agrawal, Deepak K; Schulman, Rebecca
2017-02-28
An essential motif for the assembly of biological materials such as actin at the scale of hundreds of nanometers and beyond is a network of one-dimensional fibers with well-defined geometry. Here, we demonstrate the programmed organization of DNA filaments into micron-scale architectures where component filaments are oriented at preprogrammed angles. We assemble L-, T-, and Y-shaped DNA origami junctions that nucleate two or three micron length DNA nanotubes at high yields. The angles between the nanotubes mirror the angles between the templates on the junctions, demonstrating that nanoscale structures can control precisely how micron-scale architectures form. The ability to precisely program filament orientation could allow the assembly of complex filament architectures in two and three dimensions, including circuit structures, bundles, and extended materials.
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Zhang, Jin Z; Liu, Jun; Chen, Shaowei; Liu, Gang-yu
2003-01-01
Nanostructures refer to materials that have relevant dimensions on the nanometer length scales and reside in the mesoscopic regime between isolated atoms and molecules in bulk matter. These materials have unique physical properties that are distinctly different from bulk materials. Self-Assembled Nanostructures provides systematic coverage of basic nanomaterials science including materials assembly and synthesis, characterization, and application. Suitable for both beginners and experts, it balances the chemistry aspects of nanomaterials with physical principles. It also highlights nanomaterial-based architectures including assembled or self-assembled systems. Filled with in-depth discussion of important applications of nano-architectures as well as potential applications ranging from physical to chemical and biological systems, Self-Assembled Nanostructures is the essential reference or text for scientists involved with nanostructures.
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Managing lifelike behavior in a dynamic self-assembled system
Ropp, Chad; Bachelard, Nicolas; Wang, Yuan; Zhang, Xiang
Self-organization can arise outside of thermodynamic equilibrium in a process of dynamic self-assembly. This is observed in nature, for example in flocking birds, but can also be created artificially with non-living entities. Such dynamic systems often display lifelike properties, including the ability to self-heal and adapt to environmental changes, which arise due to the collective and often complex interactions between the many individual elements. Such interactions are inherently difficult to predict and control, and limit the development of artificial systems. Here, we report a fundamentally new method to manage dynamic self-assembly through the direct external control of collective phenomena. Our system consists of a waveguide filled with mobile scattering particles. These particles spontaneously self-organize when driven by a coherent field, self-heal when mechanically perturbed, and adapt to changes in the drive wavelength. This behavior is governed by particle interactions that are completely mediated by coherent wave scattering. Compared to hydrodynamic interactions which lead to compact ordered structures, our system displays sinusoidal degeneracy and many different steady-state geometries that can be adjusted using the external field.
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So, Monica; Beyzavi, M. Hassan; Sawhney, Rohan; Shekhah, Osama; Eddaoudi, Mohamed; Al-Juaid, Salih Salem; Hupp, Joseph T.; Farha, Omar K.
2015-01-01
Herein, we demonstrate the robustness of layer-by-layer (LbL)-assembled, pillared-paddlewheel-type MOF films toward conversion to new or modified MOFs via solvent-assisted linker exchange (SALE) and post-assembly linker metalation. Further, we show that LbL synthesis can afford MOFs that have proven inaccessible through other de novo strategies.
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Energy Technology Data Exchange (ETDEWEB)
Singh, Manish Kumar; Kumar, Ashish; Prakash, Rajiv, E-mail: rprakash.mst@iitbhu.ac.in
2017-03-15
Graphical abstract: rr-PQT-12 films formed by spin coating before and after ageing (at 25 °C) showing the effect of fiber growth and significant change in charge transfer property. - Highlights: • Self-assembly of rr-PQT-12 into fiber form in chloroform marginal solvent at RT. • As assembled dispersion is processed for the fabrication of organic devices. • Processed fiber shows improvement in charge transport over its pristine one. - Abstract: This article deals with the study of self-assembly of regioregular poly (3,3‴-didodecylquarterthiophene), rr-PQT-12 into fiber form in chloroform by ageing process. Time dependent fiber growth mechanism is monitored by UV–vis absorption and confirmed by atomic force microscopy technique. It is observed that isolated rr-PQT-12 undergoes self-assembled fibril growth along π-π interaction direction and 45 min is sufficient for such assemblies in case of 0.125% w/v of rr-PQT-12 polymer in chloroform. Further the self-assembled fibril polymer is used in fabrication of Schottky diode. It exhibits ten times enhancement in forward current density (with one-fold higher mobility) and high rectification ratio compared to the isolated rr-PQT-12 due to the segmental electronic traps filling within stacking region. Our study provides a facile method of ordering of PQT-12 isolated chains in chloroform solvent and an effective way for improvement of performance of organic polymers based devices through such self-assembly.
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Facile "modular assembly" for fast construction of a highly oriented crystalline MOF nanofilm.
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.
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Inspection of pressurised nuclear equipment by certified organizations
International Nuclear Information System (INIS)
Marez, Y.
2010-01-01
The A.Q.U.A.P. is a technical association created on the 17 october 1978 grouping control organisms that define methodologies in order to apply the same procedures among their customers. It writes cards to interpret the regulation for organisms, operators and manufacturers. The areas covered by the A.Q.U.A.P. works concern the conformity evaluation of new pressure vessels, qualification of qualification of welding procedures and permanent assemblies and the qualification of the personnel realizing these assemblies, the follow up of the equipment in service. (N.C.)
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Improvement of the Threespine Stickleback Genome Using a Hi-C-Based Proximity-Guided Assembly.
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.
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Newnes electronics assembly handbook
Brindley, Keith
2013-01-01
Newnes Electronics Assembly Handbook: Techniques, Standards and Quality Assurance focuses on the aspects of electronic assembling. The handbook first looks at the printed circuit board (PCB). Base materials, basic mechanical properties, cleaning of assemblies, design, and PCB manufacturing processes are then explained. The text also discusses surface mounted assemblies and packaging of electromechanical assemblies, as well as the soldering process. Requirements for the soldering process; solderability and protective coatings; cleaning of PCBs; and mass solder/component reflow soldering are des
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Peptide Assembly-Driven Metal-Organic Framework (MOF) Motors for Micro Electric Generator
Ikezoe, Yasuhiro; Fang, Justin; Wasik, Tomasz L.; Uemura, Takashi; Zheng, Yongtai; Kitagawa, Susumu
2014-01-01
Peptide-MOF motors, whose motions are driven by anisotropic surface gradients created via peptide self-assembly around nanopores of MOFs, can rotate microscopic rotors and magnet fast enough to generate electric power of 0.1 µW. To make the peptide-MOF generator recyclable, a new MOF is applied as a host motor engine, which has a more rigid framework with higher H2O affinity so that peptide release occurs more efficiently via guest exchange without the destruction of MOF. PMID:25418936
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Photoswitching in azobenzene self-assembled monolayers capped on zinc oxide: nanodots vs nanorods.
Shah, Syed Mujtaba; Martini, Cyril; Ackermann, Jörg; Fages, Frédéric
2012-02-01
We report the synthesis and spectroscopic characterization of nanohybrid structures consisting of an azobenzene compound grafted on the surface of zinc oxide nanoparticles. Characteristic bathochromic shifts indicate that the azobenzene photochromic molecules self-assemble onto the surface of the nanocrystals. The extent of packing is dependent on the shape of the nanoparticle. ZnO nanorods, with flat facets, enable a tighter organization of the molecules in the self-assembled monolayer than in the case of nanodots that display a more curvated shape. Consistently, the efficiency of photochromic switching of the self-assembled monolayer on ZnO nanoparticles is also shown to be strongly affected by nanoparticle shape. Copyright © 2011 Elsevier Inc. All rights reserved.
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A Carbon Dioxide Bubble-Induced Vortex Triggers Co-Assembly of Nanotubes with Controlled Chirality.
Zhang, Ling; Zhou, Laicheng; Xu, Na; Ouyang, Zhenjie
2017-07-03
It is challenging to prepare co-organized nanotube systems with controlled nanoscale chirality in an aqueous liquid flow field. Such systems are responsive to a bubbled external gas. A liquid vortex induced by bubbling carbon dioxide (CO 2 ) gas was used to stimulate the formation of nanotubes with controlled chirality; two kinds of achiral cationic building blocks were co-assembled in aqueous solution. CO 2 -triggered nanotube formation occurs by formation of metastable intermediate structures (short helical ribbons and short tubules) and by transition from short tubules to long tubules in response to chirality matching self-assembly. Interestingly, the chirality sign of these assemblies can be selected for by the circulation direction of the CO 2 bubble-induced vortex during the co-assembly process. © 2017 Wiley-VCH Verlag GmbH & Co. KGaA, Weinheim.
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Laser-induced charge separation in organic nanofibers
DEFF Research Database (Denmark)
Tavares, Luciana; Behn, Dino; Kjelstrup-Hansen, Jakob
Organic semiconductors have unique properties that can be tailored via synthetic chemistry for specific applications, which combined with their low price and straight-forward processing over large areas make them interesting materials for future devices. Certain oligomers can self-assemble into c......Organic semiconductors have unique properties that can be tailored via synthetic chemistry for specific applications, which combined with their low price and straight-forward processing over large areas make them interesting materials for future devices. Certain oligomers can self......-assemble into crystalline nanofibers by vapor deposition onto muscovite mica substrates, and we have recently shown that such nanofibers can be transferred to different substrates by roll-printing and used as the active material in e.g. organic field-effect transistors (OFETs), organic light-emitting transistors (OLETs......), and organic phototransistors (OPTs). However, several device-related issues incl. charge-separation and local band structure remain poorly understood. In this work, we use electrostatic force microscopy (EFM) combined with optical microscopy to study the local surface charge of an individual organic nanofiber...
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Activation of Toll-like receptors nucleates assembly of the MyDDosome signaling hub.
Latty, Sarah Louise; Sakai, Jiro; Hopkins, Lee; Verstak, Brett; Paramo, Teresa; Berglund, Nils A; Cammorota, Eugenia; Cicuta, Pietro; Gay, Nicholas J; Bond, Peter J; Klenerman, David; Bryant, Clare E
2018-01-24
Infection and tissue damage induces assembly of supramolecular organizing centres (SMOCs)), such as the Toll-like receptor (TLR) MyDDosome, to co-ordinate inflammatory signaling. SMOC assembly is thought to drive digital all-or-none responses, yet TLR activation by diverse microbes induces anything from mild to severe inflammation. Using single-molecule imaging of TLR4-MyDDosome signaling in living macrophages, we find that MyDDosomes assemble within minutes of TLR4 stimulation. TLR4/MD2 activation leads only to formation of TLR4/MD2 heterotetramers, but not oligomers, suggesting a stoichiometric mismatch between activated receptors and MyDDosomes. The strength of TLR4 signalling depends not only on the number and size of MyDDosomes formed but also how quickly these structures assemble. Activated TLR4, therefore, acts transiently nucleating assembly of MyDDosomes, a process that is uncoupled from receptor activation. These data explain how the oncogenic mutation of MyD88 (L265P) assembles MyDDosomes in the absence of receptor activation to cause constitutive activation of pro-survival NF-κB signalling. © 2018, Latty et al.
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Energy Technology Data Exchange (ETDEWEB)
Lee, Kanghee; Kang, Heungseok; Oh, Dongseok; Yoon, Kyungho; Kim, Hyungkyu; Kim, Jaeyong [Korea Atomic Energy Research Institute, Daejeon (Korea, Republic of)
2013-10-15
This paper summary the fuel assembly damping data in air/in still water/under flow, released from foreign fuel vendors, compared our data with the published data. Some technical issues in fuel assembly damping measurement testing are also briefly discussed. Understanding of each fuel assembly damping mechanisms according to the surrounding medium and flow velocity can support the fuel design improvement in fuel assembly dynamics and structural integrity aspect. Because the upgraded requirements of the newly-developed advanced reactor system will demands to minimize fuel design margin in integrity evaluation, reduction in conservatism of fuel assembly damping can contribute to alleviate the fuel design margin for sure. Damping is an energy dissipation mechanism in a vibrating mechanical structure and prevents a resonant structure from having infinite vibration amplitudes. The sources of fuel assembly damping are various from support friction to flow contribution, and it can be increased by the viscosity or drag of surrounding fluid medium or the average velocity of water flowing. Fuel licensing requires fuel design evaluation in transient or accidental condition. Dynamic response analysis of fuel assembly is to show fuel integrity and requires information on assembly-wise damping in dry condition and under wet or water flowing condition. However, damping measurement test for the full-scale fuel assembly prototype is not easy to carry out because of the scale (fuel prototype, test facility), unsteadiness of test data (scattering, random sampling and processing), instrumentation under water flowing (water-proof response measurement), and noise. LWR fuel technology division in KAERI is preparing the infra structure for damping measurement test of full-scale fuel assembly, to support fuel industries and related research activities. Here is a preliminary summary of fuel assembly damping, published in the literature. Some technical issues in fuel assembly damping
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Table-top deterministic and collective colloidal assembly using videoprojector lithography
International Nuclear Information System (INIS)
Cordeiro, J.; Zelsmann, M.; Honegger, T.; Picard, E.; Hadji, E.; Peyrade, D.
2015-01-01
Graphical abstract: - Highlights: • Micrometric resolution substrates are made at low cost using a videoprojector. • Fabricated patterns could be used as substrates for capillary force assembly. • Arrays of organized particles are made using a table-top capillary assembly tool. • This process offers a new bridge between the colloidal domain and the chip world. - Abstract: In the field of micro- and nanotechnology, most lithography and fabrication tools coming from the microelectronic industry are expensive, time-consuming and may need some masks that have to be subcontracted. Such approach is not suitable for other fields that require rapid prototyping such as chemistry, life science or energy and may hinder research creativity. In this work, we present two table-top equipments dedicated to the fabrication of deterministic colloidal particles assemblies onto micro-structured substrates. We show that, with a limited modification of the optics of a standard videoprojector, it is possible to quickly obtain substrates with thousands of micrometric features. Then, we combine these substrates with thermodynamic colloidal assembly and generate arrays of particles without defects. This work opens the way to a simple and table-top fabrication of devices based on colloidal particles
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Table-top deterministic and collective colloidal assembly using videoprojector lithography
Energy Technology Data Exchange (ETDEWEB)
Cordeiro, J. [Univ Grenoble Alpes, F-38000 Grenoble (France); CNRS, LTM, F-38000 Grenoble (France); CEA, LETI, MINATEC Campus, F-38000 Grenoble (France); Zelsmann, M., E-mail: marc.zelsmann@cea.fr [Univ Grenoble Alpes, F-38000 Grenoble (France); CNRS, LTM, F-38000 Grenoble (France); CEA, LETI, MINATEC Campus, F-38000 Grenoble (France); Honegger, T. [Univ Grenoble Alpes, F-38000 Grenoble (France); CNRS, LTM, F-38000 Grenoble (France); CEA, LETI, MINATEC Campus, F-38000 Grenoble (France); Picard, E.; Hadji, E. [Univ Grenoble Alpes, F-38000 Grenoble (France); CEA, INAC-SP2M, F-38000 Grenoble (France); Peyrade, D. [Univ Grenoble Alpes, F-38000 Grenoble (France); CNRS, LTM, F-38000 Grenoble (France); CEA, LETI, MINATEC Campus, F-38000 Grenoble (France)
2015-09-15
Graphical abstract: - Highlights: • Micrometric resolution substrates are made at low cost using a videoprojector. • Fabricated patterns could be used as substrates for capillary force assembly. • Arrays of organized particles are made using a table-top capillary assembly tool. • This process offers a new bridge between the colloidal domain and the chip world. - Abstract: In the field of micro- and nanotechnology, most lithography and fabrication tools coming from the microelectronic industry are expensive, time-consuming and may need some masks that have to be subcontracted. Such approach is not suitable for other fields that require rapid prototyping such as chemistry, life science or energy and may hinder research creativity. In this work, we present two table-top equipments dedicated to the fabrication of deterministic colloidal particles assemblies onto micro-structured substrates. We show that, with a limited modification of the optics of a standard videoprojector, it is possible to quickly obtain substrates with thousands of micrometric features. Then, we combine these substrates with thermodynamic colloidal assembly and generate arrays of particles without defects. This work opens the way to a simple and table-top fabrication of devices based on colloidal particles.
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International Nuclear Information System (INIS)
Abe, Hideaki; Sakai, Takao; Ishida, Tomio; Yokota, Norikatsu.
1992-01-01
The lower ends of a plurality of plate-like shape memory alloys are secured at the periphery of the upper inside of the handling head of a fuel assembly. As the shape memory alloy, a Cu-Zn alloy, a Ti-Pd alloy or a Fe-Ni alloy is used. When high temperature coolants flow out to the handling head, the shape memory alloy deforms by warping to the outer side more greatly toward the upper portion thereof with the temperature increase of the coolants. As the result, the shape of the flow channel of the coolants is changed so as to enlarge at the exit of the upper end of the fuel assembly. Then, the pressure loss of the coolants in the fuel assembly is decreased by the enlargement. Accordingly, the flow rate of the coolants in the fuel assembly is increased to lower the temperature of the coolants. Further, high temperature coolants and low temperature coolants are mixed sufficiently just above the fuel assembly. This can suppress the temperature fluctuation of the mixed coolants in the upper portion of the reactor core, thereby enabling to decrease a fatigue and failures of the structural components in the upper portion of the reactor core. (I.N.)
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Soldering in electronics assembly
Judd, Mike
2013-01-01
Soldering in Electronics Assembly discusses several concerns in soldering of electronic assemblies. The book is comprised of nine chapters that tackle different areas in electronic assembly soldering. Chapter 1 discusses the soldering process itself, while Chapter 2 covers the electronic assemblies. Chapter 3 talks about solders and Chapter 4 deals with flux. The text also tackles the CS and SC soldering process. The cleaning of soldered assemblies, solder quality, and standards and specifications are also discussed. The book will be of great use to professionals who deal with electronic assem
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DEFF Research Database (Denmark)
Viciano-Chumillas, Marta; Li, Dongzhe; Smogunov, Alexander
2014-01-01
-butyl) is presented. Their electronic structure and self-assembly was studied. The organic ligands of the salen complexes are functionalized with peripheral carboxylic groups for driving molecular self-assembly through hydrogen bonding. In addition, other substituents, that is, tert-butyl and diamine bridges (2...
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Bearing assemblies, apparatuses, and motor assemblies using the same
Sexton, Timothy N.; Cooley, Craig H.; Knuteson, Cody W.
2015-12-29
Various embodiments of the invention relate to bearing assemblies, apparatuses and motor assemblies that include geometric features configured to impart a selected amount of heat transfer and/or hydrodynamic film formation. In an embodiment, a bearing assembly may include a plurality of superhard bearing pads distributed circumferentially about an axis. At least some of the plurality of superhard bearing pads may include a plurality of sub-superhard bearing elements defining a bearing surface. At least some of the plurality of sub-superhard bearing elements may be spaced from one another by one or more voids to impart a selected amount of heat transfer and hydrodynamic film formation thereon during operation. The bearing assembly may also include a support ring that carries the plurality of superhard bearing pads. In addition, at least a portion of the sub-superhard bearing elements may extend beyond the support ring.
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International Nuclear Information System (INIS)
Gjertsen, R.K.; Bassler, E.A.; Huckestein, E.A.; Salton, R.B.; Tower, S.N.
1988-01-01
A fuel assembly adapted for use with a pressurized water nuclear reactor having capabilities for fluid moderator spectral shift control is described comprising: parallel arranged elongated nuclear fuel elements; means for providing for axial support of the fuel elements and for arranging the fuel elements in a spaced array; thimbles interspersed among the fuel elements adapted for insertion of a rod control cluster therewithin; means for structurally joining the fuel elements and the guide thimbles; fluid moderator control means for providing a volume of low neutron absorbing fluid within the fuel assembly and for removing a substantially equivalent volume of reactor coolant water therefrom, a first flow manifold at one end of the fuel assembly sealingly connected to a first end of the moderator control tubes whereby the first ends are commonly flow connected; and a second flow manifold, having an inlet passage and an outlet passage therein, sealingly connected to a second end of the moderator control tubes at a second end of the fuel assembly
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Self-assembling enzymes and the origins of the cytoskeleton
Barry, Rachael; Gitai, Zemer
2011-01-01
The bacterial cytoskeleton is composed of a complex and diverse group of proteins that self-assemble into linear filaments. These filaments support and organize cellular architecture and provide a dynamic network controlling transport and localization within the cell. Here, we review recent discoveries related to a newly appreciated class of self-assembling proteins that expand our view of the bacterial cytoskeleton and provide potential explanations for its evolutionary origins. Specifically, several types of metabolic enzymes can form structures similar to established cytoskeletal filaments and, in some cases, these structures have been repurposed for structural uses independent of their normal role. The behaviors of these enzymes suggest that some modern cytoskeletal proteins may have evolved from dual-role proteins with catalytic and structural functions. PMID:22014508
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Fire resistant PV shingle assembly
Lenox, Carl J.
2012-10-02
A fire resistant PV shingle assembly includes a PV assembly, including PV body, a fire shield and a connection member connecting the fire shield below the PV body, and a support and inter-engagement assembly. The support and inter-engagement assembly is mounted to the PV assembly and comprises a vertical support element, supporting the PV assembly above a support surface, an upper interlock element, positioned towards the upper PV edge, and a lower interlock element, positioned towards the lower PV edge. The upper interlock element of one PV shingle assembly is inter-engageable with the lower interlock element of an adjacent PV shingle assembly. In some embodiments the PV shingle assembly may comprise a ventilation path below the PV body. The PV body may be slidably mounted to the connection member to facilitate removal of the PV body.
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Community assembly and coexistence in communities of arbuscular mycorrhizal fungi.
Vályi, Kriszta; Mardhiah, Ulfah; Rillig, Matthias C; Hempel, Stefan
2016-10-01
Arbuscular mycorrhizal fungi are asexual, obligately symbiotic fungi with unique morphology and genomic structure, which occupy a dual niche, that is, the soil and the host root. Consequently, the direct adoption of models for community assembly developed for other organism groups is not evident. In this paper we adapted modern coexistence and assembly theory to arbuscular mycorrhizal fungi. We review research on the elements of community assembly and coexistence of arbuscular mycorrhizal fungi, highlighting recent studies using molecular methods. By addressing several points from the individual to the community level where the application of modern community ecology terms runs into problems when arbuscular mycorrhizal fungi are concerned, we aim to account for these special circumstances from a mycocentric point of view. We suggest that hierarchical spatial structure of arbuscular mycorrhizal fungal communities should be explicitly taken into account in future studies. The conceptual framework we develop here for arbuscular mycorrhizal fungi is also adaptable for other host-associated microbial communities.
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Tailorable Exciton Transport in Doped Peptide–Amphiphile Assemblies
Energy Technology Data Exchange (ETDEWEB)
Solomon, Lee A. [Center; Sykes, Matthew E. [Center; Wu, Yimin A. [Center; Schaller, Richard D. [Center; Department; Wiederrecht, Gary P. [Center; Fry, H. Christopher [Center
2017-08-29
Light-harvesting biomaterials are an attractive target in photovoltaics, photocatalysis, and artificial photosynthesis. Through peptide self-assembly, complex nanostructures can be engineered to study the role of chromophore organization during light absorption and energy transport. To this end, we demonstrate the one-dimensional transport of excitons along naturally occurring, light-harvesting, Zn-protoporphyrin IX chromophores within self-assembled peptide-amphiphile nanofibers. The internal structure of the nanofibers induces packing of the porphyrins into linear chains. We find that this peptide assembly can enable long-range exciton diffusion, yet it also induces the formation of excimers between adjacent molecules, which serve as exciton traps. Electronic coupling between neighboring porphyrin molecules is confirmed by various spectroscopic methods. The exciton diffusion process is then probed through transient photoluminescence and absorption measurements and fit to a model for one-dimensional hopping. Because excimer formation impedes exciton hopping, increasing the interchromophore spacing allows for improved diffusivity, which we control through porphyrin doping levels. We show that diffusion lengths of over 60 nm are possible at low porphyrin doping, representing an order of magnitude improvement over the highest doping fractions.
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Binary self-assembly of highly symmetric DNA nanocages via sticky-end engineering
Institute of Scientific and Technical Information of China (English)
Xiao-Rong Wu; Chen-Wei Wu; Fei Ding; Cheng Tian; Wen Jiang; Cheng-De Mao; Chuan Zhang
2017-01-01
Discrete and symmetric three-dimensional (3D) DNA nanocages have been revoked as excellent candidates for various applications,such as guest component encapsulation and organization (e.g.dye molecules,proteins,inorganic nanoparticles,etc.) to construct new materials and devices.To date,a large variety of DNA nanocages has been synthesized through assembling small individual DNA motifs into predesigned structures in a bottom-up fashion.Most of them rely on the assembly using multiple copies of single type of motifs and a few sophisticated nanostructures have been engineered by co-assembling multi-types of DNA tiles simultaneously.However,the availability of complex DNA nanocages is still limited.Herein,we demonstrate that highly symmetric DNA nanocages consisted of binary DNA pointstar motifs can be easily assembled by deliberately engineering the sticky-end interaction between the component building blocks.As such,DNA nanocages with new geometries,including elongated tetrahedron (E-TET),rhombic dodecahedron (R-DOD),and rhombic triacontahedron (R-TRI) are successfully synthesized.Moreover,their design principle,assembly process,and structural features are revealed by polyacryalmide gel electrophoresis (PAGE),atomic force microscope (AFM) imaging,and cryogenic transmission electron microscope imaging (cryo-TEM) associated with single particle reconstruction.
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Energy Technology Data Exchange (ETDEWEB)
Gao, Zhu-Qing, E-mail: zqgao2008@163.com [School of Chemical and Biological Engineering, Taiyuan University of Science and Technology, Taiyuan 030021 (China); Li, Hong-Jin [School of Chemical and Biological Engineering, Taiyuan University of Science and Technology, Taiyuan 030021 (China); Gu, Jin-Zhong, E-mail: gujzh@lzu.edu.cn [College of Chemistry and Chemical Engineering, Lanzhou University, Lanzhou 730000 (China); Zhang, Qing-Hua [School of Chemical and Biological Engineering, Taiyuan University of Science and Technology, Taiyuan 030021 (China); Kirillov, Alexander M. [Centro de Química Estrutural, Complexo I, Instituto Superior Técnico, Universidade de Lisboa, Av. Rovisco Pais, 1049–001 Lisbon (Portugal)
2016-09-15
Four new crystalline solids, namely [Co{sub 2}(µ{sub 2}-5-Clnic){sub 2}(µ{sub 3}-5-Clnic){sub 2}(µ{sub 2}-H{sub 2}O)]{sub n} (1), [Co(5-Clnic){sub 2}(H{sub 2}O){sub 4}]·2(5-ClnicH) (2), [Pb(µ{sub 2}-5-Clnic){sub 2}(phen)]{sub n} (3), and [Cd(5-Clnic){sub 2}(phen){sub 2}]·3H{sub 2}O (4) were generated by hydrothermal self-assembly methods from the corresponding metal(II) chlorides, 5-chloronicotinic acid (5-ClnicH) as a principal building block, and 1,10-phenanthroline (phen) as an ancillary ligand (optional). All the products 1–4 were characterized by IR spectroscopy, elemental analysis, thermogravimetric (TGA), powder X-ray diffraction (PXRD) and single-crystal X-ray diffraction. Their structures range from an intricate 3D metal-organic network 1 with the 3,6T7 topology to a ladder-like 1D coordination polymer 3 with the 2C1 topology, whereas compounds 2 and 4 are the discrete 0D monomers. The structures of 2 and 4 are further extended (0D→2D or 0D→3D) by hydrogen bonds, generating supramolecular networks with the 3,8L18 and ins topologies, respectively. Synthetic aspects, structural features, thermal stability, magnetic (for 1) and luminescent (for 3 and 4) properties were also investigated and discussed. - Graphical abstract: A new series of crystalline solids was self-assembled and fully characterized; their structural, topological, luminescent and magnetic features were investigated. Display Omitted.
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Lehmann, Robert; Lightfoot, Damien J; Schunter, Celia Marei; Michell, Craig T; Ohyanagi, Hajime; Mineta, Katsuhiko; Foret, Sylvain; Berumen, Michael L.; Miller, David J; Aranda, Manuel; Gojobori, Takashi; Munday, Philip L; Ravasi, Timothy
2018-01-01
The iconic orange clownfish, Amphiprion percula, is a model organism for studying the ecology and evolution of reef fishes, including patterns of population connectivity, sex change, social organization, habitat selection and adaptation to climate change. Notably, the orange clownfish is the only reef fish for which a complete larval dispersal kernel has been established and was the first fish species for which it was demonstrated that anti-predator responses of reef fishes could be impaired by ocean acidification. Despite its importance, molecular resources for this species remain scarce and until now it lacked a reference genome assembly. Here we present a de novo chromosome-scale assembly of the genome of the orange clownfish Amphiprion percula. We utilized single-molecule real-time sequencing technology from Pacific Biosciences to produce an initial polished assembly comprised of 1,414 contigs, with a contig N50 length of 1.86 Mb. Using Hi-C based chromatin contact maps, 98% of the genome assembly were placed into 24 chromosomes, resulting in a final assembly of 908.8 Mb in length with contig and scaffold N50s of 3.12 and 38.4 Mb, respectively. This makes it one of the most contiguous and complete fish genome assemblies currently available. The genome was annotated with 26,597 protein coding genes and contains 96% of the core set of conserved actinopterygian orthologs. The availability of this reference genome assembly as a community resource will further strengthen the role of the orange clownfish as a model species for research on the ecology and evolution of reef fishes.
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Lehmann, Robert
2018-03-08
The iconic orange clownfish, Amphiprion percula, is a model organism for studying the ecology and evolution of reef fishes, including patterns of population connectivity, sex change, social organization, habitat selection and adaptation to climate change. Notably, the orange clownfish is the only reef fish for which a complete larval dispersal kernel has been established and was the first fish species for which it was demonstrated that anti-predator responses of reef fishes could be impaired by ocean acidification. Despite its importance, molecular resources for this species remain scarce and until now it lacked a reference genome assembly. Here we present a de novo chromosome-scale assembly of the genome of the orange clownfish Amphiprion percula. We utilized single-molecule real-time sequencing technology from Pacific Biosciences to produce an initial polished assembly comprised of 1,414 contigs, with a contig N50 length of 1.86 Mb. Using Hi-C based chromatin contact maps, 98% of the genome assembly were placed into 24 chromosomes, resulting in a final assembly of 908.8 Mb in length with contig and scaffold N50s of 3.12 and 38.4 Mb, respectively. This makes it one of the most contiguous and complete fish genome assemblies currently available. The genome was annotated with 26,597 protein coding genes and contains 96% of the core set of conserved actinopterygian orthologs. The availability of this reference genome assembly as a community resource will further strengthen the role of the orange clownfish as a model species for research on the ecology and evolution of reef fishes.
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International Nuclear Information System (INIS)
Marmonier, Pierre; Mesnage, Bernard; Nervi, J.C.
1975-01-01
This invention refers to fuel assemblies for a liquid metal cooled fast neutron reactor. Each assembly is composed of a hollow vertical casing, of regular polygonal section, containing a bundle of clad pins filled with a fissile or fertile substance. The casing is open at its upper end and has a cylindrical foot at its lower end for positioning the assembly in a housing provided in the horizontal diagrid, on which the core assembly rests. A set of flat bars located on the external surface of the casing enables it to be correctly orientated in its housing among the other core assemblies [fr
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Culebras, Mario; Cho, Chungyeon; Krecker, Michelle; Smith, Ryan; Song, Yixuan; Gómez, Clara M; Cantarero, Andrés; Grunlan, Jaime C
2017-02-22
In an effort to produce effective thermoelectric nanocomposites with multiwalled carbon nanotubes (MWCNT), layer-by-layer assembly was combined with electrochemical polymerization to create synergy that would produce a high power factor. Nanolayers of MWCNT stabilized with poly(diallyldimethylammonium chloride) or sodium deoxycholate were alternately deposited from water. Poly(3,4-ethylene dioxythiophene) [PEDOT] was then synthesized electrochemically by using this MWCNT-based multilayer thin film as the working electrode. Microscopic images show a homogeneous distribution of PEDOT around the MWCNT. The electrical resistance, conductivity (σ) and Seebeck coefficient (S) were measured before and after the PEDOT polymerization. A 30 bilayer MWCNT film (<1 μm thick) infused with PEDOT is shown to achieve a power factor (PF = S 2 σ) of 155 μW/m K 2 , which is the highest value ever reported for a completely organic MWCNT-based material and competitive with lead telluride at room temperature. The ability of this MWCNT-PEDOT film to generate power was demonstrated with a cylindrical thermoelectric generator that produced 5.5 μW with a 30 K temperature differential. This unique nanocomposite, prepared from water with relatively inexpensive ingredients, should open up new opportunities to recycle waste heat in portable/wearable electronics and other applications where low weight and mechanical flexibility are needed.
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Ultrathin self-assembled anionic polymer membranes for superfast size-selective separation
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
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International Nuclear Information System (INIS)
Gacoin, T; Besson, S; Boilot, J P
2006-01-01
Tremendous work achieved in the last 20 years on nanoparticle synthesis has allowed us to study many new physical properties that are found in the nanometre size range. New developments are now expected when considering assemblies of nanoparticles such as 2D or 3D organized arrays. These systems are indeed expected to exhibit original physical properties resulting from particle-particle interactions. Studies in this field are clearly dependent on the elaboration of materials with controlled particle size, organization and interparticle distance. This paper presents a strategy of elaboration that is based on the use of organized mesoporous silica films as templates. These films are made by sol-gel polymerization around surfactant assemblies and further elimination of the surfactant. This provides porous matrices with a pore organization that is the almost perfect replica of the initial micellar structure. The use of such films for the elaboration of organized arrays of nanoparticles is detailed in the case of CdS and Ag particles. The formation of particles inside the pores is achieved through impregnation with precursors that are allowed to diffuse inside the pores. This leads to particles with a size and a spatial arrangement that is directly related to the initial pore structure of the films. This process opens a wide range of investigations due to the relative ease of fabrication over large surfaces and the numerous possibilities offered by the elaboration of porous films with different pore sizes and organizations
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Energy Technology Data Exchange (ETDEWEB)
Packianathan, Charles; Katen, Sarah P.; Dann, III, Charles E.; Zlotnick, Adam (Indiana)
2010-01-12
In infected cells, virus components must be organized at the right place and time to ensure assembly of infectious virions. From a different perspective, assembly must be prevented until all components are available. Hypothetically, this can be achieved by allosterically controlling assembly. Consistent with this hypothesis, here we show that the structure of the hepatitis B virus (HBV) core protein dimer, which can spontaneously self-assemble, is incompatible with capsid assembly. Systematic differences between core protein dimer and capsid conformations demonstrate linkage between the intradimer interface and interdimer contact surface. These structures also provide explanations for the capsid-dimer selectivity of some antibodies and the activities of assembly effectors. Solution studies suggest that the assembly-inactive state is more accurately an ensemble of conformations. Simulations show that allostery supports controlled assembly and results in capsids that are resistant to dissociation. We propose that allostery, as demonstrated in HBV, is common to most self-assembling viruses.
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DEFF Research Database (Denmark)
Kiriy, N.; Bocharova, V.; Kiriy, A.
2004-01-01
This paper describes synthesis and characterization of two thiophene-based azomethines designed to optimize solubility, self-assembly, and charge carrier mobility. We found that incorporation of azomethine and amide moieties in the alpha,omega-position, and hexyl chains in the beta-position of th...... with the mobilities of the best organic semiconductors. All these significant differences in properties of related compounds can be attributed to the hydrogen bonding between QT-amide molecules responsible for the observed self-assembly....
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Prisbrey, M.; Greenhall, J.; Guevara Vasquez, F.; Raeymaekers, B.
2017-01-01
We use ultrasound directed self-assembly to organize particles dispersed in a fluid medium into a three-dimensional (3D) user-specified pattern. The technique employs ultrasound transducers that line the boundary of a fluid reservoir to create a standing ultrasound wave field. The acoustic radiation force associated with the wave field drives particles dispersed in the fluid medium into organized patterns, assuming that the particles are much smaller than the wavelength and do not interact with each other. We have theoretically derived a direct solution method to calculate the ultrasound transducer operating parameters that are required to assemble a user-specified 3D pattern of particles in a fluid reservoir of arbitrary geometry. We formulate the direct solution method as a constrained optimization problem that reduces to eigendecomposition. We experimentally validate the solution method by assembling 3D patterns of carbon nanoparticles in a water reservoir and observe good quantitative agreement between theory and experiment. Additionally, we demonstrate the versatility of the solution method by simulating ultrasound directed self-assembly of complex 3D patterns of particles. The method works for any 3D simple, closed fluid reservoir geometry in combination with any arrangement of ultrasound transducers and enables employing ultrasound directed self-assembly in a myriad of engineering applications, including biomedical and materials fabrication processes.
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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.
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Kundeti, Vamsi; Rajasekaran, Sanguthevar
2012-06-01
Efficient tile sets for self assembling rectilinear shapes is of critical importance in algorithmic self assembly. A lower bound on the tile complexity of any deterministic self assembly system for an n × n square is [Formula: see text] (inferred from the Kolmogrov complexity). Deterministic self assembly systems with an optimal tile complexity have been designed for squares and related shapes in the past. However designing [Formula: see text] unique tiles specific to a shape is still an intensive task in the laboratory. On the other hand copies of a tile can be made rapidly using PCR (polymerase chain reaction) experiments. This led to the study of self assembly on tile concentration programming models. We present two major results in this paper on the concentration programming model. First we show how to self assemble rectangles with a fixed aspect ratio ( α:β ), with high probability, using Θ( α + β ) tiles. This result is much stronger than the existing results by Kao et al. (Randomized self-assembly for approximate shapes, LNCS, vol 5125. Springer, Heidelberg, 2008) and Doty (Randomized self-assembly for exact shapes. In: proceedings of the 50th annual IEEE symposium on foundations of computer science (FOCS), IEEE, Atlanta. pp 85-94, 2009)-which can only self assembly squares and rely on tiles which perform binary arithmetic. On the other hand, our result is based on a technique called staircase sampling . This technique eliminates the need for sub-tiles which perform binary arithmetic, reduces the constant in the asymptotic bound, and eliminates the need for approximate frames (Kao et al. Randomized self-assembly for approximate shapes, LNCS, vol 5125. Springer, Heidelberg, 2008). Our second result applies staircase sampling on the equimolar concentration programming model (The tile complexity of linear assemblies. In: proceedings of the 36th international colloquium automata, languages and programming: Part I on ICALP '09, Springer-Verlag, pp 235
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Assembling large, complex environmental metagenomes
Energy Technology Data Exchange (ETDEWEB)
Howe, A. C. [Michigan State Univ., East Lansing, MI (United States). Microbiology and Molecular Genetics, Plant Soil and Microbial Sciences; Jansson, J. [USDOE Joint Genome Institute (JGI), Walnut Creek, CA (United States); Lawrence Berkeley National Lab. (LBNL), Berkeley, CA (United States). Earth Sciences Division; Malfatti, S. A. [USDOE Joint Genome Institute (JGI), Walnut Creek, CA (United States); Tringe, S. G. [USDOE Joint Genome Institute (JGI), Walnut Creek, CA (United States); Tiedje, J. M. [Michigan State Univ., East Lansing, MI (United States). Microbiology and Molecular Genetics, Plant Soil and Microbial Sciences; Brown, C. T. [Michigan State Univ., East Lansing, MI (United States). Microbiology and Molecular Genetics, Computer Science and Engineering
2012-12-28
The large volumes of sequencing data required to sample complex environments deeply pose new challenges to sequence analysis approaches. De novo metagenomic assembly effectively reduces the total amount of data to be analyzed but requires significant computational resources. We apply two pre-assembly filtering approaches, digital normalization and partitioning, to make large metagenome assemblies more computationaly tractable. Using a human gut mock community dataset, we demonstrate that these methods result in assemblies nearly identical to assemblies from unprocessed data. We then assemble two large soil metagenomes from matched Iowa corn and native prairie soils. The predicted functional content and phylogenetic origin of the assembled contigs indicate significant taxonomic differences despite similar function. The assembly strategies presented are generic and can be extended to any metagenome; full source code is freely available under a BSD license.
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3D Printing of Personalized Organs and Tissues
Ye, Kaiming
2015-03-01
Authors: Kaiming Ye and Sha Jin, Department of Biomedical Engineering, Watson School of Engineering and Applied Science, Binghamton University, State University of New York, Binghamton, NY 13902-6000 Abstract: Creation of highly organized multicellular constructs, including tissues and organs or organoids, will revolutionize tissue engineering and regenerative medicine. The development of these technologies will enable the production of individualized organs or tissues for patient-tailored organ transplantation or cell-based therapy. For instance, a patient with damaged myocardial tissues due to an ischemic event can receive a myocardial transplant generated using the patient's own induced pluripotent stem cells (iPSCs). Likewise, a type-1 diabetic patient can be treated with lab-generated islets to restore his or her physiological insulin secretion capability. These lab-produced, high order tissues or organs can also serve as disease models for pathophysiological study and drug screening. The remarkable advances in stem cell biology, tissue engineering, microfabrication, and materials science in the last decade suggest the feasibility of generating these tissues and organoids in the laboratory. Nevertheless, major challenges still exist. One of the critical challenges that we still face today is the difficulty in constructing or fabricating multicellular assemblies that recapitulate in vivo microenvironments essential for controlling cell proliferation, migration, differentiation, maturation and assembly into a biologically functional tissue or organoid structure. These challenges can be addressed through developing 3D organ and tissue printing which enables organizing and assembling cells into desired tissue and organ structures. We have shown that human pluripotent stem cells differentiated in 3D environments are mature and possess high degree of biological function necessary for them to function in vivo.
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International Nuclear Information System (INIS)
Ip, A.K.; Koyanagi, K.; Tarasuk, W.R.
1976-01-01
A method of fabricating rodded fuels suitable for use in pressure tube type reactors and in pressure vessel type reactors is described. Fuel rods are secured as an inner and an outer sub-assembly, each rod attached between mounting rings secured to the rod ends. The two sub-assemblies are telescoped together and positioned by spaced thimbles located between them to provide precise positioning while permittng differential axial movement between the sub-assemblies. Such sub-assemblies are particularly suited for mounting as bundle strings. The method provides particular advantages in the assembly of annular-section fuel pins, which includes booster fuel containing enriched fuel material. (LL)
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International Nuclear Information System (INIS)
Morgado, Mario M.; Oliveira, Monica G.N.; Ferreira Junior, Decio B.M.; Santos, Barbara O. dos; Santos, Jorge E. dos
2009-01-01
Fuel failures have been happened in Nuclear Power Plants worldwide, without lost of integrity and safety, mainly for the public, environment and power plants workers. The most common causes of these events are corrosion (CRUD), fretting and pellet cladding interaction. These failures are identified by increasing the activity of fission products, verified by chemical analyses of reactor coolant. Through these analyses, during the fourth operation cycle of Angra 2 Nuclear Power Plant, was possible to observe fuel failure indication. This indication was confirmed in the end of the cycle during the unloading of reactor core through leakage tests of fuel assembly, using the equipment called 'In Mast Sipping' and 'Box Sipping'. After confirmed, the fuel assembly reconstitution was scheduled, and happened in April, 2007, where was identified the cause and the fuel rod failure, which was substitute by dummy rods (zircaloy). The cause was fretting by 'debris'. The actions to avoid and prevent fuel assemblies failures are important. The goals of this work are to describe the methodology of fuel assembly reconstitution using the FARE (Fuel Assembly Reconstitution Equipment) system, to describe the results of this task in economic and security factors of the company and show how the fuel assembly failures are identified during operation and during the outage. (author)
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Icarus: visualizer for de novo assembly evaluation.
Mikheenko, Alla; Valin, Gleb; Prjibelski, Andrey; Saveliev, Vladislav; Gurevich, Alexey
2016-11-01
: Data visualization plays an increasingly important role in NGS data analysis. With advances in both sequencing and computational technologies, it has become a new bottleneck in genomics studies. Indeed, evaluation of de novo genome assemblies is one of the areas that can benefit from the visualization. However, even though multiple quality assessment methods are now available, existing visualization tools are hardly suitable for this purpose. Here, we present Icarus-a novel genome visualizer for accurate assessment and analysis of genomic draft assemblies, which is based on the tool QUAST. Icarus can be used in studies where a related reference genome is available, as well as for non-model organisms. The tool is available online and as a standalone application. http://cab.spbu.ru/software/icarus CONTACT: aleksey.gurevich@spbu.ruSupplementary information: Supplementary data are available at Bioinformatics online. © The Author 2016. Published by Oxford University Press. All rights reserved. For Permissions, please e-mail: journals.permissions@oup.com.
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Buildup of radioxenon isotopes in MOX-assemblies
Energy Technology Data Exchange (ETDEWEB)
Gniffke, Thomas; Kirchner, Gerald [Carl Friedrich von Weizsaecker-Centre for Science and Peace Research, Hamburg (Germany)
2015-07-01
Radioxenon is the main tracer for detection of nuclear tests conducted underground under the verification regime of the Comprehensive Nuclear Test Ban Treaty (CTBT). Since radioxenon is emitted by civilian sources too, like commercial nuclear reactors, source discrimination is still an important issue. Inventory calculations are necessary to predict which xenon isotopic ratios are built up in a reactor and how they differ from those generated by a nuclear explosion. The screening line actually used by the CTBT Organization for source discrimination is based on calculations for uranium fuel of various enrichments used in pressurized water reactors (PWRs). The usage of different fuel, especially mixed U/Pu oxide (MOX) assemblies with reprocessed plutonium, may alter the radioxenon signature of civilian reactors. In this talk, calculations of the radioxenon buildup in a MOX-assembly used in a commercial PWR are presented. Implications for the CTBT verification regimes are discussed and open questions are addressed.
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Tissue engineering by self-assembly and bio-printing of living cells
International Nuclear Information System (INIS)
Jakab, Karoly; Marga, Francoise; Forgacs, Gabor; Norotte, Cyrille; Murphy, Keith; Vunjak-Novakovic, Gordana
2010-01-01
Biofabrication of living structures with desired topology and functionality requires the interdisciplinary effort of practitioners of the physical, life and engineering sciences. Such efforts are being undertaken in many laboratories around the world. Numerous approaches are pursued, such as those based on the use of natural or artificial scaffolds, decellularized cadaveric extracellular matrices and, most lately, bioprinting. To be successful in this endeavor, it is crucial to provide in vitro micro-environmental clues for the cells resembling those in the organism. Therefore, scaffolds, populated with differentiated cells or stem cells, of increasing complexity and sophistication are being fabricated. However, no matter how sophisticated scaffolds are, they can cause problems stemming from their degradation, eliciting immunogenic reactions and other a priori unforeseen complications. It is also being realized that ultimately the best approach might be to rely on the self-assembly and self-organizing properties of cells and tissues and the innate regenerative capability of the organism itself, not just simply prepare tissue and organ structures in vitro followed by their implantation. Here we briefly review the different strategies for the fabrication of three-dimensional biological structures, in particular bioprinting. We detail a fully biological, scaffoldless, print-based engineering approach that uses self-assembling multicellular units as bio-ink particles and employs early developmental morphogenetic principles, such as cell sorting and tissue fusion. (topical review)
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Tissue engineering by self-assembly and bio-printing of living cells
Energy Technology Data Exchange (ETDEWEB)
Jakab, Karoly; Marga, Francoise; Forgacs, Gabor [Department of Physics and Astronomy, University of Missouri, Columbia, MO 65211 (United States); Norotte, Cyrille [Department of Biology, University of Missouri, Columbia, MO 65211 (United States); Murphy, Keith [Organovo, Inc., 5871 Oberlin Drive, San Diego, CA 92121 (United States); Vunjak-Novakovic, Gordana, E-mail: forgacsg@missouri.ed [Department of Biomedical Engineering, Columbia University, New York, NY 10032 (United States)
2010-06-15
Biofabrication of living structures with desired topology and functionality requires the interdisciplinary effort of practitioners of the physical, life and engineering sciences. Such efforts are being undertaken in many laboratories around the world. Numerous approaches are pursued, such as those based on the use of natural or artificial scaffolds, decellularized cadaveric extracellular matrices and, most lately, bioprinting. To be successful in this endeavor, it is crucial to provide in vitro micro-environmental clues for the cells resembling those in the organism. Therefore, scaffolds, populated with differentiated cells or stem cells, of increasing complexity and sophistication are being fabricated. However, no matter how sophisticated scaffolds are, they can cause problems stemming from their degradation, eliciting immunogenic reactions and other a priori unforeseen complications. It is also being realized that ultimately the best approach might be to rely on the self-assembly and self-organizing properties of cells and tissues and the innate regenerative capability of the organism itself, not just simply prepare tissue and organ structures in vitro followed by their implantation. Here we briefly review the different strategies for the fabrication of three-dimensional biological structures, in particular bioprinting. We detail a fully biological, scaffoldless, print-based engineering approach that uses self-assembling multicellular units as bio-ink particles and employs early developmental morphogenetic principles, such as cell sorting and tissue fusion. (topical review)
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Zhao, Kui; Yu, Xinhong; Li, Ruipeng; Amassian, Aram; Han, Yanchun
2015-01-01
The mechanistic understanding of the intrinsic molecular self-assembly of conjugated polymers is of immense importance to controlling the microstructure development in organic semiconducting thin films, with meaningful impact on charge transport
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Reflector-moderated critical assemblies
International Nuclear Information System (INIS)
Paxton, H.C.; Jarvis, G.A.; Byers, C.C.
1975-07-01
Experiments with reflector-moderated critical assemblies were part of the Rover Program at the Los Alamos Scientific Laboratory (LASL). These assemblies were characterized by thick D 2 O or beryllium reflectors surrounding large cavities that contained highly enriched uranium at low average densities. Because interest in this type of system has been revived by LASL Plasma Cavity Assembly studies, more detailed descriptions of the early assemblies than had been available in the unclassified literature are provided. (U.S.)
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Amphiphilic building blocks for self-assembly: from amphiphiles to supra-amphiphiles.
Wang, Chao; Wang, Zhiqiang; Zhang, Xi
2012-04-17
The process of self-assembly spontaneously creates well-defined structures from various chemical building blocks. Self-assembly can include different levels of complexity: it can be as simple as the dimerization of two small building blocks driven by hydrogen bonding or as complicated as a cell membrane, a remarkable supramolecular architecture created by a bilayer of phospholipids embedded with functional proteins. The study of self-assembly in simple systems provides a fundamental understanding of the driving forces and cooperativity behind these processes. Once the rules are understood, these guidelines can facilitate the research of highly complex self-assembly processes. Among the various components for self-assembly, an amphiphilic molecule, which contains both hydrophilic and hydrophobic parts, forms one of the most powerful building blocks. When amphiphiles are dispersed in water, the hydrophilic component of the amphiphile preferentially interacts with the aqueous phase while the hydrophobic portion tends to reside in the air or in the nonpolar solvent. Therefore, the amphiphiles aggregate to form different molecular assemblies based on the repelling and coordinating forces between the hydrophilic and hydrophobic parts of the component molecules and the surrounding medium. In contrast to conventional amphiphiles, supra-amphiphiles are constructed on the basis of noncovalent interactions or dynamic covalent bonds. In supra-amphiphiles, the functional groups can be attached to the amphiphiles by noncovalent synthesis, greatly speeding their construction. The building blocks for supra-amphiphiles can be either small organic molecules or polymers. Advances in the development of supra-amphiphiles will not only enrich the family of conventional amphiphiles that are based on covalent bonds but will also provide a new kind of building block for the preparation of complex self-assemblies. When polymers are used to construct supra-amphiphiles, the resulting
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Ecological assembly rules in plant communities--approaches, patterns and prospects.
Götzenberger, Lars; de Bello, Francesco; Bråthen, Kari Anne; Davison, John; Dubuis, Anne; Guisan, Antoine; Lepš, Jan; Lindborg, Regina; Moora, Mari; Pärtel, Meelis; Pellissier, Loic; Pottier, Julien; Vittoz, Pascal; Zobel, Kristjan; Zobel, Martin
2012-02-01
Understanding how communities of living organisms assemble has been a central question in ecology since the early days of the discipline. Disentangling the different processes involved in community assembly is not only interesting in itself but also crucial for an understanding of how communities will behave under future environmental scenarios. The traditional concept of assembly rules reflects the notion that species do not co-occur randomly but are restricted in their co-occurrence by interspecific competition. This concept can be redefined in a more general framework where the co-occurrence of species is a product of chance, historical patterns of speciation and migration, dispersal, abiotic environmental factors, and biotic interactions, with none of these processes being mutually exclusive. Here we present a survey and meta-analyses of 59 papers that compare observed patterns in plant communities with null models simulating random patterns of species assembly. According to the type of data under study and the different methods that are applied to detect community assembly, we distinguish four main types of approach in the published literature: species co-occurrence, niche limitation, guild proportionality and limiting similarity. Results from our meta-analyses suggest that non-random co-occurrence of plant species is not a widespread phenomenon. However, whether this finding reflects the individualistic nature of plant communities or is caused by methodological shortcomings associated with the studies considered cannot be discerned from the available metadata. We advocate that more thorough surveys be conducted using a set of standardized methods to test for the existence of assembly rules in data sets spanning larger biological and geographical scales than have been considered until now. We underpin this general advice with guidelines that should be considered in future assembly rules research. This will enable us to draw more accurate and general
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SWAP-Assembler 2: Optimization of De Novo Genome Assembler at Large Scale
Energy Technology Data Exchange (ETDEWEB)
Meng, Jintao; Seo, Sangmin; Balaji, Pavan; Wei, Yanjie; Wang, Bingqiang; Feng, Shengzhong
2016-08-16
In this paper, we analyze and optimize the most time-consuming steps of the SWAP-Assembler, a parallel genome assembler, so that it can scale to a large number of cores for huge genomes with the size of sequencing data ranging from terabyes to petabytes. According to the performance analysis results, the most time-consuming steps are input parallelization, k-mer graph construction, and graph simplification (edge merging). For the input parallelization, the input data is divided into virtual fragments with nearly equal size, and the start position and end position of each fragment are automatically separated at the beginning of the reads. In k-mer graph construction, in order to improve the communication efficiency, the message size is kept constant between any two processes by proportionally increasing the number of nucleotides to the number of processes in the input parallelization step for each round. The memory usage is also decreased because only a small part of the input data is processed in each round. With graph simplification, the communication protocol reduces the number of communication loops from four to two loops and decreases the idle communication time. The optimized assembler is denoted as SWAP-Assembler 2 (SWAP2). In our experiments using a 1000 Genomes project dataset of 4 terabytes (the largest dataset ever used for assembling) on the supercomputer Mira, the results show that SWAP2 scales to 131,072 cores with an efficiency of 40%. We also compared our work with both the HipMER assembler and the SWAP-Assembler. On the Yanhuang dataset of 300 gigabytes, SWAP2 shows a 3X speedup and 4X better scalability compared with the HipMer assembler and is 45 times faster than the SWAP-Assembler. The SWAP2 software is available at https://sourceforge.net/projects/swapassembler.
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EPA is proposing to approve a revision to the Antelope Valley Air Quality Management District portion of the California SIP concerning emissions of volatile organic compounds (VOCs) from motor vehicle assembly coating operations.
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Toward tunable doping in graphene FETs by molecular self-assembled monolayers
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
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Eziashi, Magdalene
2018-05-01
Trianglamines are triangular chiral macrocycles that were first synthesized by Gawronski’s group in Poland in the year 2000.1 Despite their unique properties; triangular pore shape, chirality, symmetric structure and tunable pore size, they are still a poorly researched class of macrocycles today. Trianglamines have yet a role to play as porous organic molecules for separation processes, as macrocyclic precursors to build increasingly complex supramolecular assemblies and as building blocks for caged porous organic structures. The aim of the Thesis work is to explore trianglamine, its derivatives, and assemblies as viable porous organic molecules for potential gas capture and separation.
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Robust forests of vertically aligned carbon nanotubes chemically assembled on carbon substrates.
Garrett, David J; Flavel, Benjamin S; Shapter, Joseph G; Baronian, Keith H R; Downard, Alison J
2010-02-02
Forests of vertically aligned carbon nanotubes (VACNTs) have been chemically assembled on carbon surfaces. The structures show excellent stability over a wide potential range and are resistant to degradation from sonication in acid, base, and organic solvent. Acid-treated single-walled carbon nanotubes (SWCNTs) were assembled on amine-terminated tether layers covalently attached to pyrolyzed photoresist films. Tether layers were electrografted to the carbon substrate by reduction of the p-aminobenzenediazonium cation and oxidation of ethylenediamine. The amine-modified surfaces were incubated with cut SWCNTs in the presence of N,N'-dicyclohexylcarbodiimide (DCC), giving forests of vertically aligned carbon nanotubes (VACNTs). The SWCNT assemblies were characterized by scanning electron microscopy, atomic force microscopy, and electrochemistry. Under conditions where the tether layers slow electron transfer between solution-based redox probes and the underlying electrode, the assembly of VACNTs on the tether layer dramatically increases the electron-transfer rate at the surface. The grafting procedure, and hence the preparation of VACNTs, is applicable to a wide range of materials including metals and semiconductors.
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Programming Cells for Dynamic Assembly of Inorganic Nano-Objects with Spatiotemporal Control.
Wang, Xinyu; Pu, Jiahua; An, Bolin; Li, Yingfeng; Shang, Yuequn; Ning, Zhijun; Liu, Yi; Ba, Fang; Zhang, Jiaming; Zhong, Chao
2018-04-01
Programming living cells to organize inorganic nano-objects (NOs) in a spatiotemporally precise fashion would advance new techniques for creating ordered ensembles of NOs and new bio-abiotic hybrid materials with emerging functionalities. Bacterial cells often grow in cellular communities called biofilms. Here, a strategy is reported for programming dynamic biofilm formation for the synchronized assembly of discrete NOs or hetero-nanostructures on diverse interfaces in a dynamic, scalable, and hierarchical fashion. By engineering Escherichia coli to sense blue light and respond by producing biofilm curli fibers, biofilm formation is spatially controlled and the patterned NOs' assembly is simultaneously achieved. Diverse and complex fluorescent quantum dot patterns with a minimum patterning resolution of 100 µm are demonstrated. By temporally controlling the sequential addition of NOs into the culture, multilayered heterostructured thin films are fabricated through autonomous layer-by-layer assembly. It is demonstrated that biologically dynamic self-assembly can be used to advance a new repertoire of nanotechnologies and materials with increasing complexity that would be otherwise challenging to produce. © 2018 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.
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Highly ordered self-assembling polymer/clay nanocomposite barrier film.
Cook, Ray; Chen, Yihong; Beall, Gary W
2015-05-27
Efforts to mimic complex-structured biologically based materials such as abalone shell have occupied substantial research time and effort in science and engineering. The majority of the efforts involve tedious and expensive techniques and processes. Layer-by-layer (LBL) is one such technique that can produce materials with quite unique physical properties, approaching, and in some cases surpassing, those seen in nature. The LBL technique, however, is quite tedious and difficult to implement commercially. We report here the discovery of an organic/inorganic spontaneous self-assembling system that forms a highly structured nanocomposite. The driving force behind this self-assembly appears to be entropy. This discovery should open up completely new avenues to designing hierarchical composites and structures. The films have been studied by X-ray diffraction and the barrier properties for oxygen diffusion measured.
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Seasonal changes in the assembly mechanisms structuring tropical fish communities.
Fitzgerald, Daniel B; Winemiller, Kirk O; Sabaj Pérez, Mark H; Sousa, Leandro M
2017-01-01
Despite growing interest in trait-based approaches to community assembly, little attention has been given to seasonal variation in trait distribution patterns. Mobile animals can rapidly mediate influences of environmental factors and species interactions through dispersal, suggesting that the relative importance of different assembly mechanisms can vary over short time scales. This study analyzes seasonal changes in functional trait distributions of tropical fishes in the Xingu River, a major tributary of the Amazon with large predictable temporal variation in hydrologic conditions and species density. Comparison of observed functional diversity revealed that species within wet-season assemblages were more functionally similar than those in dry-season assemblages. Further, species within wet-season assemblages were more similar than random expectations based on null model predictions. Higher functional richness within dry season communities is consistent with increased niche complementarity during the period when fish densities are highest and biotic interactions should be stronger; however, null model tests suggest that stochastic factors or a combination of assembly mechanisms influence dry-season assemblages. These results demonstrate that the relative influence of community assembly mechanisms can vary seasonally in response to changing abiotic conditions, and suggest that studies attempting to infer a single dominant mechanism from functional patterns may overlook important aspects of the assembly process. During the prolonged flood pulse of the wet season, expanded habitat and lower densities of aquatic organisms likely reduce the influence of competition and predation. This temporal shift in the influence of different assembly mechanisms, rather than any single mechanism, may play a large role in maintaining the structure and diversity of tropical rivers and perhaps other dynamic and biodiverse systems. © 2016 by the Ecological Society of America.
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Wang, Hui; Zhu, Wei; Li, Jian; Tian, Tian; Lan, Yue; Gao, Ning; Wang, Chen; Zhang, Meng; Faul, Charl F. J.
2015-01-01
The controlled formation of MOF-based superstructures with well-defined nanoscale sizes and exquisite morphologies represents a big challenge, but can trigger a new set of properties distinct from their bulk counterparts. Here we report on the use of a self-assembled organic object to template the first example of a nanoscale metal–organic framework (MOF) with a helical morphology. Two prototypical MOFs (HKUST-1 and MIL-100) were used to exemplify the growth of such materials on supramolecular assemblies. Interestingly, it was found that, dependent on the nature of the precursors, not only could well-defined helical MOF nanotubes be facilely fabricated, but novel helical bundle nanostructures could also be formed. These resultant MOF superstructures show additional optical properties and could be used as precursors for the preparation of chiral nanocarbons. PMID:28757993
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Speeding up the self-assembly of a DNA nanodevice using a variety of polar solvents
Kang, Di; Duan, Ruixue; Tan, Yerpeng; Hong, Fan; Wang, Boya; Chen, Zhifei; Xu, Shaofang; Lou, Xiaoding; Wei, Wei; Yurke, Bernard; Xia, Fan
2014-11-01
The specific recognition and programmable assembly properties make DNA a potential material for nanodevices. However, the more intelligent the nanodevice is, the more complicated the structure of the nanodevice is, which limits the speed of DNA assembly. Herein, to address this problem, we investigate the performance of DNA Strand Displacement Reaction (DSDR) in a mixture of polar organic solvents and aqueous buffer and demonstrate that the organic polar solvent can speed up DNA self-assembly efficiently. Taking DSDR in 20% ethanol as an example, first we have demonstrated that the DSDR is highly accelerated in the beginning of the reaction and it can complete 60% of replacement reactions (160% enhancement compared with aqueous buffer) in the first 300 seconds. Secondly, we calculated that the ΔΔG of the DSDR in 20% ethanol (-18.2 kcal mol-1) is lower than that in pure aqueous buffer (-32.6 kcal mol-1), while the activation energy is lowered by introducing ethanol. Finally, we proved that the DSDR on the electrode surface can also be accelerated using this simple strategy. More importantly, to test the efficacy of this approach in nanodevices with a complicated and slow DNA self-assembly process, we apply this strategy in the hybridization chain reaction (HCR) and prove the acceleration is fairly obvious in 20% ethanol, which demonstrates the feasibility of the proposed strategy in DNA nanotechnology and DNA-based biosensors.The specific recognition and programmable assembly properties make DNA a potential material for nanodevices. However, the more intelligent the nanodevice is, the more complicated the structure of the nanodevice is, which limits the speed of DNA assembly. Herein, to address this problem, we investigate the performance of DNA Strand Displacement Reaction (DSDR) in a mixture of polar organic solvents and aqueous buffer and demonstrate that the organic polar solvent can speed up DNA self-assembly efficiently. Taking DSDR in 20% ethanol as an
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Polymer Directed Protein Assemblies
van Rijn, Patrick
2013-01-01
Protein aggregation and protein self-assembly is an important occurrence in natural systems, and is in some form or other dictated by biopolymers. Very obvious influences of biopolymers on protein assemblies are, e. g., virus particles. Viruses are a multi-protein assembly of which the morphology is
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Core/coil assembly for use in superconducting magnets and method for assembling the same
Kassner, David A.
1979-01-01
A core/coil assembly for use in a superconducting magnet of the focusing or bending type used in syncronous particle accelerators comprising a coil assembly contained within an axial bore of the stacked, washer type, carbon steel laminations which comprise the magnet core assembly, and forming an interference fit with said laminations at the operating temperature of said magnet. Also a method for making such core/coil assemblies comprising the steps of cooling the coil assembly to cryogenic temperatures and drawing it rapidly upwards into the bore of said stacked laminations.
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De Novo Assembly of the Pea (Pisum sativum L. Nodule Transcriptome
Directory of Open Access Journals (Sweden)
Vladimir A. Zhukov
2015-01-01
Full Text Available The large size and complexity of the garden pea (Pisum sativum L. genome hamper its sequencing and the discovery of pea gene resources. Although transcriptome sequencing provides extensive information about expressed genes, some tissue-specific transcripts can only be identified from particular organs under appropriate conditions. In this study, we performed RNA sequencing of polyadenylated transcripts from young pea nodules and root tips on an Illumina GAIIx system, followed by de novo transcriptome assembly using the Trinity program. We obtained more than 58,000 and 37,000 contigs from “Nodules” and “Root Tips” assemblies, respectively. The quality of the assemblies was assessed by comparison with pea expressed sequence tags and transcriptome sequencing project data available from NCBI website. The “Nodules” assembly was compared with the “Root Tips” assembly and with pea transcriptome sequencing data from projects indicating tissue specificity. As a result, approximately 13,000 nodule-specific contigs were found and annotated by alignment to known plant protein-coding sequences and by Gene Ontology searching. Of these, 581 sequences were found to possess full CDSs and could thus be considered as novel nodule-specific transcripts of pea. The information about pea nodule-specific gene sequences can be applied for gene-based markers creation, polymorphism studies, and real-time PCR.
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Gorgescu, Walter; Tang, Jonathan; Costes, Sylvain V.; Karpen, Gary H.
2012-01-01
CENP-A (CID in flies) is the histone H3 variant essential for centromere specification, kinetochore formation, and chromosome segregation during cell division. Recent studies have elucidated major cell cycle mechanisms and factors critical for CENP-A incorporation in mitosis, predominantly in cultured cells. However, we do not understand the roles, regulation, and cell cycle timing of CENP-A assembly in somatic tissues in multicellular organisms and in meiosis, the specialized cell division cycle that gives rise to haploid gametes. Here we investigate the timing and requirements for CID assembly in mitotic tissues and male and female meiosis in Drosophila melanogaster, using fixed and live imaging combined with genetic approaches. We find that CID assembly initiates at late telophase and continues during G1 phase in somatic tissues in the organism, later than the metaphase assembly observed in cultured cells. Furthermore, CID assembly occurs at two distinct cell cycle phases during male meiosis: prophase of meiosis I and after exit from meiosis II, in spermatids. CID assembly in prophase I is also conserved in female meiosis. Interestingly, we observe a novel decrease in CID levels after the end of meiosis I and before meiosis II, which correlates temporally with changes in kinetochore organization and orientation. We also demonstrate that CID is retained on mature sperm despite the gross chromatin remodeling that occurs during protamine exchange. Finally, we show that the centromere proteins CAL1 and CENP-C are both required for CID assembly in meiosis and normal progression through spermatogenesis. We conclude that the cell cycle timing of CID assembly in meiosis is different from mitosis and that the efficient propagation of CID through meiotic divisions and on sperm is likely to be important for centromere specification in the developing zygote. PMID:23300382
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Kim, Sungjin; Kim, Jae Hong; Lee, Joon Seok; Park, Chan Beum
2015-08-12
Peptide self-assembly is an attractive route for the synthesis of intricate organic nanostructures that possess remarkable structural variety and biocompatibility. Recent studies on peptide-based, self-assembled materials have expanded beyond the construction of high-order architectures; they are now reporting new functional materials that have application in the emerging fields such as artificial photosynthesis and rechargeable batteries. Nevertheless, there have been few reviews particularly concentrating on such versatile, emerging applications. Herein, recent advances in the synthesis of self-assembled peptide nanomaterials (e.g., cross β-sheet-based amyloid nanostructures, peptide amphiphiles) are selectively reviewed and their new applications in diverse, interdisciplinary fields are described, ranging from optics and energy storage/conversion to healthcare. The applications of peptide-based self-assembled materials in unconventional fields are also highlighted, such as photoluminescent peptide nanostructures, artificial photosynthetic peptide nanomaterials, and lithium-ion battery components. The relation of such functional materials to the rapidly progressing biomedical applications of peptide self-assembly, which include biosensors/chips and regenerative medicine, are discussed. The combination of strategies shown in these applications would further promote the discovery of novel, functional, small materials. © 2015 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.
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Biomimetic Structural Materials: Inspiration from Design and Assembly.
Yaraghi, Nicholas A; Kisailus, David
2018-04-20
Nature assembles weak organic and inorganic constituents into sophisticated hierarchical structures, forming structural composites that demonstrate impressive combinations of strength and toughness. Two such composites are the nacre structure forming the inner layer of many mollusk shells, whose brick-and-mortar architecture has been the gold standard for biomimetic composites, and the cuticle forming the arthropod exoskeleton, whose helicoidal fiber-reinforced architecture has only recently attracted interest for structural biomimetics. In this review, we detail recent biomimetic efforts for the fabrication of strong and tough composite materials possessing the brick-and-mortar and helicoidal architectures. Techniques discussed for the fabrication of nacre- and cuticle-mimetic structures include freeze casting, layer-by-layer deposition, spray deposition, magnetically assisted slip casting, fiber-reinforced composite processing, additive manufacturing, and cholesteric self-assembly. Advantages and limitations to these processes are discussed, as well as the future outlook on the biomimetic landscape for structural composite materials.
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Biomimetic Structural Materials: Inspiration from Design and Assembly
Yaraghi, Nicholas A.; Kisailus, David
2018-04-01
Nature assembles weak organic and inorganic constituents into sophisticated hierarchical structures, forming structural composites that demonstrate impressive combinations of strength and toughness. Two such composites are the nacre structure forming the inner layer of many mollusk shells, whose brick-and-mortar architecture has been the gold standard for biomimetic composites, and the cuticle forming the arthropod exoskeleton, whose helicoidal fiber-reinforced architecture has only recently attracted interest for structural biomimetics. In this review, we detail recent biomimetic efforts for the fabrication of strong and tough composite materials possessing the brick-and-mortar and helicoidal architectures. Techniques discussed for the fabrication of nacre- and cuticle-mimetic structures include freeze casting, layer-by-layer deposition, spray deposition, magnetically assisted slip casting, fiber-reinforced composite processing, additive manufacturing, and cholesteric self-assembly. Advantages and limitations to these processes are discussed, as well as the future outlook on the biomimetic landscape for structural composite materials.
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Liu, Xiaoying; McBride, Sean P.; Jaeger, Heinrich M.; Nealey, Paul F.
2016-07-01
Hybrid nanomaterials comprised of well-organized arrays of colloidal semiconductor quantum dots (QDs) in close proximity to metal nanoparticles (NPs) represent an appealing system for high-performance, spectrum-tunable photon sources with controlled photoluminescence. Experimental realization of such materials requires well-defined QD arrays and precisely controlled QD-metal interspacing. This long-standing challenge is tackled through a strategy that synergistically combines lateral confinement and vertical stacking. Lithographically generated nanoscale patterns with tailored surface chemistry confine the QDs into well-organized arrays with high selectivity through chemical pattern directed assembly, while subsequent coating with a monolayer of close-packed Au NPs introduces the plasmonic component for fluorescence enhancement. The results show uniform fluorescence emission in large-area ordered arrays for the fabricated QD structures and demonstrate five-fold fluorescence amplification for red, yellow, and green QDs in the presence of the Au NP monolayer. Encapsulation of QDs with a silica shell is shown to extend the design space for reliable QD/metal coupling with stronger enhancement of 11 times through the tuning of QD-metal spatial separation. This approach provides new opportunities for designing hybrid nanomaterials with tailored array structures and multiple functionalities for applications such as multiplexed optical coding, color display, and quantum transduction.
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Nuclear fuel assemblies and fuel pins usable in such assemblies
International Nuclear Information System (INIS)
Jolly, R.
1982-01-01
A novel end cap for a nuclear fuel assembly is described in detail. It consists of a trisection arrangement which is received within a cell of a cellular grid. The cell contains abutment means with which the trisection comes into abutment. The grid also contains an abutment means for preventing the trisections from being inserted into the cell in an incorrect orientation. The present design allows fuel pins to be securely held in a hold-down grid of a sub-assembly. The design also allows easier dis-assembly of the swollen and embrittled fuel pins prior to reprocessing. (U.K.)
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Self-assembly of coiled coil peptides into nanoparticles vs 2-d plates: effects of assembly pathway
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.
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Effect of ionic contamination on climatic reliability of printed circuit board assemblies
DEFF Research Database (Denmark)
Verdingovas, Vadimas; Jellesen, Morten Stendahl; Ambat, Rajan
2012-01-01
The effect of NaCl and weak organic acids (WOAs) in “no-clean” wave solder flux residues was studied on electrochemical migration (ECM), leakage current, and corrosion on surface mount chip capacitors using a test printed circuit board assembly (PCBA) substrate having known chip components...
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Integration of Self-Assembled Microvascular Networks with Microfabricated PEG-Based Hydrogels.
Cuchiara, Michael P; Gould, Daniel J; McHale, Melissa K; Dickinson, Mary E; West, Jennifer L
2012-11-07
Despite tremendous efforts, tissue engineered constructs are restricted to thin, simple tissues sustained only by diffusion. The most significant barrier in tissue engineering is insufficient vascularization to deliver nutrients and metabolites during development in vitro and to facilitate rapid vascular integration in vivo. Tissue engineered constructs can be greatly improved by developing perfusable microvascular networks in vitro in order to provide transport that mimics native vascular organization and function. Here a microfluidic hydrogel is integrated with a self-assembling pro-vasculogenic co-culture in a strategy to perfuse microvascular networks in vitro. This approach allows for control over microvascular network self-assembly and employs an anastomotic interface for integration of self-assembled micro-vascular networks with fabricated microchannels. As a result, transport within the system shifts from simple diffusion to vessel supported convective transport and extra-vessel diffusion, thus improving overall mass transport properties. This work impacts the development of perfusable prevascularized tissues in vitro and ultimately tissue engineering applications in vivo.
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In situ studies of nucleation and assembly at soft-hard interfaces
Energy Technology Data Exchange (ETDEWEB)
Dutta, Pulak [Northwestern Univ., Evanston, IL (United States)
2013-04-01
The overall goal of this project was the exploration of new ways to make organic and hybrid (organic-inorganic) materials for energy-related applications. Towards this end, our research focused on the structure and behavior of molecular monolayers at interfaces (including floating monolayers, transferred Langmuir-Blodgett monolayers, and self-assembled monolayers), as well as the biomimetic nucleation of inorganic crystals at soft-hard interfaces. The project resulted in a number of 'firsts' and other notable achievements, which are described in the report.
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Fritz-Laylin, Lillian K; Levy, Yaron Y; Levitan, Edward; Chen, Sean; Cande, W Zacheus; Lai, Elaine Y; Fulton, Chandler
2016-03-01
Centrioles are eukaryotic organelles whose number and position are critical for cilia formation and mitosis. Many cell types assemble new centrioles next to existing ones ("templated" or mentored assembly). Under certain conditions, centrioles also form without pre-existing centrioles (de novo). The synchronous differentiation of Naegleria amoebae to flagellates represents a unique opportunity to study centriole assembly, as nearly 100% of the population transitions from having no centrioles to having two within minutes. Here, we find that Naegleria forms its first centriole de novo, immediately followed by mentored assembly of the second. We also find both de novo and mentored assembly distributed among all major eukaryote lineages. We therefore propose that both modes are ancestral and have been conserved because they serve complementary roles, with de novo assembly as the default when no pre-existing centriole is available, and mentored assembly allowing precise regulation of number, timing, and location of centriole assembly. © 2016 Wiley Periodicals, Inc.
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Bichenkova, Elena V; Sardarian, Ali R; Wilton, Amanda N; Bonnet, Pascal; Bryce, Richard A; Douglas, Kenneth T
2006-01-21
Organic intramolecular exciplexes, N-(4-dimethylaminobenzyl)-N-(1-pyrenemethyl)amine (1) and N'-4-dimethylaminonaphthyl-N-(1-pyrenemethyl)amine (2), were used as model systems to reveal major factors affecting their exciplex fluorescence, and thus lay the basis for developing emissive target-assembled exciplexes for DNA-mounted systems in solution. These models with an aromatic pyrenyl hydrocarbon moiety as an electron acceptor appropriately connected to an aromatic dimethylamino electron donor component (N,N-dimethylaminophenyl or N,N-dimethylaminonaphthyl) showed strong intramolecular exciplex emission in both non-polar and highly polar solvents. The effect of dielectric constant on the maximum wavelength for exciplex emission was studied, and emission was observed for 1 and 2 over the full range of solvent from non-polar hydrocarbons up to N-methylformamide with a dielectric constant of 182. Quantum yields were determined for these intramolecular exciplexes in a range of solvents relative to that for Hoechst 33,258. Conformational analysis of 1 was performed both computationally and via qualitative 2D NMR using (1)H-NOESY experiments. The results obtained indicated the contribution of pre-folded conformation(s) to the ground state of 1 conducive to exciplex emission. This research provides the initial background for design of self-assembled, DNA-mounted exciplexes and underpins further development of exciplex-based hybridisation bioassays.
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Next-generation transcriptome assembly
Energy Technology Data Exchange (ETDEWEB)
Martin, Jeffrey A.; Wang, Zhong
2011-09-01
Transcriptomics studies often rely on partial reference transcriptomes that fail to capture the full catalog of transcripts and their variations. Recent advances in sequencing technologies and assembly algorithms have facilitated the reconstruction of the entire transcriptome by deep RNA sequencing (RNA-seq), even without a reference genome. However, transcriptome assembly from billions of RNA-seq reads, which are often very short, poses a significant informatics challenge. This Review summarizes the recent developments in transcriptome assembly approaches - reference-based, de novo and combined strategies-along with some perspectives on transcriptome assembly in the near future.
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Human Assisted Assembly Processes
Energy Technology Data Exchange (ETDEWEB)
CALTON,TERRI L.; PETERS,RALPH R.
2000-01-01
Automatic assembly sequencing and visualization tools are valuable in determining the best assembly sequences, but without Human Factors and Figure Models (HFFMs) it is difficult to evaluate or visualize human interaction. In industry, accelerating technological advances and shorter market windows have forced companies to turn to an agile manufacturing paradigm. This trend has promoted computerized automation of product design and manufacturing processes, such as automated assembly planning. However, all automated assembly planning software tools assume that the individual components fly into their assembled configuration and generate what appear to be a perfectly valid operations, but in reality the operations cannot physically be carried out by a human. Similarly, human figure modeling algorithms may indicate that assembly operations are not feasible and consequently force design modifications; however, if they had the capability to quickly generate alternative assembly sequences, they might have identified a feasible solution. To solve this problem HFFMs must be integrated with automated assembly planning to allow engineers to verify that assembly operations are possible and to see ways to make the designs even better. Factories will very likely put humans and robots together in cooperative environments to meet the demands for customized products, for purposes including robotic and automated assembly. For robots to work harmoniously within an integrated environment with humans the robots must have cooperative operational skills. For example, in a human only environment, humans may tolerate collisions with one another if they did not cause much pain. This level of tolerance may or may not apply to robot-human environments. Humans expect that robots will be able to operate and navigate in their environments without collisions or interference. The ability to accomplish this is linked to the sensing capabilities available. Current work in the field of cooperative
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Murata, Satoshi
2012-01-01
It is man’s ongoing hope that a machine could somehow adapt to its environment by reorganizing itself. This is what the notion of self-organizing robots is based on. The theme of this book is to examine the feasibility of creating such robots within the limitations of current mechanical engineering. The topics comprise the following aspects of such a pursuit: the philosophy of design of self-organizing mechanical systems; self-organization in biological systems; the history of self-organizing mechanical systems; a case study of a self-assembling/self-repairing system as an autonomous distributed system; a self-organizing robot that can create its own shape and robotic motion; implementation and instrumentation of self-organizing robots; and the future of self-organizing robots. All topics are illustrated with many up-to-date examples, including those from the authors’ own work. The book does not require advanced knowledge of mathematics to be understood, and will be of great benefit to students in the rob...
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International Nuclear Information System (INIS)
Khun Khun, Kamalpreet; Mahajan, Aman; Bedi, R.K.
2011-01-01
Tin oxide nanostructures with well defined morphologies have been obtained through an evaporation induced self assembly process. The technique has been employed using an ultrasonic nebulizer for production of aersol and its subsequent deposition onto a heated glass substrate. The precursor used for aersol production was modified by introducing cationic and anionic surfactants namely cetyl trimethyl ammonium bromide and sodium dodecyl sulphate respectively. The effect of surfactants on the structural, electrical and optical properties of self assembled tin oxide nanostructures were investigated by using X-ray diffraction, field emission scanning electroscope microscopy, two probe technique and photoluminiscence studies. The results reveal that high concentration of surfactants in the precursor solution leads to reduction in crystallite size with significant changes in the morphology of tin oxide nanostructures. Photoluminiscence studies of the nanostructures show emissions in the visible region which exhibit marked changes in the intensities upon variation of surfactants in the precursor solutions.
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Energy Technology Data Exchange (ETDEWEB)
Khun Khun, Kamalpreet [Material Science Laboratory, Department of Physics, Guru Nanak Dev University, Amritsar 143005 (India); Mahajan, Aman, E-mail: dramanmahajan@yahoo.co.in [Material Science Laboratory, Department of Physics, Guru Nanak Dev University, Amritsar 143005 (India); Bedi, R.K. [Material Science Laboratory, Department of Physics, Guru Nanak Dev University, Amritsar 143005 (India)
2011-01-15
Tin oxide nanostructures with well defined morphologies have been obtained through an evaporation induced self assembly process. The technique has been employed using an ultrasonic nebulizer for production of aersol and its subsequent deposition onto a heated glass substrate. The precursor used for aersol production was modified by introducing cationic and anionic surfactants namely cetyl trimethyl ammonium bromide and sodium dodecyl sulphate respectively. The effect of surfactants on the structural, electrical and optical properties of self assembled tin oxide nanostructures were investigated by using X-ray diffraction, field emission scanning electroscope microscopy, two probe technique and photoluminiscence studies. The results reveal that high concentration of surfactants in the precursor solution leads to reduction in crystallite size with significant changes in the morphology of tin oxide nanostructures. Photoluminiscence studies of the nanostructures show emissions in the visible region which exhibit marked changes in the intensities upon variation of surfactants in the precursor solutions.
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Self-Assembly of Infinite Structures
Directory of Open Access Journals (Sweden)
Scott M. Summers
2009-06-01
Full Text Available We review some recent results related to the self-assembly of infinite structures in the Tile Assembly Model. These results include impossibility results, as well as novel tile assembly systems in which shapes and patterns that represent various notions of computation self-assemble. Several open questions are also presented and motivated.
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Multigeometry Nanoparticle Engineering via Kinetic Control through Multistep assembly
Chen, Yingchao; Wang, Xiaojun; Zhang, Ke; Zhang, Fuwu; Mays, Jimmy; Wooley, Karen; Pochan, Darrin
2014-03-01
Organization of block copolymers into complicated multicompartment (MCM) and multigeometry (MGM) nanostructures is of increasing interest. Multistep, co-assembly methods resulting in kinetic control processing was used to produce complex nanoparticles that are not obtained via other assembly methods. Vesicle-cylinder, separate vesicle and cylinder, disk-cylinder, and mixed vesicle nanoparticles were constructed by binary blends of distinct diblock copolymers. Initially, the vesicle former polyacrylic acid-polyisoprene and cylinder former polyacrylic acid-polystyrene which share the same hydrophilic domain but immiscible hydrophobic domain were blended in THF. Secondly, dimaine molecules are added to associate with the common hydrophilic PAA. Importantly, and lastly, by tuning the kinetic addition rate of selective, miscible solvent water, the unlike hydrophobic blocks are kinetically trapped into one particle and eventually nanophase separate to form multiple compartments and multigeometries. The effective bottom-up multistep assembly strategies can be applied in other binary/ternary blends, in which new vesicle-sphere, disk-disk and cylinder-cylinder MCM/MGM nanoparticles were programed. We are grateful for the financial support from the National Science Funding DMR-0906815 (D.J.P. and K.L.W.) and NIST METROLOGY POCHAN 2012.
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The Current Working Conditions in Ugandan Apparel Assembly Plants
Directory of Open Access Journals (Sweden)
Mike Tebyetekerwa
2017-12-01
Full Text Available Background: The present rapid shift of industrialization from developed to developing countries requires developing countries to understand issues related to work organization, management, and working conditions. There are many factors slackening production, of which working conditions is part. A complete inquiry into the workers' working conditions can enable managements to reduce risks in the workplaces and improve productivity. Understanding and awareness of the benefits of workplace research and a probe into the working conditions in the Ugandan apparel assembly plants are urgently required. Methods: A total of 103 (70 women and 33 men workers from five different plants were interviewed. Together with the top management of various plants, questionnaires about the workers' opinions of their physical working conditions were prepared. Data was collected using two methods: (1 questionnaire; and (2 observation of the workers during their work. Results: The results indicated that poor plant working conditions were mainly contributed by the workers' social factors and the management policies. Conclusion: The government, together with the management, should work to improve the working conditions in the apparel assembly plants, as it greatly affects both. Keywords: apparel assembly plants, ergonomics, musculoskeletal disorders, Uganda, working conditions
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International Nuclear Information System (INIS)
Anthony, A.J.
1980-01-01
A bimetallic spacer means is cooperatively associated with a nuclear fuel assembly and operative to resist the occurrence of in-reactor bowing of the nuclear fuel assembly. The bimetallic spacer means in one embodiment of the invention includes a space grid formed, at least principally, of zircaloy to the external surface of which are attached a plurality of stainless steel strips. In another embodiment the strips are attached to fuel pins. In each of the embodiments, the stainless steel strips during power production expand outwardly to a greater extent than do the members to which the stainless steel strips are attached, thereby forming stiff springs which abut against like bimetallic spacer means with which the other nuclear fuel assemblies are provided in a given nuclear reactor core to thus prevent the occurrence of in-reactor bowing of the nuclear fuel assemblies. (author)
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International Nuclear Information System (INIS)
Betten, P.R.
1976-01-01
Under the invention the fuel assembly is particularly suitable for liquid metal cooled fast neutron breeder reactors. Hence, according to the invention a fuel assembly cladding includes inward corrugations with respect to the remainder of the cladding according to a recurring pattern determined by the pitch of the metal wire helically wound round the fuel rods of the assembly. The parts of the cladding pressed inwards correspond to the areas in which the wire encircling the peripheral fuel rods is generally located apart from the cladding, thereby reducing the play between the cladding and the peripheral fuel rods situated in these areas. The reduction in the play in turn improves the coolant flow in the internal secondary channels of the fuel assembly to the detriment of the flow in the peripheral secondary channels and thereby establishes a better coolant fluid temperature profile [fr
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Method and apparatus for assembling a permanent magnet pole assembly
Carl, Jr., Ralph James; Bagepalli, Bharat Sampathkumaran [Niskayuna, NY; Jansen, Patrick Lee [Scotia, NY; Dawson, Richard Nils [Voorheesville, NY; Qu, Ronghai [Clifton Park, NY; Avanesov, Mikhail Avramovich [Moscow, RU
2009-08-11
A pole assembly for a rotor, the pole assembly includes a permanent magnet pole including at least one permanent magnet block, a plurality of laminations including a pole cap mechanically coupled to the pole, and a plurality of laminations including a base plate mechanically coupled to the pole.
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International Nuclear Information System (INIS)
Knutson, D.
1993-01-01
The TPX machine will be assembled in the TFTR Test Cell at the Plasma Physics Laboratory, utilizing the existing TFTR machine foundation. Preparation of the area for assembly will begin after completion of the decontamination and decommissioning phase on TFTR and certification that the radiation levels remaining, if any, are consistent with the types of operations planned. Assembly operations begin with the arrival of the first components, and conclude, approximately 24 months later, with the successful completion of the integrated systems tests and the achievement of a first plasma
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Jovanović Goran
2007-01-01
The paper presents the application of the principle of flexibility of architectonic space on the concrete example of flat composition. This example demonstrates that with a proper choice of structural spans dimensions and regular arrangement of sanitary and ventilation vertical assemblies, a structure with high flexibility in terms of flat space organization and floor space organization, can be achieved.
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Directory of Open Access Journals (Sweden)
Luis Concha-Marambio
Full Text Available Cytokinesis is the last stage in the cell cycle. In prokaryotes, the protein FtsZ guides cell constriction by assembling into a contractile ring-shaped structure termed the Z-ring. Constriction of the Z-ring is driven by the GTPase activity of FtsZ that overcomes the energetic barrier between two protein conformations having different propensities to assemble into polymers. FtsZ is found in psychrophilic, mesophilic and thermophilic organisms thereby functioning at temperatures ranging from subzero to >100°C. To gain insight into the functional adaptations enabling assembly of FtsZ in distinct environmental conditions, we analyzed the energetics of FtsZ function from mesophilic Escherichia coli in comparison with FtsZ from thermophilic Methanocaldococcus jannaschii. Presumably, the assembly may be similarly modulated by temperature for both FtsZ orthologs. The temperature dependence of the first-order rates of nucleotide hydrolysis and of polymer disassembly, indicated an entropy-driven destabilization of the FtsZ-GTP intermediate. This destabilization was true for both mesophilic and thermophilic FtsZ, reflecting a conserved mechanism of disassembly. From the temperature dependence of the critical concentrations for polymerization, we detected a change of opposite sign in the heat capacity, that was partially explained by the specific changes in the solvent-accessible surface area between the free and polymerized states of FtsZ. At the physiological temperature, the assembly of both FtsZ orthologs was found to be driven by a small positive entropy. In contrast, the assembly occurred with a negative enthalpy for mesophilic FtsZ and with a positive enthalpy for thermophilic FtsZ. Notably, the assembly of both FtsZ orthologs is characterized by a critical concentration of similar value (1-2 μM at the environmental temperatures of their host organisms. These findings suggest a simple but robust mechanism of adaptation of FtsZ, previously shown
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Development of ORIGEN libraries for mixed oxide (MOX) fuel assembly designs
International Nuclear Information System (INIS)
Mertyurek, Ugur; Gauld, Ian C.
2016-01-01
Highlights: • ORIGEN MOX library generation process is described. • SCALE burnup calculations are validated against measured MOX fuel samples from the MALIBU program. • ORIGEN MOX libraries are verified using the OECD Phase IV-B benchmark. • There is good agreement for calculated-to-measured isotopic distributions. - Abstract: ORIGEN cross section libraries for reactor-grade mixed oxide (MOX) fuel assembly designs have been developed to provide fast and accurate depletion calculations to predict nuclide inventories, radiation sources and thermal decay heat information needed in safety evaluations and safeguards verification measurements of spent nuclear fuel. These ORIGEN libraries are generated using two-dimensional lattice physics assembly models that include enrichment zoning and cross section data based on ENDF/B-VII.0 evaluations. Using the SCALE depletion sequence, burnup-dependent cross sections are created for selected commercial reactor assembly designs and a representative range of reactor operating conditions, fuel enrichments, and fuel burnup. The burnup dependent cross sections are then interpolated to provide problem-dependent cross sections for ORIGEN, avoiding the need for time-consuming lattice physics calculations. The ORIGEN libraries for MOX assembly designs are validated against destructive radiochemical assay measurements of MOX fuel from the MALIBU international experimental program. This program included measurements of MOX fuel from a 15 × 15 pressurized water reactor assembly and a 9 × 9 boiling water reactor assembly. The ORIGEN MOX libraries are also compared against detailed assembly calculations from the Phase IV-B numerical MOX fuel burnup credit benchmark coordinated by the Nuclear Energy Agency within the Organization for Economic Cooperation and Development. The nuclide compositions calculated by ORIGEN using the MOX libraries are shown to be in good agreement with other physics codes and with experimental data.
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Energy Technology Data Exchange (ETDEWEB)
Li, Jian-Rong; Yakovenko, Andrey A; Lu, Weigang; Timmons, Daren J; Zhuang, Wenjuan; Yuan, Daqiang; Zhou, Hong-Cai
2010-12-15
A systematic exploration of the assembly of Mo₂(O₂C-)₄-based metal–organic molecular architectures structurally controlled by the bridging angles of rigid organic linkers has been performed. Twelve bridging dicarboxylate ligands were designed to be of different sizes with bridging angles of 0, 60, 90, and 120° while incorporating a variety of nonbridging functional groups, and these ligands were used as linkers. These dicarboxylate linkers assemble with quadruply bonded Mo–Mo clusters acting as nodes to give 13 molecular architectures, termed metal–organic polygons/polyhedra with metal cluster node arrangements of a linear shape, triangle, octahedron, and cuboctahedron/anti-cuboctahedron. The syntheses of these complexes have been optimized and their structures determined by single-crystal X-ray diffraction. The results have shown that the shape and size of the resulting molecular architecture can be controlled by tuning the bridging angle and size of the linker, respectively. Functionalization of the linker can adjust the solubility of the ensuing molecular assembly but has little or no effect on the geometry of the product. Preliminary gas adsorption, spectroscopic, and electrochemical properties of selected members were also studied. The present work is trying to enrich metal-containing supramolecular chemistry through the inclusion of well-characterized quadruply bonded Mo–Mo units into the structures, which can widen the prospect of additional electronic functionality, thereby leading to novel properties.
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Li, Jian-Rong; Yakovenko, Andrey A; Lu, Weigang; Timmons, Daren J; Zhuang, Wenjuan; Yuan, Daqiang; Zhou, Hong-Cai
2010-12-15
A systematic exploration of the assembly of Mo2(O2C-)4-based metal-organic molecular architectures structurally controlled by the bridging angles of rigid organic linkers has been performed. Twelve bridging dicarboxylate ligands were designed to be of different sizes with bridging angles of 0, 60, 90, and 120° while incorporating a variety of nonbridging functional groups, and these ligands were used as linkers. These dicarboxylate linkers assemble with quadruply bonded Mo-Mo clusters acting as nodes to give 13 molecular architectures, termed metal-organic polygons/polyhedra with metal cluster node arrangements of a linear shape, triangle, octahedron, and cuboctahedron/anti-cuboctahedron. The syntheses of these complexes have been optimized and their structures determined by single-crystal X-ray diffraction. The results have shown that the shape and size of the resulting molecular architecture can be controlled by tuning the bridging angle and size of the linker, respectively. Functionalization of the linker can adjust the solubility of the ensuing molecular assembly but has little or no effect on the geometry of the product. Preliminary gas adsorption, spectroscopic, and electrochemical properties of selected members were also studied. The present work is trying to enrich metal-containing supramolecular chemistry through the inclusion of well-characterized quadruply bonded Mo-Mo units into the structures, which can widen the prospect of additional electronic functionality, thereby leading to novel properties.
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Wang, Yifeng; Zhou, Jing; Guo, Xuecheng; Hu, Qian; Qin, Chaoran; Liu, Hui; Dong, Meng; Chen, Yanjun
2017-12-01
In this work, a layer-by-layer (LbL) assembled biopolymer microcapsule with separate layer cavities is generated by a novel and convenient gas-liquid microfluidic approach. This approach exhibits combined advantages of microfluidic approach and LbL assembly method, and it can straightforwardly build LbL-assembled capsules in mild aqueous environments at room temperature. In particular, using this approach we can build the polyelectrolyte multilayer capsule with favorable cavities in each layer, and without the need for organic solvent, emulsifying agent, or sacrificial template. Various components (e.g., drugs, proteins, fluorescent dyes, and nanoparticles) can be respectively encapsulated in the separate layer cavities of the LbL-assembled capsules. Moreover, the encapsulated capsules present the ability as colorimetric sensors, and they also exhibit the interesting release behavior. Therefore, the LbL-assembled biopolymer capsule is a promising candidate for biomedical applications in targeted delivery, controlled release, and bio-detection. Copyright © 2017 Elsevier B.V. All rights reserved.
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Assembly Modulated by Particle Position and Shape: A New Concept in Self-Assembly
DEFF Research Database (Denmark)
Tavacoli, Joe W; Heuvingh, Julien; Du Roure, Olivia
2017-01-01
In this communication we outline how the bespoke arrangements and design of micron-sized superparamagnetic shapes provide levers to modulate their assembly under homogeneous magnetic fields. We label this new approach, 'assembly modulated by particle position and shape' (APPS). Specifically, using...... rectangular lattices of superparamagnetic micron-sized cuboids, we construct distinct microstructures by adjusting lattice pitch and angle of array with respect to a magnetic field. Broadly, we find two modes of assembly: (1) immediate 2D jamming of the cuboids as they rotate to align with the applied field...... (rotation-induced jamming) and (2) aggregation via translation after their full alignment (dipole-dipole assembly). The boundary between these two assembly pathways is independent on field strength being solely a function of the cuboid's dimensions, lattice pitch, and array angle with respect to field...
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Tuning the Cavity Size and Chirality of Self-Assembling 3D DNA Crystals
Energy Technology Data Exchange (ETDEWEB)
Simmons, Chad R.; Zhang, Fei; MacCulloch, Tara; Fahmi, Noureddine; Stephanopoulos, Nicholas; Liu, Yan; Seeman, Nadrian C. [Department; Yan, Hao
2017-08-02
The foundational goal of structural DNA nanotechnology—the field that uses oligonucleotides as a molecular building block for the programmable self-assembly of nanostructured systems—was to use DNA to construct three-dimensional (3D) lattices for solving macromolecular structures. The programmable nature of DNA makes it an ideal system for rationally constructing self-assembled crystals and immobilizing guest molecules in a repeating 3D array through their specific stereospatial interactions with the scaffold. In this work, we have extended a previously described motif (4 × 5) by expanding the structure to a system that links four double-helical layers; we use a central weaving oligonucleotide containing a sequence of four six-base repeats (4 × 6), forming a matrix of layers that are organized and dictated by a series of Holliday junctions. In addition, we have assembled mirror image crystals (l-DNA) with the identical sequence that are completely resistant to nucleases. Bromine and selenium derivatives were obtained for the l- and d-DNA forms, respectively, allowing phase determination for both forms and solution of the resulting structures to 3.0 and 3.05 Å resolution. Both right- and left-handed forms crystallized in the trigonal space groups with mirror image 3-fold helical screw axes P32 and P31 for each motif, respectively. The structures reveal a highly organized array of discrete and well-defined cavities that are suitable for hosting guest molecules and allow us to dictate a priori the assembly of guest–DNA conjugates with a specified crystalline hand.
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Huo, Lixia; Du, Pengcheng; Zhou, Hui; Zhang, Kaifeng; Liu, Peng
2017-02-01
It is well known that the self-assembled organic molecules on a solid surface exhibit the friction-reducing performance. However, the effect of the molecular size of the self-assembled organic molecules has not been established. In the present work, self-assembled monolayers (SAMs) of n-alkyltrimethoxysilanes with different alkyl chain lengths (C6, C12, or C18) were fabricated on silicon substrate. The water contact angles of the SAMs increased from 26.8° of the hydroxylated silicon substrate to near 60° after self-assembly. The atomic force microscopy (AFM) analysis results showed that the mean roughness (Ra) of the SAMs decreased with increasing the alkyl chain length. The tribological properties of the SAMs sliding against Al2O3 ball were evaluated on an UMT-2 tribometer, and the worn surfaces of the samples were analyzed by means of Nano Scratch Tester and surface profilometry. It was found that lowest friction coefficient and smallest width of wear were achieved with the SAMs of C12 alkyl chain (C12-SAM). The superior friction reduction and wear resistance of the SAMs in comparison with the bare silicon substrate are attributed to good adhesion of the self-assembled films to the substrate, especially the C12-SAM with desirable alkyl chain length.
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Nanosheet-assembled NiO microstructures for high-performance supercapacitors.
Purushothaman, Kamatchi Kamaraj; Babu, Inbamani Manohara; Sethuraman, Balasubramanian; Muralidharan, Gopalan
2013-11-13
Nanosheet-assembled NiO microstructures have been synthesized via a hydrothermal method. The presence of anionic surfactant in the fabrication process initiates the formation of lamellar micelles and a self-assembling process. This leads to the formation of NiO nanosheets and organizes it into microstructures. The effect of preparation temperature on the morphological, structural, and electrochemical properties and stability upon continuous charge/discharge cycles has been examined for supercapacitor applications. Electrochemical analysis demonstrated that NiO nanosheets prepared at 160 °C are capable of delivering a specific capacitance of 989 F g(-1) at a scan rate of 3 mV s(-1) for the potential window of 0-0.6 V. The nanosheets exhibit excellent capacity retention, 97% retention after 1000 continuous charge/discharge cycles, and an energy density of 49.45 W h kg(-1).
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Dynamic behaviour of diagnostic assemblies
International Nuclear Information System (INIS)
Pecinka, L.
1980-01-01
The methodology is shown of calculating the frequency spectrum of a diagnostic assembly. The oscillations of the assembly as a whole, of a fuel rod bundle, the assembly jacket and of the individual rods in the bundle were considered. The manufacture is suggested of a model assembly which would be used for testing forced vibrations using an experimental water loop. (M.S.)
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Selecting Operations for Assembler Encoding
Directory of Open Access Journals (Sweden)
Tomasz Praczyk
2010-04-01
Full Text Available Assembler Encoding is a neuro-evolutionary method in which a neural network is represented in the form of a simple program called Assembler Encoding Program. The task of the program is to create the so-called Network Definition Matrix which maintains all the information necessary to construct the network. To generate Assembler Encoding Programs and the subsequent neural networks evolutionary techniques are used.
The performance of Assembler Encoding strongly depends on operations used in Assembler Encoding Programs. To select the most effective operations, experiments in the optimization and the predator-prey problem were carried out. In the experiments, Assembler Encoding Programs equipped with different types of operations were tested. The results of the tests are presented at the end of the paper. -
Flashback resistant pre-mixer assembly
Laster, Walter R [Oviedo, FL; Gambacorta, Domenico [Oviedo, FL
2012-02-14
A pre-mixer assembly associated with a fuel supply system for mixing of air and fuel upstream from a main combustion zone in a gas turbine engine. The pre-mixer assembly includes a swirler assembly disposed about a fuel injector of the fuel supply system and a pre-mixer transition member. The swirler assembly includes a forward end defining an air inlet and an opposed aft end. The pre-mixer transition member has a forward end affixed to the aft end of the swirler assembly and an opposed aft end defining an outlet of the pre-mixer assembly. The aft end of the pre-mixer transition member is spaced from a base plate such that a gap is formed between the aft end of the pre-mixer transition member and the base plate for permitting a flow of purge air therethrough to increase a velocity of the air/fuel mixture exiting the pre-mixer assembly.
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International Nuclear Information System (INIS)
Sasaki, Y.; Tashima, J.
1975-01-01
A description is given of nuclear reactor fuel assemblies arranged in the form of a lattice wherein there is attached to the interface of one of two adjacent fuel assemblies a plate spring having a concave portion curved toward said interface and to the interface of the other fuel assembly a plate spring having a convex portion curved away from said interface
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Self-assembled electrical materials from contorted aromatics
Xiao, Shengxiong
This thesis describes the design, synthesis, self-assembly and electrical properties of new types of contorted polycyclic aromatic hydrocarbons. These topologically interesting contorted aromatics show promising transistor characteristics as new building blocks for organic field-effect transistors (OFETs) at different length scales. In chapter 2, a class of pentacenes that are substituted along their long edges with aromatic rings were synthesized. Their solid-state assemblies were studied by X-ray crystallography. Their performance as thin film transistors (TFTs) and single crystal field effect transistors (SCFETs) were systematically evaluated. A structure-property relationship between these highly phenylated pentacenes was found. Chapter 3 explores the new concept of whether a non-planar aromatic core could yield efficacious electronic materials, as the ultimate success in the organic electronics will require a holistic approach to creating new building blocks. Synthesis, functionalization and assembly of a new type of contorted hexabenzocoronene (HBC) whose aromatic core is heavily distorted away from planarity due to the steric congestion around its proximal carbons were discussed. Structural studies by X-ray crystallography showed that these HBC molecules stack into columnar structures in the solid state, which are ideal for conduction. Chapter 4 describes that microscale liquid crystalline thin film OFETs of tetradodecyloxy HBC showed the best transistor properties of all discotic columnar materials. Chapter 5 details the fabrication and characterization of nanoscale single crystalline fiber OFETs of octadodecyloxyl HBC. In Chapter 6 we show that a molecular scale monolayer of HBC acid chlorides could be self-assembled on SiO2 insulating layer and could be organized laterally between the ends of 2 nm carbon nanotube gaps to form high quality FETs that act as environmental and chemical sensors. Chapter 7 details the enforced one-dimensional photoconductivity
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Design of the ITER Tokamak Assembly Tools
International Nuclear Information System (INIS)
Park, Hyunki; Her, Namil; Kim, Byungchul; Im, Kihak; Jung, Kijung; Lee, Jaehyuk; Im, Kisuk
2006-01-01
ITER (International Thermonuclear Experimental Reactor) Procurement allocation among the seven Parties, EU, JA, CN, IN , KO, RF and US had been decided in Dec. 2005. ITER Tokamak assembly tools is one of the nine components allocated to Korea for the construction of the ITER. Assembly tools except measurement and common tools are supplied to assemble the ITER Tokamak and classified into 9 groups according to components to be assembled. Among the 9 groups of assembly tools, large-sized Sector Sub-assembly Tools and Sector Assembly Tools are used at the first stage of ITER Tokamak construction and need to be designed faster than seven other assembly tools. ITER IT (International Team) proposed Korea to accomplish ITA (ITER Transitional Arrangements) Task on detailed design, manufacturing feasibility and contract specification of specific, large sized tools such as Upending Tool, Lifting Tool, Sector Sub-assembly Tool and Sector Assembly Tool in Oct. 2004. Based on the concept design by ITER IT, Korea carried out ITA Task on detailed design of large-sized and specific Sector Sub-assembly and Sector Assembly Tools until Mar. 2006. The Sector Sub-assembly Tools mainly consist of the Upending, Lifting, Vacuum Vessel Support and Bracing, and Sector Sub-assembly Tool, among which the design of three tools are herein. The Sector Assembly Tools mainly consist of the Toroidal Field (TF) Gravity Support Assembly, Sector In-pit Assembly, TF Coil Assembly, Vacuum Vessel (VV) Welding and Vacuum Vessel Thermal Shield (TS) Assembly Tool, among which the design of Sector In-pit Assembly Tool is described herein
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International Nuclear Information System (INIS)
Krause, F.
1986-01-01
In the period from 1980 to 1985, in the Rheinsberg nuclear power plant experimental fuel assemblies were used on lattices at the periphery of the core. These particular fuel assemblies dispose of an extensive in-core instrumentation with different sensors. Besides this, they are fit out with a device to systematically thottle the coolant flow. The large power gradient present at the core position of the experimental fuel assembly causes a temperature profile along the fuel assemblies which is well provable at the measuring points of the outlet temperature. Along the direction of flow this temperature profile in the coolant degrades only slowly. This effect is to be taken into account when measuring the fuel assembly outlet temperature of WWER fuel assemblies. Besides this, the results of the measurements hinted both at a γ-heating of the temperature measuring points and at tolerances in the calculation of the micro power density distribution. (author)
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International Nuclear Information System (INIS)
Nagano, Mamoru; Yoshioka, Ritsuo
1983-01-01
Purpose: To effectively utilize nuclear fuels by increasing the reactivity of a fuel assembly and reduce the concentration at the central region thereof upon completion of the burning. Constitution: A fuel assembly is bisected into a central region and a peripheral region by disposing an inner channel box within a channel box. The flow rate of coolants passing through the central region is made greater than that in the peripheral region. The concentration of uranium 235 of the fuel rods in the central region is made higher. In such a structure, since the moderating effect in the central region is improved, the reactivity of the fuel assembly is increased and the uranium concentration in the central region upon completion of the burning can be reduced, fuel economy and effective utilization of uranium can be attained. (Kamimura, M.)
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International Nuclear Information System (INIS)
Nakatsuka, Masafumi; Matsuzuka, Ryuji.
1976-01-01
Object: To provide a fuel assembly which can decrease pressure loss of coolant to uniform temperature. Structure: A sectional area of a flow passage in the vicinity of an inner peripheral surface of a wrapper tube is limited over the entire length to prevent the temperature of a fuel element in the outermost peripheral portion from being excessively decreased to thereby flatten temperature distribution. To this end, a plurality of pincture-frame-like sheet metals constituting a spacer for supporting a fuel assembly, which has a plurality of fuel elements planted lengthwise and in given spaced relation within the wrapper tube, is disposed in longitudinal grooves and in stacked fashion to form a substantially honeycomb-like space in cross section. The fuel elements are inserted and supported in the space to form a fuel assembly. (Kamimura, M.)
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Welding facilities for NPP assembling
International Nuclear Information System (INIS)
Rojtenberg, S.S.
1987-01-01
Recommendations concerning the choice of equipment for welding in pre-assembling work shops, in the enlarging assembling shops and at the assembling site, are given. Advanced production automatic welders and semiautomatic machines, applied during the NPP equipment assembling as well as automatic machines specially produced for welding the main reactor components and pipelines are described. Automatic and semiautomatic machine and manual welding post supply sources are considered
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Self-assembled cellulose materials for biomedicine: A review.
Yang, Jisheng; Li, Jinfeng
2018-02-01
Cellulose-based materials have reached a growing interest for the improvement of biomedicine, due to their good biocompatibility, biodegradability, and low toxicity. Self-assembly is a spontaneous process by which organized structures with particular functions and properties could be obtained without additional complicated processing steps. This article describes the modifications, properties and applications of cellulose and its derivatives, which including a detailed review of representative types of solvents such as NMMO, DMAc/LiCl, some molten salt hydrates, some aqueous solutions of metal complexes, ionic liquids and NaOH-water system etc. The modifications were frequently performed by esterification, etherification, ATRP, RAFT, ROP and other novel methods. Stimuli-responsive cellulose-based materials, such as temperature-, pH-, light- and redox-responsive, were synthesized for their superior performance. Additionally, the applications of cellulose-based materials which can self-assemble into micelles, vesicles and other aggregates, for drug/gene delivery, bioimaging, biosensor, are also discussed. Copyright © 2017 Elsevier Ltd. All rights reserved.
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De novo Assembly and Analysis of the Chilean Pencil Catfish Trichomycterus areolatus Transcriptome
Schulze, Thomas T.; Ali, Jonathan M.; Bartlett, Maggie L.; McFarland, Madalyn M.; Clement, Emalie J.; Won, Harim I.; Sanford, Austin G.; Monzingo, Elyssa B.; Martens, Matthew C.; Hemsley, Ryan M.; Kumar, Sidharta; Gouin, Nicolas; Kolok, Alan S.; Davis, Paul H.
2016-01-01
Trichomycterus areolatus is an endemic species of pencil catfish that inhabits the riffles and rapids of many freshwater ecosystems of Chile. Despite its unique adaptation to Chile's high gradient watersheds and therefore potential application in the investigation of ecosystem integrity and environmental contamination, relatively little is known regarding the molecular biology of this environmental sentinel. Here, we detail the assembly of the Trichomycterus areolatus transcriptome, a molecular resource for the study of this organism and its molecular response to the environment. RNA-Seq reads were obtained by next-generation sequencing with an Illumina® platform and processed using PRINSEQ. The transcriptome assembly was performed using TRINITY assembler. Transcriptome validation was performed by functional characterization with KOG, KEGG, and GO analyses. Additionally, differential expression analysis highlights sex-specific expression patterns, and a list of endocrine and oxidative stress related transcripts are included. PMID:27672404
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Makam, Pandeeswar; Gazit, Ehud
2018-05-21
Molecular self-assembly is a ubiquitous process in nature and central to bottom-up nanotechnology. In particular, the organization of peptide building blocks into ordered supramolecular structures has gained much interest due to the unique properties of the products, including biocompatibility, chemical and structural diversity, robustness and ease of large-scale synthesis. In addition, peptides, as short as dipeptides, contain all the molecular information needed to spontaneously form well-ordered structures at both the nano- and the micro-scale. Therefore, peptide supramolecular assembly has been effectively utilized to produce novel materials with tailored properties for various applications in the fields of material science, engineering, medicine, and biology. To further expand the conformational space of peptide assemblies in terms of structural and functional complexity, multicomponent (two or more) peptide supramolecular co-assembly has recently evolved as a promising extended approach, similar to the structural diversity of natural sequence-defined biopolymers (proteins) as well as of synthetic covalent co-polymers. The use of this methodology was recently demonstrated in various applications, such as nanostructure physical dimension control, the creation of non-canonical complex topologies, mechanical strength modulation, the design of light harvesting soft materials, fabrication of electrically conducting devices, induced fluorescence, enzymatic catalysis and tissue engineering. In light of these significant advancements in the field of peptide supramolecular co-assembly in the last few years, in this tutorial review, we provide an updated overview and future prospects of this emerging subject.
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Composite turbine bucket assembly
Liotta, Gary Charles; Garcia-Crespo, Andres
2014-05-20
A composite turbine blade assembly includes a ceramic blade including an airfoil portion, a shank portion and an attachment portion; and a transition assembly adapted to attach the ceramic blade to a turbine disk or rotor, the transition assembly including first and second transition components clamped together, trapping said ceramic airfoil therebetween. Interior surfaces of the first and second transition portions are formed to mate with the shank portion and the attachment portion of the ceramic blade, and exterior surfaces of said first and second transition components are formed to include an attachment feature enabling the transition assembly to be attached to the turbine rotor or disk.
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Liu, Rong; Ishimatsu, Ryoichi; Yahiro, Masayuki; Adachi, Chihaya; Nakano, Koji; Imato, Toshihiko
2015-01-01
A compact photometric detector was constructed from an organic light emitting diode (OLED) based on a europium complex, europium(diben-zoylmethanato)3(bathophenanthroline) (Eu(DBM)3bath), as the light source and an organic photodiode (OPD) fabricated from a hetero-junction of two layers of copper phthalocyanine (CuPc)/fullerene (C60) as the photo-detector on a microchip prepared from poly(dimethylsiloxan) (PDMS) and was applied to the determination of phosphate. The OLED and the OPD were fabricated by a vapor deposition method on an indium tin oxide (ITO) coated glass substrate with the following layered structure; Glass (0.7 mm)/ITO (110 nm)/4,4'-bis[N-(1-naphthyl)-N-phenyl amino]-biphenyl (α-NPD) (30 nm)/4,4'-di(N-carbazolyl)biphenyl (CBP): Eu(3+) (8 wt%, 30 nm)/bathocuproine (BCP) (30 nm)/aluminum tris(8-hydroxyquinoline) (Alq3) (25 nm)/magnesium and silver (MgAg) (100 nm)/Ag (10nm) and Glass (0.7 mm)/ITO (110 nm)/CuPc (35 nm)/C60 (50 nm)/BCP (10 nm)/Ag (50 nm), respectively. The OLED based on the europium complex emitted a sharp light at the wavelength of 612 nm with a full width at half maximum (FWHM) of 8 nm. The performance of the photometric detector assembled was evaluated based on measurements of the absorbance of different concentrations of malachite green (MG) solutions for a batch system with 1cm long path length. The molar absorptive coefficient of the MG solution, calculated from the photocurrent of the OPD, was in good agreement with the value reported in the literature. A microchip with two inlets and one outlet U-shaped channel was prepared by a conventional photolithograph method. The OLED and the OPD were configured so as to face each other through the PDMS microchip in parallel in order to align the light axis of the OLED and the OPD with the flow cell (optical path length of 5mm), which was located at the end of outlet. For the determination of phosphate, an ion-association reaction between MG and a molybdenum-phosphate complex was utilized
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Controlled Synthesis of Nanowire Assemblies by Ion-Track Template Electrodeposition
Rauber, Markus
2012-01-01
The development of methods that allow the organization of nanostructures into integrated arrangements is crucial to realizing applications based on nanowires. Although various such methods exist, the direct synthesis of complex nanowire structures is one of the most suitable approaches for translating a large quantity of nanostructures into micro-/macroscale dimensions. In particular, three-dimensional (3-D) nanowire assemblies with a high integration level and adjustable connecti...
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TOOL ASSEMBLY WITH BI-DIRECTIONAL BEARING
Longhurst, G.E.
1961-07-11
A two-direction motion bearing which is incorporated in a refueling nuclear fuel element trsnsfer tool assembly is described. A plurality of bi- directional bearing assembliesare fixed equi-distantly about the circumference of the transfer tool assembly to provide the tool assembly with a bearing surface- for both axial and rotational motion. Each bi-directional bearing assembly contains a plurality of circumferentially bulged rollers mounted in a unique arrangement which will provide a bearing surface for rotational movement of the tool assembly within a bore. The bi-direc tional bearing assembly itself is capable of rational motion and thus provides for longitudinal movement of the tool assembly.
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Improving transcriptome assembly through error correction of high-throughput sequence reads
Directory of Open Access Journals (Sweden)
Matthew D. MacManes
2013-07-01
Full Text Available The study of functional genomics, particularly in non-model organisms, has been dramatically improved over the last few years by the use of transcriptomes and RNAseq. While these studies are potentially extremely powerful, a computationally intensive procedure, the de novo construction of a reference transcriptome must be completed as a prerequisite to further analyses. The accurate reference is critically important as all downstream steps, including estimating transcript abundance are critically dependent on the construction of an accurate reference. Though a substantial amount of research has been done on assembly, only recently have the pre-assembly procedures been studied in detail. Specifically, several stand-alone error correction modules have been reported on and, while they have shown to be effective in reducing errors at the level of sequencing reads, how error correction impacts assembly accuracy is largely unknown. Here, we show via use of a simulated and empiric dataset, that applying error correction to sequencing reads has significant positive effects on assembly accuracy, and should be applied to all datasets. A complete collection of commands which will allow for the production of Reptile corrected reads is available at https://github.com/macmanes/error_correction/tree/master/scripts and as File S1.
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Liposomes self-assembled from electrosprayed composite microparticles
International Nuclear Information System (INIS)
Yu Dengguang; Yang Junhe; Wang Xia; Tian Feng
2012-01-01
Composite microparticles, consisting of polyvinylpyrrolidone (PVP), naproxen (NAP) and lecithin (PC), have been successfully prepared using an electrospraying process and exploited as templates to manipulate molecular self-assembly for the synthesis of liposomes in situ. Field emission scanning electron microscope (FESEM) and transmission electron microscope (TEM) observations demonstrate that the microparticles have an average diameter of 960 ± 140 nm and a homogeneous structure. X-ray diffraction (XRD) patterns, differential scanning calorimetry (DSC) and attenuated total reflectance-Fourier transform infrared (ATR-FTIR) results verify that the building blocks NAP and PC are scattered in the polymer matrix in a molecular way owing to the very fast drying of the electrospraying process and the favorable secondary interactions among the components. FESEM, scanning probe microscope (SPM) and TEM observations demonstrate that the liposomes can be achieved through molecular self-assembly in situ when the microparticles contact water thanks to ‘like prefers like’ and by means of the confinement effect of the microparticles. The liposomes have an encapsulation rate of 91.3%, and 80.7% of the drug in the liposomes can be freed into the dissolution medium in a sustained way and by a diffusion mechanism over a period of 24 h. The developed strategy not only provides a new, facile, and effective method to assemble and organize molecules of multiple components into liposomes with electrosprayed microparticles as templates, but also opens a new avenue for nanofabrication in a step-by-step and controllable way. (paper)
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Norgal: extraction and de novo assembly of mitochondrial DNA from whole-genome sequencing data.
Al-Nakeeb, Kosai; Petersen, Thomas Nordahl; Sicheritz-Pontén, Thomas
2017-11-21
Whole-genome sequencing (WGS) projects provide short read nucleotide sequences from nuclear and possibly organelle DNA depending on the source of origin. Mitochondrial DNA is present in animals and fungi, while plants contain DNA from both mitochondria and chloroplasts. Current techniques for separating organelle reads from nuclear reads in WGS data require full reference or partial seed sequences for assembling. Norgal (de Novo ORGAneLle extractor) avoids this requirement by identifying a high frequency subset of k-mers that are predominantly of mitochondrial origin and performing a de novo assembly on a subset of reads that contains these k-mers. The method was applied to WGS data from a panda, brown algae seaweed, butterfly and filamentous fungus. We were able to extract full circular mitochondrial genomes and obtained sequence identities to the reference sequences in the range from 98.5 to 99.5%. We also assembled the chloroplasts of grape vines and cucumbers using Norgal together with seed-based de novo assemblers. Norgal is a pipeline that can extract and assemble full or partial mitochondrial and chloroplast genomes from WGS short reads without prior knowledge. The program is available at: https://bitbucket.org/kosaidtu/norgal .
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International Nuclear Information System (INIS)
Shirakawa, Ken-etsu.
1988-01-01
Purpose: To reduce the pressure loss of coolants by fuel assembly spacers. Constitution: Spacers for supporting a fuel assembly are attached by means of a plurality of wires to an outer frame. The outer frame is made of shape memory alloy such that the wires are caused to slacken at normal temperature and the slacking of the wires is eliminated in excess of the transition temperature. Since the wires slacken at the normal temperature, fuel rods can be inserted easily. After the insertion of the fuel rods, when the entire portion or the outer frame is heated by water or gas at a predetermined temperature, the outer frame resumes its previously memorized shape to tighten the wires and, accordingly, the fuel rods can be supported firmly. In this way, since the fuel rods are inserted in the slacken state of the wires and, after the assembling, the outer frame resumes its memorized shape, the assembling work can be conducted efficiently. (Kamimura, M.)
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Asadi, Kamal; Gholamrezaie, Fatemeh; Smits, Edsger C. P.; Blom, Paul W. M.; de Boer, Bert
2007-01-01
Charge carrier injection into two semiconducting polymers is investigated in field-effect transistors using gold source and drain electrodes that are modified by self-assembled monolayers of alkanethiols and perfluorinated alkanethiols. The presence of an interfacial dipole associated with the
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Structure of Hepatitis E Virion-Sized Particle Reveals an RNA-Dependent Viral Assembly Pathway
Energy Technology Data Exchange (ETDEWEB)
Xing, L.; Wall, J.; Li, T.-C.; Mayazaki, N.; Simon, M. N.; Moore, M.; Wang, C.-Y.; Takeda, N.; Wakita, T.; Miyamura, T.; Cheng, R. H.
2010-10-22
Hepatitis E virus (HEV) induces acute hepatitis in humans with a high fatality rate in pregnant women. There is a need for anti-HEV research to understand the assembly process of HEV native capsid. Here, we produced a large virion-sized and a small T=1 capsid by expressing the HEV capsid protein in insect cells with and without the N-terminal 111 residues, respectively, for comparative structural analysis. The virion-sized capsid demonstrates a T=3 icosahedral lattice and contains RNA fragment in contrast to the RNA-free T=1 capsid. However, both capsids shared common decameric organization. The in vitro assembly further demonstrated that HEV capsid protein had the intrinsic ability to form decameric intermediate. Our data suggest that RNA binding is the extrinsic factor essential for the assembly of HEV native capsids.
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Assembling Transgender Moments
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"…
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International Nuclear Information System (INIS)
Hiranuma, Hiroshi.
1976-01-01
Object: To remove limitation of the number of storage of fuel assemblies to increase the number of storage thereof so as to relatively reduce the water depth required for shielding radioactive rays. Structure: Fuel assembly storage rack containers for receiving a plurality of spent fuel assembly racks are stacked in multi-layer fashion within a storage pool filled with water for shielding radioactive rays and removing heat. (Furukawa, Y.)
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Polymer Directed Protein Assemblies
Directory of Open Access Journals (Sweden)
Patrick van Rijn
2013-05-01
Full Text Available Protein aggregation and protein self-assembly is an important occurrence in natural systems, and is in some form or other dictated by biopolymers. Very obvious influences of biopolymers on protein assemblies are, e.g., virus particles. Viruses are a multi-protein assembly of which the morphology is dictated by poly-nucleotides namely RNA or DNA. This “biopolymer” directs the proteins and imposes limitations on the structure like the length or diameter of the particle. Not only do these bionanoparticles use polymer-directed self-assembly, also processes like amyloid formation are in a way a result of directed protein assembly by partial unfolded/misfolded biopolymers namely, polypeptides. The combination of proteins and synthetic polymers, inspired by the natural processes, are therefore regarded as a highly promising area of research. Directed protein assembly is versatile with respect to the possible interactions which brings together the protein and polymer, e.g., electrostatic, v.d. Waals forces or covalent conjugation, and possible combinations are numerous due to the large amounts of different polymers and proteins available. The protein-polymer interacting behavior and overall morphology is envisioned to aid in clarifying protein-protein interactions and are thought to entail some interesting new functions and properties which will ultimately lead to novel bio-hybrid materials.
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Czech Academy of Sciences Publication Activity Database
Wimmerová, Martina; Siglerová, Věra; Šaman, David; Šlouf, Miroslav; Kaletová, Eva; Wimmer, Zdeněk
2017-01-01
Roč. 117, JAN (2017), s. 38-43 ISSN 0039-128X R&D Projects: GA MŠk LD15012; GA MŠk(CZ) LO1507 Institutional support: RVO:61389030 ; RVO:61388963 ; RVO:61389013 Keywords : glycosides * esterification * resolution * sterols * esters * foods * l. * beta-Sitosterol * Acylated steryl glycoside * Lipase * Ionic liquid * Supramolecular self-assembly * Pharmacological activity Subject RIV: CC - Organic Chemistry; CD - Macromolecular Chemistry (UMCH-V) OBOR OECD: Organic chemistry; Polymer science (UMCH-V); Organic chemistry (UOCHB-X) Impact factor: 2.282, year: 2016
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New tool to assemble repetitive regions using next-generation sequencing data
Kuśmirek, Wiktor; Nowak, Robert M.; Neumann, Łukasz
2017-08-01
The next generation sequencing techniques produce a large amount of sequencing data. Some part of the genome are composed of repetitive DNA sequences, which are very problematic for the existing genome assemblers. We propose a modification of the algorithm for a DNA assembly, which uses the relative frequency of reads to properly reconstruct repetitive sequences. The new approach was implemented and tested, as a demonstration of the capability of our software we present some results for model organisms. The new implementation, using a three-layer software architecture was selected, where the presentation layer, data processing layer, and data storage layer were kept separate. Source code as well as demo application with web interface and the additional data are available at project web-page: http://dnaasm.sourceforge.net.
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Judge, Kim; Hunt, Martin; Reuter, Sandra; Tracey, Alan; Quail, Michael A; Parkhill, Julian; Peacock, Sharon J
2016-09-01
Translating the Oxford Nanopore MinION sequencing technology into medical microbiology requires on-going analysis that keeps pace with technological improvements to the instrument and release of associated analysis software. Here, we use a multidrug-resistant Enterobacter kobei isolate as a model organism to compare open source software for the assembly of genome data, and relate this to the time taken to generate actionable information. Three software tools (PBcR, Canu and miniasm) were used to assemble MinION data and a fourth (SPAdes) was used to combine MinION and Illumina data to produce a hybrid assembly. All four had a similar number of contigs and were more contiguous than the assembly using Illumina data alone, with SPAdes producing a single chromosomal contig. Evaluation of the four assemblies to represent the genome structure revealed a single large inversion in the SPAdes assembly, which also incorrectly integrated a plasmid into the chromosomal contig. Almost 50 %, 80 % and 90 % of MinION pass reads were generated in the first 6, 9 and 12 h, respectively. Using data from the first 6 h alone led to a less accurate, fragmented assembly, but data from the first 9 or 12 h generated similar assemblies to that from 48 h sequencing. Assemblies were generated in 2 h using Canu, indicating that going from isolate to assembled data is possible in less than 48 h. MinION data identified that genes responsible for resistance were carried by two plasmids encoding resistance to carbapenem and to sulphonamides, rifampicin and aminoglycosides, respectively.
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Multi-scale coarse-graining for the study of assembly pathways in DNA-brick self-assembly
Fonseca, Pedro; Romano, Flavio; Schreck, John S.; Ouldridge, Thomas E.; Doye, Jonathan P. K.; Louis, Ard A.
2018-04-01
Inspired by recent successes using single-stranded DNA tiles to produce complex structures, we develop a two-step coarse-graining approach that uses detailed thermodynamic calculations with oxDNA, a nucleotide-based model of DNA, to parametrize a coarser kinetic model that can reach the time and length scales needed to study the assembly mechanisms of these structures. We test the model by performing a detailed study of the assembly pathways for a two-dimensional target structure made up of 334 unique strands each of which are 42 nucleotides long. Without adjustable parameters, the model reproduces a critical temperature for the formation of the assembly that is close to the temperature at which assembly first occurs in experiments. Furthermore, the model allows us to investigate in detail the nucleation barriers and the distribution of critical nucleus shapes for the assembly of a single target structure. The assembly intermediates are compact and highly connected (although not maximally so), and classical nucleation theory provides a good fit to the height and shape of the nucleation barrier at temperatures close to where assembly first occurs.
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Sequencing and De novo Draft Assemblies of the Fathead Minnow (Pimphales promelas)Reference Genome
This study was undertaken to develop genome-scale resources for the fathead minnow (Pimphales promelas) an important model organism widely used in both aquatic ecotoxicology research and in regulatory toxicity testing. We report on the first sequencing and two draft assemblies fo...
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Biomineralization of a Self-assembled, Soft-Matrix Precursor: Enamel
Snead, Malcolm L.
2015-04-01
Enamel is the bioceramic covering of teeth, a composite tissue composed of hierarchical organized hydroxyapatite crystallites fabricated by cells under physiologic pH and temperature. Enamel material properties resist wear and fracture to serve a lifetime of chewing. Understanding the cellular and molecular mechanisms for enamel formation may allow a biology-inspired approach to material fabrication based on self-assembling proteins that control form and function. A genetic understanding of human diseases exposes insight from nature's errors by exposing critical fabrication events that can be validated experimentally and duplicated in mice using genetic engineering to phenocopy the human disease so that it can be explored in detail. This approach led to an assessment of amelogenin protein self-assembly that, when altered, disrupts fabrication of the soft enamel protein matrix. A misassembled protein matrix precursor results in loss of cell-to-matrix contacts essential to fabrication and mineralization.
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Dynamic Multi-Component Hemiaminal Assembly
You, Lei; Long, S. Reid; Lynch, Vincent M.
2012-01-01
A simple approach to generating in situ metal templated tris-(2-picolyl)amine-like multi-component assemblies with potential applications in molecular recognition and sensing is reported. The assembly is based on the reversible covalent association between di-(2-picolyl)amine and aldehydes. Zinc ion is the best for inducing assembly among the metal salts investigated, while 2-picolinaldehyde is the best among the heterocyclic aldehydes studied. Although an equilibrium constant of 6.6 * 103 M-1 was measured for the assembly formed by 2-picolinaldehdye, di-(2-picolyl)amine, and zinc triflate, the equilibrium constants for other systems are in the 102 M-1 range. X-ray structural analysis revealed that zinc adopts a trigonal bipyramidal geometry within the assembled ligand. The diversity and equilibrium of the assemblies are readily altered by simply changing concentrations, varying components, or adding counter anions. PMID:21919095
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Tareq, Foysal Kabir; Fayzunnesa, Mst; Kabir, Md Shahariar; Nuzat, Musrat
2018-01-01
The aim of this investigation to preparation of silver nanoparticles organized chitosan nano polymer, which effective against microbial and pathogens, when apply to liquid medium and edible food products surface, will rescue the growth of microbes. Self-assembly approach used to synthesis of silver nanoparticles and silver nanoparticles organized chitosan nano polymer. Silver nanoparticles and silver nanoparticles organized chitosan nano polymer and film characterized using Ultra-violate visible spectrometer (UV-vis), X-ray diffraction (X-ray), and Scanning electronic microscope (SEM). The crystalline structured protein capped nano silver successfully synthesized at range of 12 nm-29 nm and organized into chitosan nano polymer. Antimicrobial ingredient in liquid medium and food product surface provide to rescue oxidative change and growth of microorganism to provide higher safety. The silver nanoparticles organized chitosan nano polymer caused the death of microorganism. The materials in nano scale synthesized successfully using self-assembly method, which showed good antimicrobial properties. Copyright © 2017 Elsevier Ltd. All rights reserved.
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Advanced gray rod control assembly
Drudy, Keith J; Carlson, William R; Conner, Michael E; Goldenfield, Mark; Hone, Michael J; Long, Jr., Carroll J; Parkinson, Jerod; Pomirleanu, Radu O
2013-09-17
An advanced gray rod control assembly (GRCA) for a nuclear reactor. The GRCA provides controlled insertion of gray rod assemblies into the reactor, thereby controlling the rate of power produced by the reactor and providing reactivity control at full power. Each gray rod assembly includes an elongated tubular member, a primary neutron-absorber disposed within the tubular member said neutron-absorber comprising an absorber material, preferably tungsten, having a 2200 m/s neutron absorption microscopic capture cross-section of from 10 to 30 barns. An internal support tube can be positioned between the primary absorber and the tubular member as a secondary absorber to enhance neutron absorption, absorber depletion, assembly weight, and assembly heat transfer characteristics.
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Multi-Robot Assembly Strategies and Metrics
MARVEL, JEREMY A.; BOSTELMAN, ROGER; FALCO, JOE
2018-01-01
We present a survey of multi-robot assembly applications and methods and describe trends and general insights into the multi-robot assembly problem for industrial applications. We focus on fixtureless assembly strategies featuring two or more robotic systems. Such robotic systems include industrial robot arms, dexterous robotic hands, and autonomous mobile platforms, such as automated guided vehicles. In this survey, we identify the types of assemblies that are enabled by utilizing multiple robots, the algorithms that synchronize the motions of the robots to complete the assembly operations, and the metrics used to assess the quality and performance of the assemblies. PMID:29497234
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Multi-Robot Assembly Strategies and Metrics.
Marvel, Jeremy A; Bostelman, Roger; Falco, Joe
2018-02-01
We present a survey of multi-robot assembly applications and methods and describe trends and general insights into the multi-robot assembly problem for industrial applications. We focus on fixtureless assembly strategies featuring two or more robotic systems. Such robotic systems include industrial robot arms, dexterous robotic hands, and autonomous mobile platforms, such as automated guided vehicles. In this survey, we identify the types of assemblies that are enabled by utilizing multiple robots, the algorithms that synchronize the motions of the robots to complete the assembly operations, and the metrics used to assess the quality and performance of the assemblies.
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Fichtman, Boris; Ramos, Corinne; Rasala, Beth; Harel, Amnon; Forbes, Douglass J
2010-12-01
Nuclear pore complexes (NPCs) are large proteinaceous channels embedded in double nuclear membranes, which carry out nucleocytoplasmic exchange. The mechanism of nuclear pore assembly involves a unique challenge, as it requires creation of a long-lived membrane-lined channel connecting the inner and outer nuclear membranes. This stabilized membrane channel has little evolutionary precedent. Here we mapped inner/outer nuclear membrane fusion in NPC assembly biochemically by using novel assembly intermediates and membrane fusion inhibitors. Incubation of a Xenopus in vitro nuclear assembly system at 14°C revealed an early pore intermediate where nucleoporin subunits POM121 and the Nup107-160 complex were organized in a punctate pattern on the inner nuclear membrane. With time, this intermediate progressed to diffusion channel formation and finally to complete nuclear pore assembly. Correct channel formation was blocked by the hemifusion inhibitor lysophosphatidylcholine (LPC), but not if a complementary-shaped lipid, oleic acid (OA), was simultaneously added, as determined with a novel fluorescent dextran-quenching assay. Importantly, recruitment of the bulk of FG nucleoporins, characteristic of mature nuclear pores, was not observed before diffusion channel formation and was prevented by LPC or OA, but not by LPC+OA. These results map the crucial inner/outer nuclear membrane fusion event of NPC assembly downstream of POM121/Nup107-160 complex interaction and upstream or at the time of FG nucleoporin recruitment.
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TAF11 assembles RISC loading complex to enhance RNAi efficiency
Liang, Chunyang; Wang, Yibing; Murota, Yukiko; Liu, Xiang; Smith, Dean; Siomi, Mikiko C.; Liu, Qinghua
2015-01-01
SUMMARY Assembly of the RNA-induced silencing complex (RISC) requires formation of the RISC loading complex (RLC), which contains Dicer-2(Dcr-2)-R2D2 complex and recruits duplex siRNA to Ago2 in Drosophila melanogaster. However, the precise composition and action mechanism of Drosophila RLC remain unclear. Here, we identified the missing factor of RLC as TATA-binding protein associated factor 11 (TAF11) by genetic screen. Although an annotated nuclear transcription factor, we found that TAF11 also associated with Dcr-2/R2D2 and localized to cytoplasmic D2 bodies. Consistent with defective RLC assembly in taf11−/− ovary extract, we reconstituted the RLC in vitro using recombinant Dcr-2-R2D2 complex, TAF11, and duplex siRNA. Furthermore, we showed that TAF11 tetramer facilitates Dcr-2-R2D2 tetramerization to enhance siRNA binding and RISC loading activities. Together, our genetic and biochemical studies define the molecular nature of Drosophila RLC and elucidate a novel cytoplasmic function of TAF11 in organizing RLC assembly to enhance RNAi efficiency. PMID:26257286
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ASSEMBLY TRANSFER SYSTEM DESCRIPTION DOCUMENT
International Nuclear Information System (INIS)
Gorpani, B.
2000-01-01
The Assembly Transfer System (ATS) receives, cools, and opens rail and truck transportation casks from the Carrier/Cask Handling System (CCHS). The system unloads transportation casks consisting of bare Spent Nuclear Fuel (SNF) assemblies, single element canisters, and Dual Purpose Canisters (DPCs). For casks containing DPCs, the system opens the DPCs and unloads the SNF. The system stages the assemblies, transfer assemblies to and from fuel-blending inventory pools, loads them into Disposal Containers (DCs), temporarily seals and inerts the DC, decontaminates the DC and transfers it to the Disposal Container Handling System. The system also prepares empty casks and DPCs for off-site shipment. Two identical Assembly Transfer System lines are provided in the Waste Handling Building (WHB). Each line operates independently to handle the waste transfer throughput and to support maintenance operations. Each system line primarily consists of wet and dry handling areas. The wet handling area includes a cask transport system, cask and DPC preparation system, and a wet assembly handling system. The basket transport system forms the transition between the wet and dry handling areas. The dry handling area includes the dry assembly handling system, assembly drying system, DC preparation system, and DC transport system. Both the wet and dry handling areas are controlled by the control and tracking system. The system operating sequence begins with moving transportation casks to the cask preparation area. The cask preparation operations consist of cask cavity gas sampling, cask venting, cask cool-down, outer lid removal, and inner shield plug lifting fixture attachment. Casks containing bare SNF (no DPC) are filled with water and placed in the cask unloading pool. The inner shield plugs are removed underwater. For casks containing a DPC, the cask lid(s) is removed, and the DPC is penetrated, sampled, vented, and cooled. A DPC lifting fixture is attached and the cask is placed
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The dentin organic matrix - limitations of restorative dentistry hidden on the nanometer scale
Energy Technology Data Exchange (ETDEWEB)
Bertassoni, Luiz E; Orgel, Joseph P.R.; Antipova, Olga; Swain, Michael V [IIT; (Sydney)
2012-07-25
The prevention and treatment of dental caries are major challenges occurring in dentistry. The foundations for modern management of this dental disease, estimated to affect 90% of adults in Western countries, rest upon the dependence of ultrafine interactions between synthetic polymeric biomaterials and nanostructured supramolecular assemblies that compose the tooth organic substrate. Research has shown, however, that this interaction imposes less than desirable long-term prospects for current resin-based dental restorations. Here we review progress in the identification of the nanostructural organization of the organic matrix of dentin, the largest component of the tooth structure, and highlight aspects relevant to understating the interaction of restorative biomaterials with the dentin substrate. We offer novel insights into the influence of the hierarchically assembled supramolecular structure of dentin collagen fibrils and their structural dependence on water molecules. Secondly, we review recent evidence for the participation of proteoglycans in composing the dentin organic network. Finally, we discuss the relation of these complexly assembled nanostructures with the protease degradative processes driving the low durability of current resin-based dental restorations. We argue in favour of the structural limitations that these complexly organized and inherently hydrated organic structures may impose on the clinical prospects of current hydrophobic and hydrolyzable dental polymers that establish ultrafine contact with the tooth substrate.
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Storage method for spent fuel assembly
International Nuclear Information System (INIS)
Tajiri, Hiroshi.
1992-01-01
In the present invention, spent fuel assemblies are arranged at a dense pitch in a storage rack by suppressing the reactivity of the assemblies, to increase storage capacity for the spent fuel assemblies. That is, neutron absorbers are filled in the cladding tube of an absorbing rod, and the diameter thereof is substantially equal with that of a fuel rod. A great amount of the absorbing rods are arranged at the outer circumference of the fuel assembly. Then, they are fixed integrally to the fuel assembly and stored in a storage rack. In this case, the storage rack may be constituted only with angle materials which are inexpensive and installed simply. With such a constitution, in the fuel assembly having absorbing rods wound therearound, neutrons are absorbed by absorbing rods and the reactivity is lowered. Accordingly, the assembly arrangement pitch in the storage rack can be made dense. As a result, the storage capacity for the assemblies is increased. (I.S.)
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Surface characterization of sulfur and alkanethiol self-assembled monolayers on Au(111)
International Nuclear Information System (INIS)
Vericat, C; Vela, M E; Benitez, G A; Gago, J A Martin; Torrelles, X; Salvarezza, R C
2006-01-01
In the last two decades surface science techniques have decisively contributed to our present knowledge of alkanethiol self-assembled monolayers (SAMs) on solid surfaces. These organic layers have been a challenge for surface scientists, in particular because of the soft nature of the organic material (which can be easily damaged by irradiation), the large number of atoms present in the molecules, and the complex physical chemistry involved in the self-assembly process. This challenge has been motivated by the appealing technological applications of SAMs that cover many fields of the emerging area of nanotechnology. Sulfur (S) is closely related to alkanethiols and can be used to understand basic aspects of the surface structure of SAMs. In this review we focus on the atomic/molecular structures of S-containing SAMs on Au(111). Particular emphasis is given to the substrate, adsorption sites, chemical state of the S-metal bond and also to the experimental and theoretical tools used to study these structures at the atomic or molecular levels. (topical review)
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Surface characterization of sulfur and alkanethiol self-assembled monolayers on Au(111)
Energy Technology Data Exchange (ETDEWEB)
Vericat, C [Instituto de Investigaciones FisicoquImicas Teoricas y Aplicadas (INIFTA), Universidad Nacional de La Plata-CONICET, Sucursal 4 Casilla de Correo 16 (1900) La Plata (Argentina); Vela, M E [Instituto de Investigaciones FisicoquImicas Teoricas y Aplicadas (INIFTA), Universidad Nacional de La Plata-CONICET, Sucursal 4 Casilla de Correo 16 (1900) La Plata (Argentina); Benitez, G A [Instituto de Investigaciones FisicoquImicas Teoricas y Aplicadas (INIFTA), Universidad Nacional de La Plata-CONICET, Sucursal 4 Casilla de Correo 16 (1900) La Plata (Argentina); Gago, J A Martin [Centro de AstrobiologIa (CSIC-INTA), 28850 Torrejon de Ardoz Madrid (Spain); Torrelles, X [Instituto de Ciencia de Materiales de Barcelona (ICMAB), Barcelona (Spain); Salvarezza, R C [Instituto de Investigaciones FisicoquImicas Teoricas y Aplicadas (INIFTA), Universidad Nacional de La Plata-CONICET, Sucursal 4 Casilla de Correo 16 (1900) La Plata (Argentina)
2006-12-06
In the last two decades surface science techniques have decisively contributed to our present knowledge of alkanethiol self-assembled monolayers (SAMs) on solid surfaces. These organic layers have been a challenge for surface scientists, in particular because of the soft nature of the organic material (which can be easily damaged by irradiation), the large number of atoms present in the molecules, and the complex physical chemistry involved in the self-assembly process. This challenge has been motivated by the appealing technological applications of SAMs that cover many fields of the emerging area of nanotechnology. Sulfur (S) is closely related to alkanethiols and can be used to understand basic aspects of the surface structure of SAMs. In this review we focus on the atomic/molecular structures of S-containing SAMs on Au(111). Particular emphasis is given to the substrate, adsorption sites, chemical state of the S-metal bond and also to the experimental and theoretical tools used to study these structures at the atomic or molecular levels. (topical review)
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International Nuclear Information System (INIS)
Vikhorev, Yu.V.; Biryukov, G.I.; Kirilyuk, N.A.; Lobanov, V.N.
1977-01-01
A fuel assembly is proposed for nuclear reactors allowing remote replacement of control rod bundles or their shifting from one assembly to another, i.e., their multipurpose use. This leads to a significant increase in fuel assembly usability. In the fuel assembly the control rod bundle is placed in guide tube channels to which baffles are attached for fuel element spacing. The remote handling of control rods is provided by a hollow cylinder with openings in its lower bottom through which the control rods pass. All control rods in a bundle are mounted to a cross beam which in turn is mounted in the cylinder and is designed for grasping the whole rod bundle by a remotely controlled telescopic mechanism in bundle replacement or shifting. (Z.M.)
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Energy Technology Data Exchange (ETDEWEB)
Graham, Emily B. [Biological Sciences Division, Pacific Northwest National Laboratory, Richland WA USA; Crump, Alex R. [Biological Sciences Division, Pacific Northwest National Laboratory, Richland WA USA; Resch, Charles T. [Geochemistry Department, Pacific Northwest National Laboratory, Richland WA USA; Fansler, Sarah [Biological Sciences Division, Pacific Northwest National Laboratory, Richland WA USA; Arntzen, Evan [Environmental Compliance and Emergency Preparation, Pacific Northwest National Laboratory, Richland WA USA; Kennedy, David W. [Biological Sciences Division, Pacific Northwest National Laboratory, Richland WA USA; Fredrickson, Jim K. [Biological Sciences Division, Pacific Northwest National Laboratory, Richland WA USA; Stegen, James C. [Biological Sciences Division, Pacific Northwest National Laboratory, Richland WA USA
2017-03-28
Subsurface zones of groundwater and surface water mixing (hyporheic zones) are regions of enhanced rates of biogeochemical cycling, yet ecological processes governing hyporheic microbiome composition and function through space and time remain unknown. We sampled attached and planktonic microbiomes in the Columbia River hyporheic zone across seasonal hydrologic change, and employed statistical null models to infer mechanisms generating temporal changes in microbiomes within three hydrologically-connected, physicochemically-distinct geographic zones (inland, nearshore, river). We reveal that microbiomes remain dissimilar through time across all zones and habitat types (attached vs. planktonic) and that deterministic assembly processes regulate microbiome composition in all data subsets. The consistent presence of heterotrophic taxa and members of the Planctomycetes-Verrucomicrobia-Chlamydiae (PVC) superphylum nonetheless suggests common selective pressures for physiologies represented in these groups. Further, co-occurrence networks were used to provide insight into taxa most affected by deterministic assembly processes. We identified network clusters to represent groups of organisms that correlated with seasonal and physicochemical change. Extended network analyses identified keystone taxa within each cluster that we propose are central in microbiome composition and function. Finally, the abundance of one network cluster of nearshore organisms exhibited a seasonal shift from heterotrophic to autotrophic metabolisms and correlated with microbial metabolism, possibly indicating an ecological role for these organisms as foundational species in driving biogeochemical reactions within the hyporheic zone. Taken together, our research demonstrates a predominant role for deterministic assembly across highly-connected environments and provides insight into niche dynamics associated with seasonal changes in hyporheic microbiome composition and metabolism.
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International Nuclear Information System (INIS)
Delafosse, Jacques.
1977-01-01
This invention relates to a nuclear fuel assembly for a light or heavy water reactor, or for a fast reactor of the kind with a bundle of cladded pins, maintained parallel to each other in a regular network by an assembly of separate supporting grids, fitted with elastic bearing surfaces on these pins [fr
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Passivation of Black Phosphorus via Self-Assembled Organic Monolayers by van der Waals Epitaxy.
Zhao, Yinghe; Zhou, Qionghua; Li, Qiang; Yao, Xiaojing; Wang, Jinlan
2017-02-01
An effective passivation approach to protect black phosphorus (BP) from degradation based on multi-scale simulations is proposed. The self-assembly of perylene-3,4,9,10-tetracarboxylic dianhydride monolayers via van der Waals epitaxy on BP does not break the original electronic properties of BP. The passivation layer thickness is only 2 nm. This study opens up a new pathway toward fine passivation of BP. © 2016 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.
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Garcia-Crespo, Andres Jose; Delvaux, John McConnell; Miller, Diane Patricia
2016-05-03
An assembly and method for affixing a turbomachine rotor blade to a rotor wheel are disclosed. In an embodiment, an adaptor member is provided disposed between the blade and the rotor wheel, the adaptor member including an adaptor attachment slot that is complementary to the blade attachment member, and an adaptor attachment member that is complementary to the rotor wheel attachment slot. A coverplate is provided, having a coverplate attachment member that is complementary to the rotor wheel attachment slot, and a hook for engaging the adaptor member. When assembled, the coverplate member matingly engages with the adaptor member, and retains the blade in the adaptor member, and the assembly in the rotor wheel.
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Magnetic nanoparticle assemblies
Trohidou, Kalliopi N
2014-01-01
Magnetic nanoparticles with diameters in the range of a few nanometers are today at the cutting edge of modern technology and innovation because of their use in numerous applications ranging from engineering to biomedicine. A great deal of scientific interest has been focused on the functionalization of magnetic nanoparticle assemblies. The understanding of interparticle interactions is necessary to clarify the physics of these assemblies and their use in the development of high-performance magnetic materials. This book reviews prominent research studies on the static and dynamic magnetic properties of nanoparticle assemblies, gathering together experimental and computational techniques in an effort to reveal their optimized magnetic properties for biomedical use and as ultra-high magnetic recording media.
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International Nuclear Information System (INIS)
Hayashi, Hiroshi; Watari, Yoshio; Hizahara, Hiroshi; Masuoka, Ryuzo.
1970-01-01
When exchanging nuclear fuel assemblies during the operation of a nuclear reactor, melting of fuel bodies, and severence of tubular claddings is halted at the time of insertion by furnishing a neutron absorbing material such as B 10 , Cd, Gd or the like at the forward end of the fuel assembly to thereby lower the power peak at the forward ends of the fuel elements to within tolerable levels and thus prevent both fuel liquification and excessive expansion. The neutron absorbing material may be attached in the form of a plate to the fuel assembly forward tie plate, or may be inserted as a pellet into the front end of the tubular cladding. (Owens, K.J.)
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International Nuclear Information System (INIS)
Anthony, A.J.; Groves, M.D.
1980-01-01
A nuclear reactor fuel assembly having a lower end fitting and actuating means interacting therewith for holding the assembly down on the core support stand against the upward flow of coolant. Locking means for interacting with projections on the support stand are carried by the lower end fitting and are actuated by the movement of an actuating rod operated from above the top of the assembly. In one embodiment of the invention the downward movement of the actuating rod forces a latched spring to move outward into locking engagement with a shoulder on the support stand projections. In another embodiment, the actuating rod is rotated to effect the locking between the end fitting and the projection. (author)
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Novel alternating polymer adsorption/surface activation self-assembled film based on hydrogen bond
Energy Technology Data Exchange (ETDEWEB)
Zhang Yongjun; Yang Shuguang; Guan Ying; Miao Xiaopeng; Cao Weixiao; Xu Jian
2003-08-01
By combining hydrogen bonding layer-by-layer self-assembly and the stepwise chemisorption method, a new alternating polymer adsorption/surface activation self-assembly method was developed. First a layer of diphenylamine-4-diazonium-formaldehyde resin (diazo resin or DR) is deposited on a substrate. In the following surface activation step, the diazonium groups on the surface couple with resorcin in the outside solution. The deposition of another layer of DR is feasible due to the formation of hydrogen bond between the diazonium group of DR and the hydroxy group of the resorcin moieties. The resulting film is photosensitive. After UV irradiation, the film becomes very stable towards polar organic solvents.
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Fuel assembly inspection device
International Nuclear Information System (INIS)
Yaginuma, Yoshitaka
1998-01-01
The present invention provides a device suitable to inspect appearance of fuel assemblies by photographing the appearance of fuel assemblies. Namely, the inspection device of the present invention measures bowing of fuel assembly or each of fuel rods or both of them based on the partially photographed images of fuel assembly. In this case, there is disposed a means which flashily projects images in the form of horizontal line from a direction intersecting obliquely relative to a horizontal cross section of the fuel assembly. A first image processing means separates the projected image pictures including projected images and calculates bowing. A second image processing means replaces the projected image pictures of the projected images based on projected images just before and after the photographing. Then, images for the measurement of bowing and images for inspection can be obtained simultaneously. As a result, the time required for the photographing can be shortened, the time for inspection can be shortened and an effect of preventing deterioration of photographing means by radiation rays can be provided. (I.S.)
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DEFF Research Database (Denmark)
Briuglia, Maria-Lucia; Urquhart, Andrew; Lamprou, Dimitrios A.
2014-01-01
and one hydrophobic that are positioned in such a well-ordered fashion allowing precise assembly into a predetermined organization. A "smart" architecture in nanostructures can represent a good opportunity to use RADA16 as a carrier system for hydrophobic drugs solving problems of drugs delivery...
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Driving Forces of the Self-Assembly of Supramolecular Systems: Partially Ordered Mesophases
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.
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International Nuclear Information System (INIS)
Dohnal, M.; Rosel, J.; Skarka, V.
1988-01-01
The mounting is described of the drive assembly of a vertical pump for nuclear power plants in areas with seismic risk. The assembly is attached to the building floor using flexible and damping elements. The design allows producing seismically resistant pumps without major design changes in the existing types of vertical pumps. (E.S.). 1 fig
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Technology for assembling and welding of top and bottom nozzles in fuel assembly
International Nuclear Information System (INIS)
Xia Chenglie; Wan Longfu
1989-10-01
The construction character, technology and sequence of assembling and welding, assembling jig used for preventing from deformation, and acceptance test of welding technology for top and bottom nozzles are presented
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Heimel, Georg; Romaner, Lorenz; Zojer, Egbert; Brédas, Jean-Luc
2007-04-01
Self-assembled monolayers (SAMs) of organic molecules provide an important tool to tune the work function of electrodes in plastic electronics and significantly improve device performance. Also, the energetic alignment of the frontier molecular orbitals in the SAM with the Fermi energy of a metal electrode dominates charge transport in single-molecule devices. On the basis of first-principles calculations on SAMs of pi-conjugated molecules on noble metals, we provide a detailed description of the mechanisms that give rise to and intrinsically link these interfacial phenomena at the atomic level. The docking chemistry on the metal side of the SAM determines the level alignment, while chemical modifications on the far side provide an additional, independent handle to modify the substrate work function; both aspects can be tuned over several eV. The comprehensive picture established in this work provides valuable guidelines for controlling charge-carrier injection in organic electronics and current-voltage characteristics in single-molecule devices.
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U.S. Department of Health & Human Services — Federal regulations require that an assembler who installs one or more certified components of a diagnostic x-ray system submit a report of assembly. This database...
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DMello, Marilyn Esclance; Sundaram, Nalini G; Kalidindi, Suresh Babu
2018-05-03
Metal-organic frameworks (MOFs) are widely known for their record storage capacities of small gas molecules (H 2 , CO 2 , and CH 4 ). Assembly of such porous materials onto well-known chemiresistive gas sensing elements such as SnO 2 could be an attractive prospect to achieve novel sensing properties as this affects the surface chemistry of SnO 2 . Cobalt-imidazole based ZIF-67 MOF was grown onto preformed SnO 2 nanoparticles to realize core-shell like architecture and explored for greenhouse gas CO 2 sensing. CO 2 sensing over SnO 2 is a challenge because its interaction with SnO 2 surface is minimal. The ZIF-67 coating over SnO 2 improved the response of SnO 2 up to 12-fold (for 50 % CO 2 ). The SnO 2 @ZIF-67 also showed a response of 16.5±2.1 % for 5000 ppm CO 2 (threshold limit value (TLV)) at 205 °C, one of the best values reported for a SnO 2 -based sensor. The observed novel CO 2 sensing characteristics are assigned to electronic structure changes at the interface of ZIF-67 and SnO 2 . © 2018 Wiley-VCH Verlag GmbH & Co. KGaA, Weinheim.
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Liu, Fan; Heck, Albert J R
2015-01-01
Proteins are involved in almost all processes of the living cell. They are organized through extensive networks of interaction, by tightly bound macromolecular assemblies or more transiently via signaling nodes. Therefore, revealing the architecture of protein complexes and protein interaction
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Alezi, Dalal
2016-10-05
The ability to direct the assembly of hexagonal building units offers great prospective to construct the awaited and looked-for hypothetical polybenzene (pbz) or “cubic graphite” structure, described 70 years ago. Here, we demonstrate the successful use of reticular chemistry as an appropriate strategy for the design and deliberate construction of a zirconium-based metal–organic framework (MOF) with the intricate pbz underlying net topology. The judicious selection of the perquisite hexagonal building units, six connected organic and inorganic building blocks, allowed the formation of the pbz-MOF-1, the first example of a Zr(IV)-based MOF with pbz topology. Prominently, pbz-MOF-1 is highly porous, with associated pore size and pore volume of 13 Å and 0.99 cm3 g–1, respectively, and offers high gravimetric and volumetric methane storage capacities (0.23 g g–1 and 210.4 cm3 (STP) cm–3 at 80 bar). Notably, the pbz-MOF-1 pore system permits the attainment of one of the highest CH4 adsorbed phase density enhancements at high pressures (0.15 and 0.21 g cm–3 at 35 and 65 bar, respectively) as compared to benchmark microporous MOFs.
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Alezi, Dalal; Spanopoulos, Ioannis; Tsangarakis, Constantinos; Shkurenko, Aleksander; Adil, Karim; Belmabkhout, Youssef; O'Keeffe, Michael; Eddaoudi, Mohamed; Trikalitis, Pantelis N.
2016-01-01
The ability to direct the assembly of hexagonal building units offers great prospective to construct the awaited and looked-for hypothetical polybenzene (pbz) or “cubic graphite” structure, described 70 years ago. Here, we demonstrate the successful use of reticular chemistry as an appropriate strategy for the design and deliberate construction of a zirconium-based metal–organic framework (MOF) with the intricate pbz underlying net topology. The judicious selection of the perquisite hexagonal building units, six connected organic and inorganic building blocks, allowed the formation of the pbz-MOF-1, the first example of a Zr(IV)-based MOF with pbz topology. Prominently, pbz-MOF-1 is highly porous, with associated pore size and pore volume of 13 Å and 0.99 cm3 g–1, respectively, and offers high gravimetric and volumetric methane storage capacities (0.23 g g–1 and 210.4 cm3 (STP) cm–3 at 80 bar). Notably, the pbz-MOF-1 pore system permits the attainment of one of the highest CH4 adsorbed phase density enhancements at high pressures (0.15 and 0.21 g cm–3 at 35 and 65 bar, respectively) as compared to benchmark microporous MOFs.
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On the influence of surface patterning on tissue self-assembly and mechanics.
Coppola, Valerio; Ventre, Maurizio; Natale, Carlo F; Rescigno, Francesca; Netti, Paolo A
2018-04-28
Extracellular matrix assembly and composition influence the biological and mechanical functions of tissues. Developing strategies to control the spatial arrangement of cells and matrix is of central importance for tissue engineering-related approaches relying on self-assembling and scaffoldless processes. Literature reports demonstrated that signals patterned on material surfaces are able to control cell positioning and matrix orientation. However, the mechanisms underlying the interactions between material signals and the structure of the de novo synthesized matrix are far from being thoroughly understood. In this work, we investigated the ordering effect provided by nanoscale topographic patterns on the assembly of tissue sheets grown in vitro. We stimulated MC3T3-E1 preosteoblasts to produce and assemble a collagen-rich matrix on substrates displaying patterns with long- or short-range order. Then, we investigated microstructural features and mechanical properties of the tissue in uniaxial tension. Our results demonstrate that patterned material surfaces are able to control the initial organization of cells in close contact to the surface; then cell-generated contractile forces profoundly remodel tissue structure towards mechanically stable spatial patterns. Such a remodelling effect acts both locally, as it affects cell and nuclear shape and globally, by affecting the gross mechanical response of the tissue. Such an aspect of dynamic interplay between cells and the surrounding matrix must be taken into account when designing material platform for the in vitro generation of tissue with specific microstructural assemblies. Copyright © 2018 John Wiley & Sons, Ltd.
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Nuclear fuel assembly seismic amplitude limiter
International Nuclear Information System (INIS)
Anthony, A.J.
1977-01-01
The ability of a nuclear reactor to withstand high seismic loading is enhanced by including, on each fuel assembly, at least one seismic grid which reduces the magnitude of the possible lateral deflection of the individual fuel elements and the entire fuel assembly. The reduction in possible deflection minimizes the possibility of impact of the spacer grids of one fuel assembly on those of an adjacent fuel assembly and reduces the magnitude of forces associated with any such impact thereby minimizing the possibility of fuel assembly damage as a result of high seismic loading. The seismic grid is mounted from the fuel assembly guide tubes, has greater external dimensions when compared to the fuel assembly spacer grids and normally does not support or otherwise contact the fuel elements. The reduction in possible deflection is achieved through reduction of the clearance between adjacent fuel assemblies made possible by the use in the seismic grid of a high strength material characterized by favorable thermal expansion characteristics and minimal irradiation induced expansion
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Chemical reactions directed Peptide self-assembly.
Rasale, Dnyaneshwar B; Das, Apurba K
2015-05-13
Fabrication of self-assembled nanostructures is one of the important aspects in nanoscience and nanotechnology. The study of self-assembled soft materials remains an area of interest due to their potential applications in biomedicine. The versatile properties of soft materials can be tuned using a bottom up approach of small molecules. Peptide based self-assembly has significant impact in biology because of its unique features such as biocompatibility, straight peptide chain and the presence of different side chain functionality. These unique features explore peptides in various self-assembly process. In this review, we briefly introduce chemical reaction-mediated peptide self-assembly. Herein, we have emphasised enzymes, native chemical ligation and photochemical reactions in the exploration of peptide self-assembly.
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Benchmark assemblies of the Los Alamos critical assemblies facility
International Nuclear Information System (INIS)
Dowdy, E.J.
1986-01-01
Several critical assemblies of precisely known materials composition and easily calculated and reproducible geometries have been constructed at the Los Alamos National Laboratory. Some of these machines, notably Jezebel, Flattop, Big Ten, and Godiva, have been used as benchmark assemblies for the comparison of the results of experimental measurements and computation of certain nuclear reaction parameters. These experiments are used to validate both the input nuclear data and the computational methods. The machines and the applications of these machines for integral nuclear data checks are described. (author)
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Benchmark assemblies of the Los Alamos Critical Assemblies Facility
International Nuclear Information System (INIS)
Dowdy, E.J.
1985-01-01
Several critical assemblies of precisely known materials composition and easily calculated and reproducible geometries have been constructed at the Los Alamos National Laboratory. Some of these machines, notably Jezebel, Flattop, Big Ten, and Godiva, have been used as benchmark assemblies for the comparison of the results of experimental measurements and computation of certain nuclear reaction parameters. These experiments are used to validate both the input nuclear data and the computational methods. The machines and the applications of these machines for integral nuclear data checks are described
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Benchmark assemblies of the Los Alamos critical assemblies facility
International Nuclear Information System (INIS)
Dowdy, E.J.
1985-01-01
Several critical assemblies of precisely known materials composition and easily calculated and reproducible geometries have been constructed at the Los Alamos National Laboratory. Some of these machines, notably Jezebel, Flattop, Big Ten, and Godiva, have been used as benchmark assemblies for the comparison of the results of experimental measurements and computation of certain nuclear reaction parameters. These experiments are used to validate both the input nuclear data and the computational methods. The machines and the applications of these machines for integral nuclear data checks are described
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Xu, Hao; Nagasaka, Shinobu; Kameta, Naohiro; Masuda, Mitsutoshi; Ito, Takashi; Higgins, Daniel A
2017-08-02
Synthetic organic nanotubes self-assembled from bolaamphiphile surfactants are now being explored for use as drug delivery vehicles. In this work, several factors important to their implementation in drug delivery are explored. All experiments are performed with the nanotubes immersed in ethanol. First, Nile Red (NR) and a hydroxylated Nile Red derivative (NR-OH) are loaded into the nanotubes and spectroscopic fluorescence imaging methods are used to determine the apparent dielectric constant of their local environment. Both are found in relatively nonpolar environments, with the NR-OH molecules preferring regions of relatively higher dielectric constant compared to NR. Unique two-color imaging fluorescence correlation spectroscopy (imaging FCS) measurements are then used along with the spectroscopic imaging results to deduce the dielectric properties of the environments sensed by mobile and immobile populations of probe molecules. The results reveal that mobile NR molecules pass through less polar regions, likely within the nanotube walls, while immobile NR molecules are found in more polar regions, possibly near the nanotube surfaces. In contrast, mobile and immobile NR-OH molecules are found to locate in environments of similar polarity. The imaging FCS results also provide quantitative data on the apparent diffusion coefficient for each dye. The mean diffusion coefficient for the NR dye was approximately two-fold larger than that of NR-OH. Slower diffusion by the latter could result from its additional hydrogen bonding interactions with polar triglycine, amine, and glucose moieties near the nanotube surfaces. The knowledge gained in these studies will allow for the development of nanotubes that are better engineered for applications in the controlled transport and release of uncharged, dipolar drug molecules.
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SP-100 nuclear assembly test: Test assembly functional requirements and system arrangement
International Nuclear Information System (INIS)
Fallas, T.T.; Gluck, R.; Motwani, K.; Clay, H.; O'Neill, G.
1991-01-01
This paper describes the functional requirements and the system that will be tested to validate the reactor, flight shield, and flight controller of the SP-100 Generic Flight System (GFS). The Nuclear Assembly Test (NAT) consists of the test article (SP-100 reactor with control devices and the flight shield) and its supporting systems. The NAT test assembly is being designed by GE. Westinghouse Hanford Company (WHC) is designing the test cell and vacuum vessel system that will contain the NAT test assembly (Renkey et al. 1989). Preliminary design reviews have been completed and the final design is under way
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International Nuclear Information System (INIS)
Jabsen, F.S.
1979-01-01
This invention is directed toward a nuclear fuel assembly guide tube arrangement which restrains spacer grid movement due to coolant flow and which offers secondary means for supporting a fuel assembly during handling and transfer operations
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Feldmesser, Ester; Rosenwasser, Shilo; Vardi, Assaf; Ben-Dor, Shifra
2014-01-01
Background The advent of Next Generation Sequencing technologies and corresponding bioinformatics tools allows the definition of transcriptomes in non-model organisms. Non-model organisms are of great ecological and biotechnological significance, and consequently the understanding of their unique metabolic pathways is essential. Several methods that integrate de novo assembly with genome-based assembly have been proposed. Yet, there are many open challenges in defining genes, particularly whe...
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Magnetic self-assembly of small parts
Shetye, Sheetal B.
Modern society's propensity for miniaturized end-user products is compelling electronic manufacturers to assemble and package different micro-scale, multi-technology components in more efficient and cost-effective manners. As the size of the components gets smaller, issues such as part sticking and alignment precision create challenges that slow the throughput of conventional robotic pick-n-place systems. As an alternative, various self-assembly approaches have been proposed to manipulate micro to millimeter scale components in a parallel fashion without human or robotic intervention. In this dissertation, magnetic self-assembly (MSA) is demonstrated as a highly efficient, completely parallel process for assembly of millimeter scale components. MSA is achieved by integrating permanent micromagnets onto component bonding surfaces using wafer-level microfabrication processes. Embedded bonded powder methods are used for fabrication of the magnets. The magnets are then magnetized using pulse magnetization methods, and the wafers are then singulated to form individual components. When the components are randomly mixed together, self-assembly occurs when the intermagnetic forces overcome the mixing forces. Analytical and finite element methods (FEM) are used to study the force interactions between the micromagnets. The multifunctional aspects of MSA are presented through demonstration of part-to-part and part-to-substrate assembly of 1 mm x 1mm x 0.5 mm silicon components. Part-to-part assembly is demonstrated by batch assembly of free-floating parts in a liquid environment with the assembly yield of different magnetic patterns varying from 88% to 90% in 20 s. Part-to-substrate assembly is demonstrated by assembling an ordered array onto a fixed substrate in a dry environment with the assembly yield varying from 86% to 99%. In both cases, diverse magnetic shapes/patterns are used to control the alignment and angular orientation of the components. A mathematical model is
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Mechanical Self-Assembly Science and Applications
2013-01-01
Mechanical Self-Assembly: Science and Applications introduces a novel category of self-assembly driven by mechanical forces. This book discusses self-assembly in various types of small material structures including thin films, surfaces, and micro- and nano-wires, as well as the practice's potential application in micro and nanoelectronics, MEMS/NEMS, and biomedical engineering. The mechanical self-assembly process is inherently quick, simple, and cost-effective, as well as accessible to a large number of materials, such as curved surfaces for forming three-dimensional small structures. Mechanical self-assembly is complementary to, and sometimes offer advantages over, the traditional micro- and nano-fabrication. This book also: Presents a highly original aspect of the science of self-assembly Describes the novel methods of mechanical assembly used to fabricate a variety of new three-dimensional material structures in simple and cost-effective ways Provides simple insights to a number of biological systems and ...
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Directed Self-Assembly of Nanodispersions
Energy Technology Data Exchange (ETDEWEB)
Furst, Eric M [University of Delaware
2013-11-15
Directed self-assembly promises to be the technologically and economically optimal approach to industrial-scale nanotechnology, and will enable the realization of inexpensive, reproducible and active nanostructured materials with tailored photonic, transport and mechanical properties. These new nanomaterials will play a critical role in meeting the 21st century grand challenges of the US, including energy diversity and sustainability, national security and economic competitiveness. The goal of this work was to develop and fundamentally validate methods of directed selfassembly of nanomaterials and nanodispersion processing. The specific aims were: 1. Nanocolloid self-assembly and interactions in AC electric fields. In an effort to reduce the particle sizes used in AC electric field self-assembly to lengthscales, we propose detailed characterizations of field-driven structures and studies of the fundamental underlying particle interactions. We will utilize microscopy and light scattering to assess order-disorder transitions and self-assembled structures under a variety of field and physicochemical conditions. Optical trapping will be used to measure particle interactions. These experiments will be synergetic with calculations of the particle polarizability, enabling us to both validate interactions and predict the order-disorder transition for nanocolloids. 2. Assembly of anisotropic nanocolloids. Particle shape has profound effects on structure and flow behavior of dispersions, and greatly complicates their processing and self-assembly. The methods developed to study the self-assembled structures and underlying particle interactions for dispersions of isotropic nanocolloids will be extended to systems composed of anisotropic particles. This report reviews several key advances that have been made during this project, including, (1) advances in the measurement of particle polarization mechanisms underlying field-directed self-assembly, and (2) progress in the
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Inverse Problem in Self-assembly
Tkachenko, Alexei
2012-02-01
By decorating colloids and nanoparticles with DNA, one can introduce highly selective key-lock interactions between them. This leads to a new class of systems and problems in soft condensed matter physics. In particular, this opens a possibility to solve inverse problem in self-assembly: how to build an arbitrary desired structure with the bottom-up approach? I will present a theoretical and computational analysis of the hierarchical strategy in attacking this problem. It involves self-assembly of particular building blocks (``octopus particles''), that in turn would assemble into the target structure. On a conceptual level, our approach combines elements of three different brands of programmable self assembly: DNA nanotechnology, nanoparticle-DNA assemblies and patchy colloids. I will discuss the general design principles, theoretical and practical limitations of this approach, and illustrate them with our simulation results. Our crucial result is that not only it is possible to design a system that has a given nanostructure as a ground state, but one can also program and optimize the kinetic pathway for its self-assembly.
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Semerdzhiev, Slav A; Shvadchak, Volodymyr V; Subramaniam, Vinod; Claessens, Mireille M A E
2017-08-09
Although the function of biopolymer hydrogels in nature depends on structural anisotropy at mesoscopic length scales, the self-assembly of such anisotropic structures in vitro is challenging. Here we show that fibrils of the protein α-synuclein spontaneously self-assemble into structurally anisotropic hydrogel particles. While the fibrils in the interior of these supra-fibrillar aggregates (SFAs) are randomly oriented, the fibrils in the periphery prefer to cross neighboring fibrils at high angles. This difference in organization coincides with a significant difference in polarity of the environment in the central and peripheral parts of the SFA. We rationalize the structural anisotropy of SFAs in the light of the observation that αS fibrils bind a substantial amount of counterions. We propose that, with the progress of protein polymerization into fibrils, this binding of counterions changes the ionic environment which triggers a change in fibril organization resulting in anisotropy in the architecture of hydrogel particles.
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Robust, directed assembly of fluorescent nanodiamonds.
Kianinia, Mehran; Shimoni, Olga; Bendavid, Avi; Schell, Andreas W; Randolph, Steven J; Toth, Milos; Aharonovich, Igor; Lobo, Charlene J
2016-10-27
Arrays of fluorescent nanoparticles are highly sought after for applications in sensing, nanophotonics and quantum communications. Here we present a simple and robust method of assembling fluorescent nanodiamonds into macroscopic arrays. Remarkably, the yield of this directed assembly process is greater than 90% and the assembled patterns withstand ultra-sonication for more than three hours. The assembly process is based on covalent bonding of carboxyl to amine functional carbon seeds and is applicable to any material, and to non-planar surfaces. Our results pave the way to directed assembly of sensors and nanophotonics devices.
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McGregor, A
1992-05-23
1200 delegates from 175 member countries attended the 45th World Health Assembly in Geneva. Everyone at the Assembly ratified measures to prevent and control AIDS. 12 countries intended to do long term planning for community based care for AIDS patients. Further the Assembly denounced instances where countries and individuals denied the gravity of the AIDS pandemic. In fact, it expressed the importance for urgent and intensive action against HIV/AIDS. The assembly backed proposals to prevent and control sexually transmitted diseases that affect AIDS patients, especially hepatitis B. For example, in countries with hepatitis B prevalence 8% (many countries in Sub-Sahara Africa, Asia, the Pacific region, and South America), health officials should introduce hepatitis B vaccine into their existing immunization programs by 1995. By 1997, this vaccine should be part of all immunization programs. The Assembly was aware of the obstacles of establishing reliable cold chains for nationwide distribution, however. Delegates in Committee A objected to the fact that 50% of the populations of developing countries continued to have limited access to essential drugs. They also expressed disapproval in implementation of WHO's 1988 ethical criteria for promotion of drugs which WHO entrusted to the Council for International Organisations of Medical Sciences (CIOMS). CIOMS lacked WHO's status and thus could not effectively monitor drug advertising. In fact, the pharmaceutical industry as well as WHO provided the funds for a meeting of 25 experts to discuss principles included in the ethical criteria. At least 4 countries insisted that WHO have the ultimate authority in monitoring drug advertising. Delegates did adopt a compromise resolution on this topic which required that industry promotion methods be reported to the 1994 Assembly via the Executive Board. The Assembly requested WHO to establish an international advisory committee on nursing and midwifery and to improve the network of
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Minerals with metal-organic framework structures.
Huskić, Igor; Pekov, Igor V; Krivovichev, Sergey V; Friščić, Tomislav
2016-08-01
Metal-organic frameworks (MOFs) are an increasingly important family of advanced materials based on open, nanometer-scale metal-organic architectures, whose design and synthesis are based on the directed assembly of carefully designed subunits. We now demonstrate an unexpected link between mineralogy and MOF chemistry by discovering that the rare organic minerals stepanovite and zhemchuzhnikovite exhibit structures found in well-established magnetic and proton-conducting metal oxalate MOFs. Structures of stepanovite and zhemchuzhnikovite, exhibiting almost nanometer-wide and guest-filled apertures and channels, respectively, change the perspective of MOFs as exclusively artificial materials and represent, so far, unique examples of open framework architectures in organic minerals.
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Bot, A.; Gilbert, E.P.; Bouwman, W.G.; Sawalha, H.I.M.; Adel, den R.; Garamus, V.M.; Venema, P.; Linden, van der E.; Flöter, E.
2012-01-01
Small-angle neutron scattering (SANS) experiments have been performed on self-assembled tubules of sitosterol and oryzanol in triglyceride oils to investigate details of their structure. Alternative organic phases (deuterated and non-deuterated decane, limonene, castor oil and eugenol) were used to
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Tetraspanin Assemblies in Virus Infection
Directory of Open Access Journals (Sweden)
Luise Florin
2018-05-01
Full Text Available Tetraspanins (Tspans are a family of four-span transmembrane proteins, known as plasma membrane “master organizers.” They form Tspan-enriched microdomains (TEMs or TERMs through lateral association with one another and other membrane proteins. If multiple microdomains associate with each other, larger platforms can form. For infection, viruses interact with multiple cell surface components, including receptors, activating proteases, and signaling molecules. It appears that Tspans, such as CD151, CD82, CD81, CD63, CD9, Tspan9, and Tspan7, coordinate these associations by concentrating the interacting partners into Tspan platforms. In addition to mediating viral attachment and entry, these platforms may also be involved in intracellular trafficking of internalized viruses and assist in defining virus assembly and exit sites. In conclusion, Tspans play a role in viral infection at different stages of the virus replication cycle. The present review highlights recently published data on this topic, with a focus on events at the plasma membrane. In light of these findings, we propose a model for how Tspan interactions may organize cofactors for viral infection into distinct molecular platforms.